Tombusviridae
Tombusviridae | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
The capsid of Tomato bushy-stunt virus |
||||||||||||||
Systematics | ||||||||||||||
|
||||||||||||||
Taxonomic characteristics | ||||||||||||||
|
||||||||||||||
Scientific name | ||||||||||||||
Tombusviridae | ||||||||||||||
Left | ||||||||||||||
|
The Tombusviridae are single-family RNA - plant viruses with positive polarity . There are currently (as of August 2019) about 70 species or more in this family, divided into over ten genera.The members can attack either monocotyledon or dicotyledonous plants ( monocotyledons or dicotyledons ), but neither species can attack both. The name is derived from the type species Tomato bushy stunt virus (TBSV) of the associated genus Tombusvirus .
construction
The RNA is enclosed in an icosahedral capsid with T = 3 symmetry . The capsid consists of 180 units of a protein ( English single coat protein ). The virion (virus particle) has a diameter of 28-35 nm and is not enveloped.
Genome
The genome of the Tombusviridae is linear and unsegmented (monopartite) in almost all representatives, only in the case of the genus Dianthovirus is known that the genome consists of two segments (bipartite segmented). The genome is approximately 4.6-4.8 kb long, has neither a 5 'cap nor a 3' polyadenine tail . It encodes 4-6 open reading frames (ORFs). The polymerase encodes an amber stop codon so that it can be read through. This enables a second product required for replication to be created. There is no helicase encoded by the virus genome .
Propagation cycle
The members of the Tombusviridae replicate in the cytoplasm , the release to the outside takes place through lysis . The replication follows the usual replication model of positive-strand RNA viruses.
After the virions were released from their capsid ( English uncoating ), the release of the viral RNA is carried in the cytoplasm . Occasionally, however, the virions are also present in the mitochondria and cell nuclei . The viral RNA is translated (on the ribosomes ) in order to first generate two proteins that are required for the synthesis of the viral RNA (replication and transcription ). The translation is carried out by leaky scanning .
The replication then takes place in the cytoplasm in membranous vesicles , the virus factories ( English viral factories ). These can be associated with the endoplasmic reticulum , or they can be found in modified organelles such as peroxisomes , mitochondria and (less often) chloroplasts .
First, a double-stranded RNA genome is generated from the (+) - single-stranded RNA genome of the virus (dsRNA genome). This dsRNA genome is then transcribed or replicated, i. H. viral messenger RNAs ( mRNAs ) and ssRNA (+) genomes are produced. The RNA-dependent RNA polymerase (RdRp) recognizes internal subgenomic promoters on the RNA of negative polarity (ssRNA (-)) to transcribe the capsid proteins and movement proteins .
The viral RNA apparently not only serves as a template for replication, but is also able to manipulate and regulate RNA synthesis. It was possible to show that the strength of the RNA synthesis is influenced by the cis elements or cis-like elements on the RNA, as in the Red clover necrotic mosaic virus (RCNMV). These include nuclear promoter sequences that determine the location where synthesis of the complementary strand of RNA begins. It is believed that this mechanism is recognized by RNA-dependent RNA polymerase (RdRp), which is encoded in the genome.
The replication process ultimately leaves an excess of RNA strands of positive polarity . It was found that Tombusviridae GAPDH , a metabolic enzyme host, for use in replication center co-opt (with added use). GAPDH can bind to the RNA (-) strand and thus keep it in the replicase complex, so that ssRNA (+) strands synthesized from it can be exported and accumulated (enriched) in the host cell. The down-regulation of GAPDH decreased the accumulation of viral RNA and eliminated the excess of ssRNA (+) copies.
The virions are assembled in the cytoplasm. A movement protein allows under certain circumstances a transfer of virions between adjacent cells of the host plant without the release of virions by lysis.
