Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias [PDF]
Molecular Biology and Evolution, 2021 Abstract Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection.
Janaina Lima de Oliveira +5 more
openaire +3 more sources
Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses [PDF]
, 2014 tRNA (tRNA) is a key molecule used for protein synthesis, with multiple points of stress-induced regulation that can include transcription, transcript processing, localization and ribonucleoside base modification.
Begley, Thomas J. +2 more
core +1 more source
Environmental shaping of codon usage and functional adaptation across microbial communities. [PDF]
, 2013 Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the ...
Achtman +63 more
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A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae [PDF]
, 2014 All authors are with the Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA -- Hal S.
Alper, Hal S. +3 more
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Mitochondrial DNA. Part B. Resources, 2020 Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly ...
Zhiwen Chen +10 more
doaj +1 more source
Zika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models. [PDF]
, 2018 Zika virus (ZIKV) infection during the large epidemics in the Americas is related to congenital abnormities or fetal demise. To date, there is no vaccine, antiviral drug, or other modality available to prevent or treat Zika virus infection.
Hu, Q +12 more
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Differences in codon bias cannot explain differences in translational power among microbes
BMC Bioinformatics, 2005 Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes,
Dethlefsen Les, Schmidt Thomas M
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Translation conditional models for protein coding sequences [PDF]
, 2000 A coding sequence is defined as a DNA sequence coding the primary structure of a protein (a polypeptide). Such a sequence must satisfy a specific constraint, which consists in coding a functional protein, As the genetic code is degenerated, there exists,
Mathé, Catherine, Rodolphe, François
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PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets [PDF]
, 2019 Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs.
Deshpande, Sumukh +4 more
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Mechanism of Virus Attenuation by Codon Pair Deoptimization
Cell Reports, 2020 Summary: Codon pair deoptimization is an efficient virus attenuation strategy, but the mechanism that leads to attenuation is unknown. The strategy involves synthetic recoding of viral genomes that alters the positions of synonymous codons, thereby ...
Nicole Groenke +10 more
doaj +1 more source