Analysis of Synonymous Codon Usage Bias in D15 Gene Encoded Surface Antigen of Riemerella Anatipestifer

2013 ◽  
Vol 641-642 ◽  
pp. 597-605
Author(s):  
Bin Feng ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Homo Sapiens ◽  
Synonymous Codon ◽  
Expression System ◽  
Evolutionary Relationship ◽  
Yeast Expression System ◽  
Riemerella Anatipestifer

In order to provide a basis for understanding the evolutionary relationship and pathogenesis of Riemerella anatipestifer and selecting a appropriate host expression systems to improve the expression of target gene in vivo and in vitro, we identified the codon bias in the newly confirmed D15 gene of Riemerella anatipestifer ATCC 11845 strain and performed comparative analysis of the codon usage bias between D15 gene in R. anatipestifer and the other 10 referenced Flavobacteriaceaes by a series of online bioinformatics softwares. The results revealed that the synonymous codons with A and T at the third codon position had widely usage in the codon of D15 gene of R. anatipestifer. In addition, there were 70 rare codons in the ORF of the D15 of R. anatipestifer, and 32 codons showing distinct usage differences between R. anatipestifer and E. coli, 30 codons between R. anatipestifer and Homo sapiens, 16 codons between R. anatipestifer and yeast, indicated the yeast expression system may be more suitable for the expression of R. anatipestifer genes. The extent of codon usage bias in the D15 gene in R. anatipestifer was highly correlated with the gene expression level, therefore the results may provide useful information for gene classification and functional studies.

Characterization of Synonymous Codon Usage in the R1 Gene of Duck Enteritis Virus

2013 ◽  
Vol 641-642 ◽  
pp. 701-711
Author(s):  
Guo Fu Lu ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Large Subunit ◽  
Expression System ◽  
Evolutionary Relationship ◽  
Duck Enteritis Virus ◽  
Yeast Expression System ◽  
R1 Gene ◽  
Enteritis Virus

In this paper, a corresponding analysis of the codon usage bias in the large subunit of ribonucleotide reductase (R1), encoded by UL39 gene from duck enteritis virus (DEV) CHv strain (Assigned Accession No.: EU071042) and 33 other reference herpesviruses was performed by using CAI, CHIPS and CUSP program of EMBOSS, aims to provide a basis for understanding the evolution and pathogenesis of DEV and for selecting appropriate host expression systems. The results showed that codon usage bias of DEV R1 gene strongly preferred to the synonymous with A and T at the third codon position; the phylogentic analysis revealed that DEV had a close evolutionary relationship with the avian Alphaherpesvirinae. In addition, the codon usage bias of DEV R1 gene was compared with those of E.coli, yeast and human. There are 17 codons showing distinct usage differences between DEV and E.coli, 13 codons between DEV and yeast, 20 codons between DEV and human. Therefore, the yeast expression system is more suitable for the target gene’s expression. The extent of codon usage bias in the DEV R1 gene was highly correlated with the gene expression level, therefore the results may provide useful information for the study of classification and function of the target gene.

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

2013 ◽  
Vol 641-642 ◽  
pp. 684-692 ◽  
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.

scholarly journals Dinucleotide evolutionary dynamics in influenza A virus

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Haogao Gu ◽  
Rebecca L Y Fan ◽  
Di Wang ◽  
Leo L M Poon
Keyword(s):  
Influenza Virus ◽  
Codon Usage ◽  
Influenza A Virus ◽  
Codon Usage Bias ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Synonymous Codon ◽  
Amino Acid Sequences ◽  
In Vivo Models

