Literature DB >> 26055156

Determinants of the rate of protein sequence evolution.

Jianzhi Zhang1, Jian-Rong Yang1.   

Abstract

The rate and mechanism of protein sequence evolution have been central questions in evolutionary biology since the 1960s. Although the rate of protein sequence evolution depends primarily on the level of functional constraint, exactly what determines functional constraint has remained unclear. The increasing availability of genomic data has enabled much needed empirical examinations on the nature of functional constraint. These studies found that the evolutionary rate of a protein is predominantly influenced by its expression level rather than functional importance. A combination of theoretical and empirical analyses has identified multiple mechanisms behind these observations and demonstrated a prominent role in protein evolution of selection against errors in molecular and cellular processes.

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Year:  2015        PMID: 26055156      PMCID: PMC4523088          DOI: 10.1038/nrg3950

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  107 in total

1.  The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate.

Authors:  Sean Chun-Chang Chen; Trees-Juen Chuang; Wen-Hsiung Li
Journal:  Mol Biol Evol       Date:  2011-03-11       Impact factor: 16.240

2.  Structural determinants of protein evolution are context-sensitive at the residue level.

Authors:  Eric A Franzosa; Yu Xia
Journal:  Mol Biol Evol       Date:  2009-07-13       Impact factor: 16.240

Review 3.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

Review 4.  Somatic mosaicism and disease.

Authors:  Steven A Frank
Journal:  Curr Biol       Date:  2014-06-16       Impact factor: 10.834

5.  The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution.

Authors:  Jean-François Gout; Daniel Kahn; Laurent Duret
Journal:  PLoS Genet       Date:  2010-05-13       Impact factor: 5.917

Review 6.  Transcription as a source of genome instability.

Authors:  Nayun Kim; Sue Jinks-Robertson
Journal:  Nat Rev Genet       Date:  2012-02-14       Impact factor: 53.242

7.  Expression level, evolutionary rate, and the cost of expression.

Authors:  Joshua L Cherry
Journal:  Genome Biol Evol       Date:  2010-09-30       Impact factor: 3.416

8.  Why is the correlation between gene importance and gene evolutionary rate so weak?

Authors:  Zhi Wang; Jianzhi Zhang
Journal:  PLoS Genet       Date:  2009-01-09       Impact factor: 5.917

9.  Evolutionary rates and centrality in the yeast gene regulatory network.

Authors:  Richard Jovelin; Patrick C Phillips
Journal:  Genome Biol       Date:  2009-04-09       Impact factor: 13.583

10.  Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.

Authors:  Jingshan Zhang; Sergei Maslov; Eugene I Shakhnovich
Journal:  Mol Syst Biol       Date:  2008-08-05       Impact factor: 11.429

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  140 in total

1.  Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales.

Authors:  Mark J Margres; Kenneth P Wray; Margaret Seavy; James J McGivern; Nathanael D Herrera; Darin R Rokyta
Journal:  Genetics       Date:  2015-11-06       Impact factor: 4.562

2.  Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Authors:  Zhen Li; Jonas Defoort; Setareh Tasdighian; Steven Maere; Yves Van de Peer; Riet De Smet
Journal:  Plant Cell       Date:  2016-01-07       Impact factor: 11.277

Review 3.  Selection on protein structure, interaction, and sequence.

Authors:  Peter B Chi; David A Liberles
Journal:  Protein Sci       Date:  2016-02-11       Impact factor: 6.725

4.  Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.

Authors:  Bryan A Moyers; Jianzhi Zhang
Journal:  Mol Biol Evol       Date:  2016-01-11       Impact factor: 16.240

5.  Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes ( Crotalus cerastes).

Authors:  Rhett M Rautsaw; Erich P Hofmann; Mark J Margres; Matthew L Holding; Jason L Strickland; Andrew J Mason; Darin R Rokyta; Christopher L Parkinson
Journal:  Proc Biol Sci       Date:  2019-07-03       Impact factor: 5.349

6.  Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins.

Authors:  Rostam M Razban
Journal:  Mol Biol Evol       Date:  2019-09-01       Impact factor: 16.240

7.  Quantifying the Mutational Robustness of Protein-Coding Genes.

Authors:  Evandro Ferrada
Journal:  J Mol Evol       Date:  2021-05-02       Impact factor: 2.395

8.  The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution.

Authors:  Amy I Gilson; Ahmee Marshall-Christensen; Jeong-Mo Choi; Eugene I Shakhnovich
Journal:  Biophys J       Date:  2017-04-11       Impact factor: 4.033

9.  Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation.

Authors:  Felix Feyertag; Patricia M Berninsone; David Alvarez-Ponce
Journal:  Mol Biol Evol       Date:  2017-03-01       Impact factor: 16.240

10.  Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins.

Authors:  Eleisha L Jackson; Amir Shahmoradi; Stephanie J Spielman; Benjamin R Jack; Claus O Wilke
Journal:  Protein Sci       Date:  2016-03-24       Impact factor: 6.725

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