| 1526 matches found in 1136 documents. Search time: 0.058 seconds. |
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Score: 17.00 |
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| Title: Differential Accumulation of Salicylic Acid and Salicylic Acid-Sensitive Catalase in Different Rice it issues .
| | Author: Chen Z Iyer S Caplan A Klessig DF Fan B | | Journal: Citation: V : 114 ( 1 ) P : 193-201 Year: 1997 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12223699 Accession (PMID): 12223699 | | Abstract: We previously proposed that salicylic acid ( SA ) -sensitive catalases serve as biological targets of SA in plant defense responses .
To further examine the role of SA-sensitive catalases , we have analyzed the relationship between SA levels and SA sensitivity of catalases in different rice ( Oryza sativa ) it issues .
We show here that , whereas rice shoots contain extremely high levels of free SA , as previously reported ( I Raskin , H Skubatz , W Tang , BJD Meeuse [ 1990 ] Ann Bot 66 : 369-373 ; P Silverman , M Seskar , D Kanter , P Schweizer , J-P Metraux , I Raskin [ 1995 ] Plant Physiol 108 : 633-639 ) , rice roots and cell-suspension cultures have very low SA levels .
Catalases from different rice it issues also exhibit differences in sensitivity to SA .
Catalase from rice shoots is insensitive to SA , but roots and cell-suspension cultures contain SA-sensitive catalase .
The difference in SA sensitivity of catalases from these different it issues correlates with the it issue-specific expression of two catalase genes , CatA and CatB , which encode highly distinctive catalase proteins .
CatA , which encodes a catalase with relatively low sequence homology to the tobacco SA-sensitive catalases , is expressed at high levels exclusively in the shoots .
On the other hand , in roots and cell-suspension cultures , with northern analysis we detected expression of only the CatB gene , which encodes a catalase with higher sequence homology to tobacco catalases .
The role of catalases in mediating some of the SA-induced responses is discussed in light of these results and the recently defined mechanisms of catalase inhibition by SA . | Matching Sentences:
[ Sen. 6, subscore: 4.00 ]: The difference in SA sensitivity of catalases from these different it issues correlates with the it issue-specific expression of two catalase genes , CatA and CatB , which encode highly distinctive catalase proteins .
[ Sen. 7, subscore: 3.00 ]: CatA , which encodes a catalase with relatively low sequence homology to the tobacco SA-sensitive catalases , is expressed at high levels exclusively in the shoots .
[ Sen. 2, subscore: 2.00 ]: To further examine the role of SA-sensitive catalases , we have analyzed the relationship between SA levels and SA sensitivity of catalases in different rice ( Oryza sativa ) it issues .
[ Sen. 5, subscore: 2.00 ]: Catalase from rice shoots is insensitive to SA , but roots and cell-suspension cultures contain SA-sensitive catalase .
[ Sen. 8, subscore: 2.00 ]: On the other hand , in roots and cell-suspension cultures , with northern analysis we detected expression of only the CatB gene , which encodes a catalase with higher sequence homology to tobacco catalases .
[ Sen. 9, subscore: 2.00 ]: The role of catalases in mediating some of the SA-induced responses is discussed in light of these results and the recently defined mechanisms of catalase inhibition by SA .
[ Sen. 1, subscore: 1.00 ]: We previously proposed that salicylic acid ( SA ) -sensitive catalases serve as biological targets of SA in plant defense responses .
[ Sen. 4, subscore: 1.00 ]: Catalases from different rice it issues also exhibit differences in sensitivity to SA .
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Score: 16.00 |
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| Title: Molecular evolution of maize catalases and their relationship to other eukaryotic and prokaryotic catalases .
| | Author: Guan L Scandalios JG .
| | Journal: J Mol .
Evol Citation: V : 42 ( 5 ) P : 570-9 Year: 1996 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8662009 Accession (PMID): 8662009 | | Abstract: We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases .
These sequences were also compared with other eukaryotic and prokaryotic catalases .
Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups .
The first , and major , group includes maize Cat1 , barley Cat1 , rice CatB , and most of the dicot catalases .
The second group is an apparent dicot-specific catalase group encompassing the tobacco Cat2 and tomato Cat .
The third is a monocot-specific catalase class including the maize Cat3 , barley Cat2 , and rice CatA .
The maize Cat2 gene is loosely related to the first group .
The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases .
Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene .
The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence .
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[ Sen. 1, subscore: 3.00 ]: We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases .
[ Sen. 10, subscore: 3.00 ]: The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence .
[ Sen. 3, subscore: 2.00 ]: Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups .
[ Sen. 6, subscore: 2.00 ]: The third is a monocot-specific catalase class including the maize Cat3 , barley Cat2 , and rice CatA .
[ Sen. 8, subscore: 2.00 ]: The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases .
[ Sen. 2, subscore: 1.00 ]: These sequences were also compared with other eukaryotic and prokaryotic catalases .
[ Sen. 4, subscore: 1.00 ]: The first , and major , group includes maize Cat1 , barley Cat1 , rice CatB , and most of the dicot catalases .
[ Sen. 5, subscore: 1.00 ]: The second group is an apparent dicot-specific catalase group encompassing the tobacco Cat2 and tomato Cat .
[ Sen. 9, subscore: 1.00 ]: Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene .
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Score: 12.00 |
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| Title: Catalytic pyrolysis of waste rice husk over mesoporous materials .
| | Author: Jeon MJ Kim SS Jeon JK Park SH Kim JM Sohn JM Lee SH Park YK | | Journal: Nanoscale Res Lett Citation: V : 7 P : 18 Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22221540 Accession (PMID): 22221540 | | Abstract: ABSTRACT : Catalytic fast pyrolysis of waste rice husk was carried out using pyrolysis-gas chromatography/mass spectrometry [ Py-GC/MS ] .
Meso-MFI zeolite [ Meso-MFI ] was used as the catalyst In addition , a 0 . 5-wt . % platinum [ Pt ] was ion-exchanged into Meso-MFI to examine the effect of Pt addition .
Using a catalytic upgrading method , the activities of the catalysts were evaluated in terms of product composition and deoxygenation .
The structure and acid site characteristics of the catalysts were analyzed by Brunauer-Emmett-Teller surface area measurement and NH3 temperature-programmed desorption analysis .
Catalytic upgrading reduced the amount of oxygenates in the product vapor due to the cracking reaction of the catalysts .
Levoglucosan , a polymeric oxygenate species , was completely decomposed without being detected .
While the amount of heavy phenols was reduced by catalytic upgrading , the amount of light phenols was increased because of the catalytic cracking of heavy phenols into light phenols and aromatics .
The amount of aromatics increased remarkably as a result of catalytic upgrading , which is attributed to the strong Bronsted acid sites and the shape selectivity of the Meso-MFI catalyst The addition of Pt made the Meso-MFI catalyst even more active in deoxygenation and in the production of aromatics .
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[ Sen. 8, subscore: 3.00 ]: The amount of aromatics increased remarkably as a result of catalytic upgrading , which is attributed to the strong Bronsted acid sites and the shape selectivity of the Meso-MFI catalyst The addition of Pt made the Meso-MFI catalyst even more active in deoxygenation and in the production of aromatics .
[ Sen. 3, subscore: 2.00 ]: Using a catalytic upgrading method , the activities of the catalysts were evaluated in terms of product composition and deoxygenation .
[ Sen. 5, subscore: 2.00 ]: Catalytic upgrading reduced the amount of oxygenates in the product vapor due to the cracking reaction of the catalysts .
[ Sen. 7, subscore: 2.00 ]: While the amount of heavy phenols was reduced by catalytic upgrading , the amount of light phenols was increased because of the catalytic cracking of heavy phenols into light phenols and aromatics .
[ Sen. 1, subscore: 1.00 ]: ABSTRACT : Catalytic fast pyrolysis of waste rice husk was carried out using pyrolysis-gas chromatography/mass spectrometry [ Py-GC/MS ] .
[ Sen. 2, subscore: 1.00 ]: Meso-MFI zeolite [ Meso-MFI ] was used as the catalyst In addition , a 0 . 5-wt . % platinum [ Pt ] was ion-exchanged into Meso-MFI to examine the effect of Pt addition .
[ Sen. 4, subscore: 1.00 ]: The structure and acid site characteristics of the catalysts were analyzed by Brunauer-Emmett-Teller surface area measurement and NH3 temperature-programmed desorption analysis .
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Score: 11.00 |
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| Title: A rural population based case-control study of senile cataract in India .
| | Author: Sreenivas V Prabhakar AK Badrinath SS Fernandez T Roy IS Sharma T Shah B | | Journal: Citation: V : 9 ( 5 ) P : 327-36 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10616266 Accession (PMID): 10616266 | | Abstract: PURPOSE : Senile cataract contributes to 75% of blindness in India and there is a growing backlog of cataract cases needing surgery .
The present study seeks clues to the etiology of senile cataract , so that strategies to prevent or even delay cataract formation could be planned .
METHODS : Using a community based case-control design , 258 cases & 308 controls from one centre and 301 cases & 591 controls from another were studied .
The subjects were from rural areas and were aged 40-60 years .
Logistic regression analysis technique was employed to study the associations between senile cataract and various variables .
RESULTS : Systolic blood pressure , duration of exposure to sunlight per day were associated with senile cataract in both the centres ( OR = 1 . 4 & 1 . 5 for systolic BP and 1 . 6 & 1 . 4 for exposure to sunlight ) .
Utilization of rice gruel ( OR = 0 . 5 ) , duration of exposure to fire & dust per day ( OR = 1 . 8 ) , family history of cataract ( OR = 5 . 0 ) , use of cheap cooking fuels ( OR = 1 . 8 ) , increased height ( OR = 0 . 7 ) and increased number of hours of work per day ( OR = 0 . 7 ) were other variables that showed significant association in either of the centres .
CONCLUSION : Senile cataract appears to have a multi factorial etiology .
Though the study provided some clues to the etiology of senile cataract , further studies are needed to know the specific role of these factors in the causation of cataract , so that any preventive or control measures could be initiated in the community .
Till such time , we have to fall back on the available surgical approach in control of senile cataract . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: PURPOSE : Senile cataract contributes to 75% of blindness in India and there is a growing backlog of cataract cases needing surgery .
[ Sen. 2, subscore: 2.00 ]: The present study seeks clues to the etiology of senile cataract , so that strategies to prevent or even delay cataract formation could be planned .
[ Sen. 9, subscore: 2.00 ]: Though the study provided some clues to the etiology of senile cataract , further studies are needed to know the specific role of these factors in the causation of cataract , so that any preventive or control measures could be initiated in the community .
[ Sen. 5, subscore: 1.00 ]: Logistic regression analysis technique was employed to study the associations between senile cataract and various variables .
[ Sen. 6, subscore: 1.00 ]: RESULTS : Systolic blood pressure , duration of exposure to sunlight per day were associated with senile cataract in both the centres ( OR = 1 . 4 & 1 . 5 for systolic BP and 1 . 6 & 1 . 4 for exposure to sunlight ) .
[ Sen. 7, subscore: 1.00 ]: Utilization of rice gruel ( OR = 0 . 5 ) , duration of exposure to fire & dust per day ( OR = 1 . 8 ) , family history of cataract ( OR = 5 . 0 ) , use of cheap cooking fuels ( OR = 1 . 8 ) , increased height ( OR = 0 . 7 ) and increased number of hours of work per day ( OR = 0 . 7 ) were other variables that showed significant association in either of the centres .
[ Sen. 8, subscore: 1.00 ]: CONCLUSION : Senile cataract appears to have a multi factorial etiology .
[ Sen. 10, subscore: 1.00 ]: Till such time , we have to fall back on the available surgical approach in control of senile cataract .
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Score: 10.00 |
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| Title: Cloning and characterization of the rice CatA catalase gene , a homologue of the maize Cat3 gene .
| | Author: Higo K Higo H | | Journal: Plant Mol . Biol . Citation: V : 30 ( 3 ) P : 505-21 Year: 1996 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub8605302 Accession (PMID): 8605302 | | Abstract: We isolated and sequenced a genomic clone ( CatA ) encoding CAT-A catalase , a homologue of the maize catalase isozyme 3 ( CAT-3 ) from rice ( Oryza sativa L ) .
The 5-upstream non-coding region had very low similarity with the maize Cat3 gene and possible cis elements and sequence motifs in the maize Cat3 gene were not evident , except for TATA and CAAT motifs .
Several sequence motifs found in the promoters of plant seed-specific genes were identified in the 5-upstream non-coding region of the CatA gene .
Northern blotting showed that the CatA gene is expressed at high levels in seeds during early development and also in young seedlings .
Methyl viologen ( paraquat ) resulted in the 3-fold induction of the CatA gene in the leaves of young seedlings , whereas abscisic acid , wounding , salicylic acid , and hydrogen peroxide had no or only slight effects .
The 1 . 9 kb 5-upstream fragment ( -1559 to +342 ) of the CatA gene was fused with the Escherichia coli beta-glucuronidase ( GUS ) gene and introduced by electroporation into protoplasts prepared from rice suspension-cultured cells , then the transient expression of the GUS gene was examined .
Deletion analysis of this chimeric gene suggested that a weak silencer is located in the region between -1564 to -699 .
Abscisic acid ( ABA ) at a final concentration of 10 ( -6 ) M doubled GUS activity in protoplasts electroporated with the chimeric DNAs having 1 . 9 to 1 . 2 kb 5-upstream regions .
A sequence highly similar to the Sph box , a motif found in genes modulated by ABA , was found at -266 to -254 .
Deletion of this region however , did not eliminate the responsiveness to ABA .
Expression of the chimeric gene in the protoplasts was not enhanced by stress such as low and high temperature , hydrogen peroxide , methyl viologen , salicylic acid , elicitor , and UV light .
The chimeric CatA-GUS plasmid DNAs amplified in the methylation-positive strain , E coli DH5alpha , showed GUS gene activities , whereas all the chimeric DNAs amplified in the methylation-deficient E coli JM110 were completely inactive in the presence or absence of ABA in the culture medium .
DNA methylation , especially of either one or both of the deoxyadenosines at the two GATC motifs ( one in the first exon and the other in the first intron of the rice CatA gene ) , appeared to be responsible for the CatA promoter activity identified in the transient assay . | Matching Sentences:
[ Sen. 1, subscore: 3.00 ]: We isolated and sequenced a genomic clone ( CatA ) encoding CAT-A catalase , a homologue of the maize catalase isozyme 3 ( CAT-3 ) from rice ( Oryza sativa L ) .
[ Sen. 13, subscore: 2.00 ]: DNA methylation , especially of either one or both of the deoxyadenosines at the two GATC motifs ( one in the first exon and the other in the first intron of the rice CatA gene ) , appeared to be responsible for the CatA promoter activity identified in the transient assay .
[ Sen. 3, subscore: 1.00 ]: Several sequence motifs found in the promoters of plant seed-specific genes were identified in the 5-upstream non-coding region of the CatA gene .
[ Sen. 4, subscore: 1.00 ]: Northern blotting showed that the CatA gene is expressed at high levels in seeds during early development and also in young seedlings .
[ Sen. 5, subscore: 1.00 ]: Methyl viologen ( paraquat ) resulted in the 3-fold induction of the CatA gene in the leaves of young seedlings , whereas abscisic acid , wounding , salicylic acid , and hydrogen peroxide had no or only slight effects .
[ Sen. 6, subscore: 1.00 ]: The 1 . 9 kb 5-upstream fragment ( -1559 to +342 ) of the CatA gene was fused with the Escherichia coli beta-glucuronidase ( GUS ) gene and introduced by electroporation into protoplasts prepared from rice suspension-cultured cells , then the transient expression of the GUS gene was examined .
[ Sen. 12, subscore: 1.00 ]: The chimeric CatA-GUS plasmid DNAs amplified in the methylation-positive strain , E coli DH5alpha , showed GUS gene activities , whereas all the chimeric DNAs amplified in the methylation-deficient E coli JM110 were completely inactive in the presence or absence of ABA in the culture medium .
