Improving genome annotation of enterotoxigenic Escherichia coli TW10598 by a label-free quantitative MS/MS approach.
The most commonly used genome annotation processes are to a great extent based on computational methods. However, those can only predict genes that have been described earlier or that have sequence signatures indicative of a gene function. Here, we report a synonymous proteogenomic approach for experimentally improving microbial genome annotation based on label-free quantitative MS/MS. The approach is exemplified by analysis of cell extracts from in vitro cultured enterotoxigenic Escherichia coli (ETEC) strain TW10598, as part of an effort to create a new reference ETEC genome sequence. The proteomic analysis yielded identification of 2060 proteins, out of which 312 proteins were originally described as hypothetical. For 84% of the identified proteins we have provided description of their relative quantitative levels, among others, for 20 abundantly expressed ETEC virulence factors. Proteogenomic mapping supported the existence of four protein-coding genes that had not been annotated, and led to correction of translation start positions of another nine. The addition of the proteomic analysis into TW10598 genome re-annotation project improved quality of the annotation, and provided experimental evidence for a significant portion of ETEC expressed proteome. Data are available via ProteomeXchange with identifier PXD002473 (http://proteomecentral.proteomexchange.org/dataset/PXD002473).
The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.
Veronika Kuchařová
VK
Pettersen
Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.|Department of Biomedicine, University of Bergen, Bergen, Norway.
Hans
H
Steinsland
The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.
Harald G
HG
Wiker
D002853:Chromatography, Liquid; D054307:Enterotoxigenic Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D037521:Virulence Factors / Q000235:genetics / Q000378:metabolism
D029968:Escherichia coli Proteins; D020543:Proteome; D037521:Virulence Factors
Enterotoxigenic Escherichia coli; Genome annotation; Label-free quantification; Microbiology; Synonymous proteogenomics