eprintid: 2854
rev_number: 11
eprint_status: archive
userid: 69
dir: disk0/00/00/28/54
datestamp: 2015-11-06 13:34:12
lastmod: 2016-05-04 10:17:33
status_changed: 2015-11-06 13:34:12
type: article
metadata_visibility: show
creators_name: Dilucca, Maddalena
creators_name: Cimini, Giulio
creators_name: Semmoloni, Andrea
creators_name: Deiana, Antonio
creators_name: Giansanti, Andrea
creators_id: 
creators_id: giulio.cimini@imtlucca.it
creators_id: 
creators_id: 
creators_id: 
title: Codon Bias Patterns of E.coli's Interacting Proteins
ispublished: pub
subjects: QH426
divisions: EIC
full_text_status: public
abstract: Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation.
date: 2015
date_type: published
publication: PloS One
volume: 10
number: 11
publisher: Public Library of Science
pagerange: e0142127
id_number: 10.1371/journal.pone.0142127
refereed: TRUE
issn: 1932-6203
official_url: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142127
citation:   Dilucca, Maddalena and Cimini, Giulio and Semmoloni, Andrea and Deiana, Antonio and Giansanti, Andrea  Codon Bias Patterns of E.coli's Interacting Proteins.  PloS One, 10 (11).  e0142127.  ISSN 1932-6203      (2015)  
document_url: http://eprints.imtlucca.it/2854/1/1507.07693v1.pdf