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Score: 7.00 |
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| Title: The role of catalase-peroxidase secreted by Magnaporthe oryzae during early infection of rice cells .
| | Author: Tanabe S Ishii-Minami N Saitoh K Otake Y Kaku H Shibuya N Nishizawa Y Minami E | | Journal: Mol Plant Microbe Interact Citation: V : 24 P : 163-71 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21043575 Accession (PMID): 21043575 | | Abstract: The biological role of a secretory catalase of the rice blast fungus Magnaporthe oryzae was studied .
The internal amino acid sequences of the partially purified catalase in the culture filtrate enabled us to identify its encoding gene as a catalase-peroxidase gene , CPXB , among four putative genes for catalase or catalase-peroxidase in M oryzae .
Knockout of the gene drastically reduced the level of catalase activity in the culture filtrate and supernatant of conidial suspension ( SCS ) , and increased the sensitivity to exogenously added HO compared with control strains , suggesting that CPXB is the major gene encoding the secretory catalase and confers resistance to HO in hyphae .
In the mutant , the rate of appressoria that induced accumulation of HO in epidermal cells of the leaf sheath increased and infection at early stages was delayed ; however , the formation of lesions in the leaf blade was not affected compared with the control strain .
These phenotypes were complimented by reintroducing the putative coding regions of CPXB driven by a constitutive promoter .
These results suggest that CPXB plays a role in fungal defense against HO accumulated in epidermal cells of rice at the early stage of infection but not in pathogenicity of M oryzae .
| Matching Sentences:
[ Sen. 2, subscore: 4.00 ]: The internal amino acid sequences of the partially purified catalase in the culture filtrate enabled us to identify its encoding gene as a catalase-peroxidase gene , CPXB , among four putative genes for catalase or catalase-peroxidase in M oryzae .
[ Sen. 3, subscore: 2.00 ]: Knockout of the gene drastically reduced the level of catalase activity in the culture filtrate and supernatant of conidial suspension ( SCS ) , and increased the sensitivity to exogenously added HO compared with control strains , suggesting that CPXB is the major gene encoding the secretory catalase and confers resistance to HO in hyphae .
[ Sen. 1, subscore: 1.00 ]: The biological role of a secretory catalase of the rice blast fungus Magnaporthe oryzae was studied .
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Score: 7.00 |
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| Title: Cloning and characterization of catalases from rice , Oryza sativa L | | Author: Wutipraditkul N Boonkomrat S Buaboocha T | | Journal: Biosci Biotechnol Biochem Citation: V : 75 P : 1900-6 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub21979082 Accession (PMID): 21979082 | | Abstract: Catalase is the major H ( 2 ) O ( 2 ) -scavenging enzyme in all aerobic organisms .
From the cDNA sequences of three rice ( Oryza sativa L ) genes that encode for predicted catalases ( OsCatA , OsCatB , and OsCatC ) , complete ORFs were subcloned into pET21a and expressed as ( His ) ( 6 ) -tagged proteins in Escherichia coli .
The recombinant ( His ) ( 6 ) -polypeptides were enriched to apparent homogeneity and characterized .
With H ( 2 ) O ( 2 ) as substrate , the highest catalase k ( cat ) value ( 20+/-1 . 71x10 ( -3 ) min ( -1 ) ) was found in recombinant OsCatB .
The optimum temperatures for catalase activity were 30 degrees C for OsCatA and OsCatC and 25 degrees C for OsCatB , while the pH optima were 8 . 0 , 7 . 5 , and 7 . 0 for OsCatA , OsCatB , and OsCatC respectively .
All the catalases were inhibited by sodium azide , beta-mercaptoethanol , and potassium cyanide , but only weakly by 3-amino-1 , 2 , 4-triazole .
The various catalases exhibited different catalase activities in the presence of different salts at different concentrations , OsCatC showing higher salt inhibitory effects than the two other OsCats .
| Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: The various catalases exhibited different catalase activities in the presence of different salts at different concentrations , OsCatC showing higher salt inhibitory effects than the two other OsCats .
[ Sen. 1, subscore: 1.00 ]: Catalase is the major H ( 2 ) O ( 2 ) -scavenging enzyme in all aerobic organisms .
[ Sen. 2, subscore: 1.00 ]: From the cDNA sequences of three rice ( Oryza sativa L ) genes that encode for predicted catalases ( OsCatA , OsCatB , and OsCatC ) , complete ORFs were subcloned into pET21a and expressed as ( His ) ( 6 ) -tagged proteins in Escherichia coli .
[ Sen. 4, subscore: 1.00 ]: With H ( 2 ) O ( 2 ) as substrate , the highest catalase k ( cat ) value ( 20+/-1 . 71x10 ( -3 ) min ( -1 ) ) was found in recombinant OsCatB .
[ Sen. 5, subscore: 1.00 ]: The optimum temperatures for catalase activity were 30 degrees C for OsCatA and OsCatC and 25 degrees C for OsCatB , while the pH optima were 8 . 0 , 7 . 5 , and 7 . 0 for OsCatA , OsCatB , and OsCatC respectively .
[ Sen. 6, subscore: 1.00 ]: All the catalases were inhibited by sodium azide , beta-mercaptoethanol , and potassium cyanide , but only weakly by 3-amino-1 , 2 , 4-triazole .
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Score: 7.00 |
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| Title: Intron loss and gain during evolution of the catalase gene family in angiosperms .
| | Author: Frugoli JA McPeek MA Thomas TL McClung CR .
| | Journal: Genetics Citation: V : 149 ( 1 ) P : 355-65 Year: 1998 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub9584109 Accession (PMID): 9584109 | | Abstract: Angiosperms ( flowering plants ) , including both monocots and dicots , contain small catalase gene families .
In the dicot , Arabidopsis thaliana , two catalase ( CAT ) genes , CAT1 and CAT3 , are tightly linked on chromosome 1 and a third , CAT2 , which is more similar to CAT1 than to CAT3 , is unlinked on chromosome 4 .
Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved , and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns .
Arabidopsis CAT2 has seven introns ; both CAT1 and CAT3 have six introns in positions conserved with CAT2 , but each has lost a different intron .
We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family .
An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1 .
CAT1 then served as the template for a second duplication , yielding CAT2 .
Intron losses from CAT1 and CAT3 followed these duplications .
One subclade of monocot catalases has lost all but the 5-most and 3-most introns , which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA .
Following this event of concerted intron loss , the Oryza sativa ( rice , a monocot ) CAT1 lineage acquired an intron in a novel position , consistent with a mechanism of intron gain at proto-splice sites . | Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved , and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns .
[ Sen. 1, subscore: 1.00 ]: Angiosperms ( flowering plants ) , including both monocots and dicots , contain small catalase gene families .
[ Sen. 2, subscore: 1.00 ]: In the dicot , Arabidopsis thaliana , two catalase ( CAT ) genes , CAT1 and CAT3 , are tightly linked on chromosome 1 and a third , CAT2 , which is more similar to CAT1 than to CAT3 , is unlinked on chromosome 4 .
[ Sen. 5, subscore: 1.00 ]: We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family .
[ Sen. 6, subscore: 1.00 ]: An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1 .
[ Sen. 9, subscore: 1.00 ]: One subclade of monocot catalases has lost all but the 5-most and 3-most introns , which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA .
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Score: 6.00 |
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| Title: Complementation of yeast Arc1p by the p43 component of the human multisynthetase complex does not require its association with yeast MetRS and GluRS .
| | Author: Golinelli-Cohen MP Zakrzewska A Mirande M | | Journal: J Mol . Biol . Citation: V : 340 ( 1 ) P : 15-27 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15184019 Accession (PMID): 15184019 | | Abstract: Yeast Arc1p , human p43 and plant methionyl-tRNA synthetase ( MetRS ) possess an EMAPII-like domain capable of non-specific interactions with tRNA .
Arc1p interacts with MetRS ( MES1 ) and GluRS and operates as a tRNA-interacting factor ( tIF ) in trans of these two synthetases .
In plant MetRS , the EMAPII-like domain is fused to the catalytic core of the synthetase and acts as a cis-acting tIF for aminoacylation .
We observed that the catalytic core of plant MetRS expressed from a centromeric plasmid can not complement a yeast arc1 ( - ) mes1 ( - ) strain .
Overexpression of the mutant enzyme from a high-copy number plasmid restored cell growth , suggesting that deletion of its C-terminal tIF domain was responsible for the poor aminoacylation efficiency of that enzyme in vivo .
Accordingly , expression of full-size plant MetRS from a centromeric plasmid , but also of fusion proteins between its catalytic core and the EMAPII-like domains of yeast Arc1p or of human p43 restored cell viability .
These data showed that homologous tIF domains from different origins are interchangeable and may act indifferently in trans or in cis of the catalytic domain of a synthetase .
Unexpectedly , co-expression of Arc1p with the catalytic core of plant MetRS restored cell viability as well , even though Arc1p did not associate with plant MetRS .
Because Arc1p also interacts with yeast GluRS , restoration of cell growth could be due at least in part to its role of cofactor for that enzyme .
However , co-expression of human p43 , a tIF that did not associate with plant MetRS or with yeast GluRS and MetRS , also restored cell viability of a yeast strain that expressed the catalytic core of plant MetRS .
These results show that p43 and Arc1p are able to facilitate tRNA aminoacylation in vivo even if they do not interact physically with the synthetases .
We propose that p43/Arc1p may be involved in sequestering tRNAs in the cytoplasm of eukaryotic cells , thereby increasing their availability for protein synthesis . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: In plant MetRS , the EMAPII-like domain is fused to the catalytic core of the synthetase and acts as a cis-acting tIF for aminoacylation .
[ Sen. 4, subscore: 1.00 ]: We observed that the catalytic core of plant MetRS expressed from a centromeric plasmid can not complement a yeast arc1 ( - ) mes1 ( - ) strain .
[ Sen. 6, subscore: 1.00 ]: Accordingly , expression of full-size plant MetRS from a centromeric plasmid , but also of fusion proteins between its catalytic core and the EMAPII-like domains of yeast Arc1p or of human p43 restored cell viability .
[ Sen. 7, subscore: 1.00 ]: These data showed that homologous tIF domains from different origins are interchangeable and may act indifferently in trans or in cis of the catalytic domain of a synthetase .
[ Sen. 8, subscore: 1.00 ]: Unexpectedly , co-expression of Arc1p with the catalytic core of plant MetRS restored cell viability as well , even though Arc1p did not associate with plant MetRS .
[ Sen. 10, subscore: 1.00 ]: However , co-expression of human p43 , a tIF that did not associate with plant MetRS or with yeast GluRS and MetRS , also restored cell viability of a yeast strain that expressed the catalytic core of plant MetRS .
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Score: 6.00 |
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| Title: Catalysis by Glomerella cingulata cutinase requires conformational cycling between the active and inactive states of its catalytic triad .
| | Author: Nyon MP Rice DW Berrisford JM Hounslow AM Moir AJ Huang H Nathan S Mahadi NM Bakar FD Craven CJ | | Journal: J Mol Biol Citation: V : 385 P : 226-35 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18983850 Accession (PMID): 18983850 | | Abstract: Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides .
Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzymes mechanism .
We have solved the crystal structure of Glomerella cingulata cutinase in the absence and in the presence of the inhibitors E600 ( diethyl p-nitrophenyl phosphate ) and PETFP ( 3-phenethylthio-1 , 1 , 1-trifluoropropan-2-one ) to resolutions between 2 . 6 and 1 . 9 A Analysis of these structures reveals that the catalytic triad ( Ser136 , Asp191 , and His204 ) adopts an unusual configuration with the putative essential histidine His204 swung out of the active site into a position where it is unable to participate in catalysis , with the imidazole ring 11 A away from its expected position .
Solution-state NMR experiments are consistent with the disrupted configuration of the triad observed crystallographically .
H204N , a site-directed mutant , was shown to be catalytically inactive , confirming the importance of this residue in the enzyme mechanism .
These findings suggest that , during its catalytic cycle , cutinase undergoes a significant conformational rearrangement converting the loop bearing the histidine from an inactive conformation , in which the histidine of the triad is solvent exposed , to an active conformation , in which the triad assumes a classic configuration .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: We have solved the crystal structure of Glomerella cingulata cutinase in the absence and in the presence of the inhibitors E600 ( diethyl p-nitrophenyl phosphate ) and PETFP ( 3-phenethylthio-1 , 1 , 1-trifluoropropan-2-one ) to resolutions between 2 . 6 and 1 . 9 A Analysis of these structures reveals that the catalytic triad ( Ser136 , Asp191 , and His204 ) adopts an unusual configuration with the putative essential histidine His204 swung out of the active site into a position where it is unable to participate in catalysis , with the imidazole ring 11 A away from its expected position .
[ Sen. 1, subscore: 1.00 ]: Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides .
[ Sen. 2, subscore: 1.00 ]: Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzymes mechanism .
[ Sen. 5, subscore: 1.00 ]: H204N , a site-directed mutant , was shown to be catalytically inactive , confirming the importance of this residue in the enzyme mechanism .
[ Sen. 6, subscore: 1.00 ]: These findings suggest that , during its catalytic cycle , cutinase undergoes a significant conformational rearrangement converting the loop bearing the histidine from an inactive conformation , in which the histidine of the triad is solvent exposed , to an active conformation , in which the triad assumes a classic configuration .
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Score: 6.00 |
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| Title: Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome .
| | Author: Rowland SJ Boocock MR McPherson AL Mouw KW Rice PA Stark WM | | Journal: Mol Microbiol Citation: V : 74 P : 282-98 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19508283 Accession (PMID): 19508283 | | Abstract: The resolvase Sin regulates DNA strand exchange by assembling an elaborate interwound synaptosome containing catalytic and regulatory Sin tetramers , and an architectural DNA-bending protein .
The crystal structure of the regulatory tetramer was recently solved , providing new insights into the structural basis for regulation .
Here we describe the selection and characterization of two classes of Sin mutations that , respectively , bypass or disrupt the functions of the regulatory tetramer .
Activating mutations , which allow the catalytic tetramer to assemble and function independently at site I ( the crossover site ) , were found at approximately 20% of residues in the N-terminal domain .
The most strongly activating mutation ( Q115R ) stabilized a catalytically active synaptic tetramer in vitro .
The positions of these mutations suggest that they act by destabilizing the conformation of the ground-state site I-bound dimers , or by stabilizing the altered conformation of the active catalytic tetramer .
Mutations that block activation by the regulatory tetramer mapped to just two residues , F52 and R54 , supporting a functional role for a previously reported crystallographic dimer-dimer interface .
We suggest how F52/R54 contacts between regulatory and catalytic subunits might promote assembly of the active catalytic tetramer within the synaptosome .
| Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: We suggest how F52/R54 contacts between regulatory and catalytic subunits might promote assembly of the active catalytic tetramer within the synaptosome .
[ Sen. 1, subscore: 1.00 ]: The resolvase Sin regulates DNA strand exchange by assembling an elaborate interwound synaptosome containing catalytic and regulatory Sin tetramers , and an architectural DNA-bending protein .
[ Sen. 4, subscore: 1.00 ]: Activating mutations , which allow the catalytic tetramer to assemble and function independently at site I ( the crossover site ) , were found at approximately 20% of residues in the N-terminal domain .
[ Sen. 5, subscore: 1.00 ]: The most strongly activating mutation ( Q115R ) stabilized a catalytically active synaptic tetramer in vitro .
[ Sen. 6, subscore: 1.00 ]: The positions of these mutations suggest that they act by destabilizing the conformation of the ground-state site I-bound dimers , or by stabilizing the altered conformation of the active catalytic tetramer .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Abrasion as a catalyst deposition technique for carbon nanotube growth .
| | Author: Alvarez NT Pint CL Hauge RH Tour JM | | Journal: J Am Chem Soc Citation: V : 131 P : 15041-8 Year: 2009 Type: PubMed-not-MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19764728 Accession (PMID): 19764728 | | Abstract: Mechanical abrasion of stainless steel ( SS ) surfaces is demonstrated as an effective technique for the deposition of catalyst to support growth of high density layers of carbon nanotubes ( CNTs ) in water-assisted catalytic chemical vapor deposition .
In all cases of Fe-containing materials abraded on Al ( 2 ) O ( 3 ) substrates , CNT growth is observed ; the 400 series of SS appears to deposit catalyst most efficiently .
