Identification and Full Genome Analysis of the First Putative Virus of Sea Buckthorn (Hippophae rhamnoides L.)

The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a viru...

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Published in:Microorganisms (Basel) Vol. 10; no. 10; p. 1933
Main Authors: Balke, Ina, Zeltina, Vilija, Zrelovs, Nikita, Kalnciema, Ieva, Resevica, Gunta, Ludviga, Rebeka, Jansons, Juris, Moročko-Bičevska, Inga, Segliņa, Dalija, Zeltins, Andris
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 28.09.2022
MDPI
Subjects:
Amino acids
Coat protein
Cysteine proteinase
Disease
DNA helicase
DNA-directed RNA polymerase
Genetic aspects
Genomes
Hippophae
Hippophae rhamnoides
Identification and classification
marafibox
Marafivirus
Methyltransferase
Nucleotide sequence
Nucleotides
Open reading frames
Papain
Pathogens
plant virus
Plant viruses
Proteins
RNA helicase
RNA polymerase
RNA viruses
RNA-directed RNA polymerase
RNA-seq
sea buckthorn
Sequence analysis
Virions
Virus diseases of plants
Virus-like particles
Viruses
Latvia
Russia
Hippophae
RNA-seq
sea buckthorn
marafibox
Marafivirus
plant virus
ISSN:2076-2607, 2076-2607
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Abstract The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of SBT for the first time. Sequence analysis of the obtained viral genome revealed high similarity with several viruses belonging to the genus Marafivirus. The genome of the new virus is 6989 nucleotides (nt) in length according to 5′, 3′ RACE (without polyA-tail), with 5′ and 3′ 133 and 109 nt long untranslated regions, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1954 amino acids with the characteristic marafivirus non-structural protein domains—methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by 6 nt, encoding the coat protein (CP) with typical signatures of minor and major forms. Both CP forms were cloned and expressed in a bacterial expression system. Only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly.
AbstractList The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of SBT for the first time. Sequence analysis of the obtained viral genome revealed high similarity with several viruses belonging to the genus Marafivirus. The genome of the new virus is 6989 nucleotides (nt) in length according to 5′, 3′ RACE (without polyA-tail), with 5′ and 3′ 133 and 109 nt long untranslated regions, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1954 amino acids with the characteristic marafivirus non-structural protein domains—methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by 6 nt, encoding the coat protein (CP) with typical signatures of minor and major forms. Both CP forms were cloned and expressed in a bacterial expression system. Only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly.
The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of SBT for the first time. Sequence analysis of the obtained viral genome revealed high similarity with several viruses belonging to the genus Marafivirus. The genome of the new virus is 6989 nucleotides (nt) in length according to 5', 3' RACE (without polyA-tail), with 5' and 3' 133 and 109 nt long untranslated regions, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1954 amino acids with the characteristic marafivirus non-structural protein domains-methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by 6 nt, encoding the coat protein (CP) with typical signatures of minor and major forms. Both CP forms were cloned and expressed in a bacterial expression system. Only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly.The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of SBT for the first time. Sequence analysis of the obtained viral genome revealed high similarity with several viruses belonging to the genus Marafivirus. The genome of the new virus is 6989 nucleotides (nt) in length according to 5', 3' RACE (without polyA-tail), with 5' and 3' 133 and 109 nt long untranslated regions, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1954 amino acids with the characteristic marafivirus non-structural protein domains-methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by 6 nt, encoding the coat protein (CP) with typical signatures of minor and major forms. Both CP forms were cloned and expressed in a bacterial expression system. Only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly.
The agricultural importance of sea buckthorn (SBT; L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of SBT for the first time. Sequence analysis of the obtained viral genome revealed high similarity with several viruses belonging to the genus . The genome of the new virus is 6989 nucleotides (nt) in length according to 5', 3' RACE (without polyA-tail), with 5' and 3' 133 and 109 nt long untranslated regions, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1954 amino acids with the characteristic marafivirus non-structural protein domains-methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by 6 nt, encoding the coat protein (CP) with typical signatures of minor and major forms. Both CP forms were cloned and expressed in a bacterial expression system. Only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly.
Audience Academic
Author Zeltins, Andris
Kalnciema, Ieva
Jansons, Juris
Moročko-Bičevska, Inga
Ludviga, Rebeka
Resevica, Gunta
Balke, Ina
Zeltina, Vilija
Zrelovs, Nikita
Segliņa, Dalija
AuthorAffiliation 1 Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
2 Plant Virology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
5 Unit of Plant Pathology and Entomology, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Graudu Street 1, LV-3701 Dobele, Latvia
6 Unit of Processing and Biochemistry, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Graudu Street 1, LV-3701 Dobele, Latvia
4 Cell Biology and Microscopy Core Facility, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
3 Bioinformatics Core Facility, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
AuthorAffiliation_xml – name: 1 Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
– name: 6 Unit of Processing and Biochemistry, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Graudu Street 1, LV-3701 Dobele, Latvia
– name: 2 Plant Virology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
– name: 3 Bioinformatics Core Facility, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
– name: 5 Unit of Plant Pathology and Entomology, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Graudu Street 1, LV-3701 Dobele, Latvia
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/36296209$$D View this record in MEDLINE/PubMed
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CitedBy_id crossref_primary_10_1371_journal_pone_0287278
crossref_primary_10_3389_fpls_2025_1533251
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Keywords Hippophae
RNA-seq
sea buckthorn
marafibox
Marafivirus
plant virus
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Snippet The agricultural importance of sea buckthorn (SBT; Hippophae rhamnoides L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have...
The agricultural importance of sea buckthorn (SBT; L.) is rapidly increasing. Several bacterial and fungal pathogens infecting SBT have been identified and...
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StartPage 1933
SubjectTerms Amino acids
Coat protein
Cysteine proteinase
Disease
DNA helicase
DNA-directed RNA polymerase
Genetic aspects
Genomes
Hippophae
Hippophae rhamnoides
Identification and classification
marafibox
Marafivirus
Methyltransferase
Nucleotide sequence
Nucleotides
Open reading frames
Papain
Pathogens
plant virus
Plant viruses
Proteins
RNA helicase
RNA polymerase
RNA viruses
RNA-directed RNA polymerase
RNA-seq
sea buckthorn
Sequence analysis
Virions
Virus diseases of plants
Virus-like particles
Viruses
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Title Identification and Full Genome Analysis of the First Putative Virus of Sea Buckthorn (Hippophae rhamnoides L.)
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