Transcriptional abundance is not the single force driving the evolution of bacterial proteins

Wen Wei,Zu-Jun Yang,Tao Zhang,Feng-Biao Guo,Dan Lin

doi:10.1186/1471-2148-13-162

Wen Wei, Zu-Jun Yang + Show 3 more

Open Access

https://doi.org/10.1186/1471-2148-13-162

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Abstract

BackgroundDespite 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.ResultsOur 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.ConclusionsDifferent 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.

Highlights

Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated
We have uncovered new relationships among evolutionary rates (ERs) in bacterial genomes related to protein subcellular localization, transmembrane helices, hydropathicity, aromaticity, and replication strand localization
We found that proteins that evolved slowly in bacterial genomes tended to avoid adopting aromatic amino acids

Summary

Introduction

Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. We have assessed the effects of 16 different biological features on the evolutionary rates (ERs) of protein-coding sequences in bacterial genomes. Rapid progress has been made in determining the most important factors that shape protein evolution, the challenge remains to assess the relative importance of various variables, such as gene expression level, essentiality (ESS) and protein interactions [1,2,3,4,5,6,7,8,9,10]. When CAI values were used as a substitute for actual expression levels in yeast [2] and bacteria [12], only a small proportion of rate variation in protein evolution can be explained by ESS. Results from another study suggest that the molecular evolution of protein-coding genes is affected by both the context of extrinsic translational expression rates and intrinsic structural-functional constraints [25]

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