The natural hosts of the Tombusviridae are plants. The routes of transmission are mechanical, seed and contact (garden tools). The viruses in this family are usually soil-borne; however, some use mushroom species of the order Chytridiales as vectors . The viruses can spread through the water as well as through root growth in infected soil and contact between plants, sometimes via pollen or seeds, depending on the virus species. From a horticultural perspective, the viruses could also be successfully transmitted by grafting and mechanical inoculation (inoculation). As expected, neither the virion alone (without genome) nor the genetic material alone is infectious.
Systematics
Internal system
According to the International Committee on Taxonomy of Viruses (ICTV) as of March 2019, the systematics of the family Tombusviridae is as follows (not all species are listed):
Area: Riboviria , Group: ssRNA (+)
- Family Tombusviridae
- Subfamily Calvusvirinae
- Genus Umbravirus
- Species Carrot mottle mimic virus (CMoMV)
- Species Carrot mottle virus (CMoV, type species)
- Species Groundnut rosette virus ( Peanut rosette virus , GRV)
- Species Lettuce speckles mottle virus (LSMV)
- Species Pea enation mosaic virus 2
- Species Tobacco bushy top virus (TBTV)
- Species Tobacco mottle virus (TMoV)
- Genus Umbravirus
- Subfamily Procedovirinae
- Genus Alphacarmovirus
- Species Angelonia flower break virus
- Species Calibrachoa mottle virus (CMoV)
- Species Carnation mottle virus (CarMV, type species)
- Species Honeysuckle ringspot virus
- Species Nootka lupine vein clearing virus (NLVCV)
- Species Pelargonium flower break virus (PFBV)
- Species Saguaro cactus virus
- Genus Alphanecrovirus
- Species olive latent virus 1 ( olive latent virus , OLV-1)
- Species Olive mild mosaic virus
- Species Tobacco necrosis virus A ( tobacco necrosis virus A , TNV-A, type species)
- Genus aureus virus
- Species Cucumber leaf spot virus
- Species Johnsongrass chlorotic stripe mosaic virus
- Species Maize white line mosaic virus (MWLMV)
- Species Pothos latent virus (PoLV, type species)
- Genus Betacarmovirus
- Species Turnip crinkle virus (TCV, type species)
- Species Cardamine chlorotic fleck virus
- Species Hibiscus chlorotic ringspot virus
- Species Japanese iris necrotic ring virus
- Species Turnip crinkle virus
- Genus Betanecrovirus
- Species Beet black scorch virus (BBSV)
- Species Leek white stripe virus (LWSV)
- Species Tobacco necrosis virus D ( tobacco necrosis virus D , TBNV-D)
- Species Turnip crinkle virus (type species)
- Genus Gallantivirus
- Species Galinsoga mosaic virus (GaMV, type species)
- Genus Gammacarmovirus
- Species Cowpea mottle virus
- Species Melon necrotic spot virus (MNSV, type species)
- Species Pea stem necrosis virus
- Species Soybean yellow mottle mosaic virus (SYMMV)
- Genus Macanavirus
- Species Furcraea necrotic streak virus (FNSV, type species)
- Genus Machlomovirus
- Species Maize chlorotic mottle virus (MCMV, type species)
- Genus Panicovirus
- Species Panicum mosaic virus ( millet mosaic virus , PMV, type species)
- Species Cocksfoot mild mosaic virus
- Species Thin paspalum asymptomatic virus
- Genus Pelarspovirus
- Species Elderberry latent virus (ElLDV)
- Species Pelargonium chlorotic ring pattern virus (PCRPV)
- Species Pelargonium line pattern virus (PLPV, type species)
- Species Pelargonium ringspot virus (PelRSV)
- Species Rosa rugosa leaf distortion virus (RrLDV)
- Genus Tombus Virus
- Species Artichoke mottled crinkle virus
- Species Carnation Italian ringspot virus
- Species Cucumber Bulgarian latent virus
- Species Cucumber necrosis virus ( Cucumber necrosis virus , CNV)
- Species Cymbidium ringspot virus
- Species Eggplant mottled crinkle virus
- Species Grapevine Algerian latent virus
- Species Havel River virus
- Species Lato River virus
- Species Limonium flower distortion virus
- Species Moroccan pepper virus
- Species Neckar River virus
- Species Pelargonium leaf curl virus
