The Codon Usage of Lowly Expressed Genes Is Subject to Natural Selection

Genome Biology and Evolution
Adi YannaiRuth Hershberg

Abstract

Codon usage bias affects the genomes of organisms from all kingdoms of life and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared with lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function. By applying tests of selection on the gene sequences of the bacterium Escherichia coli, we demonstrate that both highly and lowly expressed genes display signals of selection on codon usage. Such signals are found for both conserved and less conserved amino acid positions, even within the 10% of E. coli genes expressed at the lowest levels. We further demonstrate experimentally that single synonymous codon replacements within a lowly expressed, essential gene can carry substantial effects on bacterial fitness. Combined, our results demonstrate that even within genes expressed at relatively low levels there is substantial se...Continue Reading

Citations

Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W R Pearson, D J Lipman
Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Jan 11, 1980·Nucleic Acids Research·R GranthamA Pavé
Jun 1, 2000·Proceedings of the National Academy of Sciences of the United States of America·K A Datsenko, B L Wanner
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 10, 2006·Journal of Inherited Metabolic Disease·N Gregersen
Nov 15, 2006·Molecular Biology and Evolution·Nina Stoletzki, Adam Eyre-Walker
Nov 6, 2008·Annual Review of Genetics·Ruth Hershberg, Dmitri A Petrov
Nov 6, 2008·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Nov 27, 2008·Molecular Biology and Evolution·Mario dos Reis, Lorenz Wernisch
Apr 8, 2009·Molecular Biology and Evolution·Tong ZhouClaus O Wilke
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Apr 14, 2011·Molecular Systems Biology·Hila Gingold, Yitzhak Pilpel
Jun 6, 2013·PLoS Genetics·David S LawrieDmitri A Petrov
Feb 26, 2014·Molecular Biology and Evolution·Elad FirnbergMarc Ostermeier
Jul 18, 2015·Molecular Cell·Tessa E F QuaxJohn van der Oost
Feb 18, 2016·Molecular Biology and Evolution·Anna KnöppelDan I Andersson
Mar 11, 2016·PLoS Genetics·Gerrit Brandis, Diarmaid Hughes

Related Concepts

Conserved Sequence
Alkalescens-Dispar Group
Genome
Genes
Attentional Bias
Natural Products
Amino Acids, I.V. solution additive
Protein Biosynthesis
Beta-Lactamase
Sense Codon

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Related Papers

Molecular Biology and Evolution
Jane Charlesworth, Adam Eyre-Walker
Molecular Biology and Evolution
Adam J HockenberryMichael C Jewett
Proceedings of the National Academy of Sciences of the United States of America
Pragya MittalGrzegorz Kudla
© 2020 Meta ULC. All rights reserved