We demonstrate that this simple abrasion technique enables both micro and nanoscale accuracy in catalyst patterning as well as large area catalyst deposition for uniform , dense CNT growth .
Raman spectroscopy characterization indicates high quality CNTs grown by this approach .
This technique provides an inexpensive and simple route for addition of catalyst for Fe-based surface growth of CNTs .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Mechanical abrasion of stainless steel ( SS ) surfaces is demonstrated as an effective technique for the deposition of catalyst to support growth of high density layers of carbon nanotubes ( CNTs ) in water-assisted catalytic chemical vapor deposition .
[ Sen. 3, subscore: 2.00 ]: We demonstrate that this simple abrasion technique enables both micro and nanoscale accuracy in catalyst patterning as well as large area catalyst deposition for uniform , dense CNT growth .
[ Sen. 2, subscore: 1.00 ]: In all cases of Fe-containing materials abraded on Al ( 2 ) O ( 3 ) substrates , CNT growth is observed ; the 400 series of SS appears to deposit catalyst most efficiently .
[ Sen. 5, subscore: 1.00 ]: This technique provides an inexpensive and simple route for addition of catalyst for Fe-based surface growth of CNTs .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Nanotube nucleation versus carbon-catalyst adhesion--probed by molecular dynamics simulations .
| | Author: Ribas MA Ding F Balbuena PB Yakobson BI | | Journal: J Chem Phys Citation: V : 131 P : 224501 . Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub20001051 Accession (PMID): 20001051 | | Abstract: Catalytic nucleation of carbon nanotubes ( CNTs ) remains a challenge for the theory : Which factors and forces decide if the gathering sp ( 2 ) -network of atoms will adhere to the catalyst particle and fully cover it or the graphitic cap will liberate itself to extend into a hollow filament?
This intimate mechanism can not be seen in experiment , yet it can be investigated through comprehensive molecular dynamics .
We systematically vary the adhesion strength ( W ( ad ) ) of the graphitic cap to the catalyst and temperature T ( and C diffusion rate ) .
Observations allow us to build a statistically representative map of CNT nucleation and define the conditions for growth or metal encapsulation in a fullerene-shell ( catalyst poisoning ) .
It shows clearly that weak W ( ad ) , sufficient thermal kinetic energy ( high T ) or fast C diffusion favor the CNT nucleation .
In particular , below 600 K carbon-diffusion on the catalyst surface limits the growth , but at higher T it fully depends on cap lift-off .
Informed choice of parameters allowed us to obtain the longest simulated nanotube structures .
The study reveals a means of designing the catalyst for better CNT synthesis , potentially at desirably low temperatures .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Catalytic nucleation of carbon nanotubes ( CNTs ) remains a challenge for the theory : Which factors and forces decide if the gathering sp ( 2 ) -network of atoms will adhere to the catalyst particle and fully cover it or the graphitic cap will liberate itself to extend into a hollow filament?
[ Sen. 3, subscore: 1.00 ]: We systematically vary the adhesion strength ( W ( ad ) ) of the graphitic cap to the catalyst and temperature T ( and C diffusion rate ) .
[ Sen. 4, subscore: 1.00 ]: Observations allow us to build a statistically representative map of CNT nucleation and define the conditions for growth or metal encapsulation in a fullerene-shell ( catalyst poisoning ) .
[ Sen. 6, subscore: 1.00 ]: In particular , below 600 K carbon-diffusion on the catalyst surface limits the growth , but at higher T it fully depends on cap lift-off .
[ Sen. 8, subscore: 1.00 ]: The study reveals a means of designing the catalyst for better CNT synthesis , potentially at desirably low temperatures .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 6.00 |
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| Title: Use of traditional cooking fuels and the risk of young adult cataract in rural Bangladesh : a hospital-based case-control study .
| | Author: Tanchangya J Geater AF | | Journal: BMC Ophthalmol Citation: V : 11 P : 16 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21679452 Accession (PMID): 21679452 | | Abstract: BACKGROUND : This study aimed to investigate the independent relationship between the use of various traditional biomass cooking fuels and the occurrence of cataract in young adults in rural Bangladesh .
METHODS : A hospital-based age and sex-matched case-control study incorporating two control groups was conducted .
Cases were cataract patients aged 18 and 49 years diagnosed on the basis of any opacity of the crystalline lens or its capsule and visual acuity poorer than 6/18 on the Log Mar Visual Acuity Chart in either eye , or who had a pseudophakic lens as a result of cataract surgery within the previous 5 years .
Non-eye-disease ( NE ) controls were selected from patients from ENT or Orthopaedics departments and non-cataract eye-disease ( NC ) controls from the Ophthalmology department .
Data pertaining to history of exposure to various cooking fuels and to established risk factors for cataract were obtained by face-to-face interview and analyzed using conditional logistic regression .
RESULTS : Clean fuels were used by only 4% of subjects .
A majority of males ( 64-80% depending on group ) had never cooked , while the rest had used biomass cooking fuels , mainly wood/dry leaves , with only 6 having used rice straw and/or cow dung .
All females of each group had used wood/dry leaves for cooking .
Close to half had also used rice straw and/or cow dung .
Among females , after controlling for family history of cataract and education and combining the two control groups , case status was shown to be significantly related to lifetime exposure to rice straw , fitted as a trend variable coded as never , median of all exposed ( OR=1 . 52 , 95%CI 1 . 04-2 . 22 ) , but not to lifetime exposure to wood/dry leaves .
Case status among females showed an inverse association with ever use of cow dung as a cooking fuel ( OR 0 . 43 , 95%CI 0 . 22-0 . 81 ) .
CONCLUSIONS : In this population , where cooking is almost exclusively done using biomass fuels , cases of young adult cataract among females were more likely to have had an increased lifetime exposure to cooking with rice straw fuel and not to have cooked using cow dung fuel .
There is a possibility that these apparent associations could have been the result of uncontrolled founding , for instance by wealth .
The nature of the associations , therefore , needs to be further investigated .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Cases were cataract patients aged 18 and 49 years diagnosed on the basis of any opacity of the crystalline lens or its capsule and visual acuity poorer than 6/18 on the Log Mar Visual Acuity Chart in either eye , or who had a pseudophakic lens as a result of cataract surgery within the previous 5 years .
[ Sen. 1, subscore: 1.00 ]: BACKGROUND : This study aimed to investigate the independent relationship between the use of various traditional biomass cooking fuels and the occurrence of cataract in young adults in rural Bangladesh .
[ Sen. 5, subscore: 1.00 ]: Data pertaining to history of exposure to various cooking fuels and to established risk factors for cataract were obtained by face-to-face interview and analyzed using conditional logistic regression .
[ Sen. 10, subscore: 1.00 ]: Among females , after controlling for family history of cataract and education and combining the two control groups , case status was shown to be significantly related to lifetime exposure to rice straw , fitted as a trend variable coded as never , median of all exposed ( OR=1 . 52 , 95%CI 1 . 04-2 . 22 ) , but not to lifetime exposure to wood/dry leaves .
[ Sen. 12, subscore: 1.00 ]: CONCLUSIONS : In this population , where cooking is almost exclusively done using biomass fuels , cases of young adult cataract among females were more likely to have had an increased lifetime exposure to cooking with rice straw fuel and not to have cooked using cow dung fuel .
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Score: 6.00 |
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| Title: Expression and purification of soluble bio-active rice plant catalase-A from recombinant Escherichia coli .
| | Author: Ray M Mishra P Das P Sabat SC | | Journal: J Biotechnol Citation: V : 157 P : 12-9 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub21978604 Accession (PMID): 21978604 | | Abstract: Catalase in plants is a heme-coordinated tetrameric protein that primarily disproportionates hydrogen peroxide into water and oxygen .
It plays an important role in maintaining cellular concentration of hydrogen peroxide to a level , necessary for all aspects of normal plant growth and development .
Except for its recombinant expression in transgenic plants and insect cell line , the protein is yet to be synthesized in its bio-active form in prokaryotic expression system .
Attempts made in past for recombinant expression of plant catalase in Escherichia coli consistently resulted in formation of insoluble and inactive aggregates of inclusion body .
Here we have shown the specific requirement of a thioredoxin fusion partner , the involvement of trigger factor protein and the low temperature treatment during induction period for synthesis of completely solubilized rice plant catalase-A in recombinant E coli .
Furthermore , the bacteria required the supplementation of delta-aminolevulinic acid to produce bio-active recombinant rice catalase-A The molecular and biochemical properties of the purified recombinant protein showed the characteristic features of a typical mono-functional plant catalase .
These results attest to the usefulness of the present protocol for production of plant catalase using E coli as heterologous expression system .
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[ Sen. 6, subscore: 2.00 ]: Furthermore , the bacteria required the supplementation of delta-aminolevulinic acid to produce bio-active recombinant rice catalase-A The molecular and biochemical properties of the purified recombinant protein showed the characteristic features of a typical mono-functional plant catalase .
[ Sen. 1, subscore: 1.00 ]: Catalase in plants is a heme-coordinated tetrameric protein that primarily disproportionates hydrogen peroxide into water and oxygen .
[ Sen. 4, subscore: 1.00 ]: Attempts made in past for recombinant expression of plant catalase in Escherichia coli consistently resulted in formation of insoluble and inactive aggregates of inclusion body .
[ Sen. 5, subscore: 1.00 ]: Here we have shown the specific requirement of a thioredoxin fusion partner , the involvement of trigger factor protein and the low temperature treatment during induction period for synthesis of completely solubilized rice plant catalase-A in recombinant E coli .
[ Sen. 7, subscore: 1.00 ]: These results attest to the usefulness of the present protocol for production of plant catalase using E coli as heterologous expression system .
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Score: 6.00 |
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| Title: Crystal structure of rice rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate .
| | Author: Matsumura H Mizohata E Ishida H Kogami A Ueno T Makino A Inoue T Yokota A Mae T Kai Y | | Journal: J Mol Biol Citation: V : 422 P : 75-86 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub22609438 Accession (PMID): 22609438 | | Abstract: The key enzyme of plant photosynthesis , d-ribulose 1 , 5-bisphosphate carboxylase/oxygenase ( Rubisco ) , must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg ( 2+ ) coordination .
Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate ( NADPH ) and 6-phosphogluconate ( 6PG ) function as positive effectors to promote activation .
However , the structural mechanism remains unknown .
Here , we have determined the crystal structures of activated rice Rubisco in complex with NADPH , 6PG , or 2-carboxy-d-arabinitol 1 , 5-bisphosphate ( 2CABP ) .
The structures of the NADPH and 6PG complexes adopt open-state conformations , in which loop 6 at the catalytic site and some other loops are disordered .
The structure of the 2CABP complex is in a closed state , similar to the previous 2CABP-bound activated structures from other sources .
The catalytic sites of the NADPH and 6PG complexes are fully activated , despite the fact that bicarbonate ( NaHCO ( 3 ) ) was not added into the crystallization solution .
In the catalytic site , NADPH does not interact with Mg ( 2+ ) directly but interacts with Mg ( 2+ ) -coordinated water molecules , while 6PG interacts with Mg ( 2+ ) directly .
These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg ( 2+ ) and the carbamylated Lys201 with unique interactions and preventing its dissociation .
The structure also reveals that the relaxed complex of the effectors ( NADPH or 6PG ) , distinct from the tight-binding mode of 2CABP , would allow rapid exchange of the effectors in the catalytic sites by substrate d-ribulose 1 , 5-bisphosphate for catalysis in physiological conditions .
| Matching Sentences:
[ Sen. 10, subscore: 2.00 ]: The structure also reveals that the relaxed complex of the effectors ( NADPH or 6PG ) , distinct from the tight-binding mode of 2CABP , would allow rapid exchange of the effectors in the catalytic sites by substrate d-ribulose 1 , 5-bisphosphate for catalysis in physiological conditions .
[ Sen. 1, subscore: 1.00 ]: The key enzyme of plant photosynthesis , d-ribulose 1 , 5-bisphosphate carboxylase/oxygenase ( Rubisco ) , must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg ( 2+ ) coordination .
[ Sen. 5, subscore: 1.00 ]: The structures of the NADPH and 6PG complexes adopt open-state conformations , in which loop 6 at the catalytic site and some other loops are disordered .
[ Sen. 7, subscore: 1.00 ]: The catalytic sites of the NADPH and 6PG complexes are fully activated , despite the fact that bicarbonate ( NaHCO ( 3 ) ) was not added into the crystallization solution .
[ Sen. 8, subscore: 1.00 ]: In the catalytic site , NADPH does not interact with Mg ( 2+ ) directly but interacts with Mg ( 2+ ) -coordinated water molecules , while 6PG interacts with Mg ( 2+ ) directly .
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Score: 6.00 |
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| Title: Mechanistic role of an NS4A peptide cofactor with the truncated NS3 protease of hepatitis C virus : elucidation of the NS4A stimulatory effect via kinetic analysis and inhibitor mapping .
| | Author: Landro JA Raybuck SA Luong YP OMalley ET Harbeson SL Morgenstern KA Rao G Livingston DJ .
| | Journal: Biochemistry Citation: V : 36 ( 31 ) P : 9340-8 Year: 1997 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub9235976 Accession (PMID): 9235976 | | Abstract: Infection by hepatitis C viruses ( HCVs ) is a serious medical problem with no broadly effective treatment available for the progression of chronic hepatitis .
The catalytic activity of a viral serine protease located in the N-terminal one-third of nonstructural protein 3 ( NS3 ) is required for polyprotein processing at four site-specific junctions .
The three-dimensional crystal structure of the NS3-NS4A co-complex [ Kim , J L , Morgenstern , K A , Lin , C , Fox , T , Dwyer , M D , Landro , J A , Chambers , S P , Markland , W , Lepre , C A , OMalley , E T , Harbeson , S L , Rice , C M , Murcko , M A , Caron , P R , & Thomson , J A ( 1996 ) Cell 87 , 343-355 ] delineates a small hydrophobic region within the 54-residue NS4A protein that intercalates with and makes extensive contacts to the core of the protease .
The current investigation addresses the mechanism of NS3 protease catalytic activation by NS4A utilizing a small synthetic NS4A peptide ( residues 1678-1691 of the virus polyprotein sequence ) and the recombinantly expressed protease domain of NS3 .
The addition of NS4A dramatically increased NS3 kcat and kcat/Km catalytic parameters when measured against small peptide substrates representing the different site-specific junctions of the polyprotein .
The catalytic effect of natural and non-natural amino acid substitutions at the P1 position in a 5A/5B peptide substrate was investigated .
NS3-NS4A demonstrated a marked catalytic preference for the cysteine residue commonly found in authentic substrates .
The pH dependence of the NS3 hydrolysis reaction is not affected by the presence of NS4A .
This result suggests that NS4A does not change the pKa values of the active site residues of NS3 protease .
A steady state kinetic analysis was performed and indicated that the binding of NS4A and the peptide substrate occurs in an ordered fashion during the catalytic cycle , with NS4A binding first Two distinct kinetic classes of peptidyl inhibitors based upon the 5A/5B cleavage site were identified .
An NS4A-independent class is devoid of prime residues .
A second class of inhibitors is NS4A-dependent and contains a natural or non-natural cyclic amino acid substituted for the commonly found P1 residue serine .
These inhibitors display an up to 80-fold increase in affinity for NS3 protease in the presence of NS4A .
Sequential truncation of prime and P residues from this inhibitor class demonstrated the fact that the P4 and P1 residues are crucial for potent inhibition .
The selectivity of this NS4A effect is interpreted using a model of the 5A/5B decapeptide substrate bound to the active site of the NS3-NS4A structure .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The catalytic activity of a viral serine protease located in the N-terminal one-third of nonstructural protein 3 ( NS3 ) is required for polyprotein processing at four site-specific junctions .
[ Sen. 4, subscore: 1.00 ]: The current investigation addresses the mechanism of NS3 protease catalytic activation by NS4A utilizing a small synthetic NS4A peptide ( residues 1678-1691 of the virus polyprotein sequence ) and the recombinantly expressed protease domain of NS3 .
[ Sen. 5, subscore: 1.00 ]: The addition of NS4A dramatically increased NS3 kcat and kcat/Km catalytic parameters when measured against small peptide substrates representing the different site-specific junctions of the polyprotein .
