Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes

Sau, Keya; Deb, Arpan

doi:10.3233/isb-2009-0383

Cited by 24 publications

(8 citation statements)

References 37 publications

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“…The CUB patterns have been studied recently, especially in the case of different virus genomes [26][27] [28]. Many previous studies suggest that several factors are associated with the specific CUB patterns, including nucleotide composition [29], mutational pressure or natural selection [30][31], G+C content [32], protein secondary structure [33], translation process [34], hydrophobicity [35], tRNA abundance [36], environmental temperature [37] A limited number of studies have been published related to CUBs in SARS-CoV-2. For example, Gu et al's work on the genus betacoronavirus compared the codon usage pattern for viruses in this genus, using multivariate analysis [42].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

Tyagi

Sardar

Gupta

2021

Preprint

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The Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K) including two recently emerging strains from the United Kingdom (UK), i.e.,VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, di-nucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. When compared with human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yields a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

Tyagi

Sardar

Gupta

2021

Preprint

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“…The different frequencies among synonymous codons are called the codon usage bias (CUB). The CUB is widespread in organisms, and the degree of CUB is affected by nucleotide composition [ 9 ], DNA replication [ 10 , 11 ], translation process [ 12 , 13 ], tRNA abundance [ 14 , 15 ], gene function [ 16 ], gene length [ 17 , 18 ], protein structure [ 19 , 20 , 21 ], environmental temperature [ 22 ], selection at the amino acid level [ 23 ], and mutational and selective pressure [ 24 , 25 ]. CUB is also determined by the balance between gene mutation and natural selection [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species

Zhang

Wang

et al. 2018

IJMS

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Solanum is one of the largest genera, including two important crops—potato (Solanum tuberosum) and tomato (Solanum lycopersicum). In this study we compared the chloroplast codon usage bias (CUB) among 12 Solanum species, between photosynthesis-related genes (Photo-genes) and genetic system-related genes (Genet-genes), and between cultivated species and wild relatives. The Photo-genes encode proteins for photosystems, the photosynthetic electron transport chain, and RuBisCO, while the Genet-genes encode proteins for ribosomal subunits, RNA polymerases, and maturases. The following findings about the Solanum chloroplast genome CUB were obtained: (1) the nucleotide composition, gene expression, and selective pressure are identified as the main factors affecting chloroplast CUB; (2) all these 12 chloroplast genomes prefer A/U over G/C and pyrimidines over purines at the third-base of codons; (3) Photo-genes have higher codon adaptation indexes than Genet-genes, indicative of a higher gene expression level and a stronger adaptation of Photo-genes; (4) gene function is the primary factor affecting CUB of Photo-genes but not Genet-genes; (5) Photo-genes prefer pyrimidine over purine, whereas Genet-genes favor purine over pyrimidine, at the third position of codons; (6) Photo-genes are mainly affected by the selective pressure, whereas Genet-genes are under the underlying mutational bias; (7) S. tuberosum is more similar with Solanum commersonii than with Solanum bulbocastanum; (8) S. lycopersicum is greatly different from the analyzed seven wild relatives; (9) the CUB in codons for valine, aspartic acid, and threonine are the same between the two crop species, S. tuberosum and S. lycopersicum. These findings suggest that the chloroplast CUB contributed to the differential requirement of gene expression activity and function between Photo-genes and Genet-genes and to the performance of cultivated potato and tomato.

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“…The genetic code plays a critical role in living cells, but not all species use its built-in redundancy in the same way. Codon usage biases (CUB) are widespread across the Tree of Life and are affected by nucleotide composition [ 7 ], translation processes [ 8 ], tRNA abundance [ 9 ], gene function [ 10 ] and length [ 11 ], protein structure [ 12 ] and hydrophobicity [ 13 ], environment temperature [ 14 ] and other factors. In particular, the balance between gene mutation and natural selection determines the CUB [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

et al. 2015

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The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species.

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Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes

Cited by 24 publications

References 37 publications

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

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