Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

ABSTRACT: We present GenoSuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (MS) data from prokaryotes. To demonstrate the effectiveness of GenoSuite, we analyzed proteomics data of Bradyrhizobium japonicum (USDA110), a model organism to study agriculturally important rhizobium-legume symbiosis. Our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (TIS) and discovered 59 novel protein coding genes. Notably, a novel protein which redefined the boundary of a crucial cytochrome P450 system related operon was discovered, known to be highly expressed in the anaerobic symbiotic bacteroids. A focused analysis on N-terminally acetylated peptides indicated downstream TIS f

SUBMITTER: Kumar D 

PROVIDER: S-EPMC3820949 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature