In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases
Identifieur interne : 000360 ( Main/Exploration ); précédent : 000359; suivant : 000361In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases
Auteurs : Siddhartha Kundu [Inde] ; Rita Sharma [Inde]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
The glycoside hydrolase 9 superfamily, mainly comprising the endoglucanases, is represented in all three domains of life. The current division of GH9 enzymes, into three subclasses, namely A, B, and C, is centered on parameters derived from sequence information alone. However, this classification is ambiguous, and is limited by the paralogous ancestry of classes B and C endoglucanases, and paucity of biochemical and structural data. Here, we extend this classification schema to putative GH9 endoglucanases present in green plants, with an emphasis on identifying novel members of the class C subset. These enzymes cleave the β(1 → 4) linkage between non-terminal adjacent D-glucopyranose residues, in both, amorphous and crystalline regions of cellulose. We utilized non redundant plant GH9 enzymes with characterized molecular data, as the training set to construct Hidden Markov Models (HMMs) and train an Artificial Neural Network (ANN). The parameters that were used for predicting dominant enzyme function, were derived from this training set, and subsequently refined on 147 sequences with available expression data. Our knowledge-based approach, can ascribe differential endoglucanase activity (A, B, or C) to a query sequence with high confidence, and was used to construct a local repository of class C GH9 endoglucanases (
Url:
DOI: 10.3389/fpls.2016.01185
PubMed: 27570528
PubMed Central: 4981690
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>In silico</italic> Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases</title><author><name sortKey="Kundu, Siddhartha" sort="Kundu, Siddhartha" uniqKey="Kundu S" first="Siddhartha" last="Kundu">Siddhartha Kundu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College & Hospital</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Mathematical and Computational Biology, Information Technology Research Academy, Media Lab Asia</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>School of Computational and Integrative Sciences, Jawaharlal Nehru University</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sharma, Rita" sort="Sharma, Rita" uniqKey="Sharma R" first="Rita" last="Sharma">Rita Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>School of Computational and Integrative Sciences, Jawaharlal Nehru University</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27570528</idno><idno type="pmc">4981690</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981690</idno><idno type="RBID">PMC:4981690</idno><idno type="doi">10.3389/fpls.2016.01185</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000F33</idno><idno type="wicri:Area/Pmc/Curation">000F32</idno><idno type="wicri:Area/Pmc/Checkpoint">000286</idno><idno type="wicri:Area/Ncbi/Merge">002158</idno><idno type="wicri:Area/Ncbi/Curation">002158</idno><idno type="wicri:Area/Ncbi/Checkpoint">002158</idno><idno type="wicri:Area/Main/Merge">000360</idno><idno type="wicri:Area/Main/Curation">000360</idno><idno type="wicri:Area/Main/Exploration">000360</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic> Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases</title><author><name sortKey="Kundu, Siddhartha" sort="Kundu, Siddhartha" uniqKey="Kundu S" first="Siddhartha" last="Kundu">Siddhartha Kundu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College & Hospital</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Mathematical and Computational Biology, Information Technology Research Academy, Media Lab Asia</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>School of Computational and Integrative Sciences, Jawaharlal Nehru University</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sharma, Rita" sort="Sharma, Rita" uniqKey="Sharma R" first="Rita" last="Sharma">Rita Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>School of Computational and Integrative Sciences, Jawaharlal Nehru University</institution><country>New Delhi, India</country></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The glycoside hydrolase 9 superfamily, mainly comprising the endoglucanases, is represented in all three domains of life. The current division of GH9 enzymes, into three subclasses, namely A, B, and C, is centered on parameters derived from sequence information alone. However, this classification is ambiguous, and is limited by the paralogous ancestry of classes B and C endoglucanases, and paucity of biochemical and structural data. Here, we extend this classification schema to putative GH9 endoglucanases present in green plants, with an emphasis on identifying novel members of the class C subset. These enzymes cleave the β(1 → 4) linkage between non-terminal adjacent D-glucopyranose residues, in both, amorphous and crystalline regions of cellulose. We utilized non redundant plant GH9 enzymes with characterized molecular data, as the training set to construct Hidden Markov Models (HMMs) and train an Artificial Neural Network (ANN). The parameters that were used for predicting dominant enzyme function, were derived from this training set, and subsequently refined on 147 sequences with available expression data. Our knowledge-based approach, can ascribe differential endoglucanase activity (A, B, or C) to a query sequence with high confidence, and was used to construct a local repository of class C GH9 endoglucanases (<italic>GH</italic>9<italic>C</italic> = 241) from 32 sequenced green plants.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abbott, D W" uniqKey="Abbott D">D. W. Abbott</name></author><author><name sortKey="Hrynuik, S" uniqKey="Hrynuik S">S. Hrynuik</name></author><author><name sortKey="Boraston, A B" uniqKey="Boraston A">A. B. Boraston</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abramyan, J" uniqKey="Abramyan J">J. Abramyan</name></author><author><name sortKey="Stajich, J E" uniqKey="Stajich J">J. E. 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Kost</name></author><author><name sortKey="Chua, N H" uniqKey="Chua N">N. H. Chua</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Kundu, Siddhartha" sort="Kundu, Siddhartha" uniqKey="Kundu S" first="Siddhartha" last="Kundu">Siddhartha Kundu</name></noRegion><name sortKey="Kundu, Siddhartha" sort="Kundu, Siddhartha" uniqKey="Kundu S" first="Siddhartha" last="Kundu">Siddhartha Kundu</name><name sortKey="Kundu, Siddhartha" sort="Kundu, Siddhartha" uniqKey="Kundu S" first="Siddhartha" last="Kundu">Siddhartha Kundu</name><name sortKey="Sharma, Rita" sort="Sharma, Rita" uniqKey="Sharma R" first="Rita" last="Sharma">Rita Sharma</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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