Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions

Subramanian, Abhishek; Sarkar, Ram Rup

doi:10.1016/j.ygeno.2015.05.009

Cited by 18 publications

(20 citation statements)

References 46 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There have been many hypotheses on the cause and consequence of the usages of codons and codon pairs, such as gene expression level [85][86][87][88][89][90][91], mRNA structure [92-98], protein abundance [98][99][100][101], and mRNA/protein stability [102][103][104]. Here we demonstrated that the genetic code is nearly optimal for frameshift tolerance.…”

Section: Discussionmentioning

confidence: 66%

Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance

Wang

Dong

Chen

et al. 2016

Preprint

View full text Add to dashboard Cite

Frameshift mutation yields truncated, dysfunctional product proteins, leading to loss-of-function, genetic disorders or even death. Frameshift mutations have been considered as mostly harmful and of little importance for the molecular evolution of proteins. Frameshift protein sequences, encoded by the alternative reading frames of a coding gene, have been therefore considered as meaningless. However, existing studies had shown that frameshift genes/proteins are widely existing and sometimes functional. It is puzzling how a frameshift kept its structure and functionality while its amino-acid sequence is changed substantially. Here we demonstrate that the protein sequences of the frameshifts are highly conservative when compared with the wild-type protein sequence, and the similarities among the three protein sequences encoded in the three reading frames of a coding gene are defined mainly by the genetic code. In the standard genetic code, amino acid substitutions assigned to frameshift codon substitutions are far more conservative than those assigned to random substitutions. The frameshift tolerability of the standard genetic code ranks in the top 1.0-5.0% of all possible genetic codes, showing that the genetic code is optimal in terms of frameshift tolerance. In some higher species, the shiftability is further optimized at gene- or genome-level by a biased usage of codons and codon pairs, in which frameshift-tolerable codons/codon pairs are overrepresented in their genomes.

show abstract

Section: Discussionmentioning

confidence: 66%

Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance

Wang

Dong

Chen

et al. 2016

Preprint

View full text Add to dashboard Cite

show abstract

“…The notion of gene expression by CAI values was proposed for a long time ago, however, in recent years, the methods have been widely used to qualitatively assess high-level expression genes in prokaryote and eukaryote [38,39,40,41]. Fast development of the whole-genome analysis technologies, especially whole genome sequencing as well as proteomics has made it possible to compare computational data of codon usage and expression ability with experimental evidence.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Liu

Zhu

et al. 2016

IJMS

View full text Add to dashboard Cite

Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.

show abstract

“…The predominant impact of selection pressure on CUB of tyrosinase genes was further supported by plots between ENC and GC 3 , and between ENC and CAI (Fig. 2) [20,31]. …”

Section: Discussionmentioning

confidence: 88%

“…(a=0.0580; R=0.2391) and S. mediterranea (a=0.0508; R=0.1690). Taken together, these data strongly suggested that the selection pressure, such as translational selection rather than mutational bias, was the main force governing bias in nucleotide composition of tyrosinase codons (refer [31] and references therein), even though it was apparent that mutational bias also provided significant force causing the bias at least in the C. sinensis and O. viverrini genes. The predominant impact of selection pressure on CUB of tyrosinase genes was further supported by plots between ENC and GC 3 , and between ENC and CAI (Fig.…”

Section: Discussionmentioning

confidence: 90%

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

Bae

2017

Korean J Parasitol

View full text Add to dashboard Cite

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC12 and GC3 was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC3 vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

show abstract

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions

Cited by 18 publications

References 46 publications

Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance

Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

Contact Info

Product

Resources

About