Viroid

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Viroids are the smallest known infectious subcellular pathogens with a genome , 80 to 100 times smaller than the smallest viruses. They do not count as living beings ( organisms ) because they do not have their own metabolism and can only multiply within living cells. Viroids generally have the ability to control their replication and the ability to evolve .

All known viroids are inhabitants of higher plants and mostly cause diseases, the economic significance of which for humans is very different. Some of them are important plant pathogens in agriculture . The American Phytopathological Society has (in a compilation of the most important milestones of the past millennium in plant pathology published in 2000) recognized Theodor Otto Diener's discovery of viroids in 1971 as one of the ten most important pathogen discoveries of the millennium.

history

Theodor O. servant in front of a TEM image of the PSTVd (short rods), and for comparison, a double-stranded bacteriophage - DNA (long loop)

Efforts to isolate and characterize the causative agent of spindle tuber addiction in the potato plant led to the discovery of the first viroid . This disease was first observed in potatoes in the US states of New York and New Jersey in the early 1920s . The infectious nature of the disease was recognized in 1923 by Eugene S. Schultz and Donald Folsom , but the particular nature of the pathogen initially remained unknown and it was assigned to the plant viruses .

The plant pathologist Theodor O. Diener, who works at the Pioneering Laboratory for Plant Virology of the Agricultural Research Service in Beltsville, Maryland, succeeded in 1971 in isolating and characterizing the pathogen as an RNA that was unusually small, protein-free and independently replicating at the time of knowledge . Diener suggested the name Viroid - that is, virus-like - for this group of pathogens.

In the years that followed, servants and other groups elucidated many of the molecular properties of viroids. In 1971, Stollar and Diener were able to use immunological tests to show that viroids are not double-stranded but single-stranded RNA and that no viroid-specific RNA- DNA hybrids exist. Sogo et al. investigated viroid RNA using electron microscopy in 1973 and confirmed the single-stranded nature of RNA and the circular secondary structure of RNA.

Heinz L. Singer et al. were able to prove the structure of the viroids as covalently closed , single-stranded RNA rings with specific base pairings within the RNA strand in 1976 at the Institute of Virology at the Justus Liebig University in Giessen . Henco et al. detected helically wound sections within the RNA ring, with which the special energetic stability of the RNA could be explained. In 1978 Hans Joachim Gross et al. the first nucleotide sequence of a viroid - the PSTVd. Since then, viroids have been named with the usual three- or four-digit abbreviation to which a “d” is added - PSTVd ​​for Potato Spindle Tuber Viroid.

properties

Viroids only consist of a single-stranded ribonucleic acid (RNA) closed in a ring . In contrast to viruses , viroids have no additional proteins or lipids for packaging in the form of a shell or capsid . Viroids can only multiply within living cells ( obligatory intracellular parasites ), which is why they form the group of subcellular pathogens together with viruses, virusoids and prions . For viroids, together with viroid-like satellite RNA, the International Committee for Taxonomy of Viruses (ICTV) has defined a separate classification of subviral pathogens .

The RNA of the viroids is between 241 and 401 nucleotides long. Typically, no mRNA is transcribed from this genomic RNA during multiplication in the cell , and thus no viroid-specific proteins are produced. The viroid RNA has its own catalytic activity, among other things in the form of a ribozyme . The mechanism of RNA replication and interaction with cellular components is a model for studying the functionality of RNA in the cell. These mechanisms of the viroids are considered by many to be a molecular fossil from an early stage in chemical evolution .

Genome and structure

Structural comparison of PSTVd, HSVd and PLMVd

The RNA of the viroids contains many complementary areas, as a result of which double-stranded, linear structures are formed, which can be observed under the electron microscope as rod-shaped structures about 50 nm long.

The genome of the PSTVd ​​is divided into five areas: terminal left (TL), pathogenicity (P), central (C), variable (V) and terminal right (TR). Within the central region lies the conserved sequence of the central conserved region (CCR), in which there is a UV- sensitive E-loop motif with unusual base pairing. The highly conserved RNA sequence GAAAC, which occurs in all viroids, is located within the central conserved region .

