Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host

Wang, Qianqian; Lyu, Xueliang; Chéng, Jiāsēn; Fù, Yànpíng; Lin, Yang; Abdoulaye, Assane Hamidou; Xiè, Jiǎtāo

doi:10.3390/ijms23137441

Cited by 17 publications

(11 citation statements)

References 69 publications

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“…All eight CpG-encompassing codons are found to be underrepresented in the Nipah virus [ 74 ]. RSCU values analysis of six codons containing TpA (TTA, CTA, ATA, GTA, TAT, and TAC) indicated that these are not preferred in Mycoviral genes [ 75 ]. HCV also showed a significant tendency to not prefer the codons with CpG or TpA dinucleotides [ 76 ], and many researchers have reported similar results [ 77 , 78 , 79 , 80 ] establishing a correlation between the presence of CpG and TpA and lower RSCU.…”

Section: Resultsmentioning

confidence: 99%

A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons

Gurjar¹,

Karuvantevida

Rzhepakovsky

et al. 2023

Vaccines

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The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes’ spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes.

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Section: Resultsmentioning

confidence: 99%

A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons

Gurjar¹,

Karuvantevida

Rzhepakovsky

et al. 2023

Vaccines

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“…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.…”

Section: Discussionmentioning

confidence: 99%

The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes

Pawlak

Błażej

Mackiewicz

et al. 2023

IJMS

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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.

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“…dianthimycovirus 1, Heterobasidion partitivirus 13 strain an1, Phytophthora endornavirus 2 (PEV2), and PEV3 show that the high titer of mycoviruses can induce more severe symptoms in the host than mycoviruses with low titer [ 43 , 44 , 45 ]. Some researchers have hypothesized that hypovirulence-associated mycoviruses causing the hypovirulence of hosts result from the codon usage of mycovirus and host was similar which was beneficial to increase mycovirus accumulation [ 46 ]. In some cases that may be true, but here the codon usage was not the key reason.…”

Section: Discussionmentioning

confidence: 99%

Extending the Host Range of Fusarium Poae Virus 1 from Fusarium poae to other Fusarium Species in the Field

Song

Sun

Gao

et al. 2022

Viruses

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Fusarium poae virus 1 (FpV1, a betapartitivirus) is one of the mycoviruses which is discovered earlier. Due to the vegetative incompatibility barrier that often exists between different species or strains of filamentous fungi, FpV1 has been thought to be limited to its host, F. poae, as a non-hypovirulence mycovirus in the past 20 years in the field. Here, a novel strain of FpV1 (FpV1-Fa) with two dsRNA segments (2157-and 2080-nt) was consistently identified in F. asiaticum isolates in the field. FpV1-Fa induced abnormal morphology and hypovirulence of F. asiaticum, along with a high viral load. FpV1-Fa was detected only from the F. asiaticum and F. tricinctum strains at a FpV1-Fa sampling site (119.014289, 33.8261), while the other strains from other sites were not identified FpV1-Fa. A horizontal transmission experiment showed that FpV1-Fa can transfer from F. asiaticum to F. poae and F. tricinctum, but not to F. graminearum. The selection analysis of FpV1-Fa revealed RdRP and CP were under strong purifying selection, and the C-terminal side of RdRP was under positive selection. In these regions, 9 amino acid mutations in RdRP and 21 mutations in CP appeared to cause the variation of host range and virulence in FpV1-Fa.

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Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host

Cited by 17 publications

References 69 publications

A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons

A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons

The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes

Extending the Host Range of Fusarium Poae Virus 1 from Fusarium poae to other Fusarium Species in the Field

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