[ Sen. 6, subscore: 1.00 ]: The catalytic effect of natural and non-natural amino acid substitutions at the P1 position in a 5A/5B peptide substrate was investigated .
[ Sen. 7, subscore: 1.00 ]: NS3-NS4A demonstrated a marked catalytic preference for the cysteine residue commonly found in authentic substrates .
[ Sen. 10, subscore: 1.00 ]: A steady state kinetic analysis was performed and indicated that the binding of NS4A and the peptide substrate occurs in an ordered fashion during the catalytic cycle , with NS4A binding first Two distinct kinetic classes of peptidyl inhibitors based upon the 5A/5B cleavage site were identified .
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Score: 5.00 |
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| Title: Acetylation of rice straw with or without catalysts and its characterization as a natural sorbent in oil spill cleanup .
| | Author: Sun XF Sun R Sun JX .
| | Journal: J Agric .
Food Chem .
Citation: V : 50 ( 22 ) P : 6428-33 Year: 2002 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12381129 Accession (PMID): 12381129 | | Abstract: An investigation of the acetylation of rice straw with acetic anhydride at 100 and 120 degrees C for 1-4 h with four tertiary amine catalysts ( pyridine , 4-dimethylaminopyridine , N-methylpyrrolidine , and N-methylpyrrolidinone ) or without catalyst in a solvent-free system was undertaken , and the extent of acetylation was measured by weight percent gain , which increased with the extent of reaction time and temperature and the amounts of catalyst used .
4-Dimethylaminopyridine was found to be the most effective catalyst of those studied .
At a concentration of 7% of the catalyst in acetic anhydride , a weight percent gain of 15 . 4% was realized , compared with 11 . 2% for the noncatalyst reaction , after 0 . 5 h of exposure to the system at 120 degrees C Characterization of acetylated straw was performed by FT-IR , CP MAS ( 13 ) C NMR , and thermal studies .
Interestingly , the acetylated straw is significantly hydrophobic and does not get wet with water , thereby offering potential for the better utilization of cheap waste materials as natural sorbents in oil cleanup . | Matching Sentences:
[ Sen. 1, subscore: 3.00 ]: An investigation of the acetylation of rice straw with acetic anhydride at 100 and 120 degrees C for 1-4 h with four tertiary amine catalysts ( pyridine , 4-dimethylaminopyridine , N-methylpyrrolidine , and N-methylpyrrolidinone ) or without catalyst in a solvent-free system was undertaken , and the extent of acetylation was measured by weight percent gain , which increased with the extent of reaction time and temperature and the amounts of catalyst used .
[ Sen. 2, subscore: 1.00 ]: 4-Dimethylaminopyridine was found to be the most effective catalyst of those studied .
[ Sen. 3, subscore: 1.00 ]: At a concentration of 7% of the catalyst in acetic anhydride , a weight percent gain of 15 . 4% was realized , compared with 11 . 2% for the noncatalyst reaction , after 0 . 5 h of exposure to the system at 120 degrees C Characterization of acetylated straw was performed by FT-IR , CP MAS ( 13 ) C NMR , and thermal studies .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Iron incorporated heterogeneous catalyst from rice husk ash .
| | Author: Adam F Kandasamy K Balakrishnan S | | Journal: Citation: V : 304 ( 1 ) P : 137-43 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16996077 Accession (PMID): 16996077 | | Abstract: Silica supported iron catalyst was prepared from rice husk ash ( RHA ) via the sol-gel technique using an aqueous solution of iron ( III ) salt in 3 . 0 M HNO ( 3 ) .
The sample was dried at 110 degrees C and labeled as RHA-Fe .
A sample of RHA-Fe was calcined at 700 degrees C for 5 h and labeled as RHA-Fe700 .
X-ray diffraction spectrogram showed that both RHA-Fe and RHA-Fe700 were amorphous .
The SEM/EDX results showed that the metal was present as agglomerates and the Fe ions were not homogeneously distributed in RHA-Fe but RHA-Fe700 was shown to be homogeneous .
The specific surface areas for RHA-Fe and RHA-Fe700 were determined by BET nitrogen adsorption studies and found to be 87 . 4 and 55 . 8 m ( 2 ) g ( -1 ) , respectively .
Both catalysts showed high activity in the reaction between toluene and benzyl chloride .
The mono-substituted benzyltoluene was the major product and both catalysts yielded more than 92% of the product .
The GC showed that both the ortho and para-substituted monoisomers were present in about equal quantities .
The minor products consisting of 16 di-substituted isomers were also observed in the GC-MS spectra of both catalytic products .
The catalyst was found to be reusable without loss of activity and with no leaching of the metal | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Silica supported iron catalyst was prepared from rice husk ash ( RHA ) via the sol-gel technique using an aqueous solution of iron ( III ) salt in 3 . 0 M HNO ( 3 ) .
[ Sen. 7, subscore: 1.00 ]: Both catalysts showed high activity in the reaction between toluene and benzyl chloride .
[ Sen. 8, subscore: 1.00 ]: The mono-substituted benzyltoluene was the major product and both catalysts yielded more than 92% of the product .
[ Sen. 10, subscore: 1.00 ]: The minor products consisting of 16 di-substituted isomers were also observed in the GC-MS spectra of both catalytic products .
[ Sen. 11, subscore: 1.00 ]: The catalyst was found to be reusable without loss of activity and with no leaching of the metal
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Enzymatic synthesis of cello-oligosaccharides by rice BGlu1 { beta } -glucosidase glycosynthase mutants .
| | Author: Hommalai G Withers SG Chuenchor W Cairns JR Svasti J | | Journal: Citation: V : ( ) P : Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17405771 Accession (PMID): 17405771 | | Abstract: Rice ( BGlu1 ) beta-glucosidase is a glycosyl hydrolase family 1 enzyme that acts as an exoglucanase on beta- ( 1 , 4 ) - and short beta- ( 1 , 3 ) -linked gluco-oligosaccharides .
Mutations of BGlu1 beta-glucosidase at glutamate residue 414 of its natural precursor destroyed the enzymes catalytic activity , but the enzyme could be rescued in the presence of the anionic nucleophiles formate and azide , which verifies that this residue is the catalytic nucleophile .
The catalytic activities of three candidate mutants , E414G , E414S , and E414A , in the presence of the nucleophiles were compared .
The E414G mutant had approximately 25 and 1400-fold higher catalytic efficiency than E414A and E414S , respectively .
All three mutants could catalyze the synthesis of mixed length oligosaccharides by transglucosylation , when alpha-glucosyl fluoride was used as donor and pNP-cellobioside as acceptor .
The E414G mutant gave the fastest transglucosylation rate , which was approximately 3 and 19 fold faster than E414S and E414A , respectively , and gave yields of up to 70-80 % insoluble products with a donor : acceptor ratio of 5 : 1 .
( 13 ) C-NMR , methylation analysis and electrospray ionization mass spectrometry showed that the insoluble products were beta- ( 1 , 4 ) -linked oligomers with a degree of polymerization ( DP ) of 5 to at least 11 .
The BGlu1 E414G glycosynthase was found to prefer longer chain length oligosaccharides that occupy at least three sugar residue binding subsites as acceptors for productive transglucosylation .
This is the first report of a beta-glucansynthase derived from an exoglycosidase that can produce long chain cello-oligosaccharides , which likely reflects the extended oligosaccharide binding site of rice BGlu1 beta-glucosidase .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: Mutations of BGlu1 beta-glucosidase at glutamate residue 414 of its natural precursor destroyed the enzymes catalytic activity , but the enzyme could be rescued in the presence of the anionic nucleophiles formate and azide , which verifies that this residue is the catalytic nucleophile .
[ Sen. 3, subscore: 1.00 ]: The catalytic activities of three candidate mutants , E414G , E414S , and E414A , in the presence of the nucleophiles were compared .
[ Sen. 4, subscore: 1.00 ]: The E414G mutant had approximately 25 and 1400-fold higher catalytic efficiency than E414A and E414S , respectively .
[ Sen. 5, subscore: 1.00 ]: All three mutants could catalyze the synthesis of mixed length oligosaccharides by transglucosylation , when alpha-glucosyl fluoride was used as donor and pNP-cellobioside as acceptor .
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Score: 5.00 |
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| Title: Growth , new growth , and amplification of carbon nanotubes as a function of catalyst composition .
| | Author: Crouse CA Maruyama B Colorado R Jr Back T Barron AR | | Journal: J Am Chem Soc Citation: V : 130 P : 7946-54 Year: 2008 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub18507464 Accession (PMID): 18507464 | | Abstract: Carbon nanotubes ( CNTs ) have been grown using Fe , Co , Ni , and Co/Fe spin-on-catalyst ( SOC ) systems , involving the metal salt dispersed with a spin-on-glass precursor .
During initial growth runs ( CH4/H2/900 degrees C ) , the CNT yield followed the order Co-SOC > Fe-SOC >> Ni-SOC .
The Fe catalysts produced the longest nanotubes at the expense of a larger average CNT diameter and broader diameter distribution than the Co-SOC system .
A series of Co/Fe-SOCs were prepared where as the atomic percentage of Co is increased nucleation of CNT increases but the CNT length decreases .
The linear relationship between the diameter and length of CNTs grown from the Co/Fe-SOC suggests that slow growth is beneficial with respect to control over CNT diameter .
After initial CNT growth , the original samples were subjected to additional growth runs .
Four individual reactions were observed in the Fe-SOC and binary Co/Fe-SOC : regrowth ( amplification ) , double growth ( a second CNT growing from a previously active catalyst ) , CNT etching , and nucleation from initially inactive catalysts ( new growth ) .
CNT etching was observed for the mixed catalyst systems ( Co/Fe-SOC ) but not for either Fe-SOC or Co-SOC .
During the regrowth experiments , CNTs were observed that were not present after the initial growth run ( and were not as a result of amplification or double growth ) .
Thus , catalysts , which were initially inactive toward nucleation of CNTs in the original growth run , are capable of becoming activated when placed back into the furnace and submitted to regrowth under identical conditions .
| Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Four individual reactions were observed in the Fe-SOC and binary Co/Fe-SOC : regrowth ( amplification ) , double growth ( a second CNT growing from a previously active catalyst ) , CNT etching , and nucleation from initially inactive catalysts ( new growth ) .
[ Sen. 3, subscore: 1.00 ]: The Fe catalysts produced the longest nanotubes at the expense of a larger average CNT diameter and broader diameter distribution than the Co-SOC system .
[ Sen. 8, subscore: 1.00 ]: CNT etching was observed for the mixed catalyst systems ( Co/Fe-SOC ) but not for either Fe-SOC or Co-SOC .
[ Sen. 10, subscore: 1.00 ]: Thus , catalysts , which were initially inactive toward nucleation of CNTs in the original growth run , are capable of becoming activated when placed back into the furnace and submitted to regrowth under identical conditions .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Co-expression of GroEL/ES enhances the expression of plant catalase in bacterial cytosol .
| | Author: Mondal P Ray M Sahu S Sabat SC | | Journal: Protein Pept Lett Citation: V : 15 P : 1075-8 Year: 2008 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19075818 Accession (PMID): 19075818 | | Abstract: Expression of plant proteins in E coli is frequently unsuccessful , but soluble and functional rice catalase-B can be produced in E coli when it is co-expressed with the chaperone GroEL/ES .
The rice catalase exhibited properties typical for a catalase including the decomposition of H ( 2 ) O ( 2 ) and inhibition by aminotriazole , a specific inhibitor for plant and animal catalases .
This achievement records for first time the successful expression of a both native and variant rice plant catalase in bacterial cytosol suggesting that it may be an option to be considered for the expression of other plant proteins in E coli .
| Matching Sentences:
[ Sen. 2, subscore: 3.00 ]: The rice catalase exhibited properties typical for a catalase including the decomposition of H ( 2 ) O ( 2 ) and inhibition by aminotriazole , a specific inhibitor for plant and animal catalases .
[ Sen. 1, subscore: 1.00 ]: Expression of plant proteins in E coli is frequently unsuccessful , but soluble and functional rice catalase-B can be produced in E coli when it is co-expressed with the chaperone GroEL/ES .
[ Sen. 3, subscore: 1.00 ]: This achievement records for first time the successful expression of a both native and variant rice plant catalase in bacterial cytosol suggesting that it may be an option to be considered for the expression of other plant proteins in E coli .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis .
| | Author: Zhu G Ye N Zhang J | | Journal: Plant Cell Physiol Citation: V : 50 P : 644-51 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19208695 Accession (PMID): 19208695 | | Abstract: Both glucose and ABA play crucial roles in the regulation of seed germination and post-germination development .
In Arabidopsis thaliana , up-regulation of ABA biosynthesis is suggested as one of the possible mechanisms mediating the glucose-induced delay in seed germination .
Since the endogenous ABA level is controlled by the equilibrium between ABA biosynthesis and catabolism , we investigated how this equilibrium is related to the regulation of seed germination by glucose in rice .
When ABA biosynthesis was inhibited by nordihydroguaiaretic acid ( NDGA ) , an inhibitor of the ABA anabolic enzyme 9-cis-epoxycarotenoid dioxygenase ( NCED ) , rice seed germination showed no response .
In contrast , inhibition of ABA catabolism by diniconazole significantly arrested seed germination , suggesting that the regulation of ABA catabolism plays a major role .
Further experiments indicated that the expression of OsABA8ox3 , a key gene in ABA catabolism and encoding ABA 8-hydroxylase in rice , was significantly increased during the first 6 h of imbibition , which was consistent with the decline of ABA content in the imbibed seeds .
Expression of OsABA8ox genes , especially OsABA8ox2 and OsABA8ox3 , was sensitively suppressed in the presence of exogenously supplied glucose .
In contrast , the expression profiles of OsNCED genes that control the limiting step of ABA biosynthesis showed no significant changes in response to low levels of glucose .
Our results demonstrated that the glucose-induced delay of seed germination is a result of the suppression of ABA catabolism rather than any enhancement of ABA biosynthesis during rice seed germination .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: In contrast , inhibition of ABA catabolism by diniconazole significantly arrested seed germination , suggesting that the regulation of ABA catabolism plays a major role .
[ Sen. 3, subscore: 1.00 ]: Since the endogenous ABA level is controlled by the equilibrium between ABA biosynthesis and catabolism , we investigated how this equilibrium is related to the regulation of seed germination by glucose in rice .
[ Sen. 6, subscore: 1.00 ]: Further experiments indicated that the expression of OsABA8ox3 , a key gene in ABA catabolism and encoding ABA 8-hydroxylase in rice , was significantly increased during the first 6 h of imbibition , which was consistent with the decline of ABA content in the imbibed seeds .
[ Sen. 9, subscore: 1.00 ]: Our results demonstrated that the glucose-induced delay of seed germination is a result of the suppression of ABA catabolism rather than any enhancement of ABA biosynthesis during rice seed germination .
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Score: 5.00 |
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| Title: Catalytic conversion of sugarcane bagasse , rice husk and corncob in the presence of TiO2 , ZrO2 and mixed-oxide TiO2-ZrO2 under hot compressed water ( HCW ) condition .
| | Author: Chareonlimkun A Champreda V Shotipruk A Laosiripojana N | | Journal: Bioresour Technol Citation: V : 101 P : 4179-86 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20137923 Accession (PMID): 20137923 | | Abstract: The simultaneous hydrolysis/dehydration reaction of sugarcane bagasse , rice husk and corncob was studied under hot compressed water in the presence of TiO ( 2 ) , ZrO ( 2 ) and TiO ( 2 ) -ZrO ( 2 ) at 473-673K .
Among them , the reaction of corncob at 573K in the presence of TiO ( 2 ) -ZrO ( 2 ) produced the highest furfural and 5-hydroxymethylfurfural ( HMF ) yields ( 10 . 3% and 8 . 6% ) with less by-products ( ie glucose , fructose , xylose , and 1 , 6-anhydroglucose ) selectivities .
It was found that the catalyst preparation procedure and calcination temperature strongly affected its reactivity .
Catalysts prepared by ( co- ) precipitation method gained higher reactivity than those prepared by sol-gel and physical mixing methods .
The suitable calcination temperature for TiO ( 2 ) and ZrO ( 2 ) was at 773K , whereas that for TiO ( 2 ) -ZrO ( 2 ) was at 873K ; the XRD patterns revealed that different portions of phase formation were observed over catalysts with different calcination temperature .
