| 1526 matches found in 1136 documents. Search time: 0.048 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 .
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[ 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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