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The graph shows the RSCUs of human cell cycle regulated (CCR) genes and non-cell cycle regulated (NCCR) genes, compared with the RSCUs of RNA viruses.
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The codon usage pattern is a specific characteristic of each species; however, the codon usage of all of the genes in a genome is not uniform. Intriguingly, most viruses have codon usage patterns that are vastly different from the optimal codon usage of their hosts. How viral genes with different codon usage patterns are efficiently expressed durin...
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... genes cycling at the protein level and non-cycle regulated genes (NCCRs) that were found not to cycle at the protein level were selected from previous studies ( Table 3). The RSCUs of the CCR and NCCR genes were plotted on a graph and compared with the RSCUs of RNA viruses ( Figure 5). The results showed that the CCR genes were located with -ssRNA, dsRNA, and some þssRNA viruses, indicating similar codon usage patterns, while the RSCUs of the NCCR genes were distributed all over the graph with no resemblance to RNA viruses. ...
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... Genome composition in RNA viruses reflects codon usage and therefore CUB is considered to be mainly under mutational pressure (Jenkins and Holmes, 2003;Belalov and Lukashev, 2013;Yao et al., 2020). Apart from the genome composition, limited evidence of host-specific translational selection pressure also has been reported in human RNA viruses (Jitobaom et al., 2020), in the MERS-CoV (Hussain et al., 2020) and influenza virus H1N1 (Wong et al., 2010). A recent study reported the coevolution of virus and host codon usage . ...
... However, numerous studies have demonstrated that the use of synonymous codons is a non-random process [8] and that some codons are employed more preferentially than others during translation [9][10][11]. This phenomenon of codon usage preference contains not only simple random mutations in base composition, but also corresponding functions that can explain the occurrence of different codon usage patterns in distinct species at a biological level [12]. It describes why similar codon selection strategies might be employed, thus complementing the molecular data with biological significance. ...
... The results revealed a high expression capability of foreign genes and an optimal frequency of codon usage in both strains. These findings provide strong evidence of their adaptability in the host and suggest a potential correlation with virus-host infection [12]. While numerous studies look for similarities between virus and host genomes, most of these similarities are more closely related to a biological function rather than codon usage [12]. ...
... These findings provide strong evidence of their adaptability in the host and suggest a potential correlation with virus-host infection [12]. While numerous studies look for similarities between virus and host genomes, most of these similarities are more closely related to a biological function rather than codon usage [12]. Whereas, it is not unusual for there to be different codon usage biases between viruses and host that correlate with the range of hosts infected, host translation and virulence, for example [24][25][26]. ...
Porcine reproductive and respiratory syndrome (PRRS) is a problem that has significant economic impact on the global pig industry. In recent years, there has been an increased importation of pork into China, contributing to the emergence of novely imported porcine reproductive and respiratory syndrome virus (PRRSV) sub-types. Nevertheless, codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain elusive. To investigate this, we employed a Bayesian approach to analyze two novel imported PRRSV sub-types, namely, NADC30-like and NADC34-like viruses. These sub-types have different codon preferences. Besides, the Effective Number of Codon (ENC) analysis revealed that both NADC30-like and NADC34-like fall within the expected curve distribution, describing a balanced codon usage for both NADC30-like and NADC34-like virus. Based on the Codon Adaptation Index (CAI), NADC30-like showed the highest similarity to the host, aligning with the main prevalence trend of the host. In contrast, NADC34-like exhibited the highest frequency of optimal codon usage; this analysis is based on Frequency of Optimal Codons (FOP). Moreover, the Relative Codon Deoptimization Index (RCDI) indicates that NADC30-like sub-types have a greater degree of inverse optimization sub-type. These findings suggest that mutational pressure affects codon usage preferences of genes in newly imported PRRSV, and that natural selection plays a vital role in determining PRRSV gene codon preferences. Our study provides new insights into the disease, origin, evolutionary patterns, and host adaptation of these newly imported PRRSV sub-types in China. It also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.
... The higher similarity of viral codon usage to the host can facilitate the replication of these pathogenic agents. The usage is similar to specific host genes [81,82] and is visible especially in viruses infecting a narrow spectrum of hosts [83,84]. Therefore, dynamic changes in codon usage in the hosts, e.g., due to changes in mutational pressure, can protect them against infectious agents. ...
Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation–selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used.
... It should be expected that the synonymous codon usage pattern of viruses would be shaped by selecting specific codon subsets to match the most abundant host transfer RNAs (tRNAs). However, the codon usage of many viruses is very different from the optimal codons present in the host [30]. Interestingly, it was recently reported that codon usage in virus IDRs is less optimized for the host than in ORs [31]. ...
Intrinsically disordered regions (IDRs) are abundant in the proteome of RNA viruses. The multifunctional properties of these regions are widely documented and their structural flexibility is associated with the low constraint in their amino acid positions. Therefore, from an evolutionary stand point, these regions could have a greater propensity to accumulate non-synonymous mutations (NS) than highly structured regions (ORs, or ‘ordered regions’). To address this hypothesis, we compared the distribution of non-synonymous mutations (NS), which we relate here to mutational robustness, in IDRs and ORs in the genome of potyviruses, a major genus of plant viruses. For this purpose, a simulation model was built and used to distinguish a possible selection phenomenon in the biological datasets from randomly generated mutations. We analyzed several short-term experimental evolution datasets. An analysis was also performed on the natural diversity of three different species of potyviruses reflecting their long-term evolution. We observed that the mutational robustness of IDRs is significantly higher than that of ORs. Moreover, the substitutions in the ORs are very constrained by the conservation of the physico-chemical properties of the amino acids. This feature is not found in the IDRs where the substitutions tend to be more random. This reflects the weak structural constraints in these regions, wherein an amino acid polymorphism is naturally conserved. In the course of evolution, potyvirus IDRs and ORs follow different evolutive paths with respect to their mutational robustness. These results have forced the authors to consider the hypothesis that IDRs and their associated amino acid polymorphism could constitute a potential adaptive reservoir.
