Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins

Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein co-translational folding. In this work, we explore how codon variants affect the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA. By analyzing over 14,000 bacterial, archaeal, and fungal ORFeomes, we found that Bacteria and Archaea exhibit an exponential ramp of hydrogen bonding at the 5′-end of CDSs, while a similar ramp was not found in Fungi. The ramp develops within the first 20 codon positions in prokaryotes, eventually reaching a steady carrying capacity of hydrogen bonding that does not differ from Fungi. Selection against uniformity tests proved that selection acts against synonymous codons with high content of hydrogen bonding at the 5′-end of prokaryotic ORFeomes. Overall, this study provides novel insights into the molecular feature of hydrogen bonding that is governed by the genetic code at the 5′-end of CDSs. A web-based application to analyze the position-dependent hydrogen bonding of ORFeomes has been developed and is publicly available (https://juanvillada.shinyapps.io/hbonds/).

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Codon usage of highly expressed genes affects proteome-wide translation efficiency

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1719375115 ◽

2018 ◽

Vol 115 (21) ◽

pp. E4940-E4949 ◽

Cited By ~ 57

Author(s):

Idan Frumkin ◽

Marc J. Lajoie ◽

Christopher J. Gregg ◽

Gil Hornung ◽

George M. Church ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Codon Usage ◽

Codon Usage Bias ◽

Protein Translation ◽

Translation Efficiency ◽

Synonymous Codons ◽

Codon Composition ◽

Theoretical Predictions ◽

Highly Expressed Genes

Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes inEscherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.

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Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes

Marine Genomics ◽

10.1016/j.margen.2016.10.001 ◽

2017 ◽

Vol 32 ◽

pp. 31-39 ◽

Cited By ~ 8

Author(s):

Ratna Prabha ◽

Dhananjaya P. Singh ◽

Swati Sinha ◽

Khurshid Ahmad ◽

Anil Rai

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Codon Usage Bias ◽

Genome Wide ◽

Codon Context

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Codon Usage Bias of the Wheat Flower Development Gene WAG-2 and Other AGAMOUS Group Genes

Journal of Agricultural Science ◽

10.5539/jas.v9n9p56 ◽

2017 ◽

Vol 9 (9) ◽

pp. 56

Author(s):

Wenhan Hu ◽

Shuhong Wei

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Target Genes ◽

Expression System ◽

Functional Studies ◽

Codon Preference ◽

Synonymous Codons ◽

The Difference ◽

Relationship Of

Analyzing codon usage bias of WAG-2 gene in wheat three-pistil (TP) mutant may provide a basis for selecting the appropriate host expression systems to improve the expression of target genes. In the present study, we analyzed the codon bias of the complete coding sequence (CDS) of the WAG-2 gene in TP using Codon W program, and compared the results with AGAMOUS (AG) group genes of other plant species. Results showed that the WAG-2 gene in TP and other monocot AG group genes preferably used codons ending with G/C bases, but Arabidopsis thaliana, Nicotiana tabacum, and other dicot crops were biased toward the synonymous codons with A/T. The clustering results based on codon bias were consistent with those based on CDS of the AG group genes, indicating that the difference in codon preference of AG group genes sequences was closely associated with the genetic relationship of the species. The Euclidean distance coefficients of WAG-2 with A. thaliana and N. tabacum were 9.255 and 5.730, respectively, indicating that N. tabacum may be more suitable for the expression of WAG-2. There were 37 codons showing distinct usage differences between WAG-2 and genome of yeast, 23 between WAG-2 and Escherichia coli. Therefore, the E. coli was the superior protein expression system. These results may improve our understanding of codon usage bias and functional studies of WAG-2.

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Analysis of Synonymous Codon Usage in the US2 Gene of Duck Plague Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.647.220 ◽

2013 ◽

Vol 647 ◽

pp. 220-226

Author(s):

Jie Gao ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Expression System ◽

Synonymous Codon Usage ◽

Eukaryotic Expression ◽

Eukaryotic Expression System ◽

Duck Plague Virus

The codon usage bias of DPV-CHv US2 gene (GenBank Accession No. EU195086) will be analysed in this study, and a comparative analysis of DPV-CHv US2 gene and those of other 15 alphaherpesvirus US2 genes was performed. We also analysed the RSCU, ENC, GC3s value of those US2 genes in herpesvirus, some data were analysed specifically in the article. Consequently, we found that the eukaryotic expression system——the yeast is more suitable for the expression of DPV US2 gene.

