ArticleGenome biology and evolution2012
Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
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- The Evolution of G-quadruplex Structure in mRNA Untranslated Region.Evolutionary bioinformatics online · 2021Article
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life.Genome biology · 2020Article
- Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis.Poultry science · 2019Article
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- Tuning recombinant protein expression to match secretion capacity.Microbial cell factories · 2018Article
- Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands.Molecular biology and evolution · 2018Article
- Effects of mRNA secondary structure on the expression of HEV ORF2 proteins in Escherichia coli.Microbial cell factories · 2017Article
- Incorporation of a tag helps to overcome expression variability in a recombinant host.Biotechnology reports (Amsterdam, Netherlands) · 2016Article
- Prediction of ribosome footprint profile shapes from transcript sequences.Bioinformatics (Oxford, England) · 2016Article
- Distribution and diversity of ribosome binding sites in prokaryotic genomes.BMC genomics · 2015Article
- Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.Molecular systems biology · 2014Article
- Quantifying position-dependent codon usage bias.Molecular biology and evolution · 2014Article
- Efficient translation initiation dictates codon usage at gene start.Molecular systems biology · 2013Article
- Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
Several recent studies have found that selection acts on synonymous mutations at the beginning of genes to reduce mRNA secondary-structure stability, presumably to aid in translation initiation. This observation suggests that a metric of relative mRNA secondary-structure stability, Z(ΔG), could be used to test whether putative genes are likely to be functionally important. Using the Escherichia coli genome, we compared the mean Z(ΔG) of genes with known functions, genes with known orthologs, genes where function and orthology are unknown, and pseudogenes. Genes in the first two categories demonstrated similar levels of selection for reduced stability (increased Z(ΔG)), whereas for pseudogenes stability did not differ from our null expectation. Surprisingly, genes where function and orthology were unknown were also not different from the null expectation, suggesting that many of these open reading frames are not functionally important. We extended our analysis by constructing a Bayesian phylogenetic mixed model based on data from 145 prokaryotic genomes. As in E. coli, genes with no known function had consistently lower Z(ΔG), even though we expect that many of the currently unannotated genes will ultimately have their functional utility discovered. Our findings suggest that functional genes tend to evolve increased Z(ΔG), whereas nonfunctional ones do not. Therefore, Z(ΔG) may be a useful metric for identifying genes of potentially important function and could be used to target genes for further functional study.
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