Secondary structure of the potato-spindle-tuber-viroid with numerous base pairings (lines) and CCR region (yellow)

In density gradient centrifugation , the sedimentation coefficients for PSTVd ​​are 6.7 ± 0.1 S (359 nt length), for CEVd 6.7 ± 0.1 S (371 nt length), for CCCVd-1s 5.9 S ( 247 nt length), for CCCVd-1l at 6.3 ± 0.1 S (302 nt length), for CCCVd-2s at 7.6 ± 0.1 S (494 nt length) and for CCCVd-2l at 8, 2 S (604 nt length). Assuming an ellipsoidal shape of the viroids, the axial ratio (a / b) is 20. The partial specific volume v 2 of the viroids was determined to be 0.53 cm 3 / g.

Replication

Unlike viruses, viroids do not encode proteins . This is why they are exclusively dependent on enzymes from the host plant for their replication and transport . This fundamentally distinguishes viroids from satellite viruses , which rely on helper viruses to replicate .

The replication takes place via rolling circle replication by the cellular RNA polymerase II , which normally uses DNA as a template. The mutation rate in the replication of viroids is the highest among all nucleic acid - replicon . Due to the inaccuracy of replication, viroids occur as quasi-species within an organism . However, many mutations have an impact on infectivity and pathogenicity . The rolling circle replication creates a long strand of RNA from several serial copies of the genome (a multimer ), which is presumably only cut into the individual genomes by the cellular RNase ( DCL1 and DCL4 hydrolyze Pospiviroidae, DCL2 and DCL3 in all viroids) ( to the monomer ). The viroids from the Avsunviroidae group can also hydrolyze autocatalytically . The ring closure of the newly generated viroid RNA is presumably carried out by a cellular DNA ligase , which normally uses DNA as a template. In Avsunviroidae, ligation is autocatalytic.

The hepatitis D virus (HDV) has ribozyme activity similar to that of viroids.

Pathogenicity

The exact mechanism by which the viroid RNA has a pathogenic effect on plants is not yet known. Various models have been proposed (e.g. RNA silencing ). An overexpression of a non-infectious shRNA with a specific sequence of PSTVd leads to similar symptoms such as infection with PSTVd. In addition, a partial sequence of the PSTVd ​​is complementary to certain mRNA from plants. During an infection with viroids, short RNA fragments ( vd-sRNA ) are formed in the course of the plant's defense against the viroid by Dicer -like and AGO -proteins of the plant . These short fragments weaken the host plant's resistance .

transmission

Viroids are transmitted mechanically or through a smear infection , especially after injury, but also through pollen and seeds, the proportion of the transmission routes being unknown. If the plant is co-infected with PSTVd ​​and the potato leafroll virus ( PLRV , a polerovirus ) or the velvet tobacco mottle virus ( VTMoV , a sobemovirus ), the transmission of PSTVd ​​is increased, presumably by packaging the viroid in the virus capsid. In addition, it was suspected that it was transmitted by green aphids (Aphididae) or bumblebees . The spread within a plant occurs via plasmodesmata . The infection is lifelong ( persistent ).

Systematics

On the basis of sequence comparisons of already characterized viroid RNAs (currently 29 species and a large number of variants) and their different catalytic and structural properties, the viroids are divided into two virus families and eight genera. The prototypical representative of the Pospiviroids is the PSTVd ​​and that for the Avsunviroids is Avocado sunblotch viroid (ASBVd). While Pospiviroids replicate in the cell nucleus , Avsunviroids arise in the chloroplast .

In contrast to real viruses, the official names of the viroid taxa have “viroid” instead of just “vir” as part of the name ending, the abbreviations end in “Vd” instead of “V”, possibly followed by a number (not Roman , but Arabic). As of ICTV November 2018, the following ranks are in use:

Family ( ... viroidae )
Genus or genus ( ... viroid )
Species or species ( ... viroid )

The taxonomy is in detail as follows:

  • ASBVd ( Avocado sunblotch viroid )
  • ELVd ( Eggplant latent viroid )
  • CChMVd ( Chrysanthemum chlorotic mottle viroid )
  • PLMVd ( Peach latent mosaic viroid )
  • ADFVd ( Apple dimple fruit viroid )
  • ASSVd ( Apple scar skin viroid )
  • AGVd ( Australian grapevine viroid )
  • CBLVd ( Citrus bent leaf viroid )
  • CDVd ( Ccitrus dwarfing viroid ), formerly CVd-III ( Citrus viroid III )
  • CVd-V ( Citrus viroid V )
  • CVd-VI ( Citrus viroid VI )
  • GYSVd 1 ( Ggrapevine yellow speckle viroid 1 )
  • GYSVd 2 ( Grapevine yellow speckle viroid 2 )
  • PBCVd ( Pear blister canker viroid )
  • CBCVd ( Citrus bark cracking viroid ), formerly CVd-IV ( Citrus viroid IV )
  • CCCVd ( Coconut cadang-cadang viroid )
  • CTiVd ( Coconut tinangaja viroid )
  • HLVd ( VHop latent viroid )
  • CbVd 1 ( Coleus blumei viroid 1 )
  • CbVd 2 ( Coleus blumei viroid 2 )
  • CbVd 3 ( Coleus blumei viroid 3 )
  • DLVd ( Dahlia latent viroid )
  • HSVd ( Hop stunt viroid )
  • CSVd ( Chrysanthemum stunt viroid )
  • CEVd ( Citrus exocortis viroid )
  • CLVd ( Columnea latent viroid )
  • IrVd ( Iresine viroid 1 )
  • PCFVd ( Pepper chat fruit viroid )
  • PSTVd ( Potato spindle tuber viroid )
  • TASVd ( Tomato apical stunt viroid )
  • TCDVd ( Tomato chlorotic dwarf viroid )
  • TPMVd ( Tomato planta macho viroid ), synonymous with previously differentiated MPVd ( Mexican papita viroid )

Biological importance

Viroids occur only as pathogens in vascular plants ( plant pathogens ). Viroids cause over 30 diseases of vascular plants. The infections affect many different cultivated plants , and depending on the environmental conditions and host- pathogen ratio , the resulting disease may either not break out or break out only mildly, or it may lead to severe damage and death of the plants. The economic damage caused by viroids mainly affects potato plants, tomatoes, citrus fruits, grapes, hops and ornamental plants. Viroids have not yet been discovered in animals. A typical example is the potato spindle tuber viroid Potato Spindle Tuber Viroid (abbr. PSTVd), which affects potatoes, tomatoes and many other plant species and causes great economic damage.

Diagnostics and therapy

Individual viroids are identified via a Northern blot with a hybridization probe and increasingly also via RT-PCR and qRT-PCR . Therapy consists of the exclusion or eradication of the infected plants.

Environmental stability

The tenacity of the viroids depends on the strain. PSTVd ​​is inactivated by repeated freezing and thawing . Viroids are generally sensitive to bleaching agents , chaotropes in higher concentrations and denaturation by heating, whereby the structure of the viroids is stabilized by divalent magnesium ions and the denaturation temperature increases by up to 30 ° C depending on the concentration.

literature

  • David M. Knipe, Peter M. Howley (eds.-in-chief): Fields' Virology . 5th edition, Philadelphia 2007, ISBN 0-7817-6060-7 .
  • B. Ding, A. Itaya: Viroid: a useful model for studying the basic principles of infection and RNA biology . Mol Plant Microbe Interact. (2007) 20 (1): pp. 7-20 (Review), PMID 17249418 .
  • EM Tsagris, AE Martínez de Alba, M. Gozmanova, K. Kalantidis: Viroids . Cell Microbiol. (2008) 10 (11): pp. 2168-2179 (review), PMID 18764915 .
  • F. Di Serio, R. Flores, JT Verhoeven, SF Li, V. Pallás, JW Randles, T. Sano, G. Vidalakis, RA Owens: Current status of viroid taxonomy. In: Archives of virology. Volume 159, Number 12, December 2014, pp. 3467-3478, doi : 10.1007 / s00705-014-2200-6 , PMID 25216773 .

