Peptidoglycan Hydrolases
The bacterial cell wall consists of a glycan strands which are cross-linked by flexible peptide side chains, providing strength and rigidity to the bacterial cell wall. The peptidoglycan of both gram-positive and gram-negative bacteria comprises of repeating units of N-acetylglucosamine (NAG) and β-(1-4)-N-acetylmuramic acid (NAM) cross-linked by peptide stem chains attached to the NAM residues. Peptidoglycan hydrolases are the enzymes responsible for cleaving the bonds within peptidoglycan chain and side-chain branches, therefore, are responsible for maintaining overall cell wall peptidoglycan turnover. Recently, peptidoglycan hydrolases have been proposed as potential alternative for antibiotics due to their bacteriolytic activity.
Class         Name                                                                Site of action
"A"                 N-acetylmuramoyl-L-alanine amidases             Glycan-Peptide bond
"B"                 Peptidases                                                         Stem peptide
"C"                 Enzymes acting on Peptidoglycan chain            Glycan strand
"D"                 Unclassified                                                         Not known
Motivation to develop a better, comprehensive and efficient software
Identification and characterization of novel peptidoglycan hydrolases in the completely sequenced genomes becomes difficult due to the lack of homology of these hydrolases with the previously well characterized peptidoglycan hydrolases. Therefore, in the present work, a machine learning based approach using Random Forest has been used and demonstrated for the identification and classification of novel peptidoglycan hydrolases from genomic and metagenomic data. The predicted novel peptidoglycan hydrolases belonging to different classes would provide leads for further characterization and potential application as antibacterial agents specifically against various bacterial species. The developed 'Hype' tool helps in the identification and classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs. To our knowledge, this is the only tool available for the prediction of peptidoglycan hydrolases from genomic and metagenomic data. HyPe is also available as stand-alone tool.
How to cite:
Sharma, Ashok K., Sanjiv Kumar, K. Harish, Darshan B. Dhakan, and Vineet K. Sharma. "Prediction of peptidoglycan hydrolases-a new class of antibacterial proteins." BMC genomics 17, no. 1 (2016): 1.