The complete genome sequence of a novel virus, bellflower veinal mottle virus, suggests the existence of a new genus within the family Potyviridae

Seo, Jang‐Kyun; Kwak, Hae-Ryun; Kim, Mi-Kyeong; Kim, Jeong-Soo; Choi, Hongsoo

doi:10.1007/s00705-017-3374-5

Cited by 16 publications

(9 citation statements)

References 7 publications

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“…This element was necessary for the internal initiation function of the TriMV 5= UTR both in vitro and in vivo. Phylogenetic analysis of members of the Potyviridae family and functional comparisons between the TriMV 5= UTR and that of the Bellflower veinal mottle virus (BVMoV), a newly discovered potyvirus of bellflower (34), suggest a possible remnant motif among potyviruses. To our knowledge, this is the first evidence of a IRES-driven motif-based mechanism for translation conserved in both plant-and animal-hosted picornaviruses.…”

mentioning

confidence: 99%

The Triticum Mosaic Virus Internal Ribosome Entry Site Relies on a Picornavirus-Like YX-AUG Motif To Designate the Preferred Translation Initiation Site and To Likely Target the 18S rRNA

Jaramillo-Mesa

Gannon

Holshbach

et al. 2019

J Virol

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Several viruses encode an internal ribosome entry site (IRES) at the 5′ end of their RNA, which, unlike most cellular mRNAs, initiates translation in the absence of a 5′ m7GpppG cap. Here, we report a uniquely regulated translation enhancer found in the 739-nucelotide (nt) sequence of the Triticum mosaic virus (TriMV) leader sequence that distinguishes the preferred initiation site from a plethora of IRES-encoded AUG triplets. Through deletion mutations of the TriMV 5′ untranslated region (UTR), we show that the TriMV 5′ UTR encodes acis-acting picornaviral Y16-X11-AUG-like motif with a 16-nt polypyrimidine CU-tract (Y16), at a precise, 11-nt distance (X11) from the preferred 13th AUG. Phylogenetic analyses indicate that this motif is conserved among potyviral leader sequences with multiple AUGs. Consistent with a broadly conserved mechanism, the motif could be functionally replaced with known picornavirus YX-AUG motifs and is predicted to function as target sites for the 18S rRNA by direct base pairing. Accordingly, mutations that disrupted overall complementarity to the 18S rRNA markedly reduced TriMV IRES activity, as did the delivery of antisense oligonucleotides designed to block YX-AUG accessibility. To our knowledge, this is the first report of a plant viral IRES YX-AUG motif, and our findings suggest that a conserved mechanism regulates translation for multiple economically important plant and animal positive single-stranded RNA viruses.IMPORTANCEUncapped viral RNAs often rely on their 5′ leader sequences to initiate translation, and the Triticum mosaic virus (TriMV) devotes an astonishing 7% of its genome to directing ribosomes to the correct AUG. Here we uncover a novel mechanism by which a TriMVcis-regulatory element controls cap-independent translation. The upstream region of the functional AUG contains a 16-nt polypyrimidine tract located 11 nt from the initiation site. Based on functional redundancy with similar motifs derived from human picornaviruses, the motif is likely to operate by directing ribosome targeting through base pairing with 18S rRNA. Our results provide the first report of a broad-spectrum mechanism regulating translation initiation for both plant- and animal-hosted picornaviruses.

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mentioning

confidence: 99%

The Triticum Mosaic Virus Internal Ribosome Entry Site Relies on a Picornavirus-Like YX-AUG Motif To Designate the Preferred Translation Initiation Site and To Likely Target the 18S rRNA

Jaramillo-Mesa

Gannon

Holshbach

et al. 2019

J Virol

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“…Although goji berry has been grown worldwide, viruses infecting goji berry are rather unknown. Thus, to identify the causal agent(s), the total RNA extracted from this sample was subjected to RNA-Seq as described previously [ 10 , 16 ].…”

Section: Resultsmentioning

confidence: 99%

“…RNA-Seq was performed using an Illumina HiSeq2000 sequencer (Illumina, Inc., USA). De novo assembly of the quality filtered RNA-Seq reads was performed using the Trinity pipeline and assembled contigs were analyzed by BLASTn and BLASTx searches against the viral reference genome database in GenBank [ 10 , 16 ]. The entire RNA-Seq procedure was performed by Macrogen Inc. (Seoul, South Korea).…”

Section: Methodsmentioning

confidence: 99%

Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families

Kwon

Choi

et al. 2018

PLoS ONE

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An unusual novel plant virus provisionally named goji berry chlorosis virus (GBCV) was isolated from goji berry plants (Lycium chinense Miller) showing chlorosis symptoms and its complete genome sequence was determined. The viral genome consists of a positive-sense single-stranded RNA of 10,100 ribonucleotides and contains six open reading frames (ORFs). Electron microscopy showed that the viral genome is packaged as a filamentous particle with an average length of approximately 850 nm. Phylogenetic analysis and amino acid similarity analysis of the encoded ORFs revealed that this new virus could be classified in an intermediate position between the families Benyviridae and Virgaviridae. The GBCV 200-kDa replicase (ORF1) is more similar to benyvirus replicases than to virgavirus replicases, while its 17-kDa coat protein (CP, ORF2) is more closely related with virgavirus CPs than benyvirus CPs. ORF3 was predicted to produce a C-terminally extended protein from ORF2 via frameshifting. While ORF4 (45-kDa), ORF5 (44-kDa), and ORF6 (16-kDa) have no apparent sequence homology with other known viruses, ORF5 is predicted to encode a movement protein (MP) that is phylogenetically related to the furovirus MP and ORF6 was experimentally proven to encode a viral suppressor of RNA silencing. These unusual characteristics suggest that GBCV may represent an evolutionary link between the families Benyviridae and Virgaviridae and indicate the existence of a novel, unidentified virus group.

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“…The other 11 genera each contain one to ten recognized species. The genus Bevemovirus has a single approved species, the Bellflower veinal mottle virus (BVMoV), which was isolated from a bellflower (Campanula takesimana) (Seo et al, 2017). The BVMoV polyprotein is predicted to be cleaved to produce nine mature proteins, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb, and CP; this is the same as that of macluravirus polyproteins.…”

Section: Introductionmentioning

confidence: 99%

“…The BVMoV polyprotein is predicted to be cleaved to produce nine mature proteins, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb, and CP; this is the same as that of macluravirus polyproteins. Phylogenetic analysis using BVMoV and selected potyvirid polyprotein sequences suggested that the genus Bevemovirus is the sister taxon of the genus Macluravirus (Seo et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

Choi¹,

Shin²,

Shirasu³

et al. 2022

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The complete genome sequence of a novel virus, bellflower veinal mottle virus, suggests the existence of a new genus within the family Potyviridae

Cited by 16 publications

References 7 publications

The Triticum Mosaic Virus Internal Ribosome Entry Site Relies on a Picornavirus-Like YX-AUG Motif To Designate the Preferred Translation Initiation Site and To Likely Target the 18S rRNA

The Triticum Mosaic Virus Internal Ribosome Entry Site Relies on a Picornavirus-Like YX-AUG Motif To Designate the Preferred Translation Initiation Site and To Likely Target the 18S rRNA

Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

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