Codon usage and amino acid usage influence genes expression level

Pavlidis, Paul; Malakar, Arup Kumar; Chakraborty, Supriyo

doi:10.1007/s10709-017-9996-4

Cited by 17 publications

(11 citation statements)

References 47 publications

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“…There have been quite some hypotheses on the cause and consequence of the usages of codons/codon pairs, such as gene expression level [45], mRNA structure [46], mRNA stability [47], and protein abundance [48]. Here we demonstrated that the shiftability of a gene or a genome is adjusted through the usage of codons and codon pairs, suggesting that many genes and certain genomes were optimized for frameshift tolerance.…”

Section: Discussionmentioning

confidence: 70%

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

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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.

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Section: Discussionmentioning

confidence: 70%

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

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show abstract

“…In total, four mutations (one synonymous mutation) were identified in the α-factor prepro-leader, and thirteen mutations (5 synonymous mutations) were detected in the laccase gene ( Table 1 ). Corresponding to data in the Codon Usage Database ( ), four of the six synonymous mutations favored codon usage in S. cerevisiae , which improved the translation and expression of the laccase gene in yeast [ 25 , 26 ].…”

Section: Resultsmentioning

confidence: 99%

Directed Evolution of a Homodimeric Laccase from Cerrena unicolor BBP6 by Random Mutagenesis and In Vivo Assembly

Zhang

et al. 2018

IJMS

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Laccases have great potential for industrial applications due to their green catalytic properties and broad substrate specificities, and various studies have attempted to improve the catalytic performance of these enzymes. Here, to the best of our knowledge, we firstly report the directed evolution of a homodimeric laccase from Cerrena unicolor BBP6 fused with α-factor prepro-leader that was engineered through random mutagenesis followed by in vivo assembly in Saccharomyces cerevisiae. Three evolved fusion variants selected from ~3500 clones presented 31- to 37-fold increases in total laccase activity, with better thermostability and broader pH profiles. The evolved α-factor prepro-leader enhanced laccase expression levels by up to 2.4-fold. Protein model analysis of these variants reveals that the beneficial mutations have influences on protein pKa shift, subunit interaction, substrate entrance, and C-terminal function.

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“…Given the significant biological effects of different codon patterns, identifying these patterns in a given gene or genome is important to understand the molecular mechanisms of gene expression and to uncover the effects of long-term evolution on the genome [ 15 , 45 , 46 ]. Moreover, identifying these patterns is helpful for the phylogenetic analysis of species and to improve the expression of a target gene by optimizing codons [ 23 , 47 – 49 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

Wang

Mao

et al. 2021

BMC Genomics

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Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

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Codon usage and amino acid usage influence genes expression level

Cited by 17 publications

References 47 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

Directed Evolution of a Homodimeric Laccase from Cerrena unicolor BBP6 by Random Mutagenesis and In Vivo Assembly

Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

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