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Selection-driven cost-efficiency optimisation of transcripts modulates gene evolutionary rate in bacteria

https://doi.org/10.1101/136861
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf01731487openalex-snapshot
Evolutionary processes and evolutionary noise at the molecular level
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Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: Codon usage, map position, and concerted evolution
inferredcites →https://doi.org/10.1016/0022-2836(89)90260-xopenalex-snapshot
Codon usage determines translation rate in Escherichia coli
inferredcites →https://doi.org/10.1016/j.cell.2008.05.042openalex-snapshot
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
inferredcites →https://doi.org/10.1016/j.febslet.2009.11.052openalex-snapshot
Deciphering synonymous codons in the three domains of life: Co‐evolution with specific tRNA modification enzymes
inferredcites →https://doi.org/10.1016/j.tig.2012.07.006openalex-snapshot
Speeding with control: codon usage, tRNAs, and ribosomes
inferredcites →https://doi.org/10.1016/s0021-9258(18)60966-4openalex-snapshot
Missense misreading of asparagine codons as a function of codon identity and context.
inferredcites →https://doi.org/10.1016/s1672-0229(10)60008-3openalex-snapshot
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
inferredcites →https://doi.org/10.1038/ncomms11334openalex-snapshot
Energy efficiency trade-offs drive nucleotide usage in transcribed regions
inferredcites →https://doi.org/10.1038/nrg2662openalex-snapshot
The evolutionary consequences of erroneous protein synthesis
inferredcites →https://doi.org/10.1073/pnas.0308594100openalex-snapshot
Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes
inferredcites →https://doi.org/10.1073/pnas.1016719108openalex-snapshot
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.185openalex-snapshot
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
inferredcites →https://doi.org/10.1093/dnares/dsu017openalex-snapshot
Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias
inferredcites →https://doi.org/10.1093/genetics/136.3.927openalex-snapshot
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.
inferredcites →https://doi.org/10.1093/genetics/158.2.927openalex-snapshot
Highly Expressed Genes in Yeast Evolve Slowly
inferredcites →https://doi.org/10.1093/molbev/msj038openalex-snapshot
A Single Determinant Dominates the Rate of Yeast Protein Evolution
inferredcites →https://doi.org/10.1093/nar/gkg897openalex-snapshot
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
inferredcites →https://doi.org/10.1093/nar/gkh834openalex-snapshot
Solving the riddle of codon usage preferences: a test for translational selection
inferredcites →https://doi.org/10.1093/nar/gki366openalex-snapshot
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040443openalex-snapshot
The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias.
inferredcites →https://doi.org/10.1101/gr.10.2.228openalex-snapshot
Thermophilic Bacteria Strictly Obey Szybalski's Transcription Direction Rule and Politely Purine-Load RNAs with Both Adenine and Guanine
inferredcites →https://doi.org/10.1101/gr.2896904openalex-snapshot
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
inferredcites →https://doi.org/10.1111/evo.12597openalex-snapshot
A generation-time effect on the rate of molecular evolution in bacteria
inferredcites →https://doi.org/10.1111/j.1432-1033.1976.tb10639.xopenalex-snapshot
The Energetics of Escherichia coli during Aerobic Growth in Continuous Culture
inferredcites →https://doi.org/10.1126/science.1191701openalex-snapshot
Differential Arginylation of Actin Isoforms Is Regulated by Coding Sequence–Dependent Degradation
inferredcites →https://doi.org/10.1126/science.1241934openalex-snapshot
Causes and Effects of N-Terminal Codon Bias in Bacterial Genes
inferredcites →https://doi.org/10.1186/1471-2105-13-1openalex-snapshot
GuiTope: an application for mapping random-sequence peptides to protein sequences
inferredcites →https://doi.org/10.1186/1471-2164-9-1openalex-snapshot
Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host
inferredcites →https://doi.org/10.1186/gb-2011-12-1-r1openalex-snapshot
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
inferredcites →https://doi.org/10.1186/s13059-015-0805-zopenalex-snapshot
ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
inferredcites →https://doi.org/10.1371/journal.pgen.1005926openalex-snapshot
The Selective Advantage of Synonymous Codon Usage Bias in Salmonella
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
inferredcites →https://doi.org/10.1371/journal.pone.0058393openalex-snapshot
Codon Optimization Significantly Improves the Expression Level of a Keratinase Gene in Pichia pastoris
inferredcites →https://doi.org/10.1534/genetics.167.1.543openalex-snapshot
Natural Selection Affects Frequencies of AG and GT Dinucleotides at the 5′ and 3′ Ends of Exons

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/molbev/msy043openalex-snapshot
The Amount of Nitrogen Used for Photosynthesis Modulates Molecular Evolution in Plants
inferred← citeshttps://doi.org/10.1101/162693openalex-snapshot
The amount of nitrogen used for photosynthesis governs molecular evolution in plants
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