... Codon usage bias is generally highly expressed here than other genes through RSCU (Relative Synonymous Codon Usage) calculation. This calculation was done from the protein coding sequences of the human genes and RNA viruses and then PCA (Principal Coefficient Analysis) was performed to assess the codon usage bias of a gene (Jitobaom et al 2020). ...
... Jitobaom et al 2020). Several researches are going on to find out the reason of using different codons for the translation of viral proteins in the host. ...
With the increase of COVID-19 as pandemic throughout the world causing several deaths in several countries, researches are going on to find out the ways in the origin of mutations in SARS-CoV-2 genome. The process of mutation and origin of new variants have been discussed. Again the Codon Usage Pattern in the present virus has also been described. Lastly different modern methods for the prediction of mutations in the virus have been mentioned. New technologies are used to study genomic changes and changes in the sequence of amino acids of the viral protein are used to predict the origin of future mutations. The information for the prediction of mutations will definitely help to synthesize the specific drugs for the Coronavirus as well as in the manufacture of proper vaccine.
... Unlike completely identical or opposite patterns, some viruses have evolved a mixture of coincident and antagonistic codons, for instance, Citrus tristeza virus [18], Zika virus [25], and chikungunya virus [54]. Jitobaom et al. (2020) analyzed codon usage similarity between human RNA viruses and human genes, which demonstrated that the codon usage of cell-cycle-regulated genes are similar to that of human RNA viruses, indicating that human RNA viral genes may be efficiently expressed at the certain stages of the cell cycle [55]. In this study, we found that the fungal genes involved in nucleobase-containing compound metabolic/biosynthetic process, heterocycle biosynthetic process, RNA biosynthetic process, and transcription that have similar codon usage pattern to mycoviruses are significantly enriched. ...
... Human genes that have similar codon usage to human immunodeficiency virus type 1, Zika virus, influenza A virus, and dengue virus serotype 2 may be upregulated in viral infections [55]. In our analysis, 9 and 13 GO terms of S. sclerotiorum and F. graminearum genes that have similar codon usage pattern to mycoviruses have been found to be identical to the GO terms of upregulated S. sclerotiorum and F. graminearum genes in SsMYRV4 and FgV2 infection, respectively; FgV1 infection can also upregulate F. graminearum transcriptional genes that with similar codon usage to mycoviruses, while there was no effect on the F. graminearum genes that have similar codon usage pattern to mycoviruses during FgV3, FgV4, and FgHV1 infections. ...
Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.
... Codon usage bias is generally highly expressed here than other genes through RSCU (Relative Synonymous Codon Usage) calculation. This calculation was done from the protein coding sequences of the human genes and RNA viruses and then PCA (Principal Coefficient Analysis) was performed to assess the codon usage bias of a gene (Jitobaom et al 2020). ...
The widely spread pandemic of COVID-19 throughout the world is due to the Corona virus known as Sars-CoV-2 which was first detected in the Wuhan district of China at the end of 2019. With the increase of pandemic in 2020 all countries of the world are facing serious threats to public health and economic crisis. So far seven types of coronavirus have been detected such as SARS-CoV, MERS- CoV, HKU1, NL 63, OC 43, 229 E and recent one SARS-CoV-2. Of these coronaviruses, SARS-COV, MERS-CoV and SARS-CoV-2 cause severe diseases to humans and other viruses show mild symptoms.
... Viruses tend to use different codon usage patterns to improve overall virus survival and evade the host immune system (Moratorio et al. 2013). Previous studies indicated that similarities of relative synonymous codon usage (RSCU) of genes between pathogens and their host can impact gene expression in the host and that the pathogens depend on their hosts for their multiplication (Alonso and Diambra 2020;Jitobaom et al. 2020;Kula et al. 2018;Michely et al. 2013;Miller et al. 2017;Nambou and Anakpa 2020;Pepin et al. 2008). Recently, codon usage similarities between viral genes and human genes has been demonstrated and indicated that the infection (viral proteins engaging the host cell proteins) may induce pathological effects as a result of the expression and translation of RNA transcripts and the effects of proteins from these transcripts (Maldonado et al. 2021). ...
Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options.
... Codon usage similarity between viral and host genomes has been shown as an indicator for adaptation to the host as optimized use of the available endogenous amino acids allows more efficient translation of viral genes [41,42]. The codon usage of the canonical SARS-CoV-2 genes has been determined to correlate well with the human, bat and pangolin amino acid pools [43,44]. ...
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.
... (31). Essas semelhanças podem influenciar processos biológicos importantes já que conhecidamente sabe-se que genes humanos com padrões de uso de códons semelhantes aos vírus de RNA em condições de infecção são influenciados a nível de regulação e expressão de proteínas (17), por exemplo, genes exógenos com com viés do uso de códons sinônimos (CUB) muito semelhantes ao hospedeiro podem impedir consideravelmente a tradução do hospedeiro (35). Apesar do modelo que replicamos não se basear em CUB, é possível notar que ocorre essa competição por recursos na célula hospedeira e que isso influencia no processo de tradução. ...
Análise das diferenças de preferências de códons nos arbovírus em relação ao hospedeiro humano e identificação do melhores códons para inibir os tRNAs cognatos visando a redução da taxa de tradução das proteínas virais e assim a taxa de replicação viral.
