Predicting Gene Expression Level from Codon Usage Bias

Henry, Ian; Sharp, Paul M.

doi:10.1093/molbev/msl148

Cited by 64 publications

(59 citation statements)

References 21 publications

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“…Slight differences were also found for the His CAC codon usage, which was 35 % in the whole genome and 41 % in highly transcribed transposon insertions. However, these differences are very small and support previous computer analyses indicating that highly expressed genes of several species, including M. genitalium, have no discernible differences in codon usage compared to other genes (Henry & Sharp, 2007).…”

Section: Monitoring Gene Expression Level Using the Promoterless Vectorsupporting

confidence: 85%

A new promoterless reporter vector reveals antisense transcription in Mycoplasma genitalium

et al. 2007

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The mechanisms that promote and regulate transcription in mycoplasmas are poorly understood. Here, a promoter-probe vector based on the pMTnTetM438 minitransposon and containing a promoterless lacZ reporter gene was constructed to analyse Mycoplasma genitalium transcription in vivo. Recovered transposon insertions were in monocopy, with 16 % expressing enough b-galactosidase (b-Gal) to yield colonies exhibiting a detectable blue colour. A sample of 52 blue colonies was propagated and selected for further analyses. The b-Gal activity of the corresponding cultures was measured to quantify, in a reproducible way, the transcription levels of the interrupted ORFs. Several insertions were found in sense with the interrupted ORF, but surprisingly there was also a number of insertions in non-coding regions, many of them in repetitive DNA regions known as MgPa islands. Moreover, 30 % of the analysed transposon insertions had the lacZ gene in the opposite orientation to the coding frame, suggesting the existence of antisense transcripts that may be involved in the control of gene expression in M. genitalium.

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Section: Monitoring Gene Expression Level Using the Promoterless Vectorsupporting

confidence: 85%

A new promoterless reporter vector reveals antisense transcription in Mycoplasma genitalium

et al. 2007

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“…Codon usage is compared between a set of 40 highly expressed genes (high; see Sharp et al 2005) and the genome as a whole (all); the data are relative synonymous codon usage values (the ratio of the observed number to that expected if all codons for an amino acid were used equally). Nineteen codons occurring at significantly higher frequencies (see Henry & Sharp 2007) replicated by different mechanisms with different mutation rates (Fijalkowska et al 1998), which could lead to the observed differences in base composition. Alternatively, since there is an excess of genes located on the leading strand in many bacteria (Brewer 1988;Tillier & Collins 2000), biases in transcriptioncoupled repair could lead to a skew between the strands in nucleotide composition (Francino et al 1996).…”

Section: Variation In Codon Usage Bias Among Bacteriamentioning

confidence: 99%

Forces that influence the evolution of codon bias

Sharp

Emery

Zeng

2010

Phil. Trans. R. Soc. B

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322

246

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The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the variation among species appears to be due to biased patterns of mutation. The strength of selection on codon usage can be estimated by two different approaches. First, the extent of bias in favour of translationally optimal codons in highly expressed genes, compared to that in genes where selection is weak, reveals the longterm effectiveness of selection. Here we show that the strength of selected codon usage bias is highly correlated with bacterial growth rate, suggesting that selection has favoured translational efficiency. Second, the pattern of bias towards optimal codons at polymorphic sites reveals the ongoing action of selection. Using this approach we obtained results that were completely consistent with the first method; importantly, the frequency spectra of optimal codons at polymorphic sites were similar to those predicted under an equilibrium model. Highly expressed genes in Escherichia coli appear to be under continuing strong selection, whereas selection is very weak in genes expressed at low levels.

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“…Optimal codons were identified as those occurring significantly more frequently in the HE genes than across all genes, using x 2 -tests with sequential Bonferroni correction [10]. Codon adaptation index (CAI; [18]) values were computed using codon fitness values from the HE gene set.…”

Section: Methodsmentioning

confidence: 99%

“…Karlin et al [9] used codon-usage analyses to predict HE genes in 19 archaeal genomes. However, their approach (i) assumed translational selection without first testing for its presence and (ii) is expected to give anomalous results, even in species where selection has shaped codon usage [10]. Some Archaea have been included in larger analyses mainly focused on genomes from Bacteria.…”

Section: Introductionmentioning

confidence: 99%

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

Emery

Sharp

2010

Biol. Lett.

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Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis . Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli , the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli : in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.

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Predicting Gene Expression Level from Codon Usage Bias

Cited by 64 publications

References 21 publications

A new promoterless reporter vector reveals antisense transcription in Mycoplasma genitalium

A new promoterless reporter vector reveals antisense transcription in Mycoplasma genitalium

Forces that influence the evolution of codon bias

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

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