Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae
Abstract
:1. Introduction
2. Results
2.1. Genome Organization of Reclovirids
2.2. Protein Domains in the Replicases of Reclovirids
2.3. Protein Domains and Motifs in Non-Replicative Proteins of Reclovirids
3. Discussion
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Gilmer, D.; Ratti, C. ICTV Virus Taxonomy Profile: Benyviridae. J. Gen. Virol. 2017, 98, 1571–1572. [Google Scholar] [CrossRef] [PubMed]
- Solovyev, A.G.; Morozov, S.Y. Uncovering Plant Virus Species Forming Novel Provisional Taxonomic Units Related to the Family Benyviridae. Viruses 2022, 14, 2680. [Google Scholar] [CrossRef] [PubMed]
- Valach, M.; Moreira, S.; Petitjean, C.; Benz, C.; Butenko, A.; Flegontova, O.; Nenarokova, A.; Prokopchuk, G.; Batstone, T.; Lapébie, P.; et al. Recent expansion of metabolic versatility in Diplonema papillatum the model species of a highly speciose group of marine eukaryotes. BMC Biol. 2023, 21, 99. [Google Scholar] [CrossRef] [PubMed]
- Benites, L.F.; Stephens, T.G.; Bhattacharya, D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol. 2022, 8, veac101. [Google Scholar] [CrossRef]
- Veglia, A.J.; Bistolas, K.S.I.; Voolstra, C.R.; Hume, B.C.C.; Ruscheweyh, H.J.; Planes, S.; Allemand, D.; Boissin, E.; Wincker, P.; Poulain, J.; et al. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun. Biol. 2023, 6, 566. [Google Scholar] [CrossRef]
- Mifsud, J.C.O.; Gallagher, R.V.; Holmes, E.C.; Geoghegan, J.L. Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom. J. Virol. 2022, 96, e0026022. [Google Scholar] [CrossRef]
- Morozov, S.Y.; Solovyev, A.G. Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-cistron Movement Block. Biomolecules 2022, 12, 861. [Google Scholar] [CrossRef]
- Kwon, S.-J.; Choi, G.-S.; Choi, B.; Seo, J.-K. Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families. PLoS ONE 2018, 13, e0206382. [Google Scholar] [CrossRef]
- Solovyev, A.G.; Morozov, S.Y. Non-replicative integral membrane proteins encoded by plant alpha-like viruses: Emergence of diverse orphan ORFs and movement protein genes. Front. Plant. Sci. 2017, 8, 1820. [Google Scholar] [CrossRef]
- Atabekova, A.K.; Lazareva, E.A.; Lezzhov, A.A.; Solovieva, A.D.; Golyshev, S.A.; Skulachev, B.I.; Solovyev, I.D.; Savitsky, A.P.; Heinlein, M.; Morozov, S.Y.; et al. Interaction between Movement Proteins of Hibiscus green spot virus. Viruses 2022, 14, 2742. [Google Scholar] [CrossRef]
- Ramos-González, P.L.; Arena, G.D.; Tassi, A.D.; Chabi-Jesus, C.; Kitajima, E.W.; Freitas-Astúa, J. Kitaviruses: A Window to Atypical Plant Viruses Causing Nonsystemic Diseases. Annu. Rev. Phytopathol. 2023. [Google Scholar] [CrossRef] [PubMed]
- Mushegian, A. Methyltransferases of Riboviria. Biomolecules 2022, 12, 1247. [Google Scholar] [CrossRef] [PubMed]
- Baliji, S.; Cammer, S.A.; Sobral, B.; Baker, S.C. Detection of nonstructural protein 6 in murine coronavirus-infected cells and analysis of the transmembrane topology by using bioinformatics and molecular approaches. J. Virol. 2009, 83, 6957–6962. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Reid, C.R.; Airo, A.M.; Hobman, T.C. The Virus-Host Interplay: Biogenesis of +RNA Replication Complexes. Viruses 2015, 7, 4385–4413. [Google Scholar] [CrossRef] [Green Version]