The portion of these phase formations affected the acidity-basicity of catalyst and thus the catalyst reactivity .
| Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: The portion of these phase formations affected the acidity-basicity of catalyst and thus the catalyst reactivity .
[ Sen. 3, subscore: 1.00 ]: It was found that the catalyst preparation procedure and calcination temperature strongly affected its reactivity .
[ Sen. 4, subscore: 1.00 ]: Catalysts prepared by ( co- ) precipitation method gained higher reactivity than those prepared by sol-gel and physical mixing methods .
[ Sen. 5, subscore: 1.00 ]: The suitable calcination temperature for TiO ( 2 ) and ZrO ( 2 ) was at 773K , whereas that for TiO ( 2 ) -ZrO ( 2 ) was at 873K ; the XRD patterns revealed that different portions of phase formation were observed over catalysts with different calcination temperature .
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Score: 5.00 |
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| Title: Preparation of biodiesel from rice bran fatty acids catalyzed by heterogeneous cesium-exchanged 12-tungstophosphoric acids .
| | Author: Srilatha K Sree R Prabhavathi Devi BL Sai Prasad PS Prasad RB Lingaiah N | | Journal: Bioresour Technol Citation: V : 116 P : 53-7 Year: 2012 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub22609655 Accession (PMID): 22609655 | | Abstract: Biodiesel synthesis from rice bran fatty acids ( RBFA ) was carried out using cesium exchanged 12-tungstophosphoric acid ( TPA ) catalysts .
The physico-chemical properties of the catalysts were derived from X-ray diffraction ( XRD ) , Fourier transform infrared ( FTIR ) , temperature programmed desorption ( TPD ) of NH ( 3 ) and scanning electron microscopy ( SEM ) .
The characterization techniques revealed that the Keggin structure of TPA remained intact as Cs replaced protons .
The partial exchange of Cs for protons resulted in an increase in acidity and the catalysts with one Cs ( + ) ( Cs ( 1 ) H ( 2 ) PW ( 12 ) O ( 40 ) ) showed highest acidity .
Under optimized conditions about 92% conversion of RBFA was obtained .
The catalyst was reused for five times and retained of its original activity .
Pseudo-first order model was applied to correlate the experimental kinetic data .
Modified tungstophosphoric acids are efficient solid acid catalysts for the synthesis of biodiesel from the oils containing high FFA .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Biodiesel synthesis from rice bran fatty acids ( RBFA ) was carried out using cesium exchanged 12-tungstophosphoric acid ( TPA ) catalysts .
[ Sen. 2, subscore: 1.00 ]: The physico-chemical properties of the catalysts were derived from X-ray diffraction ( XRD ) , Fourier transform infrared ( FTIR ) , temperature programmed desorption ( TPD ) of NH ( 3 ) and scanning electron microscopy ( SEM ) .
[ Sen. 4, subscore: 1.00 ]: The partial exchange of Cs for protons resulted in an increase in acidity and the catalysts with one Cs ( + ) ( Cs ( 1 ) H ( 2 ) PW ( 12 ) O ( 40 ) ) showed highest acidity .
[ Sen. 6, subscore: 1.00 ]: The catalyst was reused for five times and retained of its original activity .
[ Sen. 8, subscore: 1.00 ]: Modified tungstophosphoric acids are efficient solid acid catalysts for the synthesis of biodiesel from the oils containing high FFA .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: A comparative proteomic approach to analyse structure , function and evolution of rice chitinases : a step towards increasing plant fungal resistance .
| | Author: Sarma K Dehury B Sahu J Sarmah R Sahoo S Sahu M Sen P Modi MK Barooah M | | Journal: J Mol Model Citation: V : P : Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22684798 Accession (PMID): 22684798 | | Abstract: Glycoside hydrolase family 19 chitinases ( EC 3 . 2 . 1 . 14 ) widely distributed in plants , bacteria and viruses catalyse the hydrolysis of chitin and play a major role in plant defense mechanisms and development .
Rice possesses several classes of chitinase , out of which a single structure of class I has been reported in PDB to date .
In the present study an attempt was made to gain more insight into the structure , function and evolution of class I , II and IV chitinases of GH family 19 from rice .
The three-dimensional structures of chitinases were modelled and validated based on available X-ray crystal structures .
The structural study revealed that they are highly alpha-helical and bilobed in nature .
These enzymes are single or multi domain and multi-functional in which chitin-binding domain ( CBD ) and catalytic domain ( CatD ) are present in class I and IV whereas class II lacks CBD .
The CatD possesses a catalytic triad which is thought to be involved in catalytic process .
Loop III , which is common in all three classes of chitinases , reflects that it may play a significant role in their function .
Our study also confirms that the absence and presence of different loops in GH family 19 of rice may be responsible for various sized products .
Molecular phylogeny revealed chitinases in monocotyledons and dicotyledons differed from each other forming two different clusters and may have evolved differentially .
More structural study of this enzyme from different plants is required to enhance the knowledge of catalytic mechanism and substrate binding .
| Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: The CatD possesses a catalytic triad which is thought to be involved in catalytic process .
[ Sen. 1, subscore: 1.00 ]: Glycoside hydrolase family 19 chitinases ( EC 3 . 2 . 1 . 14 ) widely distributed in plants , bacteria and viruses catalyse the hydrolysis of chitin and play a major role in plant defense mechanisms and development .
[ Sen. 6, subscore: 1.00 ]: These enzymes are single or multi domain and multi-functional in which chitin-binding domain ( CBD ) and catalytic domain ( CatD ) are present in class I and IV whereas class II lacks CBD .
[ Sen. 11, subscore: 1.00 ]: More structural study of this enzyme from different plants is required to enhance the knowledge of catalytic mechanism and substrate binding .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Screening of rice genes from the cDNA catalog using the data obtained by protein sequencing .
| | Author: Hirano H | | Journal: J Protein Chem .
Citation: V : 16 ( 5 ) P : 533-6 Year: 1997 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub9246640 Accession (PMID): 9246640 | | Abstract: The partial amino acid sequences of 121 rice proteins separated by two-dimensional gel electrophoresis ( 2D-PAGE ) , were determined for a protein sequence data file .
In the Rice Genome Research Program ( RGP ) , more than 20 , 000 cDNA clones randomly selected from rice cDNA libraries have been sequenced to construct a cDNA catalog .
Complimentary DNAs encoding about 30% of proteins in the protein sequence data file could be identified in the catalog by computer search .
It was deduced that 20 , 000-40 , 000 genes are present in the rice genome .
Only half of about 20 , 000 cDNAs sequenced in the RGP , corresponding to 1/4-1/2 of genes present in the entire rice genome , should have unique sequences after considering gene redundancy .
This is consistent with the fact that the cDNAs encoding about 30% of the sequenced proteins could be identified in the catalog .
If the size of the cDNA catalog is enlarged further , cDNAs encoding all proteins separated by 2D-PAGE could be easily identified from the catalog by using the protein sequence data . | Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: If the size of the cDNA catalog is enlarged further , cDNAs encoding all proteins separated by 2D-PAGE could be easily identified from the catalog by using the protein sequence data .
[ Sen. 2, subscore: 1.00 ]: In the Rice Genome Research Program ( RGP ) , more than 20 , 000 cDNA clones randomly selected from rice cDNA libraries have been sequenced to construct a cDNA catalog .
[ Sen. 3, subscore: 1.00 ]: Complimentary DNAs encoding about 30% of proteins in the protein sequence data file could be identified in the catalog by computer search .
[ Sen. 6, subscore: 1.00 ]: This is consistent with the fact that the cDNAs encoding about 30% of the sequenced proteins could be identified in the catalog .
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Score: 4.00 |
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| Title: Catalytic mechanism of scytalone dehydratase : site-directed mutagenisis , kinetic isotope effects , and alternate substrates .
| | Author: Basarab GS Steffens JJ Wawrzak Z Schwartz RS Lundqvist T Jordan DB .
| | Journal: Biochemistry Citation: V : 38 ( 19 ) P : 6012-24 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10320327 Accession (PMID): 10320327 | | Abstract: On the basis of the X-ray crystal structure of scytalone dehydratase complexed with an active center inhibitor [ Lundqvist , T , Rice , J , Hodge , C N , Basarab , G S , Pierce , J and Lindqvist , Y ( 1994 ) Structure ( London ) 2 , 937-944 ] , eight active-site residues were mutated to examine their roles in the catalytic mechanism .
All but one residue ( Lys73 , a potential base in an anti elimination mechanism ) were found to be important to catalysis or substrate binding .
Steady-state kinetic parameters for the mutants support the native roles for the residues ( Asn131 , Asp31 , His85 , His110 , Ser129 , Tyr30 , and Tyr50 ) within a syn elimination mechanism .
Relative substrate specificities for the two physiological substrates , scytalone and veremelone , versus a Ser129 mutant help assign the orientation of the substrates within the active site .
His85Asn was the most damaging mutation to catalysis consistent with its native roles as a general base and a general acid in a syn elimination .
The additive effect of Tyr30Phe and Tyr50Phe mutations in the double mutant is consistent with their roles in protonating the substrates carbonyl through a water molecule .
Studies on a synthetic substrate , which has an anomeric carbon atom which can better stabilize a carbocation than the physiological substrate ( vermelone ) , suggest that His110Asn prefers this substrate over vermelone in order to balance the mutation-imposed weakness in promoting the elimination of hydroxide from substrates .
All mutant enzymes bound a potent active-site inhibitor in near 1 : 1 stoichiometry , thereby supporting their active-site integrity .
An X-ray crystal structure of the Tyr50Phe mutant indicated that both active-site waters were retained , likely accounting for its residual catalytic activity .
Steady-state kinetic parameters with deuterated scytalone gave kinetic isotope effects of 2 . 7 on kcat and 4 . 2 on kcat/Km , suggesting that steps after dehydration partially limit kcat .
Pre-steady-state measurements of a single-enzyme turnover with scytalone gave a rate that was 6-fold larger than kcat . kcat/Km with scytalone has a pKa of 7 . 9 similar to the pKa value for the ionization of the substrates C6 phenolic hydroxyl , whereas kcat was unaffected by pH , indicating that the anionic form of scytalone does not bind well to enzyme .
With an alternate substrate having a pKa above 11 , kcat/Km had a pKa of 9 . 3 likely due to the ionization of Tyr50 .
The non-enzyme-catalyzed rate of dehydration of scytalone was nearly a billion-fold slower than the enzyme-catalyzed rate at pH 7 . 0 and 25 degrees C The non-enzyme-catalyzed rate of dehydration of scytalone had a deuterium kinetic isotope effect of 1 . 2 at pH 7 . 0 and 25 degrees C , and scytalone incorporated deuterium from D2O in the C2 position about 70-fold more rapidly than the dehydration rate .
Thus , scytalone dehydrates through an E1cb mechanism off the enzyme .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: On the basis of the X-ray crystal structure of scytalone dehydratase complexed with an active center inhibitor [ Lundqvist , T , Rice , J , Hodge , C N , Basarab , G S , Pierce , J and Lindqvist , Y ( 1994 ) Structure ( London ) 2 , 937-944 ] , eight active-site residues were mutated to examine their roles in the catalytic mechanism .
[ Sen. 2, subscore: 1.00 ]: All but one residue ( Lys73 , a potential base in an anti elimination mechanism ) were found to be important to catalysis or substrate binding .
[ Sen. 5, subscore: 1.00 ]: His85Asn was the most damaging mutation to catalysis consistent with its native roles as a general base and a general acid in a syn elimination .
[ Sen. 9, subscore: 1.00 ]: An X-ray crystal structure of the Tyr50Phe mutant indicated that both active-site waters were retained , likely accounting for its residual catalytic activity .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular plant vigna angularis | | Author: Kimura S Laosinchai W Itoh T Cui X Linder CR Brown RM .
| | Journal: Citation: V : 11 ( 11 ) P : 2075-86 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10559435 Accession (PMID): 10559435 | | Abstract: The catalytic subunit of cellulose synthase is shown to be associated with the putative cellulose-synthesizing complex ( rosette terminal complex [ TC ] ) in vascular plants .
The catalytic subunit domain of cotton cellulose synthase was cloned using a primer based on a rice expressed sequence tag ( D41261 ) from which a specific primer was constructed to run a polymerase chain reaction that used a cDNA library from 24 days postanthesis cotton fibers as a template .
The catalytic region of cotton cellulose synthase was expressed in Escherichia coli , and polyclonal antisera were produced .
Colloidal gold coupled to goat anti-rabbit secondary antibodies provided a tag for visualization of the catalytic region of cellulose synthase during transmission electron microscopy .
With a freeze-fracture replica labeling technique , the antibodies specifically localized to rosette TCs in the plasma membrane on the P-fracture face .
Antibodies did not specifically label any structures on the E-fracture face .
Significantly , a greater number of immune probes labeled the rosette TCs ( ie , gold particles were 20 nm or closer to the edge of the rosette TC ) than did preimmune probes .
These experiments confirm the long-held hypothesis that cellulose synthase is a component of the rosette TC in vascular plants , proving that the enzyme complex resides within the structure first described by freeze fracture in 1980 .
In addition , this study provides independent proof that the CelA gene is in fact one of the genes for cellulose synthase in vascular plants .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The catalytic subunit of cellulose synthase is shown to be associated with the putative cellulose-synthesizing complex ( rosette terminal complex [ TC ] ) in vascular plants .
[ Sen. 2, subscore: 1.00 ]: The catalytic subunit domain of cotton cellulose synthase was cloned using a primer based on a rice expressed sequence tag ( D41261 ) from which a specific primer was constructed to run a polymerase chain reaction that used a cDNA library from 24 days postanthesis cotton fibers as a template .
[ Sen. 3, subscore: 1.00 ]: The catalytic region of cotton cellulose synthase was expressed in Escherichia coli , and polyclonal antisera were produced .
[ Sen. 4, subscore: 1.00 ]: Colloidal gold coupled to goat anti-rabbit secondary antibodies provided a tag for visualization of the catalytic region of cellulose synthase during transmission electron microscopy .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Crystal structure of rice alpha-galactosidase complexed with D-galactose .
| | Author: Fujimoto Z Kaneko S Momma M Kobayashi H Mizuno H | | Journal: J Biol . Chem . Citation: V : 278 ( 22 ) P : 20313-8 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12657636 Accession (PMID): 12657636 | | Abstract: alpha-Galactosidases catalyze the hydrolysis of alpha-1 , 6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto- ( gluco ) mannans .
The crystal structure of rice alpha-galactosidase has been determined at 1 . 5A resolution using the multiple isomorphous replacement method .
The structure consisted of a catalytic domain and a C-terminal domain and was essentially the same as that of alpha-N-acetylgalactosaminidase , which is the same member of glycosyl hydrolase family 27 .
The catalytic domain had a ( beta/alpha ) 8-barrel structure , and the C-terminal domain was made up of eight beta-strands containing a Greek key motif .
The structure was solved as a complex with d-galactose , providing a mode of substrate binding in detail .
The d-galactose molecule was found bound in the active site pocket on the C-terminal side of the central beta-barrel of the catalytic domain .
The d-galactose molecule consisted of a mixture of two anomers present in a ratio equal to their natural abundance .
Structural comparisons of rice alpha-galactosidase with chicken alpha-N-acetylgalactosaminidase provided further understanding of the substrate recognition mechanism in these enzymes . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: alpha-Galactosidases catalyze the hydrolysis of alpha-1 , 6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto- ( gluco ) mannans .
[ Sen. 3, subscore: 1.00 ]: The structure consisted of a catalytic domain and a C-terminal domain and was essentially the same as that of alpha-N-acetylgalactosaminidase , which is the same member of glycosyl hydrolase family 27 .
[ Sen. 4, subscore: 1.00 ]: The catalytic domain had a ( beta/alpha ) 8-barrel structure , and the C-terminal domain was made up of eight beta-strands containing a Greek key motif .
[ Sen. 6, subscore: 1.00 ]: The d-galactose molecule was found bound in the active site pocket on the C-terminal side of the central beta-barrel of the catalytic domain .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: In silico modeling and hydrogen peroxide binding study of rice catalase .
| | Author: Sekhar PN Kishor PB Reddy LA Mondal P Dash AK Kar M Mohanty S Sabat SC .
| | Journal: In Silico Biol .
