Clustering of low usage codons in the translation initiation region of hepatitis C virus

Zhou, Jian; Su, Jun Hong; Chen, Hao Tai; Zhang, Jie; na, Li; Ding, Yiliang; Stipkovits, L.; Szathmáry, Susan; Pejsak, Z.; Liu, Yong sheng

doi:10.1016/j.meegid.2013.03.043

Cited by 9 publications

(8 citation statements)

References 51 publications

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“…During the course of translation of the polyprotein of EMCV, the IRES controls binding of the 40S ribosomal subunit to initiate this translation (Jackson and Kaminski, 1995;Kaminski et al, 1994). The influence of the UTR on the codon usage pattern of the ITR of a particular gene has been reported by previous studies (Zhou et al, 2010(Zhou et al, , 2013b. Although evolutionary studies generally suggest that the viral genes with efficient expression represent high codon adaptation in host cell environment, the precise fitness of viral genome associated with translationally adapted codons remains a topic of active debate (Kudla et al, 2009;Stanssens et al, 1986).…”

Section: Introductionmentioning

confidence: 76%

The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

Xx¹,

Yp²,

Jl³

et al. 2014

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Summary. -The synonymous codon usage patterns in the initial and terminal translation regions (ITR, TTR) of the whole coding sequence of encephalomyocarditis virus (EMCV) were analyzed in relation to those in its natural hosts using the sequences accessible in databases. In general, some low-usage host codons were found overrepresented in the ITR and TTR of the virus, while some high-usage host codons were found under-represented in the two viral regions. These relationships are thought to participate in the regulation of the speed of translation of viral proteins and in the suppression of ribosomal traffic jams, both aiming at the increase of virus yields. Keywords: encephalomyocarditis virus; initial translation region; terminal translation region; synonymous codon usage * Corresponding author. E-mail: maxiaoxia956@163.com, mzr@ xbmu.edu.cn; phone: +86-931-2938311. Abbreviations: EMCV = encephalomyocarditis virus; IRES = internal ribosome entry site; ITR = initial translation region; RSCU = relative synonymous codon usage value; TTR = terminal translation region; UTR = untranslated region

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Section: Introductionmentioning

confidence: 76%

The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

Xx¹,

Yp²,

Jl³

et al. 2014

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“…As for the life cycle of viruses, production of viral proteins is often influenced by their host cell environments and translation initiation strategies (Davy and Doorbar, 2007;Jackson et al, 2010;Firth and Brierley, 2012;Zhou et al, 2013b). Synonymous codon usage in the TIR of CSFV has been examined for 59 codons; we found that although the synonymous GAG (Glu) and UUG (Leu) codons showed a slight tendency to exist in the first 10 codon positions of TIR, the 2nd and 3rd codon positions showed a strong tendency to select them.…”

Section: Discussionmentioning

confidence: 92%

Genetic features of a translation initiation system composed of IRES element, nucleotide context surrounding the initiation codon, and translation initiation region of classical swine fever virus RNA

Xx¹,

Yp²,

Yq³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism.

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“…Codons with the same name were mixed and recorded in FASTA format, after which the new rearranged sequences were structured and calculated using the CAI index formula to represent the codon distribution at different positions . Additionally, to analyze the synonymous codon usage bias in the translation initiation region (the 2nd to 10th codon positions), which comprises the aligned codons located at the 2nd codon position, 3rd codon position, 4th codon position, …, 8th codon position, 9th codon position, and 10th codon position of ORFs in the B. burgdorferi genome, we referred to the formula for synonymous codon usage bias in the specific coding region and established a simple formula for estimating the synonymous codon usage bias of each codon position in the translation initiation region. Thus,

Y = \ln (\frac{X_{n} / Y_{n}}{X / Y})

where X n is the sum of a particular synonymous codon at a specific codon position in the translation initiation region of B. burgdorferi , Y n is the sum of the corresponding amino acids in the given position, X is the sum of the synonymous codons in the B. burgdorferi genome and, Y is the sum of the corresponding amino acid in the given genome.…”

Section: Methodsmentioning

confidence: 99%

“…. ., 8th codon position, 9th codon position, and 10th codon position of ORFs in the B. burgdorferi genome, we referred to the formula for synonymous codon usage bias in the specific coding region [42,43] and established a simple formula for estimating the synonymous codon usage bias of each codon position in the translation initiation region. Thus,…”

Section: Synonymous Codon Usage In the Translation Initiation Regiomentioning

confidence: 99%

Adaptation of Borrelia burgdorferi to its natural hosts by synonymous codon and amino acid usage

Chang

et al. 2018

J Basic Microbiol

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Lyme disease, caused by Borrelia burgdorferi, is a focally endemic tick‐transmitted zoonotic infection. In this study, the major factors underlying synonymous codon‐related amino acid usage in the B. burgdorferi genome and bias in synonymous codon usage of the translation initiation region of coding sequences were analyzed. Additionally, adaptation of B. burgdorferi to several of its hosts was analyzed in the context of synonymous codon usage. Principal component analysis (PCA) revealed that nucleotide content at the third synonymous position of a codon influenced the synonymous codon usage pattern, but the strand‐specific factor did not influence the synonymous codon usage pattern of B. burgdorferi. In terms of the low GC content of B. burgdorferi coding sequences, the effective number of codons (ENC) showed a significant correlation with GC3 content (at the synonymous position). For the amino acid usage pattern for B. burgdorferi, PCA showed that the strand‐specific factor did not contribute to this pattern, while the properties (aromaticity and hydrophobicity) of the amino acids themselves showed strong correlations with this pattern. Under‐represented codons, which were frequently selected in the translation initiation region, possibly play roles in regulating gene expression in B. burgdorferi. In terms of co‐evolution and synonymous codon usage patterns, adaptation of B. burgdorferi to different intermediate hosts was apparent to different degrees, and the degree of adaptation of this spirochete to wild animals was stronger than that of humans or mice.

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Clustering of low usage codons in the translation initiation region of hepatitis C virus

Cited by 9 publications

References 51 publications

The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

Genetic features of a translation initiation system composed of IRES element, nucleotide context surrounding the initiation codon, and translation initiation region of classical swine fever virus RNA

Adaptation of Borrelia burgdorferi to its natural hosts by synonymous codon and amino acid usage

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