Ribosomal Frameshift Signals in Viral Genomes

Plant, Ewan P.

doi:10.5772/26550

Cited by 7 publications

(4 citation statements)

References 157 publications

(230 reference statements)

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“…This phenomenon is termed ribosomal frameshift [235]. The ribosome can slip one or two nucleotides (−1 or −2 frameshifts) to the 5 end or one or two nucleotides (+1 or +2 frameshifts) to the 3 end [25,[236][237][238], in which the programmed −1 ribosomal frameshift is the type with detailed characteristics [239]. Programmed −1 ribosomal frameshift was first described by the expression of the Gag-Pol polyprotein of the rous sarcoma alpharetrovirus, which is a chimeric product of overlapping gag and pol ORFs [240,241].…”

Section: Ribosomal Frameshiftmentioning

confidence: 99%

Translation of Plant RNA Viruses

Geng

Wang

Liu

et al. 2021

Viruses

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Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.

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Section: Ribosomal Frameshiftmentioning

confidence: 99%

Translation of Plant RNA Viruses

Geng

Wang

Liu

et al. 2021

Viruses

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“…The 5' two-thirds of the genome code for two polyproteins, pp1a and pp1ab, which are then proteolytically cleaved in several nonstructural proteins. Production of the pp1ab requires the translating ribosome to change the reading frame at the frameshift signal that bridges ORF1a and ORF1ab 2 . The nal one-third of the genome encodes a set of four structural protein genes, in the order of spike (S), envelope (E), membrane (M) and nucleocapsid (N).…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 And Other Human Coronavirus Show Genome Patterns Previously Associated to Reduced Viral Recognition and Altered Immune Response

Franzo

2021

Preprint

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A new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.

show abstract

“…The 5' two-thirds of the genome code for two polyproteins, pp1a and pp1ab, which are then proteolytically cleaved in several nonstructural proteins. Production of the pp1ab requires the translating ribosome to change the reading frame at the frameshift signal that bridges ORF1a and ORF1ab 2 . The final one-third encodes a set of four structural protein genes, in the order of spike (S), envelope (E), membrane (M) and nucleocapsid (N).…”

Section: Introductionmentioning

confidence: 99%

The features of SARS-CoV-2 and other human coronavirus genomes could affect interferon production and immune response

Franzo¹

2020

Preprint

View full text Add to dashboard Cite

A new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented.The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2.Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.

show abstract

Ribosomal Frameshift Signals in Viral Genomes

Cited by 7 publications

References 157 publications

Translation of Plant RNA Viruses

Translation of Plant RNA Viruses

SARS-CoV-2 And Other Human Coronavirus Show Genome Patterns Previously Associated to Reduced Viral Recognition and Altered Immune Response

The features of SARS-CoV-2 and other human coronavirus genomes could affect interferon production and immune response

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