- Species Pelargonium necrotic spot virus
- Species Petunia asteroid mosaic virus (PetAMV)
- Species Sitke waterborne virus
- Species Tomato bushy stunt virus ( Tomato bushy stunt virus , tomato dwarf bush virus , TBSV, type species)
- Genus Zeavirus
- Species Maize necrotic streak virus (MNeSV)
- with no assigned genus
- Species Ahlum waterborne virus
- Species Bean mild mosaic virus
- Species Chenopodium necrosis virus ( Chenopodium necrosis virus , CPNV)
- Species Cucumber soil-borne virus
- Species trailing lespedeza virus 1 (TLV1)
- Species Weddel waterborne virus
- Genus Alphacarmovirus
- Subfamily Regressovirinae
- Genus Dianthovirus
- Species Carnation ringspot virus (CRSV, type species)
- Species Red clover necrotic mosaic virus (RCNMV)
- Species Sweet clover necrotic mosaic virus
- Genus Dianthovirus
- with no assigned subfamily
- Genus Avenavirus
- Species Oat chlorotic stunt virus (OCSV, type species)
- Genus Avenavirus
- proposed, but still operated by ICTV to date:
- Species " Carnation yellow stripe virus " (" Carnation yellow stripe virus ", CYSV)
- Subfamily Calvusvirinae
External system
Koonin et al (2015) suspect that the Flaviviridae originate from the relatives they postulate, negative-strand RNA viruses ; this group corresponds to today's Phylum Negarnaviricota . Proposed sister group of the Flaviviridae would then be the family of Tombusviridae . According to this proposal, they all together form the supergroup “Flavivirus-like superfamily” postulated by the authors.
Shi et al (2016) similarly refer to the further relationship of the Flaviviridae as " Flavi-like viruses ".
These suggestions have since been superseded by the ICTV Master Species List # 35 of March 2020. A comparison of the cladograms can be found in Tymovirales §ICTV Master Species List # 35 .
Remarks
DI molecules ( English defective interfering RNA ) are prepared from the viral genome, but which cells are unable due to shortening and other defects, (such as a virus) infecting RNAs alone. Instead, like a satellite virus, they must be co-infected with an intact helper virus . Research has shown that tombus virus infection of plants contains DI RNAs that are derived directly from the viral RNA genome and not from a host genome. Viral DI RNAs with their small size and the cis-acting elements are good templates for the study of RNA replication both in vivo and in vitro.
In the synthesis of some proteins, subgenomic RNA ( English sub-genomic RNA , sgRNA) is used. It arises from the premature termination of the (-) strand synthesis. SgRNAs and sgRNA negative sense templates were found in infected cells.
Individual evidence
- ^ P. Hopper, SC Harrison, RT Sauer: Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. . In: Journal of Molecular Biology . 177, No. 4, August 25, 1984, pp. 701-713. doi : 10.1016 / 0022-2836 (84) 90045-7 . PMID 6481803 .
- ↑ a b ICTV Master Species List 2018b v2 MSL # 34v, March 2019
- ↑ a b c d ICTV: ICTV Taxonomy history: Carrot mottle mimic virus , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
- ↑ a b c d e f Viral Zone . ExPASy. Retrieved August 28, 2019.
- ^ ICTV: Virus Taxonomy . Retrieved August 28, 2019.
- ↑ a b c ICTV : Family - Tombusviridae , in: Virus Taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses 2012, pp 1111–1138, 23 November 2011, doi: 10.1016 / B978-0-12-384684-6.00096-3
- ↑ habili, N. and Symons, RH (1989). Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs in their putative RNA polymerases and nucleic acid helicases. Nucleic Acids Research 17 : 23, pp 9543-9555
- ↑ a b c ICTVdB — The Universal Virus Database, version 3 00.074. Tombusviridae
- ^ Wiley InterScience Encyclopedia of Life Sciences: Tombusviridae
- ↑ Lommel SA, Weston-Fina M, Xiong Z, Lomonossoff GP: The nucleotide sequence and gene organization of red clover necrotic mosaic virus RNA-2 . In: Nucleic Acids Res . 16, No. 17, September 1988, pp. 8587-602. doi : 10.1093 / nar / 16.17.8587 . PMID 3047682 . PMC 338578 (free full text).
