Genome Sequences of Spinach Deltapartitivirus 1, Spinach Amalgavirus 1, and Spinach Latent Virus Identified in Spinach Transcriptome

Park, Dongbin; Hahn, Yoonsoo

doi:10.4014/jmb.1703.03043

Cited by 20 publications

(9 citation statements)

References 35 publications

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“…A BLASTx search of the NCBI non-redundant protein database confirmed the contig was related to plant amalgaviruses, including Blueberry latent virus (BLV), Zostera marina amalgavirus 1 (ZmAV1), Zostera marina amalgavirus 2 (ZmAV2), Allium cepa amalgavirus 1 (AcAV1), Allium cepa amalgavirus 2 (AcAV2), Spinach amalgavirus 1 (SpAV1), STV, and Rhododendron virus A (RHV-A) (Martin et al, 2011;Nibert et al, 2016;Park et al, 2018;Park and Hahn, 2017b;Sabanadzovic et al, 2009Sabanadzovic et al, , 2010. The contig was therefore considered to be derived from a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1).…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

Goh¹,

Park²,

Lee³

et al. 2018

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Amalgaviridae is a family of double-stranded, monosegmented RNA viruses that are associated with plants, fungi, microsporidians, and animals. A sequence contig derived from the transcriptome of a eudicot, Cistus incanus (the family Cistaceae; commonly known as hoary rockrose), was identified as the genome sequence of a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1). Sequence comparison and phylogenetic analysis indicated that CiRV1 is a novel species of the genus Amalgavirus in the family Amalgaviridae. The CiRV1 genome contig has two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. An ORF1+2 fusion protein, which functions in viral RNA replication, is produced by a +1 programmed ribosomal frameshifting (PRF) mechanism. A +1 PRF motif UUU_CGU, which matches the conserved amalgavirus +1 PRF consensus sequence UUU_CGN, was found at the boundary of CiRV1 ORF1 and ORF2. Comparison of 25 amalgavirus ORF1+2 fusion proteins revealed that only three different positions within a 13-amino acid segment were recurrently used at the boundary, possibly being selected so as not to interfere with correct folding and function of the fusion protein. CiRV1 is the first virus found to be associated with the Cistus species and may be useful for studying amalgaviruses.

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Section: Resultsmentioning

confidence: 99%

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

Goh¹,

Park²,

Lee³

et al. 2018

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“…These selected non-RefSeq CDS sequences were extracted from corresponding genome sequences. In cases where a programmed ribosomal frameshift occurred [ 49 , 50 ], the skipped nucleotide was removed or the repeated nucleotide was added to generate the complete ORF. These sequences were designated as “variant” CDS sequences.…”

Section: Methodsmentioning

confidence: 99%

Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

Park

Hahn

2021

BMC Bioinformatics

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Background RNA viruses possess remarkable evolutionary versatility driven by the high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. Results In this study, we systematically analyzed publicly available viral genome sequences and identified compensatory frameshift events in hundreds of viral protein-coding sequences. Compensatory frameshift events resulted in large-scale amino acid differences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were significantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in different locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic relationships between variant viruses. Conclusions Our results imply that the compensatory frameshift is one of the mechanisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.

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“…When total RNA from plant samples was extracted for transcriptomic analysis, viral genome RNAs were isolated together with the host RNAs. As a result, many plant RNA-seq datasets contain associated RNA virus sequences, which can be identified by comprehensive bioinformatic analysis ( Kim et al, 2014 ; Liu et al, 2012 ; Park and Hahn, 2017a , 2017b ). In this study, two novel amalgaviruses were identified in a transcriptome dataset obtained for the common eelgrass ( Kong et al, 2014 ).…”

mentioning

confidence: 99%

“…The second protein encoded by amalgaviruses is an ORF1+2 fusion protein that uses a +1 PRF mechanism for proper translation. A +1 PRF motif sequence, UUU_CGN (underline, codon boundary for ORF1; N, any nucleotide; CGN, a rare arginine codon), is prevalent in plant amalgaviruses ( Nibert et al, 2016 ; Park and Hahn, 2017b ). The same +1 PRF motif was observed in other RNA viruses such as Zygosaccharomyces bailii virus Z (ZbV-Z) and influenza A viruses ( Depierreux et al, 2016 ; Firth et al, 2012 ).…”

mentioning

confidence: 99%

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

et al. 2018

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Genome Sequences of Spinach Deltapartitivirus 1, Spinach Amalgavirus 1, and Spinach Latent Virus Identified in Spinach Transcriptome

Cited by 20 publications

References 35 publications

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

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