( Gedrukt ) Citation: V : 6 ( 5 ) P : 435-47 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17274773 Accession (PMID): 17274773 | | Abstract: Homology modeling of the catalase , CatC cloned and sequenced from rice ( Oryza sativa L , cv Ratna an Indica cultivar ) has been performed based on the crystal structure of the catalase CatF ( PDB code 1m7s ) by using the software MODELLER .
With the aid of molecular mechanics and molecular dynamics methods , the final model is obtained and is further assessed by PROCHECK and VERIFY - 3D graph , which show that the final refined model is reliable .
With this model , a flexible docking study with the hydrogen peroxide , the substrate for catalase , is performed and the results indicate that Arg310 , Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate .
These hydrogen-bonding interactions play an important role for the stability of the complex Our results may be helpful for further experimental investigations .
| Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Homology modeling of the catalase , CatC cloned and sequenced from rice ( Oryza sativa L , cv Ratna an Indica cultivar ) has been performed based on the crystal structure of the catalase CatF ( PDB code 1m7s ) by using the software MODELLER .
[ Sen. 3, subscore: 2.00 ]: With this model , a flexible docking study with the hydrogen peroxide , the substrate for catalase , is performed and the results indicate that Arg310 , Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Binding and catalytic contributions to site recognition by flp recombinase .
| | Author: Whiteson KL Rice PA | | Journal: J Biol Chem Citation: V : 283 P : 11414-23 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18276592 Accession (PMID): 18276592 | | Abstract: Flp catalyzes site-specific recombination in a highly sequence-specific manner despite making few direct contacts to the bases within its binding site .
Sequence discrimination could take place in the binding and/or the catalytic steps .
In this study , we independently measure the binding affinity and initial cleavage rate of Flp recombinase with approximately 20 designed alternate target DNA sequences .
Our results show that Flp specificity is largely , although not entirely , imparted at the binding step and is the result of a combination of direct and indirect readout .
The Flp binding site includes an A/T-rich region that displays a characteristically narrow minor groove .
We find that many A --> T changes are tolerated at the binding step , whereas C or G substitutions tend to decrease binding affinity .
The effects of the latter can be alleviated by replacing guanine with inosine , which removes the N2 amino group that protrudes into the minor groove .
Some A --> T changes reduce binding affinity , due to clashing with nearby residues , reinforcing that specificity requires avoiding negative contacts as well as creating positive ones .
A tracts , which can lead to unusually rigid DNA structure , are tolerated during the binding step when placed within the region where the minor groove is already narrow .
However , most A tracts slow catalysis more than C or G substitutions .
Understanding what kind of sequence variation is tolerated in the binding and catalytic steps helps us understand how the target DNA is recognized by Flp and will be useful in guiding the design of Flp variants with altered specificities .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Flp catalyzes site-specific recombination in a highly sequence-specific manner despite making few direct contacts to the bases within its binding site .
[ Sen. 2, subscore: 1.00 ]: Sequence discrimination could take place in the binding and/or the catalytic steps .
[ Sen. 10, subscore: 1.00 ]: However , most A tracts slow catalysis more than C or G substitutions .
[ Sen. 11, subscore: 1.00 ]: Understanding what kind of sequence variation is tolerated in the binding and catalytic steps helps us understand how the target DNA is recognized by Flp and will be useful in guiding the design of Flp variants with altered specificities .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Catalase and superoxide dismutase activities in a Stenotrophomonas maltophilia WZ2 resistant to herbicide pollution .
| | Author: Lu Z Sang L Li Z Min H | | Journal: Ecotoxicol Environ Saf Citation: V : 72 P : 136-43 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18304632 Accession (PMID): 18304632 | | Abstract: Quinclorac bensulfuron-methyl is a mixed herbicide widely used on paddy rice field to effectively control barnyard grass and most broad-leaved grasses and sedges .
We analyzed superoxide dismutase ( SOD ) and catalase activities in the quinclorac-highly degrading strain Stenotrophomonas maltophilia WZ2 and Gram-negative standard strain Escherichia coli K12 in an attempt to understand antioxidant enzymes in bacteria are produced in response to quinclorac or bensulfuron-methyl , which increases the virulence of the bacteria .
MnSOD and two additional catalase isozymes were induced by quinclorac or bensulfuron-methyl in S maltophilia WZ2 , but not in E coli K12 .
Quinclorac turned out to be a more sensitive inducer of SOD , whereas bensulfuron-methyl is a more sensitive one of catalase .
A mixture of both has effects similar to quinclorac .
Results indicate that catalase has a much weakly role in the defense against quinclorac or bensulfuron-methyl induced oxidative stress , whereas SOD could be critical | Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: We analyzed superoxide dismutase ( SOD ) and catalase activities in the quinclorac-highly degrading strain Stenotrophomonas maltophilia WZ2 and Gram-negative standard strain Escherichia coli K12 in an attempt to understand antioxidant enzymes in bacteria are produced in response to quinclorac or bensulfuron-methyl , which increases the virulence of the bacteria .
[ Sen. 3, subscore: 1.00 ]: MnSOD and two additional catalase isozymes were induced by quinclorac or bensulfuron-methyl in S maltophilia WZ2 , but not in E coli K12 .
[ Sen. 4, subscore: 1.00 ]: Quinclorac turned out to be a more sensitive inducer of SOD , whereas bensulfuron-methyl is a more sensitive one of catalase .
[ Sen. 6, subscore: 1.00 ]: Results indicate that catalase has a much weakly role in the defense against quinclorac or bensulfuron-methyl induced oxidative stress , whereas SOD could be critical
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: His-311 and Arg-559 are key residues involved in fatty acid oxygenation in pathogen-inducible oxygenase .
| | Author: Koszelak-Rosenblum M Krol AC Simmons DM Goulah CC Wroblewski L Malkowski MG | | Journal: J Biol Chem Citation: V : 283 P : 24962-71 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18596034 Accession (PMID): 18596034 | | Abstract: Pathogen-inducible oxygenase ( PIOX ) oxygenates fatty acids into 2R-hydroperoxides .
PIOX belongs to the fatty acid alpha-dioxygenase family , which exhibits homology to cyclooxygenase enzymes ( COX-1 and COX-2 ) .
Although these enzymes share common catalytic features , including the use of a tyrosine radical during catalysis , little is known about other residues involved in the dioxygenase reaction of PIOX .
We generated a model of linoleic acid ( LA ) bound to PIOX based on computational sequence alignment and secondary structure predictions with COX-1 and experimental observations that governed the placement of carbon-2 of LA below the catalytic Tyr-379 .
Examination of the model identified His-311 , Arg-558 , and Arg-559 as potential molecular determinants of the dioxygenase reaction .
Substitutions at His-311 and Arg-559 resulted in mutant constructs that retained virtually no oxygenase activity , whereas substitutions of Arg-558 caused only moderate decreases in activity .
Arg-559 mutant constructs exhibited increases of greater than 140-fold in Km , whereas no substantial change in Km was observed for His-311 or Arg-558 mutant constructs .
Thermal shift assays used to measure ligand binding affinity show that the binding of LA is significantly reduced in a Y379F/R559A mutant construct compared with that observed for Y379F/R558A construct .
Although Oryza sativa PIOX exhibited oxygenase activity against a variety of 14-20-carbon fatty acids , the enzyme did not oxygenate substrates containing modifications at the carboxylate , carbon-1 , or carbon-2 .
Taken together , these data suggest that Arg-559 is required for high affinity binding of substrates to PIOX , whereas His-311 is involved in optimally aligning carbon-2 below Tyr-379 for catalysis .
| Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Although these enzymes share common catalytic features , including the use of a tyrosine radical during catalysis , little is known about other residues involved in the dioxygenase reaction of PIOX .
[ Sen. 4, subscore: 1.00 ]: We generated a model of linoleic acid ( LA ) bound to PIOX based on computational sequence alignment and secondary structure predictions with COX-1 and experimental observations that governed the placement of carbon-2 of LA below the catalytic Tyr-379 .
[ Sen. 10, subscore: 1.00 ]: Taken together , these data suggest that Arg-559 is required for high affinity binding of substrates to PIOX , whereas His-311 is involved in optimally aligning carbon-2 below Tyr-379 for catalysis .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescence .
| | Author: Ougham H Hortensteiner S Armstead I Donnison I King I Thomas H Mur L | | Journal: Plant Biol ( Stuttg ) Citation: V : 10 Suppl 1 P : 4-14 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18721307 Accession (PMID): 18721307 | | Abstract: The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail .
In the last few years , genes encoding a number of the catabolic enzymes have been characterized , including the key ring-opening activities , phaeophorbide a oxygenase ( PaO ) and red chlorophyll catabolite reductase ( RCCR ) .
Recently , a gene that modulates disassembly of chlorophyll-protein complexes and activation of pigment ring-opening has been isolated by comparative mapping in monocot species , positional cloning exploiting rice genomics resources and functional testing in Arabidopsis .
The corresponding gene in pea has been identified as Mendels I locus ( green/yellow cotyledons ) .
Mutations in this and other chlorophyll catabolic genes have significant consequences , both for the course of leaf senescence and senescence-like stress responses , notably hypersensitivity to pathogen challenge .
Loss of chlorophyll can occur via routes other than the PaO/RCCR pathway , resulting in changes that superficially resemble senescence .
Such pseudosenescence responses tend to be pathological rather than physiological and may differ from senescence in fundamental aspects of biochemistry and regulation .
| Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: In the last few years , genes encoding a number of the catabolic enzymes have been characterized , including the key ring-opening activities , phaeophorbide a oxygenase ( PaO ) and red chlorophyll catabolite reductase ( RCCR ) .
[ Sen. 1, subscore: 1.00 ]: The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail .
[ Sen. 5, subscore: 1.00 ]: Mutations in this and other chlorophyll catabolic genes have significant consequences , both for the course of leaf senescence and senescence-like stress responses , notably hypersensitivity to pathogen challenge .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Cloning , characterisation and comparative analysis of a starch synthase IV gene in wheat : functional and evolutionary implications .
| | Author: Leterrier M Holappa LD Broglie KE Beckles DM | | Journal: BMC Plant Biol Citation: V : 8 P : 98 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18826586 Accession (PMID): 18826586 | | Abstract: BACKGROUND : Starch is of great importance to humans as a food and biomaterial , and the amount and structure of starch made in plants is determined in part by starch synthase ( SS ) activity .
Five SS isoforms , SSI , II , III , IV and Granule Bound SSI , have been identified , each with a unique catalytic role in starch synthesis .
The basic mode of action of SSs is known ; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete .
To gain a better understanding of the differences in SS sequences that underscore their specificity , the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done .
RESULTS : The wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement .
The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock .
Phylogenetic analysis showed that in plants , SSIV is closely related to SSIII , while SSI , SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation .
Further , identified differences at the amino acid level in their glycosyltransferase domains , predicted secondary structures , global conformations and conserved residues might be indicative of intragroup functional associations .
CONCLUSION : Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases ( GSs ) , it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI , SSI and SSII .
In GBSSI , the Ile485 residue may partially explain that enzymes unique catalytic features .
The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Five SS isoforms , SSI , II , III , IV and Granule Bound SSI , have been identified , each with a unique catalytic role in starch synthesis .
[ Sen. 9, subscore: 1.00 ]: CONCLUSION : Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases ( GSs ) , it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI , SSI and SSII .
[ Sen. 10, subscore: 1.00 ]: In GBSSI , the Ile485 residue may partially explain that enzymes unique catalytic features .
[ Sen. 11, subscore: 1.00 ]: The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Pain catastrophizing and pain-related fear in osteoarthritis patients : relationships to pain and disability .
| | Author: Somers TJ Keefe FJ Pells JJ Dixon KE Waters SJ Riordan PA Blumenthal JA McKee DC LaCaille L Tucker JM Schmitt D Caldwell DS Kraus VB Sims EL Shelby RA Rice JR | | Journal: J Pain Symptom Manage Citation: V : 37 P : 863-72 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19041218 Accession (PMID): 19041218 | | Abstract: This study examined the degree to which pain catastrophizing and pain-related fear explain pain , psychological disability , physical disability , and walking speed in patients with osteoarthritis ( OA ) of the knee .
Participants in this study were 106 individuals diagnosed as having OA of at least one knee , who reported knee pain persisting for six months or longer .
Results suggest that pain catastrophizing explained a significant proportion ( all Ps < or = 0 . 05 ) of variance in measures of pain ( partial r ( 2 ) [ pr ( 2 ) ] = 0 . 10 ) , psychological disability ( pr ( 2 ) = 0 . 20 ) , physical disability ( pr ( 2 ) = 0 . 11 ) , and gait velocity at normal ( pr ( 2 ) = 0 . 04 ) , fast ( pr ( 2 ) = 0 . 04 ) , and intermediate speeds ( pr ( 2 ) = 0 . 04 ) .
Pain-related fear explained a significant proportion of the variance in measures of psychological disability ( pr ( 2 ) = 0 . 07 ) and walking at a fast speed ( pr ( 2 ) = 0 . 05 ) .
Pain cognitions , particularly pain catastrophizing , appear to be important variables in understanding pain , disability , and walking at normal , fast , and intermediate speeds in knee OA patients .
Clinicians interested in understanding variations in pain and disability in this population may benefit by expanding the focus of their inquiries beyond traditional medical and demographic variables to include an assessment of pain catastrophizing and pain-related fear .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: This study examined the degree to which pain catastrophizing and pain-related fear explain pain , psychological disability , physical disability , and walking speed in patients with osteoarthritis ( OA ) of the knee .
[ Sen. 3, subscore: 1.00 ]: Results suggest that pain catastrophizing explained a significant proportion ( all Ps < or = 0 . 05 ) of variance in measures of pain ( partial r ( 2 ) [ pr ( 2 ) ] = 0 . 10 ) , psychological disability ( pr ( 2 ) = 0 . 20 ) , physical disability ( pr ( 2 ) = 0 . 11 ) , and gait velocity at normal ( pr ( 2 ) = 0 . 04 ) , fast ( pr ( 2 ) = 0 . 04 ) , and intermediate speeds ( pr ( 2 ) = 0 . 04 ) .
[ Sen. 5, subscore: 1.00 ]: Pain cognitions , particularly pain catastrophizing , appear to be important variables in understanding pain , disability , and walking at normal , fast , and intermediate speeds in knee OA patients .
[ Sen. 6, subscore: 1.00 ]: Clinicians interested in understanding variations in pain and disability in this population may benefit by expanding the focus of their inquiries beyond traditional medical and demographic variables to include an assessment of pain catastrophizing and pain-related fear .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Effects of catalase on the accumulation of H ( 2 ) O ( 2 ) in rice cells inoculated with rice blast fungus , Magnaporthe oryzae .
| | Author: Tanabe S Nishizawa Y Minami E | | Journal: Physiol Plant Citation: V : 137 P : 148-54 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19719483 Accession (PMID): 19719483 | | Abstract: Roles of H ( 2 ) O ( 2 ) in the infection process of Magnaporthe oryzae on rice were investigated .
In a leaf sheath assay for up to 48 h post-inoculation , the absence or presence of catalase in the conidia suspension was correlated with the level of accumulated H ( 2 ) O ( 2 ) in infected leaf cells , as observed by staining with 3 , 3-diaminobenzidine tetrahydrochloride .
In the incompatible interaction , the appearance of autofluorescence or frequency of cell death characterized by granulation ( symptoms characteristic of hypersensitive responses ) was not significantly affected by the presence of catalase in the conidia suspension .
In the leaf blade assay , inoculation of compatible conidia in the presence of catalase produced more severe symptoms than that of conidia in the absence of catalase at 6 days post-inoculation .
These results suggest that , in this host-parasite interaction , the primary role of host-produced H ( 2 ) O ( 2 ) is in limiting hyphal growth after penetration through toxic action .
Furthermore , in incompatible interactions , H ( 2 ) O ( 2 ) is implied not to be a major mediator of hypersensitive cell death .
| Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: In the leaf blade assay , inoculation of compatible conidia in the presence of catalase produced more severe symptoms than that of conidia in the absence of catalase at 6 days post-inoculation .
