background and objectives: the aim of this study was to investigate the significance of multiple-mutations in the katg gene, predominant nucleotide changes and its correlation with high level of resistance to isoniazid in mycobacterium tuberculosis isolates that were randomly collected from sputa of 42 patients with primary and secondary active pulmonary tuberculosis from different geographic r...

In eukaryotes, gene expression is a complex, multi-step process involving transcription, splicing, translation, and post-translational modifications. At each individual step, errors can occur that lead to nonfunctional and potentially toxic proteins. Therefore, eukaryotes have evolved a wide array of solutions to minimize the risk of error. There are two fundamental strategies to minimize the p...

Circulating animal coronaviruses occasionally infect humans. The SARS-CoV-2 is responsible for the current worldwide outbreak of COVID-19 that has resulted in 2 112 844 deaths as late January 2021. We compared genetic code preferences 496 viruses, including 34 and 242 corresponding hosts, to uncover patterns distinguish single- ‘promiscuous’ multiple-host-infecting viruses. Based on a codon usa...

Context-dependent codon bias and its relationship with messenger RNA (mRNA) longevity was examined in 4,648 mRNA transcripts of the Saccharomyces cerevisiae transcriptome for which mRNA half-lives have been empirically determined. Surprisingly, rare codon usage (codons used <13 times per 1,000 codons in the genome) increased with mRNA half-life. However, it is shown that this pattern was not du...

The optimal context for translation initiation in mammalian species is GCCRCCaugG (where R = purine and "aug" is the initiation codon), with the -3R and +4G being particularly important. The presence of +4G has been interpreted as necessary for efficient translation initiation. Accumulated experimental and bioinformatic evidence has suggested an alternative explanation based on amino acid const...

We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo. Low frequency effects of so-called "silent" codon changes and codon neighbor (context) effects could be measured using this assay. An advantage of this system is that translation speed is unaffected by t...

The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the model indicated that the direction of code evolution changed on expansion from the N-fixers code (stage 2). Growth of the code from 16 codons in the NAN colum...

Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical analyses, based on co...

The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bact...