Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli

Biochemical and Biophysical Research Communications
Regina M Goetz, Anders Fuglsang

Abstract

Although codon usage is often represented by a 61-dimensional vector, the ability of determining the codon bias in a gene relies on a uni-dimensional vector which measures the total bias in usage of synonymous codons. Codon usage is receiving more and more focus because codon biases might be valuable tools to predict and optimize gene/protein expression. How good any of these measures is for correlating codon usage with gene and protein expression has yet to be investigated. In this study, we correlated gene transcript levels in Escherichia coli with codon usage, using a number of different codon bias measures. We found that there is a significant correlation between transcript levels and codon bias measures, suggesting that these measures can be used to assess or predict gene expression. The codon bias measure performing best in this context was the codon adaptation index.

References

Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Jan 11, 1980·Nucleic Acids Research·R GranthamA Pavé
Apr 1, 1997·The International Journal of Biochemistry & Cell Biology·I G IvanovM G Abouhaidar
Jul 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan A BernsteinStanley N Cohen
Apr 15, 2004·Biochemical and Biophysical Research Communications·Anders Fuglsang
Oct 7, 2004·Biochemical and Biophysical Research Communications·Sayed-Amir Marashi, Hamed Shateri Najafabadi

Citations

Apr 6, 2006·Journal of Molecular Evolution·Björn SällströmSiv G E Andersson
May 25, 2005·Biochemical and Biophysical Research Communications·Qing-Shan FuLing-Ling Chen
Sep 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ming-Wei ChenDavid D Ho
Nov 1, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yousheng RaoXiquan Zhang
Jul 26, 2013·Molecular Biology and Evolution·Aoife Doherty, James O McInerney
Apr 19, 2007·Nucleic Acids Research·Pere PuigbòSantiago Garcia-Vallvé
Nov 6, 2008·Annual Review of Genetics·Ruth Hershberg, Dmitri A Petrov
Jan 31, 2008·BMC Bioinformatics·Pere PuigbòSantiago Garcia-Vallvé
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Dec 20, 2005·Genetics·Cristina E PopescuRobert W Lee
Jun 11, 2010·Evolutionary Bioinformatics Online·Soohyun LeeChangwon Kang
Sep 30, 2014·FEBS Letters·Adrian Gabriel TorresLluís Ribas de Pouplana
Oct 27, 2015·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·David B Carlini, Matthew Makowski
Jan 23, 2016·The Korean Journal of Parasitology·Xing YangXuepeng Cai
May 23, 2007·Biochemical and Biophysical Research Communications·Gang WuStephen J Freeland
Mar 10, 2015·Annual Review of Biophysics·Julie L Chaney, Patricia L Clark
Jun 7, 2015·Enzyme and Microbial Technology·Han Bin PekDong-Yup Lee
Mar 13, 2014·The Journal of Steroid Biochemistry and Molecular Biology·Tamara Fernández-CaleroMónica Marin
Apr 19, 2015·BMC Genomics·Marcelo BaezaVíctor Cifuentes
Aug 28, 2012·Trends in Genetics : TIG·Eva Maria Novoa, Lluís Ribas de Pouplana
Sep 16, 2016·Journal of Biomolecular Structure & Dynamics·Bidhan Chandra Roy, Ashutosh Mukherjee
Mar 11, 2016·PLoS Genetics·Gerrit Brandis, Diarmaid Hughes
Nov 28, 2013·Scientific Reports·Pedro ChanJim Warwicker
May 17, 2017·The Korean Journal of Parasitology·Young-An Bae
Jan 27, 2017·G3 : Genes - Genomes - Genetics·Paweł BłażejPaweł Mackiewicz
Nov 19, 2020·Genome Biology·Nhan HuynhKirst King-Jones
Oct 1, 2019·Computers in Biology and Medicine·R PriyaRamamoorthy Siva

Related Concepts

Sense Codon
Alkalescens-Dispar Group
RNA, Bacterial
Poly(A) Tail
Transcription, Genetic

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