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Plant Biotechnology Journal, Volume 24, Issue 7, Page 4528-4545, July 2026.ABSTRACT Protoberberine alkaloids are a characteristic group of natural products in Coptis plants known for their notable pharmacological activities. However, the structural similarity and the substrate promiscuity of their biosynthetic enzymes have left the precise synthetic pathways remain unclarified, posing challenges to regulate product formation.
Jun Song +14 more
wiley +1 more source
Codon Usage Bias and Phylogenetic Analysis of the Mitochondrial Genomes in Two <i>Enicurus</i> Species. [PDF]
Genes (Basel)Qian L +5 more
europepmc +1 more source
Lifestyle shapes genome architecture and codon usage bias in <i>Staphylococcus aureus</i> bacteriophages, suggesting stronger host adaptation in their virulent lineages. [PDF]
Front MicrobiolGamkrelidze A +4 more
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Molecular Biology Reports, 2021 Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism.
Sujatha Thankeswaran Parvathy +2 more
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Annual Review of Genetics, 2008
In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias. Population genetic studies have shown that synonymous sites are under weak selection and that codon bias is maintained by a balance between selection, mutation, and genetic drift.
Ruth Hershberg, Dmitri A Petrov
exaly +3 more sources
In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias. Population genetic studies have shown that synonymous sites are under weak selection and that codon bias is maintained by a balance between selection, mutation, and genetic drift.
Ruth Hershberg, Dmitri A Petrov
exaly +3 more sources
Codon bias and gene expression [PDF]
FEBS Letters, 1991 The frequencies with which individual synonymous codons are used to code their cognate amino acids is quite variable from genome to genome and within genomes, from gene to gene. One particularly well documented codon bias is that associated with highly expressed genes in bacteria as well as in yeast; this is the so‐called major codon bias.
C G Kurland
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Codon Usage Bias: An Endless Tale
Journal of Molecular Evolution, 2021Since the genetic code is degenerate, several codons are translated to the same amino acid. Although these triplets were historically considered to be "synonymous" and therefore expected to be used at rather equal frequencies in all genomes, we now know that this is not the case. Indeed, since several coding sequences were obtained in the late '70s and
Andrés Iriarte +2 more
openaire +2 more sources
Codon bias from minimization of codon–anticodon interaction
Biosystems, 2016Inequalities between codon usage probabilities for quartets of codons are derived using a minimum principle for codon-anticodon interaction and a probability sum rule in the framework of the Crystal Basis Model of the genetic code. Performing this study separately for the Early and for the Eukaryotic Genetic Code, we observe a consistency in the ...
Sciarrino, Antonino, Sorba, Paul
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Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Evolutionary Bioinformatics, 2010 We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon ...
Soohyun Lee, Changwon Kang
exaly +5 more sources