Web links

Individual evidence

  1. ↑ The prions , also subcellular pathogens, are even smaller, but do not have their own genetic material.
  2. ↑ a b c d e f g h R. Flores, RA Owens: Viroids . In: Brian WJ Mahy and Marc H. van Regenmortel (eds.): Encyclopedia of Virology , 3rd Edition, San Diego 2008, Volume 5, pp. 332-342, ISBN 978-0-12-373935-3 .
  3. ↑ Karin Mölling: Superpower of Life. Travel to the amazing world of viruses. 1st edition, Beck, Munich 2015, ISBN 978-3-406-66969-9 .
  4. ↑ From Y1K to 2K: Millennial Milestones in Plant Pathology, American Phytopathological Society Publications, APSnet Features, (written by Thor Kommedahl, University of Minnesota), 2000, 7pp. On-line. DOI: 10.1094 / APSFeature-2000-0100.
  5. ^ RA Owens, J. Th. J. Verhoeven: Potato Spindle Tuber. In: Plant Health Instructor. 2009, doi : 10.1094 / PHI-I-2009-0804-01 .
  6. ↑ ES Schultz, D. Folsom: A "spindling-tuber disease" of Irish potatoes. Science (1923) 2; 57 (1466): p. 149, PMID 17831586 .
  7. ↑ a b T. O. Diener: Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA. In: Virology. Volume 45, Number 2, August 1971, pp. 411-428, PMID 5095900 .
  8. ↑ BD Stollar, TO Diener: Potato spindle tuber viroid. V. Failure of immunological tests to disclose double-stranded RNA or RNA-DNA hybrids. In: Virology. Volume 46, Number 1, October 1971, pp. 168-170, PMID 5166353 .
  9. ↑ TO Diener: Potato spindle tuber viroid. 8. Correlation of infectivity with a UV-absorbing component and thermal denaturation properties of the RNA. In: Virology. Volume 50, Number 2, November 1972, pp. 606-609, PMID 4636118 .
  10. ↑ JM Sogo, T. Koller, TO Diener: Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy. In: Virology. Volume 55, Number 1, September 1973, pp. 70-80, PMID 4728831 .
  11. ^ HL Singer, G. Klotz, D. Riesner, HJ Gross, AK Kleinschmidt: Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. In: Proceedings of the National Academy of Sciences . Volume 73, Number 11, November 1976, pp. 3852-3856, PMID 1069269 , PMC 431239 (free full text).
  12. ↑ K. Henco, D. Riesner, HL Singer: Conformation of viroids . Nucleic Acids Res . (1977) 4 (1): pp. 177-194, PMID 866174 , PMC 342418 (free full text).
  13. ↑ a b H. J. Gross, H. Domdey, C. Lossow, P. Jank, M. Raba, H. Alberty, HL Singer: Nucleotide sequence and secondary structure of potato spindle tuber viroid. In: Nature. Volume 273, Number 5659, May 1978, pp. 203-208, PMID 643081 .
  14. ↑ AMQ King, MJ Adams, EB Carstens, EJ Lefkovitz, et al .: Virus Taxonomy . Elsevier Academic Press, 2012. pp. 1221-1259, TN: 949565
  15. ↑ TO Diener: Viroids: "living fossils" of primordial RNAs? In: Biology direct. Volume 11, number 1, March 2016, p. 15, doi : 10.1186 / s13062-016-0116-7 , PMID 27016066 , PMC 4807594 (free full text).
  16. ^ B. Ding, A. Itaya: Viroid: a useful model for studying the basic principles of infection and RNA biology . Mol Plant Microbe Interact. (2007) 20 (1): pp. 7-20 (review), PMID 17249418 (full text) .
  17. ↑ a b c d e f A. Hadidi, R. Flores, JW Randles, JS Semancik: Viroids. Csiro Publishing, 2003, ISBN 978-0-643-06789-9 , pp. 18, 38.
  18. ↑ EM Tsagris, AE Martínez de Alba, M. Gozmanova, K. Kalantidis: Viroids. In: Cellular microbiology. Volume 10, Number 11, November 2008, pp. 2168-2179, doi : 10.1111 / j.1462-5822.2008.01231.x , PMID 18764915 .
  19. ↑ Ricardo Flores, Francesco DiSerio, Carmen Hernández: viroid: The noncoding genome . In: Seminars in Virology . 8, No. 1, February 1997, pp. 65-73. doi : 10.1006 / smvy.1997.0107SA .