Abstract Significant biases of dinucleotide composition in many RNA viruses including influenza A virus have been reported in recent years. Previous studies have showed that a codon-usage-altered influenza mutant with elevated CpG usage is attenuated in mammalian in vitro and in vivo models. However, the relationship between dinucleotide preference and codon usage bias is not entirely clear and changes in dinucleotide usage of influenza virus during evolution at segment level are yet to be investigated. In this study, a Monte Carlo type method was applied to identify under-represented or over-represented dinucleotide motifs, among different segments and different groups, in influenza viral sequences. After excluding the potential biases caused by codon usage and amino acid sequences, CpG and UpA were found under-represented in all viral segments from all groups, whereas UpG and CpA were found over-represented. We further explored the temporal changes of usage of these dinucleotides. Our analyses revealed significant decrease of CpG frequency in Segments 1, 3, 4, and 5 in seasonal H1 virus after its re-emergence in humans in 1977. Such temporal variations were mainly contributed by the dinucleotide changes at the codon positions 3-1 and 2-3 where silent mutations played a major role. The depletions of CpG and UpA through silent mutations consequently led to over-representations of UpG and CpA. We also found that dinucleotide preference directly results in significant synonymous codon usage bias. Our study helps to provide details on understanding the evolutionary history of influenza virus and selection pressures that shape the virus genome.

Analysis of Synonymous Codon Usage in the UL14 Gene of Duck Enteritis Virus

2012 ◽  
Vol 424-425 ◽  
pp. 680-689
Author(s):  
Fang Jie Li ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
Its Gene ◽  
Close Relationship ◽  
Enteritis Virus ◽  
High Level

The codon usage of DEV UL14 gene was analyzed by using CAI, CHIPS and CUSP program of EMBOSS. The results showed that codon usage bias in the DEV UL14 gene was a high level of diversity in codon usage bias towards the synonymous with C and G at the third codon position existed for coding the Glu, Gly, Asn and Tyr amino acids. The cluster analysis demonstrated that the codon usage bias of DEV UL14 gene has a very close relationship with its gene function and gene type. In addition, the E.coli expression system is more suitable for heterologous expression of the DEV UL14 gene.

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

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.

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

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.

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

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.

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

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.

scholarly journals Synonymous codon substitutions perturb co-translational protein foldingin vivoand impair cell fitness

2019 ◽  
Author(s):  
Ian M. Walsh ◽  
Micayla A. Bowman ◽  
Iker F. Soto ◽  
Anabel Rodriguez ◽  
Patricia L. Clark
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Cellular Protein ◽  
Synonymous Codon Usage ◽  
Folding Mechanism ◽  
C Terminus ◽  
Essential Enzyme

AbstractIn the cell, proteins are synthesized from N- to C-terminus and begin to fold during translation. Co-translational folding mechanisms are therefore linked to elongation rate, which varies as a function of synonymous codon usage. However, synonymous codon substitutions can affect many distinct cellular processes, which has complicated attempts to deconvolve the extent to which synonymous codon usage can promote or frustrate proper protein foldingin vivo. Although previous studies have shown that some synonymous changes can lead to different final structures, other substitutions will likely be more subtle, perturbing predominantly the protein folding pathway without radically altering the final structure. Here we show that synonymous codon substitutions encoding a single essential enzyme lead to dramatically slower cell growth. These mutations do not prevent active enzyme formation; instead, they predominantly alter the protein folding mechanism, leading to enhanced degradationin vivo. These results support a model where synonymous codon substitutions can impair cell fitness by significantly perturbing co-translational protein folding mechanisms, despite the chaperoning provided by the cellular protein homeostasis network.SignificanceMany proteins that are incapable of refoldingin vitronevertheless fold efficiently to their native state in the cell. This suggests that more information than the amino acid sequence is required to properly fold these proteins. Here we show that synonymous mRNA mutations can alter a protein folding mechanismin vivo, leading to changes in cellular fitness. This work demonstrates that synonymous codon selection can play an important role in supporting efficient protein productionin vivo.

scholarly journals A Comparative Analysis of Synonymous Codon Usage Bias Pattern in Human Albumin Superfamily

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Hoda Mirsafian ◽  
Adiratna Mat Ripen ◽  
Aarti Singh ◽  
Phaik Hwan Teo ◽  
Amir Feisal Merican ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Protein Secondary Structure ◽  
Human Albumin ◽  
Synonymous Codon Usage ◽  
Domains Of Life ◽  
Synonymous Codon Usage Bias

Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin,α-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC) suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure.

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