title: Transcriptional abundance is not the single force driving the evolution of bacterial proteins.
abstract: BACKGROUND
  Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. In this study, we have assessed the effects of 16 different biological features on the evolutionary rates (ERs) of protein-coding sequences in bacterial genomes.
  
  
  RESULTS
  Our analysis of 18 bacterial species revealed new correlations between ERs and constraining factors. Previous studies have suggested that transcriptional abundance overwhelmingly constrains the evolution of yeast protein sequences. This transcriptional abundance leads to selection against misfolding or misinteractions. In this study we found that there was no single factor in determining the evolution of bacterial proteins. Not only transcriptional abundance (codon adaptation index and expression level), but also protein-protein associations (PPAs), essentiality (ESS), subcellular localization of cytoplasmic membrane (SLM), transmembrane helices (TMH) and hydropathicity score (HS) independently and significantly affected the ERs of bacterial proteins. In some species, PPA and ESS demonstrate higher correlations with ER than transcriptional abundance.
  
  
  CONCLUSIONS
  Different forces drive the evolution of protein sequences in yeast and bacteria. In bacteria, the constraints are involved in avoiding a build-up of toxic molecules caused by misfolding/misinteraction (transcriptional abundance), while retaining important functions (ESS, PPA) and maintaining the cell membrane (SLM, TMH and HS). Each of these independently contributes to the variation in protein evolution.
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054 Chengdu, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wei
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.forename: Dan
authors.initials: D
authors.lastname: Lin
authors.forename: Zu-Jun
authors.initials: ZJ
authors.lastname: Yang
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D003062:Codon / Q000378:metabolism; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D003062:Codon
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