Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

Genome Biology
Maya Botzman, Hanah Margalit


It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codons. This phenomenon, termed codon usage bias, is common to many organisms and has been recognized as influencing cellular fitness. This suggests that the global extent of codon usage bias of an organism might be associated with its phenotypic traits. To test this hypothesis we used a simple measure for assessing the extent of codon bias of an organism, and applied it to hundreds of sequenced prokaryotes. Our analysis revealed a large variability in this measure: there are organisms showing very high degrees of codon usage bias and organisms exhibiting almost no differential use of synonymous codons among different genes. Remarkably, we found that the extent of codon usage bias corresponds to the lifestyle of the organism. Especially, organisms able to live in a wide range of habitats exhibit high extents of codon usage bias, consistent with their need to adapt efficiently to different environments. Pathogenic prokaryotes also demonstrate higher extents of codon usage bias than non-pathogenic prokaryotes, in accord with the ...Continue Reading


Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Jan 11, 1980·Nucleic Acids Research·R GranthamA Pavé
Apr 12, 2000·International Journal of Systematic and Evolutionary Microbiology·Y SekiguchiH Harada
Oct 17, 2003·Nature·Sina GhaemmaghamiJonathan S Weissman
Dec 6, 2003·Genome Research·Gila Lithwick, Hanah Margalit
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Jul 13, 2004·Trends in Biotechnology·Claes GustafssonJeremy Minshull
Sep 28, 2004·Nucleic Acids Research·Mario dos ReisLorenz Wernisch
Feb 25, 2005·Nucleic Acids Research·Paul M SharpR Elizabeth Sockett
Mar 4, 2006·Science·Francesca D CiccarelliPeer Bork
Dec 7, 2006·Nucleic Acids Research·Donna MaglottTatiana Tatusova
Aug 10, 2007·Genome Biology·Ruth HershbergDmitri A Petrov
Aug 2, 2008·Genome Research·Huifeng JiangZhenglong Gu
Nov 27, 2008·Molecular Biology and Evolution·Mario dos Reis, Lorenz Wernisch
Apr 11, 2009·Science·Grzegorz KudlaJoshua B Plotkin
Jun 2, 2009·BMC Bioinformatics·Haruo SuzukiMasaru Tomita
Jun 9, 2009·Genome Biology·Shiri FreilichEytan Ruppin
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Jan 22, 2010·PLoS Genetics·Sara Vieira-Silva, Eduardo P C Rocha
Jun 30, 2010·PLoS Genetics·Fran SupekTomislav Smuc


Jan 8, 2013·Nucleic Acids Research·Svetlana A ShabalinaAnna Kashina
Sep 4, 2012·Nucleic Acids Research·Hila GingoldYitzhak Pilpel
Aug 8, 2013·Nucleic Acids Research·Masa RollerKristian Vlahovicek
Nov 10, 2013·PloS One·Alexandra MouraRui Alves
Mar 10, 2016·Microbiome·Naseer SangwanJack A Gilbert
Nov 26, 2013·Journal of Molecular Evolution·Siddhartha Sankar SatapathySuvendra Kumar Ray
Oct 6, 2012·Environmental Microbiology·Ben BusbyEugene V Koonin
Dec 17, 2014·Extremophiles : Life Under Extreme Conditions·Deeya SahaTapash Chandra Ghosh
Jan 5, 2013·Microbiology·Andrés IriarteHéctor Musto
Jun 27, 2015·BioMed Research International·Tatiana TatarinovaAlexander Bolshoy
Apr 7, 2015·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Sumit MukherjeeTapash Chandra Ghosh
Dec 6, 2014·PloS One·Chandra Shekhar Kumar, Sachin Kumar
Feb 6, 2017·ELife·Thomas BadetSylvain Raffaele
Sep 30, 2017·Molecular Biology and Evolution·Liam Abrahams, Laurence D Hurst
Nov 7, 2017·Molecular Biology and Evolution·Sergey V Venev, Konstantin B Zeldovich
Aug 21, 2018·Annual Review of Cell and Developmental Biology·Roni RakYitzhak Pilpel
Mar 8, 2019·Annals of the New York Academy of Sciences·Arif UddinSupriyo Chakraborty
Sep 9, 2016·G3 : Genes - Genomes - Genetics·Chuyue YangLuís A N Amaral
Apr 19, 2018·Nature Communications·Ricardo J Eloy AlvesChrista Schleper
Oct 20, 2017·Frontiers in Microbiology·Alexei Y KostygovVyacheslav Yurchenko
Jan 30, 2019·BMC Genomics·Nancy MerinoHaruo Suzuki
Sep 29, 2017·Molecular Biology and Evolution·Maxime DéraspeJacques Corbeil
Sep 21, 2018·Frontiers in Microbiology·Alba Pérez-CataluñaMaria J Figueras

Related Concepts

Biological Adaptation
G+C Composition
Sense Codon
Genome, Bacterial
Evolution, Molecular
Computational Molecular Biology
Genome, Archaeal

Related Feeds


Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.