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Characterization of Codon Usage Bias in UL13 Gene of the Duck Plague Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.393-395.641 ◽

2011 ◽

Vol 393-395 ◽

pp. 641-650

Author(s):

Xi Xia Hu ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Position ◽

Expression System ◽

Expression Systems ◽

Yeast Expression System ◽

E Coli ◽

Synonymous Codons ◽

Suitable Expression

A comprehensive analysis of codon usage bias of DPV UL13 gene (GenBank Accession No. EU195098) was performed to provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting suitable expression systems to improve the expression of UL13 genes. Our study showed that codon usage bias of DPV UL13 gene strongly prefered to the synonymous with A and T at the third codon position. And ENC value and GC3s contents of the codon usage bias of UL13 gene in DPV were significantly different compared with those in other 21 reference herpesviruses. The phylogentic analysis about the putative protein of DPV UL13 and the 21 reference herpesviruses revealed that DPV was evolutionarily closer to the AnHV-1. In addition, the codon usage bias of DPV UL13 gene was compared with those of E. coli, yeast and human. There are 23 codons showing distinct usage differences between DPV and E. coli, 12 codons between DPV and yeast, 21 codons between DPV and human. Therefore, the yeast expression system is more appropriate for heterologous expression of the DPV UL13 gene.

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Comparative analysis of nuclear tRNA genes ofNasonia vitripennisand other arthropods, and relationships to codon usage bias

Insect Molecular Biology ◽

10.1111/j.1365-2583.2009.00933.x ◽

2010 ◽

Vol 19 ◽

pp. 49-58 ◽

Cited By ~ 17

Author(s):

S. K. Behura ◽

M. Stanke ◽

C. A. Desjardins ◽

J. H. Werren ◽

D. W. Severson

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Codon Usage Bias ◽

Trna Genes

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A detailed comparative analysis of codon usage bias in Zika virus

Virus Research ◽

10.1016/j.virusres.2016.06.022 ◽

2016 ◽

Vol 223 ◽

pp. 147-152 ◽

Cited By ~ 19

Author(s):

Juan Cristina ◽

Alvaro Fajardo ◽

Martín Soñora ◽

Gonzalo Moratorio ◽

Héctor Musto

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Zika Virus ◽

Codon Usage Bias

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Comparisons of Coding and Noncoding Sequences to infer the Origin of Codon usage Bias

10.1101/174359 ◽

2017 ◽

Author(s):

Prashant Mainali ◽

Sobita Pathak

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Gc Content ◽

Mutation Bias ◽

Translation Process ◽

Noncoding Regions ◽

Coding Regions ◽

Synonymous Codons ◽

Shed Light

ABSTRACTCodon usage bias is the preferential use of the subset of synonymous codons during translation. In this paper, the comparisons of normalized entropy and GC content between the sequence of coding regions of Escherichia coli k12 and noncoding regions (ncRNA, rRNA) of various organisms were done to shed light on the origin of the codon usage bias.The normalized entropy of the coding regions was found significantly higher than the noncoding regions, suggesting the role of the translation process in shaping codon usage bias. Further, when the position specific GC content of both coding and noncoding regions was analyzed, the GC2 content in coding regions was lower than GC1 and GC2 while in noncoding regions, the GC1, GC2, GC3 contents were approximately equal. This discrepancy is explained by the biased mutation coupled with the presence and absence of selection pressure. The accumulation of CG content occurs in the sequences due to mutation bias in DNA repair and recombination process. In noncoding regions, the mutation is harmful and thus, selected against while due to the degeneracy of codons in coding regions, a mutation in GC3 is neutral and hence, not selected. Thus, the accumulation of GC content occurs in coding regions, and thus codon usage bias occurs.

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