- Sá-Moura, B.; Kornprobst, M.; Kharde, S.; Ahmed, Y.L.; Stier, G.; Kunze, R.; Sinning, I.; Hurt, E. Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLoS ONE 2017, 12, e0183272. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tellinghuisen, T.L.; Paulson, M.S.; Rice, C.M. The NS5A protein of bovine viral diarrhea virus contains an essential zinc-binding site similar to that of the hepatitis C virus NS5A protein. J. Virol. 2006, 80, 7450–7458. [Google Scholar] [CrossRef] [Green Version]
- LeDesma, R.; Heller, B.; Biswas, A.; Maya, S.; Gili, S.; Higgins, J.; Ploss, A. Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication. eLife 2023, 12, e80529. [Google Scholar] [CrossRef]
- Kumar, G.; Dasgupta, I. Variability, Functions and Interactions of Plant Virus Movement Proteins: What Do We Know So Far? Microorganisms 2021, 9, 695. [Google Scholar] [CrossRef]
- Huang, C.; Heinlein, M. Function of Plasmodesmata in the Interaction of Plants with Microbes and Viruses. Methods Mol. Biol. 2022, 2457, 23–54. [Google Scholar]
- Hajikhezri, Z.; Darweesh, M.; Akusjärvi, G.; Punga, T. Role of CCCH-Type Zinc Finger Proteins in Human Adenovirus Infwctions. Viruses 2020, 12, 1322. [Google Scholar] [CrossRef]
- Wang, G.; Zheng, C. Zinc finger proteins in the host-virus interplay: Multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol. Rev. 2021, 45, fuaa059. [Google Scholar] [CrossRef]
- Neuhaus, D. Zinc finger structure determination by NMR: Why zinc fingers can be handful. Prog. Nucl. Magn. Reson. Spectrosc. 2022, 130–131, 62–105. [Google Scholar] [CrossRef] [PubMed]
- Siré, C.; Bangratz-Reyser, M.; Fargette, D.; Brugidou, C. Genetic diversity and silencing suppression effects of Rice yellow mottle virus and the P1 protein. Virol. J. 2008, 5, 55. [Google Scholar] [CrossRef] [Green Version]
- Gillet, F.X.; Cattoni, D.I.; Petiot-Bécard, S.; Delalande, F.; Poignavent, V.; Brizard, J.P.; Bessin, Y.; Dorsselaer, A.V.; Declerck, N.; Sanglier-Cianférani, S.; et al. The RYMV-encoded viral suppressor of RNA silencing P1 is a zinc-binding protein with redox-dependent flexibility. J. Mol. Biol. 2013, 425, 2423–2435. [Google Scholar] [CrossRef] [PubMed]
- Poignavent, V.; Hoh, F.; Terral, G.; Yang, Y.; Gillet, F.X.; Kim, J.H.; Allemand, F.; Lacombe, E.; Brugidou, C.; Cianferani, S.; et al. A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread. J. Mol. Biol. 2022, 434, 167715. [Google Scholar] [CrossRef] [PubMed]
- Tsirigos, K.D.; Peters, C.; Shu, N.; Käll, L.; Elofsson, A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 2015, 43, W401–W407. [Google Scholar] [CrossRef]
- Bejerman, N.; Debat, H. Exploring the tymovirales landscape through metatranscriptomics data. Arch. Virol. 2022, 167, 1785–1803. [Google Scholar] [CrossRef] [PubMed]
- Fukuhara, T. Endornaviruses: Persistent dsRNA viruses with symbiotic properties in diverse eukaryotes. Virus Genes 2019, 55, 165–173. [Google Scholar] [CrossRef] [PubMed]
- Kwon, S.J.; Bodaghi, S.; Dang, T.; Gadhave, K.R.; Ho, T.; Osman, F.; Al Rwahnih, M.; Tzanetakis, I.E.; Simon, A.E.; Vidalakis, G. Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV). Front. Microbiol. 2021, 12, 683130. [Google Scholar] [CrossRef]
