Near-Complete Genome Sequence of Ryegrass Mottle Virus from Irrigation Water in Ecuador

Guevara, Fiama; Flores, Francisco

doi:10.1128/mra.00037-21

Cited by 4 publications

(6 citation statements)

References 12 publications

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“…Ryegrass mottle virus (RGMoV) belongs to the family Solemoviridae , genus Sobemovirus , and infects monocotyledons, such as Italian ryegrass ( Lolium multiflorum ), cocksfoot ( Dactylis glomerata ), wheat ( Triticum aestivum ), barley ( Hordeum vulgare ), oats ( Avena sativa ), rye ( Secale cerdeale ), and Italian millet ( Setaria italica ) [ 1 , 2 ]. RGMoV was isolated from Italian ryegrass and cocksfoot in Japan [ 1 ] and was also found in irrigation waters in Ecuador in 2021 [ 3 ]. Its genome is a monocistronic single-stranded positive-sense RNA that is 4212 or 4247 nucleotides in length [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

“…RGMoV was isolated from Italian ryegrass and cocksfoot in Japan [ 1 ] and was also found in irrigation waters in Ecuador in 2021 [ 3 ]. Its genome is a monocistronic single-stranded positive-sense RNA that is 4212 or 4247 nucleotides in length [ 3 , 4 ]. Sobemovirus genomic RNA (gRNA) encodes five open reading frames (ORF), where ORF1, ORFx, ORF2a, and ORF2b are translated from the gRNA, and ORF3, which encodes the coat protein (CP), is translated from a subgenomic RNA (sgRNA) [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

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VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure

Kalnins

Ludviga

Kalnciema

et al. 2023

IJMS

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Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro–VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro–VPg complex during interaction is lacking. Here, we solved a full Pro–VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory effects on the Pro cleavage activity.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure

Kalnins

Ludviga

Kalnciema

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

Section: Introductionmentioning

confidence: 99%

“…RGMoV was isolated from Italian ryegrass and cocksfoot in Japan [1] and was also found in irrigation waters in Ecuador in 2021 [3]. Its genome is a monocistronic single-stranded positive-sense RNA that is 4212 or 4,247 bp in length [3, 4]. Sobemovirus genomic RNA (gRNA) encodes five open reading frames (ORF), where ORF1, ORFx, ORF2a, and ORF2b are translated from the gRNA, and ORF3, which encodes the coat protein (CP), is translated from a subgenomic RNA (sgRNA) [5, 6].…”

Section: Introductionmentioning

confidence: 99%

VPg impact on Ryegrass mottle virus serine-like 3C protease proteolysis and structure

Kalnins

Ludviga

Kalnciema

et al. 2023

Preprint

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Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). NMR studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full ProVPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory activities on the Pro cleavage activity.

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“…The distribution of RGMoV is no longer limited to Japan. Through high throughput sequencing (HTS), RGMoV has been detected in various samples worldwide, including the United Kingdom (GenBank ID MW588198.1), USA (GenBank ID OK424596.1), Australia (GenBank ID MT129760.1), Ecuador (GenBank ID MW411579.1; [45]), and by ELISA and IEM in Germany [46]. The widespread presence of RGMoV in different regions indicates it is a plant pathogen of concern.…”

Section: Introductionmentioning

confidence: 99%

Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods– 3′ RACE and RNA-Seq

Balke,

Silamikelis,

Radovica-Spalvina

et al. 2023

PLoS ONE

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Ryegrass mottle virus (RGMoV; genus: Sobemovirus) is a single-stranded positive RNA virus with a 30 nm viral particle size. It exhibits T = 3 symmetry with 180 coat protein (CP) subunits forming a viral structure. The RGMoV genome comprises five open reading frames that encode P1, Px, a membrane-anchored 3C-like serine protease, a viral genome-linked protein, P16, an RNA-dependent RNA polymerase, and CP. The RGMoV genome size varies, ranging from 4175 nt (MW411579.1) to 4253 nt (MW411579.1) in the deposited sequences. An earlier deposited RGMoV complete genome sequence of 4212 nt length (EF091714.1) was used to develop an infectious complementary DNA (icDNA) construct for in vitro gRNA transcription from the T7 promoter. However, viral infection was not induced when the transcribed gRNA was introduced into oat plants, indicating the potential absence of certain sequences in either the 5’ or 3’ untranslated regions (UTR) or both. The complete sequence of the 3’ UTR was determined through 3’ end RACE, while the 5’ UTR was identified using high-throughput sequencing (HTS)-RNA-Seq to resolve the potential absences. Only the icDNA vector containing the newly identified UTR sequences proved infectious, resulting in typical viral infection symptoms and subsequent propagation of progeny viruses, exhibiting the ability to cause repeated infections in oat plants after at least one passage. The successful generation of icDNA highlighted the synergistic potential of utilizing both methods when a single approach failed. Furthermore, this study demonstrated the reliability of HTS as a method for determining the complete genome sequence of viral genomes.

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Near-Complete Genome Sequence of Ryegrass Mottle Virus from Irrigation Water in Ecuador

Cited by 4 publications

References 12 publications

VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure

VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure

VPg impact on Ryegrass mottle virus serine-like 3C protease proteolysis and structure

Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods– 3′ RACE and RNA-Seq

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