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...

Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and non-synonymous substitutions. Another modeling approach, known as the mutation-selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some approaches allowing for heterogeneity in these...

Base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of Aquifex aeolicus and Bacillus subtilis, having different optimal growth temperatures. These two bacteria do not have significant difference in overall GC composition, but GC(1+2) and GC3 levels were found to vary significantly. Significant increments in purine content and GC3 compositi...

Introduction RNA genomes versus DNA genomes Quasispecies theory and virus adaptation RNA Processing in the Nucleus Capping Splicing Polyadenylation and Nuclear Export Cytoplasmic Transcription Translation in Eukaryotes Post-transcriptional Control Leaky Scanning Ribosomal Frameshifting Stop Codon Readthrough Concluding Remarks

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins such as cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary crite...

Facts and ideas presented in this short review concern some recent developments at the interface between sequence analysis, gene expression prediction and genome comparison carried on in our group. The guiding line to all results presented here is to derive biological information from genome sequences by means of a purely statistical analysis and an appropriate design of algorithms. 1 Some back...

Mutual interference among linked genetic sites subject to selection may reduce the level of adaptation. A recent study detected this effect using data on protein sequence evolution and codon usage in Drosophila.

Recent analyses indicate that differences in protein concentrations are only 20%-40% attributable to variable mRNA levels, underlining the importance of posttranscriptional regulation. Generally, protein concentrations depend on the translation rate (which is proportional to the translational activity, TA) and the degradation rate. By integrating 12 publicly available large-scale datasets and a...

The mature core protein of the Hepatitis C virus (HCVC173) carrying pelB as a signal peptide (PelB::core) was overexpressed in Escherichia coli as 18% and 23.3% of the host’s total protein, in flask and fermentor cultivation, respectively. A final specific yield of 25 ± 1 mg HCVC173/g dry cell weight and an overallproductivity of 51±1 mg HCVC173/l/h were obtained in the stirred-tank ferme...

Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neuros...