Tombusviridae

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Tombusviridae
2tbv capsid ray.png

The capsid of Tomato bushy-stunt virus
with three distinguishable by their orientation
coat protein - monomer (p41),
orange, green and blue colored.

Systematics
Classification : Viruses
Area : Riboviria
Empire : Orthornavirae
Phylum : Kitrinoviricota
Class : Tolucaviricetes
Order : Tolivirales
Family : Tombusviridae
Taxonomic characteristics
Genome : (+) ss RNA
Baltimore : Group 4
Symmetry : icosahedral
Cover : no
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 (+)

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

  1. ^ 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 .
  2. a b ICTV Master Species List 2018b v2 MSL # 34v, March 2019
  3. a b c d ICTV: ICTV Taxonomy history: Carrot mottle mimic virus , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
  4. a b c d e f Viral Zone . ExPASy. Retrieved August 28, 2019.
  5. ^ ICTV: Virus Taxonomy . Retrieved August 28, 2019.
  6. 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
  7. 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
  8. a b c ICTVdB — The Universal Virus Database, version 3 00.074. Tombusviridae
  9. ^ Wiley InterScience Encyclopedia of Life Sciences: Tombusviridae
  10. 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).
  11. 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).
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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.
  17. ^ 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
  18. 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).
  19. ICTV: ICTV Master Species List 2019.v1 , New MSL including all taxa updates since the 2018b release, March 2020 (MSL # 35)
  20. 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 .
  21. 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 .
  22. 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)

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