Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid

Babbitt, Gregory A.; Alawad, Mohammed; Schulze, Katharina; Hudson, André O.

doi:10.1093/nar/gku811

Cited by 23 publications

(29 citation statements)

References 77 publications

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“…The alternative synonymous codons do not occur equally; they instead follow a special codon usage pattern, a phenomenon termed codon usage bias [9]. Several factors are known to contribute to codon usage bias, such as mutational bias, translational and transcriptional selection, protein structure, tRNA abundance, RNA stability, GC content, gene expression level, and gene length [10–12].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.

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Section: Introductionmentioning

confidence: 99%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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“…Then, given the relevance between the synonymous code usage bias and the intrinsic DNA flexibility, we employed the ωGC3 value to estimate the strength of selection pressure which the two groups endured. The ωGC3 value represents the strength of natural selection acting on intrinsic DNA flexibility according to Babbitt's method (Babbitt et al ., ), which was calculated based on the mutational impact ( dTRX obs ) and the simulated neutral impact ( dTRX neutral ) on the intrinsic flexibility of synonymous sites. The box plot showed that the ωGC3 values for the T MGT ≤ 20°C group were higher than those for the T MGT > 20°C group ( P < 0.002) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, intrinsic DNA flexibility was most important to the optimization of local DNA molecular dynamics. From the above, we can conclude that the GC content at synonymous sites (≈GC3) is strongly associated with intrinsic DNA flexibility and optimization of local DNA molecular dynamics (Babbitt et al ., ).…”

Section: Discussionmentioning

confidence: 97%

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Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier‐inhabitingCryobacteriumstrains

Liu

Song

Zhou

et al. 2020

Environmental Microbiology

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Summary The link between guanine–cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (TMGT) and genomics of 78 Cryobacterium strains to avoid unreliable conclusions resulting from distantly phylogenetic groups. Phylogenomic analysis revealed this taxon had much higher diversification than we knew. Interestingly, these strains showed thermotolerance divergence with phylogenetic cohesion. A significant difference was found between TMGT ≤ 20°C strains and TMGT > 20°C strains in genomic GC content which mainly caused by variation of GC3. TMGT ≤ 20°C strains tended to use synonymous codons ended with A/U, but TMGT > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of TMGT ≤ 20°C strains could provide lower intrinsic DNA flexibility which strongly associated with optimal molecular dynamics, and then guarantee DNA function at lower growth temperatures. This analysis of codon bias revealed close relationships for thermal adaptation, GC content at synonymous sites (≈GC3), intrinsic DNA flexibility and optimal DNA dynamics. Natural selection was main force driving this codon bias; strains with lower TMGT endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.

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“…In both prokaryotic and eukaryotic genes, the synonymous codon usage is non-random [24,25]. It has been postulated that genes in any genome follow a particular codon usage pattern that is similar within the same organism and members of related species [24,26].…”

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confidence: 99%

Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus

2015

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Infectious bursal disease virus (IBDV) is an important poultry pathogen. The VP2 protein of IBDV is the major host-protective immunogen. Although the functions of the VP2 protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the VP2 gene have not yet been reported. In the present study, we have analyzed the relative synonymous codon usage and effective number of codons (ENC) using 69 IBDV VP2 genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of ENC values and GC3s as well as the correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in the VP2 gene. In addition, other factors, such as the aromaticity, hydrophobicity and aliphatic index also influence the codon usage variation of the VP2 gene. This study represents a comprehensive analysis of IBDV VP2 gene codon usage patterns and provides a basic understanding of the codon usage bias.

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Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid

Cited by 23 publications

References 77 publications

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier‐inhabitingCryobacteriumstrains

Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus

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