- ↑ Mizumoto H, Tatsuta M, Kaido M, Mise K, Okuno T: Cap-independent translational enhancement by the 3 'untranslated region of red clover necrotic mosaic virus RNA1 . In: J. Virol. . 77, No. 22, November 2003, pp. 12113-12121. doi : 10.1128 / JVI.77.22.12113-12121.2003 . PMID 14581548 . PMC 254280 (free full text).
- ↑ a b Beth L. Nicholson, Pui Kei K. Lee, KA White: Internal RNA replication elements are prevalent in Tombusviridae , in: Front. Microbiol., August 6, 2012, doi: 10.3389 / fmicb.2012.00279
- ↑ K. Andrew White, Peter D. Nagy: Advances in the Molecular Biology of Tombusviruses: Gene Expression, Genome Replication, and Recombination , in: Progress in Nucleic Acid Research and Molecular Biology, Volume 78, 2004, pp. 187-226, doi: 10.1016 / S0079-6603 (04) 78005-8
- ↑ Wang, R. and Nagy, P. (2008) Tomato bushy stunt virus Co-Opts the RNA-Binding Function of a Host Metabolic Enzyme for Viral Genomic RNA Synthesis. Cell Host & Microbe 3 : 3, pp. 178-187
- ↑ a b Castaño A, Ruiz L, Hernández C (2009) Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus. Virology 386 (2), pp. 417-426
- ↑ Since this supergroup (called by the authors as English superfamily ) contains a phylum with the Nagarnaviricota , their rank must necessarily be higher and should not be understood as a superfamily . Ranks higher than order (such as Phylum) were not specified by the ICTV at the time of the 2015 work.
- ^ Eugene V. Koonin, Valerian V. Dolja, Mart Krupovic: Origins and evolution of viruses of eukaryotes: The ultimate modularity , in: Virology from May 2015; 479-480. 2-25, Epub March 12, 2015, PMC 5898234 (free full text), PMID 25771806
- ↑ Mang Shi, Xian-Dan Lin, Nikos Vasilakis, Jun-Hua Tian, Ci-Xiu Li, Liang-Jun Chen, Gillian Eastwood, Xiu-Nian Diao, Ming-Hui Chen, Xiao Chen, Xin-Cheng Qin, Steven G. Widen, Thomas G Wood, Robert B Tesh, Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang: Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses . In: Journal of Virology . 90, No. 2, 2016, pp. 659-69. doi : 10.1128 / JVI.02036-15 . PMID 26491167 . PMC 4702705 (free full text).
- ↑ ICTV: ICTV Master Species List 2019.v1 , New MSL including all taxa updates since the 2018b release, March 2020 (MSL # 35)
- ↑ Yoshimi Yamamura, Herman B. Scholthof: Tomato bushy stunt virus: a resilient model system to study virus-plant interactions . In: Molecular Plant Pathology . 6, No. 5, September 1, 2005, pp. 491-502. doi : 10.1111 / j.1364-3703.2005.00301.x . PMID 20565674 .
- ↑ Karen-Beth G. Scholthof, Herman B. Scholthof, Andrew O. Jackson: The Effect of Defective Interfering RNAs on the Accumulation of Tomato Bushy Stunt Virus Proteins and Implications for Disease Attenuation . In: Virology . 211, No. 1, August 1, 1995, pp. 324-328. doi : 10.1006 / viro.1995.1410 . PMID 7645230 .
- ↑ NCBI: Defective interfering RNA-4 of tomato bushy stunt virus (TBSV-P DI-4) and Defective interfering RNA-5 of tomato bushy stunt virus (TBSV-P DI-5)