Ribosome Traffic in E. coli and Regulation of Gene Expression

Lesnik, Thierry; Solomovici, Jean; Deana, Atilio; Ehrlich, Ricardo; Reiss, Claude

doi:10.1006/jtbi.1999.1047

Cited by 54 publications

(36 citation statements)

References 31 publications

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“…In some unicellular organisms, highly expressed genes have a strong selective preference for the codons complementary to the most abundant tRNA species, whereas lower expressed genes display more uniform codon usage patterns largely compatible with the mutational bias in the absence of translational selection [10,46]. In mammals and birds, the diverse patterns of codon usage may arise from compositional constraints of the genomes [47][48][49].…”

Section: Discussionmentioning

confidence: 99%

“…Studies of the synonymous codon usage are not used equally both within and between genomes [1][2][3]. While several factors such as mutational bias [4][5][6], translational selection [7][8][9][10], secondary structure of proteins [11][12][13], replicational and transcriptional selection [14,15], and environmental factors [16,17] have been reported to influence the codon usage in various organisms. In contrast, amino acid usage has been demonstrated to be influenced by factors such as hydrophobicity, aromaticity, cysteine residue (Cys) content, and mean molecular weight [16,18], growth temperature, etc.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

et al. 2008

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The analysis on codon usage bias of UL24 gene of duck enteritis virus (DEV) may improve our understanding of the evolution and pathogenesis of DEV 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. The codon usage bias of UL24 genes of DEV and 27 reference herpesviruses were analyzed. The results showed that codon of UL24 gene of DEV was strong bias toward 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 UL24 gene of herpesviruses was constrained by the G + C content. The phylogentic analysis suggested that DEV was evolutionarily closer to Alphaherpesvirinae and that there was no significant deviation in codon usage in different virus strains. There were 20 codons showing distinct usage differences between DEV and Escherichia coli, 23 between DEV and Homo sapiens, but only 16 codons between DEV and yeast. Therefore the yeast expression system may be more suitable for the expression of DEV genes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

et al. 2008

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“…In general, translation selection in nature and compositional constraints are thought to be the two major factors accounting for variation of codon usage pattern among genomes in various organisms (Karlin and Mrázek 1996;Lesnik et al 2000;). Comparison with pattern of synonymous codon usage in different mammals, compositional constraints of the genomes play a weak role in some unicellular organisms (such as Escherichia coli & Sacchromyces cerevisiae) and high expression genes have a obvious selective discrepancy for codon usage with a high concentration of the particular acceptor tRNA molecular, in contrast, low expressed genes show a obviously similar codon usage pattern (Gouy and Gautier 1982;Grantham et al 1981;Ghosh et al 2000;Lesnik et al 2000;Majumdar et al 1999;Ohno et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Analysis of synonymous codon usage in foot-and-mouth disease virus

et al. 2010

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In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C & O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.

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“…In E. coli and yeast, synonymous codon usage patterns are related to the abundance of isoaccepting tRNAs [7,56] , where highly expressed genes have a strong selective preference for the codons complementary to the most abundant tRNA species, whereas lowly expressed genes display more uniform codon usage patterns largely compatible with the mutational bias in the absence of translational selection [57,58] . In mammals and birds, the diverse patterns of codon usage may arise from the compositional constraints of the genomes [19,59,60] .…”

Section: Discussionmentioning

confidence: 99%

Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene

et al. 2009

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Objective: The aim was to identify the codon usage bias between the newly identified duck plague virus (DPV) UL35 gene (GenBank accession No. EF643558) and the UL35-like genes of 27 other reference herpesviruses. Methods: A comparative analysis of the codon usage bias of the 28 herpesviruses was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). Results: The results showed obvious differences of the synonymous codon usage bias in the 28 herpesviruses indicated by the Codon Adaptation Index, effective number of codons (ENc), and the value of G + C content at the 3rd codon position. The codon usage pattern of the DPV UL35 gene was phylogenetically conserved and similar to that of the UL35-like genes of the avian α-herpesvirus, with a strong bias towards the codons with A and T at the 3rd codon position. A cluster analysis of codon usage pattern of the DPV UL35 gene with other reference herpesviruses demonstrated that the codon usage bias of the UL35 genes of the 28 herpesviruses had a very close relation with their gene function. The ENc-plot revealed that the genetic heterogeneity in the DPV UL35 gene and the 27 reference herpesviruses were constrained by G + C content, while gene length exerted relatively weaker influences. In addition, comparisons of the codon preferences in the UL35 gene of DPV with those of Escherichia coli, yeast and humans revealed that there were 33 codons showing distinct usage differences between the DPV and yeast, and 38 between the DPV and humans, but only 31 between the DPV and E. coli. Therefore, the E. coli system may be more suitable for the expression of the DPV UL35 gene. Conclusion: Together, these results may improve our understanding of the evolution, pathogenesis and functional studies of DPV, as well as contribute significantly to the area of herpesvirus research and possibly studies with other viruses.

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Ribosome Traffic in E. coli and Regulation of Gene Expression

Cited by 54 publications

References 31 publications

Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

Analysis of synonymous codon usage in foot-and-mouth disease virus

Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene

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