[ Sen. 2, subscore: 1.00 ]: In a leaf sheath assay for up to 48 h post-inoculation , the absence or presence of catalase in the conidia suspension was correlated with the level of accumulated H ( 2 ) O ( 2 ) in infected leaf cells , as observed by staining with 3 , 3-diaminobenzidine tetrahydrochloride .
[ Sen. 3, subscore: 1.00 ]: In the incompatible interaction , the appearance of autofluorescence or frequency of cell death characterized by granulation ( symptoms characteristic of hypersensitive responses ) was not significantly affected by the presence of catalase in the conidia suspension .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Kinetic basis for the conjugation of auxin by a GH3 family indole-acetic acid-amido synthetase .
| | Author: Chen Q Westfall CS Hicks LM Wang S Jez JM | | Journal: J Biol Chem Citation: V : 285 P : 29780-6 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20639576 Accession (PMID): 20639576 | | Abstract: The GH3 family of acyl-acid-amido synthetases catalyze the ATP-dependent formation of amino acid conjugates to modulate levels of active plant hormones , including auxins and jasmonates .
Initial biochemical studies of various GH3s show that these enzymes group into three families based on sequence relationships and acyl-acid substrate preference ( I , jasmonate-conjugating ; II , auxin and salicylic acid-conjugating ; III , benzoate-conjugating ) ; however , little is known about the kinetic and chemical mechanisms of these enzymes .
Here we use GH3-8 from Oryza sativa ( rice ; OsGH3-8 ) , which functions as an indole-acetic acid ( IAA ) -amido synthetase , for detailed mechanistic studies .
Steady-state kinetic analysis shows that the OsGH3-8 requires either Mg ( 2+ ) or Mn ( 2+ ) for maximal activity and is specific for aspartate but accepts asparagine as a substrate with a 45-fold decrease in catalytic efficiency and accepts other auxin analogs , including phenyl-acetic acid , indole butyric acid , and naphthalene-acetic acid , as acyl-acid substrates with 1 . 4-9-fold reductions in k ( cat ) /K ( m ) relative to IAA .
Initial velocity and product inhibition studies indicate that the enzyme uses a Bi Uni Uni Bi Ping Pong reaction sequence .
In the first half-reaction , ATP binds first followed by IAA .
Next , formation of an adenylated IAA intermediate results in release of pyrophosphate .
The second half-reaction begins with binding of aspartate , which reacts with the adenylated intermediate to release IAA-Asp and AMP .
Formation of a catalytically competent adenylated-IAA reaction intermediate was confirmed by mass spectrometry .
These mechanistic studies provide insight on the reaction catalyzed by the GH3 family of enzymes to modulate plant hormone action .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The GH3 family of acyl-acid-amido synthetases catalyze the ATP-dependent formation of amino acid conjugates to modulate levels of active plant hormones , including auxins and jasmonates .
[ Sen. 4, subscore: 1.00 ]: Steady-state kinetic analysis shows that the OsGH3-8 requires either Mg ( 2+ ) or Mn ( 2+ ) for maximal activity and is specific for aspartate but accepts asparagine as a substrate with a 45-fold decrease in catalytic efficiency and accepts other auxin analogs , including phenyl-acetic acid , indole butyric acid , and naphthalene-acetic acid , as acyl-acid substrates with 1 . 4-9-fold reductions in k ( cat ) /K ( m ) relative to IAA .
[ Sen. 9, subscore: 1.00 ]: Formation of a catalytically competent adenylated-IAA reaction intermediate was confirmed by mass spectrometry .
[ Sen. 10, subscore: 1.00 ]: These mechanistic studies provide insight on the reaction catalyzed by the GH3 family of enzymes to modulate plant hormone action .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: | | Author: Wu M Shariat-Madar B Haron MH Wu M Khan IA Dasmahapatra AK | | Journal: Comp Biochem Physiol C Toxicol Pharmacol Citation: V : 153 P : 159-67 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20965276 Accession (PMID): 20965276 | | Abstract: Although the mechanism of ethanol toxicity during embryogenesis is unknown , our earlier studies on Japanese rice fish ( Oryzias latipes ) embryos indicated that the effects might be mediated through oxidative stress .
In this study we have determined the oxidative stress and the mRNA content of four antioxidant enzymes ( catalase , glutathione reductase , glutathione-S-transferase , and superoxide dismutase ) during Japanese rice fish embryogenesis ( from 0 day post-fertilization to hatching ) and after exposing the embryos to ethanol ( 100 and 300 mM ) for 48 h at three stages ( 0-2 , 1-3 and 4-6 days post-fertilization , dpf ) of organogenesis .
We observed that oxidative stress was minimal in blastula , gastrula or neurula stages , increased gradually with the advancement of morphogenesis and reached its maximum level in hatchlings .
The antioxidant enzyme mRNAs were constitutively expressed throughout development ; however , the expression pattern was not identical among the enzymes .
Catalase and superoxide dismutase ( SOD ) mRNAs were minimal in the fertilized eggs , but increased significantly in 1 dpf and then either sharply dropped ( SOD ) or maintained a steady-state ( catalase ) .
Glutathione-S-transferase ( GST ) was very high in fertilized eggs and sharply dropped 1 dpf and then gradually increased thereafter .
Glutathione reductase ( GR ) maintained a steady-state throughout the development .
Ethanol was able to attenuate oxidative stress in embryos exposed only to 300 mM 1-3 dpf ; no significant difference with controls was observed in other ethanol-treated groups .
The antioxidant enzyme mRNAs also remained unaltered after ethanol treatment .
From these data we conclude that the attenuation of oxidative stress by ethanol is probably due to the inhibition of normal growth of the embryos rather than by inhibiting catalase , GST , GR or SOD-dependent activities .
| Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Catalase and superoxide dismutase ( SOD ) mRNAs were minimal in the fertilized eggs , but increased significantly in 1 dpf and then either sharply dropped ( SOD ) or maintained a steady-state ( catalase ) .
[ Sen. 2, subscore: 1.00 ]: In this study we have determined the oxidative stress and the mRNA content of four antioxidant enzymes ( catalase , glutathione reductase , glutathione-S-transferase , and superoxide dismutase ) during Japanese rice fish embryogenesis ( from 0 day post-fertilization to hatching ) and after exposing the embryos to ethanol ( 100 and 300 mM ) for 48 h at three stages ( 0-2 , 1-3 and 4-6 days post-fertilization , dpf ) of organogenesis .
[ Sen. 10, subscore: 1.00 ]: From these data we conclude that the attenuation of oxidative stress by ethanol is probably due to the inhibition of normal growth of the embryos rather than by inhibiting catalase , GST , GR or SOD-dependent activities .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Structural basis for the one-pot formation of the diarylheptanoid scaffold by curcuminoid synthase from Oryza sativa .
| | Author: Morita H Wanibuchi K Nii H Kato R Sugio S Abe I | | Journal: Proc Natl Acad Sci U S A Citation: V : 107 P : 19778-83 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21041675 Accession (PMID): 21041675 | | Abstract: Curcuminoid synthase ( CUS ) from Oryza sativa is a plant-specific type III polyketide synthase ( PKS ) that catalyzes the remarkable one-pot formation of the C ( 6 ) -C ( 7 ) -C ( 6 ) diarylheptanoid scaffold of bisdemethoxycurcumin , by the condensation of two molecules of 4-coumaroyl-CoA and one molecule of malonyl-CoA .
The crystal structure of O sativa CUS was solved at 2 . 5-A resolution , which revealed a unique , downward expanding active-site architecture , previously unidentified in the known type III PKSs .
The large active-site cavity is long enough to accommodate the two C ( 6 ) -C ( 3 ) coumaroyl units and one malonyl unit .
Furthermore , the crystal structure indicated the presence of a putative nucleophilic water molecule , which forms hydrogen bond networks with Ser351-Asn142-H ( 2 ) O-Tyr207-Glu202 , neighboring the catalytic Cys174 at the active-site center .
These observations suggest that CUS employs unique catalytic machinery for the one-pot formation of the C ( 6 ) -C ( 7 ) -C ( 6 ) scaffold .
Thus , CUS utilizes the nucleophilic water to terminate the initial polyketide chain elongation at the diketide stage .
Thioester bond cleavage of the enzyme-bound intermediate generates 4-coumaroyldiketide acid , which is then kept within the downward expanding pocket for subsequent decarboxylative condensation with the second 4-coumaroyl-CoA starter , to produce bisdemethoxycurcumin .
The structure-based site-directed mutants , M265L and G274F , altered the substrate and product specificities to accept 4-hydroxyphenylpropionyl-CoA as the starter to produce tetrahydrobisdemethoxycurcumin .
These findings not only provide a structural basis for the catalytic machinery of CUS but also suggest further strategies toward expanding the biosynthetic repertoire of the type III PKS enzymes .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Curcuminoid synthase ( CUS ) from Oryza sativa is a plant-specific type III polyketide synthase ( PKS ) that catalyzes the remarkable one-pot formation of the C ( 6 ) -C ( 7 ) -C ( 6 ) diarylheptanoid scaffold of bisdemethoxycurcumin , by the condensation of two molecules of 4-coumaroyl-CoA and one molecule of malonyl-CoA .
[ Sen. 4, subscore: 1.00 ]: Furthermore , the crystal structure indicated the presence of a putative nucleophilic water molecule , which forms hydrogen bond networks with Ser351-Asn142-H ( 2 ) O-Tyr207-Glu202 , neighboring the catalytic Cys174 at the active-site center .
[ Sen. 5, subscore: 1.00 ]: These observations suggest that CUS employs unique catalytic machinery for the one-pot formation of the C ( 6 ) -C ( 7 ) -C ( 6 ) scaffold .
[ Sen. 9, subscore: 1.00 ]: These findings not only provide a structural basis for the catalytic machinery of CUS but also suggest further strategies toward expanding the biosynthetic repertoire of the type III PKS enzymes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Biochemical and enzymatic study of rice BADH wild-type and mutants : an insight into fragrance in rice .
| | Author: Wongpanya R Boonyalai N Thammachuchourat N Horata N Arikit S Myint KM Vanavichit A Choowongkomon K | | Journal: Protein J Citation: V : 30 P : 529-38 Year: 2011 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub21959793 Accession (PMID): 21959793 | | Abstract: Betaine aldehyde dehydrogenase 2 ( BADH2 ) is believed to be involved in the accumulation of 2-acetyl-1-pyrroline ( 2AP ) , one of the major aromatic compounds in fragrant rice .
The enzyme can oxidize omega-aminoaldehydes to the corresponding omega-amino acids .
This study was carried out to investigate the function of wild-type BADHs and four BADH2 mutants : BADH2_Y420 , containing a Y420 insertion similar to BADH2 . 8 in Myanmar fragrance rice , BADH2_C294A , BADH2_E260A and BADH2_N162A , consisting of a single catalytic-residue mutation .
Our results showed that the BADH2_Y420 mutant exhibited less catalytic efficiency towards gamma-aminobutyraldehyde but greater efficiency towards betaine aldehyde than wild-type .
We hypothesized that this point mutation may account for the accumulation of gamma-aminobutyraldehyde/Delta ( 1 ) -pyrroline prior to conversion to 2AP , generating fragrance in Myanmar rice .
In addition , the three catalytic-residue mutants confirmed that residues C294 , E260 and N162 were involved in the catalytic activity of BADH2 similar to those of other BADHs .
| Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: In addition , the three catalytic-residue mutants confirmed that residues C294 , E260 and N162 were involved in the catalytic activity of BADH2 similar to those of other BADHs .
[ Sen. 3, subscore: 1.00 ]: This study was carried out to investigate the function of wild-type BADHs and four BADH2 mutants : BADH2_Y420 , containing a Y420 insertion similar to BADH2 . 8 in Myanmar fragrance rice , BADH2_C294A , BADH2_E260A and BADH2_N162A , consisting of a single catalytic-residue mutation .
[ Sen. 4, subscore: 1.00 ]: Our results showed that the BADH2_Y420 mutant exhibited less catalytic efficiency towards gamma-aminobutyraldehyde but greater efficiency towards betaine aldehyde than wild-type .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Catalytic protein modification with dirhodium metallopeptides : specificity in designed and natural systems .
| | Author: Chen Z Vohidov F Coughlin JM Stagg LJ Arold ST Ladbury JE Ball ZT | | Journal: J Am Chem Soc Citation: V : 134 P : 10138-45 Year: 2012 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub22621321 Accession (PMID): 22621321 | | Abstract: In this study , we present advances in the use of rhodium ( II ) metallopeptides for protein modification .
Site-specific , proximity-driven modification is enabled by the unique combination of peptide-based molecular recognition and a rhodium catalyst capable of modifying a wide range of amino-acid side chains .
We explore catalysis based on coiled-coil recognition in detail , providing an understanding of the determinants of specificity and culminating in the demonstration of orthogonal modification of separate proteins in cell lysate .
In addition , the concepts of proximity-driven catalysis are extended to include modification of the natural Fyn SH3 domain with metallopeptides based on a known proline-rich peptide ligand .
The development of orthogonal catalyst-substrate pairs for modification in lysate , and the extension of these methods to new natural protein domains , highlight the capabilities for new reaction design possible in chemical approaches to site-specific protein modification .
| Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Site-specific , proximity-driven modification is enabled by the unique combination of peptide-based molecular recognition and a rhodium catalyst capable of modifying a wide range of amino-acid side chains .
[ Sen. 3, subscore: 1.00 ]: We explore catalysis based on coiled-coil recognition in detail , providing an understanding of the determinants of specificity and culminating in the demonstration of orthogonal modification of separate proteins in cell lysate .
[ Sen. 4, subscore: 1.00 ]: In addition , the concepts of proximity-driven catalysis are extended to include modification of the natural Fyn SH3 domain with metallopeptides based on a known proline-rich peptide ligand .
[ Sen. 5, subscore: 1.00 ]: The development of orthogonal catalyst-substrate pairs for modification in lysate , and the extension of these methods to new natural protein domains , highlight the capabilities for new reaction design possible in chemical approaches to site-specific protein modification .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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| Title: Stereochemical studies of D-glucal hydration by alpha-glucosidases and exo-alpha-glucanases : indications of plastic and conserved phases in catalysis by glycosylases .
| | Author: Chiba S Brewer CF Okada G Matsui H Hehre EJ .
| | Journal: Biochemistry Citation: V : 27 ( 5 ) P : 1464-9 Year: 1988 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub3284583 Accession (PMID): 3284583 | | Abstract: Alpha-Glucosidases from Aspergillus niger , pig serum , ungerminated rice , buckwheat , and sugar beet seeds ( but not from brewers yeast or honeybee ) were found to catalyze the hydration of D-glucal Each reactive alpha-glucosidase , incubated with D-glucal in D2O , was shown to protonate ( deuteriate ) this prochiral substrate from above its re face , ie , from a direction opposite that assumed for protonating alpha-D-glucosidic substrates .
At the same time , D-glucal hydration catalyzed by three of the alpha-glucosidases that acted rapidly enough in D2O to determine product configuration was found to yield 2-deoxy-D-glucose of the same specific ( alpha- ) configuration as the D-glucose produced from alpha-D-glucosidic substrates .
These findings substantially extend those reported earlier for the hydration of D-glucal by one ( Candida tropicalis ) alpha-glucosidase preparation .
Together with other recent results , they suggest that the process of catalysis by alpha-glucosidases ( and perhaps glycosylases in general ) may comprise two separate and separately controlled parts , namely , a "plastic" phase concerned with substrate protonation and a substrate-unrelated "conserved" phase concerned with the creation of product configuration .
In contrast to the alpha-glucosidases , three "inverting" exo-alpha-glucanases ( Arthrobacter globiformis glucodextranase ; Rhizopus niveus and Paecilomyces varioti glucoamylase ) were found to protonate D-glucal from below its si face .
Further , whereas the catalysis of D-glucal hydration by the alpha-glucosidases was intensively inhibited by excess substrate , that promoted by the exo-glucanases showed no detectable substrate inhibition .
