Codon usage bias in human cytomegalovirus and its biological implication

Hu, Changyuan; Chen, Jing; Ye, Lulu; Chen, Renpin; Zhang, Lifang; Xue, Xiangyang

doi:10.1016/j.gene.2014.05.018

Cited by 25 publications

(22 citation statements)

References 105 publications

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“…To maintain the high G + C content an alternative strategy was used in which the nine amino acids that have more than two codons were changed to the codons least preferred by K181 but with the highest GC content (BAC70 403Cys and BAC70 403Tyr ; Table ). This was chosen since the MCMV primase codon usage is very similar to the preferred codon usage of betaherpesvirinae in general (Table ), overall human cytomegalovirus codon usage, and in particular the HCMV UL70 primase gene (G + C 63%, GC3% 80, Enc 39)[RoyChoudury and Mukherjee, ; Hu et al, ] and thus appears to be independent of the host. This produced an M70 ORF with a G + C content of 66%, a CpG of 379, a GC3% of 90 and an Enc (effective number of codons) of 39.38 compared to a G + C of 64%, a CpG of 381, a GC3% of 85, and an Enc of 43.04 for K181 (Perth); 403 of the 964 codons (42%) were changed.…”

Section: Resultsmentioning

confidence: 99%

“…The effective number of codons (Enc) estimates how far the gene or genome departs from equal usage of synonymous codons. It correlates with the overall G + C content (GC%) and the GC content at the third synonymous codon position (GC3%) of the gene [RoyChoudury and Mukherjee, ; Hu et al, ]. Enc values range from 20 (when only one codon per amino acid is used for a gene signifying extreme bias) to 61 (when using all available synonymous codons and signifying zero bias).…”

Section: Methodsmentioning

confidence: 99%

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Further studies on the role of the residue 890 cysteine to tyrosine mutation in the M70 primase ORF of the temperature‐sensitive mutant (tsm5) of murine cytomegalovirus

Al-Ali

Sweet

2016

Journal of Medical Virology

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A mutation (C890Y) introduced into the M70 primase gene of murine cytomegalovirus (MCMV) resulted in reduced viral replication in murine embryo fibroblasts at 40°C and the mutant was severely attenuated in vivo. The attenuated replication of the M70 mutant was also observed in Raw 264.7 macrophages at 37°C, demonstrating that the mutation produced a defective rather than an unstable protein possibly reducing the amount of functional protein under different environmental conditions. Many synonymous mutations were introduced into this ORF by changing codon preferences that should reduce the efficiency of gene translation, but not change protein sequence or structure. Two Bacterial Artificial Chromosome (BAC) constructs were produced with 155 codons (at the distal third of the M70 gene) changed to MCMV less preferred codons and with either cysteine (BAC70(155Cys) ) or tyrosine (BAC70(155Tyr) ) at residue 890. Upon transfection of these BACs into NIH 3T3 cells, only BAC70(155Cys) produced virus and this mutant Mt70(155Cys) replicated similarly to its revertant and the wt MCMV K181 (Perth) variant. A metagenomic analysis of the protein structure of the primase using PredictProtein showed that the change from cysteine (M70Cys) to tyrosine (M70Tyr) has a marked effect on protein structure. However, when the cysteine residue was replaced by serine (M70Ser) or methionine (M70Met), which produced mutant viruses with a wild-type phenotype, the predicted structure was similar to the wild-type structure. J. Med. Virol. 88:1613-1621, 2016. © 2016 Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Further studies on the role of the residue 890 cysteine to tyrosine mutation in the M70 primase ORF of the temperature‐sensitive mutant (tsm5) of murine cytomegalovirus

Al-Ali

Sweet

2016

Journal of Medical Virology

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“…Natural selection and/or mutation pressure for efficiency and accuracy are the fundamental forces that influence synonymous codon usage (Jenkins and Holmes, 2003;Hu et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Analysis of factors affecting codon usage bias in human papillomavirus

Kamatani¹,

Shirota²

2018

J. Bioinform. Seq. Anal.

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“…In general, 61 codons can encode 20 different amino acids, so most of them are synonymous codons. Many studies have suggested that each codon was applied in different rates within different individuals and even within various genes of one genome [14][15][16][17][18][19][20][21]. This phenomenon was regarded as codon usage bias.…”

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confidence: 99%

Evolution of codon usage in 2019-new coronavirus causing human infection

Yao

Guan

et al. 2020

Preprint

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Background: The recent emergence of viral pneumonia was caused by the novel coronavirus (SARS-Cov-2), which has spread to many countries and threated the global public health.Results: In the current study, we provide a primary evolutionary analysis based on the codon usage patterns of SARS-Cov-2 genome sequences. We employed bioinformatics technologies to measure the nucleotide compositions, the relative synonymous codon usage (RSCU), the codon adaptation index (CAI), and other indices. Our results reflected that there were some similarities of codon usage bias between SARS-Cov-2 and its natural reservoirs, suggesting that SARS-Cov-2 was tended to evolve its codon usage which was comparable to that of its hosts. Additionally, various degree of adaptation to the SARS-Cov-2 host and vector were estimated, even different genes have different codon adaptation to their reservoirs. We further suggested that SARS-Cov-2 isolates were evolving at a rapid substitution rate under their translation selection pressure of their hosts.Conclusions: The findings of the present study will provide help for the understanding of the elements leading to viral evolution and adaptation to reservoirs.

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Codon usage bias in human cytomegalovirus and its biological implication

Cited by 25 publications

References 105 publications

Further studies on the role of the residue 890 cysteine to tyrosine mutation in the M70 primase ORF of the temperature‐sensitive mutant (tsm5) of murine cytomegalovirus

Further studies on the role of the residue 890 cysteine to tyrosine mutation in the M70 primase ORF of the temperature‐sensitive mutant (tsm5) of murine cytomegalovirus

Analysis of factors affecting codon usage bias in human papillomavirus

Evolution of codon usage in 2019-new coronavirus causing human infection

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