1
|
Xu Z, Gao Y, Teng K, Ge H, Zhang X, Wu M, Li R, Wu Z, Zheng L. Identification and Genome Characterization of a Novel Virus within the Genus Totivirus from Chinese Bayberry ( Myrica rubra). Viruses 2024; 16:283. [PMID: 38400058 PMCID: PMC10893191 DOI: 10.3390/v16020283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to identify viruses in M. rubra leaves exhibiting yellowing and irregular margin symptoms collected in Fuzhou, a city located in China's Fujian province in the year 2022. As a consequence, a novel member of the genus Totivirus was identified and tentatively named "Myrica rubra associated totivirus 1" (MRaTV1). The genome sequencing of MRaTV1 was determined by overlapping reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The two deduced proteins encoded by MRaTV1 have the highest amino acid (aa) sequence identity to the coat protein (CP) and RNA-dependent RNA polymerase (RdRP) of Panax notoginseng virus A (PNVA), a member of the genus Totivirus within the family Totiviridae, at 49.7% and 61.7%, respectively. According to the results of the phylogenetic tree and the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV) for the genus Totivirus, MRaTV1 is considered a new member of the genus Totivirus.
Collapse
Affiliation(s)
- Zhongtian Xu
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yi'nan Gao
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Kun Teng
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Huoyang Ge
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Xiaoqi Zhang
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Mengjing Wu
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA
| | - Zujian Wu
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Luping Zheng
- Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| |
Collapse
|
2
|
Khalifa ME, MacDiarmid RM. Molecular Characterization of Two Totiviruses from the Commensal Yeast Geotrichum candidum. Viruses 2023; 15:2150. [PMID: 38005831 PMCID: PMC10674808 DOI: 10.3390/v15112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Mycoviruses can infect many of the major taxa of fungi including yeasts. Mycoviruses in the yeast fungus Geotrichum candidum are not well studied with only three G. candidum-associated viral species characterized to date, all of which belong to the Totiviridae genus Totivirus. In this study, we report the molecular characteristics of another two totiviruses co-infecting isolate Gc6 of G. candidum. The two totiviruses were tentatively named Geotrichum candidum totivirus 2 isolate Gc6 (GcTV2-Gc6) and Geotrichum candidum totivirus 4 isolate Gc6 (GcTV4-Gc6). Both viruses have the typical genome organization of totiviruses comprising two ORFs encoding capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) at the N and C termini, respectively. The genomes of GcTV2-Gc6 and GcTV4-Gc6 are 4592 and 4530 bp long, respectively. Both viruses contain the-frameshifting elements and their proteins could be expressed as a single fusion protein. GcTV2-Gc6 is closely related to a totivirus isolated from the same host whereas GcTV4-Gc6 is related to insect-associated totiviruses. The phylogenetic analysis indicated that GcTV2-Gc6 and GcTV4-Gc6 belong to two different sister clades, I-A and I-B, respectively. It is interesting that all viruses identified from G. candidum belong to the genus Totivirus; however, this might be due to the lack of research reporting the characterization of mycoviruses from this fungal host. It is possible that the RNA interference (RNAi) mechanism cannot actively suppress totivirus accumulation in G. candidum Gc6.
Collapse
Affiliation(s)
- Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta 34517, Egypt;
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| |
Collapse
|
3
|
Tan H, Zhao R, Wang H, Huang X. Identification and molecular characterization of a novel member of the genus Totivirus from Areca catechu L. Arch Virol 2023; 168:247. [PMID: 37676322 DOI: 10.1007/s00705-023-05867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023]
Abstract
In previous work, RNA-seq was applied to identify the causal agent of yellow leaf disease (YLD) in areca palm (Areca catechu L.), resulting in the identification of areca palm velarivirus 1 (APV1) associated with YLD. Additionally, RNA-seq revealed a totivirus-like virus in areca palm. This work revealed that the totivirus-like virus is prevalent in asymptomatic areca palms. Therefore, it was tentatively named "areca palm latent totivirus 1" (APLTV1). The complete genome sequence of APLTV1 was determined and found to be 4754 base pairs (bp) in length, containing two ORFs whose encoded proteins share 55% and 69% amino acid (aa) sequence identity with the capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), respectively, of Bursera graveolens-associated totivirus 1 (BgAT1). Phylogenetic analysis based on alignment of the CP and RdRp sequences revealed that APLTV1 clustered with other members of the genus Totivirus, suggesting that APLTV1 represents a novel species of the genus Totivirus, family Totiviridae.
Collapse
Affiliation(s)
- Hang Tan
- College of Tropical Agriculture and Forest, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Ruibai Zhao
- College of Tropical Agriculture and Forest, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Hongxing Wang
- College of Tropical Agriculture and Forest, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Xi Huang
- College of Tropical Agriculture and Forest, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.
| |
Collapse
|
4
|
Abstract
In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly refined, species-specific relationship between Xrn1p and the "L-A" totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, the activity of Xrn1p against totiviruses is not simply an incidental consequence of the enzymatic activity of Xrn1p, but rather Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. Consistent with this, we demonstrated that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs.
Collapse
Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Brandon Ho
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sarah Bushong
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Arlen Johnson
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|