title: In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases.
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 (GH9C = 241) from 32 sequenced green plants.
authors: Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College & HospitalNew Delhi, India; Mathematical and Computational Biology, Information Technology Research Academy, Media Lab AsiaNew Delhi, India; School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India.
authors: Siddhartha
authors: S
authors: Kundu
authors: School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi, India.
authors: Rita
authors: R
authors: Sharma
keywords: artificial neural network; carbohydrate binding module; cellulose; endoglucanase; glycoside hydrolase; hidden markov models