Transcription, mRNA export and immune evasion shape the codon usage of viruses
Christine Mordstein,Laura Cano,Atahualpa Castillo Morales,Bethan Young,Bethan Young,Alexander T Ho,Alan M. Rice,Michael Liss,Laurence D. Hurst,Grzegorz Kudla +9 more
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TLDR
This paper analyzed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation, and found that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses.Abstract:
The nucleotide composition, dinucleotide composition, and codon usage of many viruses differs from their hosts. These differences arise because viruses are subject to unique mutation and selection pressures that do not apply to host genomes; however, the molecular mechanisms that underlie these evolutionary forces are unclear. Here, we analysed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation. We find that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses. In an experimental follow-up, we find that the effects of GC content on gene expression depend on whether the genetic material is delivered to the cell as DNA or mRNA, whether it is transcribed by endogenous or exogenous RNA polymerase, and whether transcription takes place in the nucleus or cytoplasm. Our results suggest that viral codon usage cannot be explained by a simple adaptation to the codon usage of the host - instead, it reflects the combination of multiple selective and mutational pressures, including the need for efficient transcription, export, and immune evasion.read more
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Causes and consequences of purifying selection on SARS-CoV-2.
Atahualpa Castillo Morales,Alan M. Rice,Alexander T Ho,Christine Mordstein,Christine Mordstein,Christine Mordstein,Stefanie Mühlhausen,Samir F Watson,Laura Cano,Bethan Young,Bethan Young,Grzegorz Kudla,Laurence D. Hurst +12 more
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Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species.
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Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype
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Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases
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References
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TL;DR: It is shown that the m6A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells, and supports an emerging paradigm of m 6A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.