  20. ↑ R. Flores, P. Serra, S. Minoia, F. Di Serio, B. Navarro: Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs. In: Frontiers in microbiology. Volume 3, 2012, p. 217, doi : 10.3389 / fmicb.2012.00217 , PMID 22719735 , PMC 3376415 (free full text).
  21. ↑ JA Daros, SF Elena, R. Flores: Viroids: an Ariadne's thread into the RNA labyrinth. In: EMBO reports. Volume 7, Number 6, June 2006, pp. 593-598, doi : 10.1038 / sj.embor.7400706 , PMID 16741503 , PMC 1479586 (free full text).
  22. ↑ B. Ding: Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. In: Wiley interdisciplinary reviews. RNA. Volume 1, Number 3, 2010 Nov-Dec, pp. 362-375, doi : 10.1002 / wrna.22 , PMID 21956936 .
  23. ↑ RW Hammond: Analysis of the virulence modulating region of potato spindle tuber viroid (PSTVd) by site-directed mutagenesis. In: Virology. Volume 187, Number 2, April 1992, pp. 654-662, PMID 1546460 .
  24. ↑ MV Nayudu: Plant Viruses. Tata McGraw-Hill Education, 2008, ISBN 978-0-070-65660-4 , p. 454.
  25. ↑ a b Nicholas H. Acheson. Fundamentals of Molecular Virology. 2nd Edition. John Wiley & Sons, 2011, ISBN 978-0-470-90059-8 , pp. 379-383.
  26. ↑ R. Flores, S. Minoia, A. Carbonell, A. Gisel, S. Delgado, A. López-Carrasco, B. Navarro, F. Di Serio: Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. In: Virus research. Volume 209, November 2015, pp. 136-145, doi : 10.1016 / j.virusres.2015.02.027 , PMID 25738582 .
  27. ↑ C. Alves, C. Branco, C. Cunha: Hepatitis delta virus: a peculiar virus. In: Advances in virology. Volume 2013, 2013, p. 560105, doi : 10.1155 / 2013/560105 , PMID 24198831 , PMC 3807834 (free full text).
  28. ↑ MB Wang, XY Bian, LM Wu, LX Liu, NA Smith, D. Isenegger, RM Wu, C. Masuta, VB Vance, JM Watson, A. Rezaian, ES Dennis, PM Waterhouse: On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. In: Proceedings of the National Academy of Sciences . Volume 101, number 9, March 2004, pp. 3275-3280, doi : 10.1073 / pnas.0400104101 , PMID 14978267 , PMC 365780 (free full text).
  29. ^ V. Pallas, G. Martinez, G. Gomez: The interaction between plant viroid-induced symptoms and RNA silencing. In: Methods in molecular biology. Volume 894, 2012, pp. 323-343, doi : 10.1007 / 978-1-61779-882-5_22 , PMID 22678590 .
  30. ^ WA Miller, R. Shen, W. Staplin, P. Kanodia: Noncoding RNAs of Plant Viruses and Viroids: Sponges of Host Translation and RNA Interference Machinery. In: Molecular plant-microbe interactions: MPMI. Volume 29, number 3, March 2016, pp. 156-164, doi : 10.1094 / MPMI-10-15-0226-FI , PMID 26900786 , PMC 5410770 (free full text).
  31. ↑ JA Bokx, PGM Piron: Transmission of potato spindle tuber viroid by aphids. In: Netherlands Journal of Plant Pathology. 87, 1981, p. 31, doi : 10.1007 / bf01976653 .
  32. ^ PD Sharma: Microbiology & Plant Pathology. Rastogi Publications, 2010, ISBN 978-8-171-33740-8 , p. 202.
  33. ↑ SIB: Circular Single Strand RNA Viruses: Viroids , on: ViralZone
  34. ↑ SIB: Avsunviroidae , on: ViralZone
  35. ↑ SIB: Pospiviroidae , on: ViralZone
  36. ^ Taxonomic Proposal to the ICTV Executive Committee To rename an existing Virus Name
  37. ↑ Jeffrey C. Pommerville: Fundamentals of Microbiology . Jones and Bartlett Learning, Burlington, MA 2014, ISBN 978-1-284-03968-9 , p. 482.
  38. ^ A b c R. W. Hammond, RA Owens: Viroids: New and Continuing Risks for Horticultural and Agricultural Crops. . In: APSnet Feature Articles . 2006. doi : 10.1094 / APSnetFeature-2006-1106 .