Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv

Abstract

Original genome annotations need to be regularly updated if the information they contain is to remain accurate and relevant. Here the complete reannotation of the genome sequence of Mycobacterium tuberculosis strain H37Rv is presented almost 4 years after the first submission. Eighty-two new protein-coding sequences (CDS) have been included and 22 of these have a predicted function. The majority were identified by manual or automated reanalysis of the genome and most of them were shorter than the 100 codon cutoff used in the initial genome analysis. The functional classification of 643 CDS has been changed based principally on recent sequence comparisons and new experimental data from the literature. More than 300 gene names and over 1000 targeted citations have been added and the lengths of 60 genes have been modified. Presently, it is possible to assign a function to 2058 proteins (52 % of the 3995 proteins predicted) and only 376 putative proteins share no homology with known proteins and thus could be unique to M. tuberculosis.

Mycobacterium tuberculosisFunctional Network Analysis by Global Subcellular Protein Profiling

“…So far proteomic studies of Mtb and other organisms have mainly involved two-dimensional PAGE (2DGE) to resolve proteins followed by mass spectrometry (MS) to identify them (Kaji et al, 2000;Taoka et al, 2000;Mattow et al, 2001aMattow et al, , 2001b). However, because of the limitations of 2DGE-based separation methods, only 341 proteins have so far been identified in the Mtb proteome Mattow et al, 2001aMattow et al, , 2001b thus far, compared with the 3924 protein coding sequences (CDS) predicted from the genome (Camus et al, 2002). Only recently has SDS-PAGE been used to separate membrane proteins of Mtb for further liquid chromatography (LC)-MS/MS analyses (Gu et al, 2003a).…”

Succinylome Analysis Reveals the Involvement of Lysine Succinylation in Metabolism in Pathogenic Mycobacterium tuberculosis*

“…Because Mtb H37Rv is the first sequenced Mtb strain (40) and has been extensively used for studies in dissecting the roles of individual genes in pathogenesis (41), it was selected as a test case. We analyzed the succinylome of Mtb H37Rv by using high accuracy nano-LC-MS/MS in combination with the enrichment of succinylated peptides from digested cell lysates and subsequent peptide identification.…”

A Systematic Review Of Gyrase Mutations Associated With Fluoroquinolone-Resistant Mycobacterium Tuberculosis And A Proposed Gyrase Numbering System

“…We propose that the GyrB sequence that was re-annotated in 2002 34 should be used as the reference sequence (Table 1 and Figure S3).…”

“…34 Regarding the QRDR of GyrA, some publications used the E. coli numbering system to describe substitution location. 38 -41 In this systematic review, all substitution locations in GyrA were standardized to the genome M. tuberculosis numbering system, in which the QRDR of GyrA ranges from codon 74 to 113.…”

“…36 When the entire genome of M. tuberculosis was published in 1998, the start codon of gyrB was 28 codons upstream of the codon that had been used earlier. Due to the absence of some amino acids in E. coli that are present in M. tuberculosis, the 34 Systematic review 821 JAC first codon of the GyrB QRDR was five codons upstream of the codon that had been used earlier; the QRDR therefore ranged from amino acid 500 to 538 2 (see gi|1552558|emb|CAB02426.1 in Figure S3). Of the studies reviewed, most authors used the 500-538 numbering system to identify mutation location.…”