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[ Sen. 1, subscore: 1.00 ]: Alpha-Glucosidases from Aspergillus niger , pig serum , ungerminated rice , buckwheat , and sugar beet seeds ( but not from brewers yeast or honeybee ) were found to catalyze the hydration of D-glucal Each reactive alpha-glucosidase , incubated with D-glucal in D2O , was shown to protonate ( deuteriate ) this prochiral substrate from above its re face , ie , from a direction opposite that assumed for protonating alpha-D-glucosidic substrates .
[ Sen. 2, subscore: 1.00 ]: At the same time , D-glucal hydration catalyzed by three of the alpha-glucosidases that acted rapidly enough in D2O to determine product configuration was found to yield 2-deoxy-D-glucose of the same specific ( alpha- ) configuration as the D-glucose produced from alpha-D-glucosidic substrates .
[ Sen. 4, subscore: 1.00 ]: Together with other recent results , they suggest that the process of catalysis by alpha-glucosidases ( and perhaps glycosylases in general ) may comprise two separate and separately controlled parts , namely , a "plastic" phase concerned with substrate protonation and a substrate-unrelated "conserved" phase concerned with the creation of product configuration .
[ Sen. 6, subscore: 1.00 ]: Further , whereas the catalysis of D-glucal hydration by the alpha-glucosidases was intensively inhibited by excess substrate , that promoted by the exo-glucanases showed no detectable substrate inhibition .
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Score: 4.00 |
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| Title: Factors determining steric course of enzymic glycosylation reactions : glycosyl transfer products formed from 2 , 6-anhydro-1-deoxy-D-gluco-hept-1-enitol by alpha-glucosidases and an inverting exo-alpha-glucanase .
| | Author: Schlesselmann P Fritz H Lehmann J Uchiyama T Brewer CF Hehre EJ .
| | Journal: Biochemistry Citation: V : 21 ( 25 ) P : 6606-14 Year: 1982 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub6758847 Accession (PMID): 6758847 | | Abstract: Glycosyl transfer products were formed from 2 , 6-anhydro-1-deoxy-D-gluco-hept-1-enitol ( heptenitol ) by purified alpha-glucosidases from Candida tropicalis and rice and by an inverting exo-alpha-glucanase ( glucodextranase ) from Arthrobacter globiformis .
The products were structurally defined through 1H and 13C NMR ( nuclear magnetic resonance ) spectra of their crystalline per-O-acetates in comparison with those of authentic methyl 1-deoxy-alpha and methyl 1-deoxy-beta-D-gluco-heptuloside .
1-Deoxy-alpha-D-gluco-heptulosyl- ( 2 leads to 7 ) -heptenitol and 1-deoxy-alpha-D-gluco-heptulosyl- ( 2 leads to 7 ) -D-gluco-heptulose were produced by both the Candida alpha-glucosidase and the glucodextranase ; 1-deoxy-alpha-D-gluco-heptulosyl- ( 2 leads to 5 ) - and 1-deoxy-alpha-D-gluco-heptulosyl- ( 2 leads to 7 ) -D-gluco-heptuloses by the rice alpha-glucosidase .
These results , together with our earlier findings of sterospecific hydration of heptenitol catalyzed by the same enzymes [ Hehre , E J , Brewer , C F , Uchiyama , T , Schlesselmann , P , & Lehmann , J ( 1980 ) Biochemistry 19 , 3557-3564 ] , show the inadequacy of the long-accepted notion that carbohydrase-catalyzed reactions always lead to retention ( or always lead to inversion ) of substrate configuration .
In particular , the finding that glucodextranase forms transfer products of alpha configuration and a hydration product of beta configuration from the same substrate provides a clear example of the functioning of acceptors rather than donor substrates in selecting the steric course of reactions catalyzed by a glycosylase .
The circumstances under which acceptor cosubstrates might be expected to show this significant effect are discussed .
The opportunity presumably would exist whenever carbonium ion mediated reactions are catalyzed by glycosylases that provide oppositely oriented approaches of different acceptors to the catalytic center .
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[ Sen. 7, subscore: 2.00 ]: The opportunity presumably would exist whenever carbonium ion mediated reactions are catalyzed by glycosylases that provide oppositely oriented approaches of different acceptors to the catalytic center .
[ Sen. 4, subscore: 1.00 ]: These results , together with our earlier findings of sterospecific hydration of heptenitol catalyzed by the same enzymes [ Hehre , E J , Brewer , C F , Uchiyama , T , Schlesselmann , P , & Lehmann , J ( 1980 ) Biochemistry 19 , 3557-3564 ] , show the inadequacy of the long-accepted notion that carbohydrase-catalyzed reactions always lead to retention ( or always lead to inversion ) of substrate configuration .
[ Sen. 5, subscore: 1.00 ]: In particular , the finding that glucodextranase forms transfer products of alpha configuration and a hydration product of beta configuration from the same substrate provides a clear example of the functioning of acceptors rather than donor substrates in selecting the steric course of reactions catalyzed by a glycosylase .
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Score: 4.00 |
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| Title: Molecular cloning of the cDNA for the catalytic subunit of plant DNA polymerase alpha and its cell-cycle dependent expression .
| | Author: Yokoi M Ito M Izumi M Miyazawa H Nakai H Hanaoka F | | Journal: Genes Cells Citation: V : 2 ( 11 ) P : 695-709 Year: 1997 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub9491803 Accession (PMID): 9491803 | | Abstract: BACKGROUND : DNA polymerase alpha has been studied in considerable detail in yeast and animals .
Genetic and biochemical analyses reveal that this enzyme is composed of a heterotetramer and is necessary for replicon initiation and primer synthesis in lagging strand synthesis .
In spite of the fact that modes of DNA replication in plants seem to be similar to those in other eukaryotes , very little is known about the biochemical components that participate in DNA replication of plants , including DNA polymerases .
RESULTS : Using a 561-base pair DNA fragment , obtained by polymerase chain reaction amplification from a rice cDNA library as a probe , we isolated and sequenced a cDNA homologous to the cDNA for the catalytic subunit of rice DNA polymerase alpha .
The encoded polypeptide has extensive homology with the catalytic subunit of DNA polymerase alpha from several species .
Furthermore , when the cDNA was expressed in eukaryotic transcription/translation systems , the protein products showed DNA polymerase activity which was inhibited by a monoclonal antibody specific for DNA polymerase alpha .
Using RNA gel blot analysis , we found that the levels of mRNA of the catalytic subunit of this enzyme is regulated during the cell-cycle in plant cells .
CONCLUSION : This is the first report which describes the cDNA cloning of plant DNA polymerase .
We conclude that the principal features of the DNA polymerase alpha catalytic subunit are conserved in plants . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: RESULTS : Using a 561-base pair DNA fragment , obtained by polymerase chain reaction amplification from a rice cDNA library as a probe , we isolated and sequenced a cDNA homologous to the cDNA for the catalytic subunit of rice DNA polymerase alpha .
[ Sen. 5, subscore: 1.00 ]: The encoded polypeptide has extensive homology with the catalytic subunit of DNA polymerase alpha from several species .
[ Sen. 7, subscore: 1.00 ]: Using RNA gel blot analysis , we found that the levels of mRNA of the catalytic subunit of this enzyme is regulated during the cell-cycle in plant cells .
[ Sen. 9, subscore: 1.00 ]: We conclude that the principal features of the DNA polymerase alpha catalytic subunit are conserved in plants .
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Score: 3.00 |
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| Title: Cloning and characterization of a cDNA encoding catalase in wheat .
| | Author: Saruyama H Matsumura T | | Journal: DNA Seq .
Citation: V : 10 ( 1 ) P : 31-5 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10565542 Accession (PMID): 10565542 | | Abstract: We determined the nucleotide sequence of a cDNA encoding the catalase ( CAT ) isolated from wheat ( Triticum aestivum L ) .
The deduced amino acid sequence suggests that this wheat catalase isozyme shared higher amino acid homology with group I CATs of barley CAT-1 , rice CAT B and maize CAT-1 and CAT-2 but lower homology with group II CATs of barley CAT-2 , rice CAT A and maize CAT-3 .
Both group I and II specific sequences of Ser-Arg-Leu and Ser-Ser-Ser , respectively considered as peroxisomal targeting signals were found first in monocot plant of wheat .
Functionally important amino acids at active center and heme-binding sites detected in all other plant catalase were conserved .
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[ Sen. 1, subscore: 1.00 ]: We determined the nucleotide sequence of a cDNA encoding the catalase ( CAT ) isolated from wheat ( Triticum aestivum L ) .
[ Sen. 2, subscore: 1.00 ]: The deduced amino acid sequence suggests that this wheat catalase isozyme shared higher amino acid homology with group I CATs of barley CAT-1 , rice CAT B and maize CAT-1 and CAT-2 but lower homology with group II CATs of barley CAT-2 , rice CAT A and maize CAT-3 .
[ Sen. 4, subscore: 1.00 ]: Functionally important amino acids at active center and heme-binding sites detected in all other plant catalase were conserved .
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Score: 3.00 |
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| Title: Cloning of a gene for an acyl-CoA dehydrogenase from Pisum sativum L and purification and characterization of its product as an isovaleryl-CoA dehydrogenase .
| | Author: Reinard T Janke V Willard J Buck F Jacobsen HJ Vockley J | | Journal: J Biol . Chem . Citation: V : 275 ( 43 ) P : 33738-43 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10913142 Accession (PMID): 10913142 | | Abstract: Isovaleryl-CoA dehydrogenase ( IVD , EC ) catalyzes the third step in the catabolism of leucine in mammals .
Deficiency of this enzyme leads to the clinical disorder isovaleric acidemia .
IVD has been purified and characterized from human and rat liver , and the x-ray crystallographic structure of purified recombinant human IVD has been reported .
Nothing is known about IVD activity in plants , although cDNA clones from Arabidopsis thaliana and partial sequences from Gossypium hirsutum and Oryza sativa have been identified as putative IVDs based on sequence homology and immuno cross-reactivity .
In this report we describe the identification and characterization of an IVD from pea , purification of the enzyme using a novel and rapid auxin affinity chromatography matrix , and cloning of the corresponding gene .
At the amino acid level , pea IVD is 60% similar to human and rat IVD .
The specific activity and abundance of plant IVD was found to be significantly lower than for its human counterpart and exhibits developmental regulation .
Substrate specificity of the plant enzyme is similar to the human IVD , and it cross-reacts to anti-human IVD antibodies .
Molecular modeling of the pea enzyme based on the structure of human IVD indicates a high degree of structural similarity among these enzymes .
Glu-244 , shown to function as the catalytic base in human IVD along with most of the amino acids that make up the acyl CoA binding pocket , is conserved in pea IVD .
The genomic structure of the plant IVD gene consists of 13 exons and 12 introns , spanning approximately 4 kilobases , and the predicted RNA splicing sites exhibit the extended consensus sequence described for other plant genes . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Isovaleryl-CoA dehydrogenase ( IVD , EC ) catalyzes the third step in the catabolism of leucine in mammals .
[ Sen. 10, subscore: 1.00 ]: Glu-244 , shown to function as the catalytic base in human IVD along with most of the amino acids that make up the acyl CoA binding pocket , is conserved in pea IVD .
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Score: 3.00 |
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| Title: Regulation of alcoholic fermentation in coleoptiles of two rice cultivars differing in tolerance to anoxia .
| | Author: Gibbs J Morrell S Valdez A Setter TL Greenway H | | Journal: J Exp . Bot . Citation: V : 51 ( 345 ) P : 785-96 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10938871 Accession (PMID): 10938871 | | Abstract: To investigate regulation of anaerobic carbohydrate catabolism in anoxia-tolerant plant it issue , rate of alcoholic fermentation and maximum catalytic activities of four key enzymes were assessed in coleoptiles of two rice cultivars that differ in tolerance to anoxia .
The enzymes were ATP-dependent phosphofructokinase ( PFK ) , pyrophosphate-dependent phosphofructokinase ( PFP ) , pyruvate decarboxylase ( PDC ) , and alcohol dehydrogenase ( ADH ) .
During anoxia , rates of coleoptile elongation and ethanol synthesis were faster in the more tolerant variety Calrose than in IR22 .
Calrose coleoptiles , in contrast to IR22 , also showed a sustained Pasteur effect , with the estimated rate of glycolysis during anoxia being 1 . 4-1 . 7-fold faster than that of aerobic coleoptiles .
In Calrose after 5 d anoxia , maximum catalytic activities of crude enzyme extracts were ( in mumol substrate g-1 fresh weight min . -1 ) 170-240 for ADH , 4-6 for PDC and PFP and 0 . 4-0 . 7 for PFK .
During anoxia , activity per coleoptile of all four enzymes increased 3-5 . 5-fold , suggesting that PFK , and PFP , like PDC and ADH , are synthesised in anoxic rice coleoptiles .
Enzyme activities , on a fresh weight basis , were lower in IR22 than in Calrose .
In vivo activities of PDC and PFK in anoxic coleoptiles from both cultivars were calculated using in vitro activities , estimated substrate levels , cytoplasmic pH , and S0 . 5 ( the substrate level at which 0 . 5Vmax is reached , without inferring Michaelis-Menten kinetics ) .
Data indicated that potential carbon flux through PFK , rather than through PDC , more closely approximated rates of alcoholic fermentation .
That PFK is an important site of regulation was supported further for Calrose coleoptiles by a decrease in the concentration of its substrate pool ( F-6-P + G-6-P ) following the onset of anoxia .
By contrast , in IR22 , there was little evidence for control by PFK , consistent with recent evidence that suggests substrate supply limits alcoholic fermentation in this cultivar . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: To investigate regulation of anaerobic carbohydrate catabolism in anoxia-tolerant plant it issue , rate of alcoholic fermentation and maximum catalytic activities of four key enzymes were assessed in coleoptiles of two rice cultivars that differ in tolerance to anoxia .
[ Sen. 5, subscore: 1.00 ]: In Calrose after 5 d anoxia , maximum catalytic activities of crude enzyme extracts were ( in mumol substrate g-1 fresh weight min . -1 ) 170-240 for ADH , 4-6 for PDC and PFP and 0 . 4-0 . 7 for PFK .
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Score: 3.00 |
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| Title: The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase .
| | Author: Piotrowski M Schnfelder S Weiler EW .
| | Journal: J Biol . Chem . Citation: V : 276 ( 4 ) P : 2616-21 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11060302 Accession (PMID): 11060302 | | Abstract: Nitrilases ( nitrile aminohydrolases , EC ) are enzymes that catalyze the hydrolysis of nitriles to the corresponding carbon acids .
Among the four known nitrilases of Arabidopsis thaliana , the isoform NIT4 is the most divergent one , and homologs of NIT4 are also known from species not belonging to the Brassicaceae like Nicotiana tabacum and Oryza sativa .
We expressed A thaliana NIT4 as hexahistidine tag fusion protein in Escherichia coli .
The purified enzyme showed a strong substrate specificity for beta-cyano-l-alanine ( Ala ( CN ) ) , an intermediate product of cyanide detoxification in higher plants .
Interestingly , not only aspartic acid but also asparagine were identified as products of NIT4-catalyzed Ala ( CN ) hydrolysis .
Asn itself was no substrate for NIT4 , indicating that it is not an intermediate but one of two reaction products .
NIT4 therefore has both nitrilase and nitrile hydratase activity .
Several lines of evidence indicate that the catalytic center for both reactions is the same .
The NIT4 homologs of N tabacum were found to catalyze the same reactions and protein extracts of A thaliana , N tabacum and Lupinus angustifolius also converted Ala ( CN ) to Asp and Asn in vitro .
NIT4 may play a role in cyanide detoxification during ethylene biosynthesis because extracts from senescent leaves of A thaliana showed higher Ala ( CN ) hydratase/nitrilase activities than extracts from nonsenescent it issue . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Nitrilases ( nitrile aminohydrolases , EC ) are enzymes that catalyze the hydrolysis of nitriles to the corresponding carbon acids .
[ Sen. 8, subscore: 1.00 ]: Several lines of evidence indicate that the catalytic center for both reactions is the same .
[ Sen. 9, subscore: 1.00 ]: The NIT4 homologs of N tabacum were found to catalyze the same reactions and protein extracts of A thaliana , N tabacum and Lupinus angustifolius also converted Ala ( CN ) to Asp and Asn in vitro .
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