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

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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Characterization of Codon Usage Bias in the RA Ragb/SusD Gene

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.641-642.654 ◽

2013 ◽

Vol 641-642 ◽

pp. 654-665

Author(s):

Si Si Yang ◽

De Kang Zhu ◽

Xiao Jia Wang ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Target Genes ◽

Synonymous Codon ◽

Expression System ◽

Synonymous Codon Usage ◽

Effective Number ◽

E Coli ◽

Synonymous Codons ◽

Effective Number Of Codons

The analysis on codon usage bias of Riemerella anatipestifer (RA) RagB/SusD gene (GenBank accession No. NC_017045.1) may improve our understanding of the evolution and pathogenesis of RA and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. In this study, the synonymous codon usage in the RagB/SusD gene of RA and 19 reference bacteroidetes have been investigated. The results showed that codon usage bias in the RagB/SusD gene was strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in RagB/SusD gene of bacteroidetes was constrained by the G + C content. The codon adaptation index (CAI), effective number of codons (ENC), and GC3S values indicated synonymous codon usage bias in the RagB/SusD gene of bacteroidetes, and this synonymous bias was correlated with host evolution. The phylogentic analysis suggested that RagB/SusD was evolutionarily closer to Ornithobacterium rhinotracheale and that there was no significant deviation in codon usage in different bacteroidetes. There are 25 codons showing distinct usage differences between RA RagB/SusD and E. coli, 30 between RA RagB/SusD and Homo sapiens, 26 codons between RA RagB/SusD and yeast. Therefore the yeast and E. coli expression system may be suitable for the expression of RA RagB/SusD gene if some codons could be optimized.

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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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Characterization of Synonymous Codon Usage Bias in the UL1 Gene of Duck Plague Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.641-642.693 ◽

2013 ◽

Vol 641-642 ◽

pp. 693-700

Author(s):

Ling Jie Zuo ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Expression System ◽

Synonymous Codon Usage ◽

E Coli ◽

Synonymous Codons ◽

Compositional Constraint ◽

Main Factor

In this study, we calculated the codon usage bias in DPV CHv UL1 gene and performed a comparative analysis of synonymous codon patterns in UL1 of DPV CHv strain and other 19 reference herpesviruses. The results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL1 gene of DPV CHv. G + C compositional constraint was the main factor that determined the codon usage bias in UL1 gene. In addition, the codon usage bias of DPV CHv UL1 gene was compared with those of E. coli, yeast and human. There are 25 codons showing distinct usage differences between DPV and E. coli, 26 codons between DPV and yeast, and 21 codons between DPV and human. Therefore, the Human expression system is more suitable for heterologous expression of the DPV UL1 gene.

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Characterization of Codon Usage Bias in the UL17 Gene of Duck Enteritis Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.641-642.666 ◽

2013 ◽

Vol 641-642 ◽

pp. 666-674

Author(s):

Ting Wen ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Position ◽

Expression System ◽

Duck Enteritis Virus ◽

Yeast Expression System ◽

E Coli ◽

Synonymous Codons ◽

Enteritis Virus

The analysis on codon usage bias of UL17 gene of duck enteritis virus (DEV) may provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting appropriate host expression systems to improve the expression of DEV UL17 gene. In this study the results indicate that codon usage bias of DEV UL17 gene strongly preferred to the synonymous with A and T at third codon position. The ENC values and GC3S contents of the codon usage bias of UL17 genes in DEV and the 20 reference herpesviruses were obviously different. In addition, we compared the codon usage bias of DEV UL17 gene with E.coli, yeast and human. There are 25 codons showing distinct usage differences between DEV and E. coli, 17 codons between DEV and yeast, 23 codons between DEV and human. Therefore, the yeast expression system is more suitable for heterologous expression of the DEV UL17 gene.

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Characterization of Synonymous Codon Usage Bias in the Riemerella Anatipestifer OmpA/MotB Gene

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.641-642.684 ◽

2013 ◽

Vol 641-642 ◽

pp. 684-692 ◽

Cited By ~ 1

Author(s):

Pan Xu ◽

An Chun Cheng ◽

Ming Shu Wang ◽

De Kang Zhu ◽

Xiao Jia Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Target Genes ◽

Synonymous Codon ◽

Expression System ◽

Synonymous Codon Usage ◽

Effective Number ◽

Riemerella Anatipestifer ◽

Synonymous Codon Usage Bias

The analysis on codon usage bias of OmpA/MotB gene of Riemerella anatipestifer (RA) may provide a basis for understanding the evolution and pathogenesis of RA and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In our study, a comparative analysis of the codon usage bias in the newly discovered RA OmpA/MotB gene and the OmpA/MotB gene of 20 reference flavobacteriaceae was performed. The results of the codon adaptation indes (CAI), effective number of codon (ENC), and GC3s values indicated that synonymous codon usage bias in the OmpA/MotB gene of flavobacteriaceae. The results showed that codon usage bias in the RA OmpA/MotB gene was strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the G+C compositional constraint is the main factor that determines the codon usage bias in OmpA/MotB gene of flavobacteriaceae. Comparison of the codon usage in the OmpA/MotB gene of different organisms revealed that there were 31 codons showing distinct codon usage differences between the RA and E. coli, 41 between the RA and humans, but 29 between the RA and yeast. Therefore the yeast expression system may be more suitable for the expression of RA OmpA/MotB gene. These results may improve our understanding of the evolution, pathogenesis and functional studies of RA, as well as contribute significantly to the area of flavobacteriaceae research.

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Codon bias (codon preference, codon usage bias)

The Dictionary of Genomics, Transcriptomics and Proteomics ◽

10.1002/9783527678679.dg02066 ◽

2015 ◽

pp. 1-1

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Codon Preference

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Analysis of synonymous codon usage of transcriptome database in Rheum palmatum

PeerJ ◽

10.7717/peerj.10450 ◽

2021 ◽

Vol 9 ◽

pp. e10450

Author(s):

Xiaowei Huo ◽

Sisi Liu ◽

Yimin Li ◽

Hao Wei ◽

Jing Gao ◽

...

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Synonymous Codon ◽

Expression System ◽

Evolutionary Mechanisms ◽

Mutation Pressure ◽

Rheum Palmatum ◽

Optimal Codons

Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

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Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

10.1101/2021.03.03.433699 ◽

2021 ◽

Author(s):

Neetu Tyagi ◽

Rahila Sardar ◽

Dinesh Gupta

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Gc Content ◽

Respiratory Illness ◽

Respiratory Viruses ◽

Nucleotide Composition ◽

Health Crisis ◽

Study Results ◽

Usage Patterns ◽

The Difference

AbstractThe Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

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Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomes

10.1101/811612 ◽

2019 ◽

Author(s):

Juan C. Villada ◽

Maria F. Duran ◽

Patrick K. H. Lee

Keyword(s):

Hydrogen Bonding ◽

Codon Usage ◽

Codon Usage Bias ◽

Translation Efficiency ◽

Molecular Processes ◽

Molecular Feature ◽

Web Based ◽

Synonymous Codons ◽

Double Stranded Dna ◽

Codon Positions

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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