- Liu, J.; Carino, E.; Bera, S.; Gao, F.; May, J.P.; Simon, A.E. Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs. Viruses 2021, 13, 646. [Google Scholar] [CrossRef]
Plant Order/Family | Virus Host Plant | Accession Number |
---|---|---|
Asparagales; Orchidaceae | Dactylorhiza hatagirea | BK013327 |
Gymnadenia rhellicani | GHXH01324014 | |
Gymnadenia rhellicani | GHXH01128483 | |
Platanthera guangdongensis | SRX14997078 | |
Ophrys sphegodes | GHXJ01414654 | |
Ophrys fusca | GHXI01129489 | |
Liliales; Melanthiaceae | Daiswa yunnanensis | GFOY01013898 |
Ericales; Theaceae | Camellia reticulate | GEER01003429 |
Ericales; Ericaceae | Sarcodes sanguinea | SERM-2010905 * |
Asterales; Asteraceae | Leontopodium alpinum | DOVJ-2063723 * |
Leontopodium alpinum | DOVJ-2063722 * | |
Lamiales; Lamiaceae | Scutellaria montana | ATYL-2017654 * |
Lamiales; Orobanchaceae | Cistanche tubulosa | GJRS01079843 |
Melampyrum roseum | IADV01103213 | |
Striga hermonthica | ICPL01009187 | |
Apiales; Apiaceae | Daucus carota | OM419188; SRX13122999 |
Coriandrum sativum | GGPN01001998 | |
Caryophyllales; Chenopodiaceae | Atriplex prostrata | AAXJ-2011446 * |
Silene dioica | GFCG01071918 | |
Santalales; Viscaceae | Arceuthobium sichuanense | BK059270 |
Viscum album | GJLG01028288 | |
Viscum album | GJLG01014603; SRX12291946 | |
Malpighiales; Podostemaceae | Rhyncholacis cf. penicillata | ICSC01000014 |
Rhyncholacis cf. penicillata | ICSC01056734 | |
Fabales; Fabaceae | Vicia faba | GISP01006645; SRX10153333 |
Astragalus canadensis | GGNK01006218 | |
Trifolium pretense | MG596242 |
VLRA, Accession Number | Percentage of Identity/Gaps | Domain Position *, E-Value |
---|---|---|
Dactylorhiza hatagirea virus, BK013327 | 32/5 | 342, 3e−41 |
Gymnadenia rhellicani, GHXH01324014 | 31/7 | 331, 1e−33 |
Ophrys sphegodes, GHXJ01414654 | 30/5 | 341, 3e−33 |
Ophrys fusca, GHXI01129489 | 29/5 | 341, 1e−32 |
Camellia reticulate, GEER01003429 | 33/5 | 226, 6e−36 |
Coriandrum sativum, GGPN01001998 | 31/5 | 289, 5e−31 |
Rhyncholacis cf. penicillata Rhyc16, ICSC01000014 | 31/8 | 315, 8e−31 |
Rhyncholacis cf. penicillata Rhyc2783, ICSC01056734 | 32/5 | 372, 1e−30 |
Silene dioica, GFCG01071918 | 31/16 | 364, 1e−26 |
Red clover RNA virus 1, MG596242 | 31/5 | 311, 9e−34 |
Arceuthobium sichuanense virus 3, BK059270 | 30/10 | 231, 2e−29 |
Striga hermonthica, ICPL01009187 | 29/5 | 317, 9e−22 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Morozov, S.Y.; Lezzhov, A.A.; Solovyev, A.G. Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae. Int. J. Mol. Sci. 2023, 24, 12161. https://doi.org/10.3390/ijms241512161
Morozov SY, Lezzhov AA, Solovyev AG. Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae. International Journal of Molecular Sciences. 2023; 24(15):12161. https://doi.org/10.3390/ijms241512161
Chicago/Turabian StyleMorozov, Sergey Y., Alexander A. Lezzhov, and Andrey G. Solovyev. 2023. "Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae" International Journal of Molecular Sciences 24, no. 15: 12161. https://doi.org/10.3390/ijms241512161