Christie-Oleza, Joseph Alexander, Miotello, Guylaine and Armengaud, Jean (2012) High-throughput proteogenomics of Ruegeria pomeroyi : seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics, Volume 13 (Number 1). Article number 73. doi:10.1186/1471-2164-13-73 ISSN 1471-2164.

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Abstract

Background
The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade.

Results
A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs) that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated.

Conclusions
By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera), we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase the reliability of the future annotation of marine bacterial genomes.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology
Divisions:	Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Marine bacteria -- Genome mapping, Proteomics, Genomics
Journal or Publication Title:	BMC Genomics
Publisher:	BioMed Central Ltd.
ISSN:	1471-2164
Official Date:	15 February 2012
Dates:	Date Event 15 February 2012 Published 15 February 2012 Accepted 25 July 2012 Submitted
Volume:	Volume 13
Number:	Number 1
Article Number:	Article number 73
DOI:	10.1186/1471-2164-13-73
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	27 December 2015
Date of first compliant Open Access:	27 December 2015
Funder:	Fundación Ramón Areces, France. Commissariat à l'énergie atomique et aux énergies alternatives, France. Ministère des affaires étrangères et européennes
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