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Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species.
Front Genet
August 2021
School of Life Science, Shanxi University, Taiyuan, China.
The synonymous codons usage shows a characteristic pattern of preference in each organism. This codon usage bias is thought to have evolved for efficient protein synthesis. Synonymous codon usage was studied in genes of the hexaploid wheat (AABBDD) and its progenitor species, (AA), (DD), and (AABB).
View Article and Find Full Text PDFContext-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.
BMC Ecol Evol
April 2021
College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian, Beijing, China.
Background: Synonymous mutations do not alter the amino acids and therefore are regarded as neutral for a long time. However, they do change the tRNA adaptation index (tAI) of a particular codon (independent of its context), affecting the tRNA availability during translation. They could also change the isoaccepting relationship with its neighboring synonymous codons in particular context, which again affects the local translation process.
View Article and Find Full Text PDFSubstrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment.
RNA Biol
August 2021
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Colicin D is a plasmid-encoded bacteriocin that specifically cleaves tRNA of sensitive cells. has four isoaccepting tRNAs; the cleavage occurs at the 3' end of anticodon-loop, leading to translation impairment in the sensitive cells. tRNAs form a common L-shaped structure and have many conserved nucleotides that limit tRNA identity elements.
View Article and Find Full Text PDFParsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias.
BMC Plant Biol
October 2019
College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
Background: Synonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated codon could base pair with the same anticodon as the original, the mutation is termed an isoaccepting mutation.
View Article and Find Full Text PDFRole of codon usage and tRNA changes in rat cytomegalovirus latency and (re)activation.
J Basic Microbiol
June 2016
Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, 70126, Italy.
Herpesviruses can remain in their hosts by establishing a latent infection with a low pattern of viral gene expression. Passage from latency to reactivation may occur under particular conditions such as immunosuppressive treatments or during fetal development, and often is accompanied by heavy pathologic sequelae. To investigate the molecular basis underlying herpesvirus latency and (re)activation, codon usage of rat cytomegalovirus was comparatively analyzed with respect to the rat codon usage.
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