Analyzing Gene Expression and Codon Usage Bias in Diverse Genomes Using a Variety of Models
Synonymous codon usage has long been known as a factor that affects the average expression level of proteins
in microorganisms. A systematic approach to study the role of codon usage bias underlying gene expression has been
described. Facts and ideas presented in this short review are to derive biological information from genome sequences by
means of various statistical analyses and appropriate design of algorithms. Using codon usage bias as a numerical
estimator of gene expression, a comparative analysis of predicted highly expressed (PHE) genes was performed in
bacteria, cyanobacteria, archaea, lower eukaryotes and higher eukaryotes. Here, it is suggested that both codon usage and
as well as base compositions at three codon sites regulate the individual gene expression. Any correlation between gene
length and expression level, however, remains unexplained. Relationship between gene expression levels and synonymous
codon usage provides an important line of evidence for translational selection and suggests some general mechanism
underlying protein evolution.
Keywords: Archaea, bacteria, codon usage, eukaryotes, GC content, gene expression, highly expressed genes predicted.
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