Improving genome annotation of enterotoxigenic Escherichia coli TW10598 by a label-free quantitative MS/MS approach

Proteomics
Veronika Kuchařová PettersenHarald G Wiker

Abstract

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...Continue Reading

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Citations

Apr 20, 2016·Frontiers in Microbiology·Matthys G PotgieterJonathan M Blackburn
Sep 2, 2017·Journal of Proteome Research·Nadia G D'LimaSarah A Slavoff

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