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Carmoviruses (Tombusviridae) Feng Qu University of Nebraska-Lincoln, Qu.28@Osu.Edu University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 1999 Carmoviruses (Tombusviridae) Feng Qu University of Nebraska-Lincoln, [email protected] Thomas Jack Morris University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub Part of the Immunology and Infectious Disease Commons, Molecular Biology Commons, and the Virology Commons Qu, Feng and Morris, Thomas Jack, "Carmoviruses (Tombusviridae)" (1999). Faculty Publications in the Biological Sciences. 414. https://digitalcommons.unl.edu/bioscifacpub/414 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Encyclopedia of Virology, 2nd edition, ed. R.G. Webster & A. Granoff, Academic Press, 1999. Copyright © 1999 Academic Press. Used by permission digitalcommons.unl.edudigitalcommons.unl.edu Carmoviruses (Tombusviridae) Feng Qu and T. Jack Morris School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USA Taxonomy, Classification and Evolutionary necrotic mosaic virus, RCNMV) are significant and include Relationships sequence similarity of CP as well as similarity in subunit to- pology and interactions within the virion. There also exists Carmovirus is one of two officially recognized genera of a marked sequence similarity in the RNA-dependent RNA Tombusviridae. Members of Tombusviridae all have icosahe- polymerase (RDRP) genes of carmoviruses and viruses of the dral virions of about 30 nm in diameter with T = 3 symmetry following genera: Dianthovirus, Necrovirus (e.g. tobacco ne- that consists of 180 coat protein (CP) subunits of about 38- crosis virus, TNV), Machlomovirus (e.g. maize chlorotic mot- 43 kDa and a single-stranded (ss) RNA genome ranging in tle virus, MCMV) and Luteovirus (e.g. barley yellow dwarf size from 4.0 to 4.7 kb. Carmoviruses share recognizable se- viruses of the PAV type). Several newly sequenced viruses quence similarity in both the polymerase and structural genes have been proposed for consideration as new genera of Tom- with members of the other genus, Tombusvirus. Sequence busviridae, based primarily on similarities of nucleotide se- comparisons and phylogenetic analysis of these genes sup- quences and genome organization (e.g. pathos latent virus, oat port the view that the genera are distinct but closely related. chlorotic stunt virus and panicum mosaic virus). In a broader In addition, the genome organization of the carmoviruses is context, phylogenetic comparisons of viral RNA polymerase characteristically different from that of the tombusviruses. genes have identified the Tombusviridae as a representative Carmoviruses contain a single-component positive-sense plant virus cluster for one of three RNA virus supergroups genome of about 4.0 kb. The genome, as exemplified by tur- with relatedness to animal viruses of Flaviviridae and the fam- nip crinkle virus (TCV) in Figure 1, consists of five open ily of small RNA phage (Leviviridae). reading frames (ORFs) which encode proteins of about 28, 88, 8, 9 and 38 kDa from the 5’ to the 3’ end, respectively. Distribution, Host Range, Transmission and The virions are icosahedral and consist of 180 CP subunits of Economic Significance approximately 38 kDa. The genus name is derived from the first member of the genus to be sequenced, carnation mot- Carmoviruses occur worldwide and are generally reported to tle virus (CarMV). Much more detailed knowledge about vi- cause mild asymptomatic infections on relatively restricted rus structure and genome function is, however, known for natural host ranges. Most accumulate to high concentrations TCV because its crystal structure has been determined and in infected tissues and are mechanically transmitted with fa- it was the first carmovirus for which infectious transcripts cility. Beetle transmission has been reported for a number of were produced from a cDNA clone of the genome. To date, members, as has transmission in association with soil and/or the nucleotide sequences of six definitive carmoviruses have irrigation water, and in some cases in association with fungal been determined (Table 1). These sequenced members share zoospores. Most of the viruses have been reported to cause similar morphological and physicochemical properties with diseases in a limited number of plants or plant types. about 20 other viruses listed in Table 1 that are recognized A number of carmoviruses have been identified in asso- as species or tentative species, depending on the character- ciation with ornamental hosts and have been widely distrib- ized molecular detail of the viruses. Unlike the majority of uted in such hosts by vegetative propagation. CarMY is the tombusviruses, carmoviruses are sufficiently distant from most noteworthy, being widespread in cultivated carnations, each other to prevent them cross reacting in standard RNA and recognized as one of the more important components of hybridization or serological tests. viral disease complexes in this crop worldwide. It accumu- Carmoviruses and tombusviruses share properties with nu- lates to high concentrations without producing severe symp- merous other small spherical RNA viruses. Structural similar- toms and spreads primarily by contact transmission and veg- ities with members of the Dianthovirus genus (e.g. red clover etative propagation. It has a broad experimental host range 243 244 Qu & Morris in Encyclopedia of Virology, 1999 Figure 1. Genome organization of a typical carmovirus as represented by turnip crinkle virus. The genomic and subgenomic RNAs are depicted as solid lines and the sizes of the RNAs are noted. The ORFs are indicated by the boxes, with the numbers in the boxes identifying the polypeptide encoded by the ORF. The numbers above and below the diagrams give the transcriptional start sites for the sgRNAs and the nucleotide locations of the codons defining each ORF. that includes over 30 species in 15 plant families. PFBV is concentrations, often approaching a level equivalent to 0.5% widespread in vegetatively propagated Pelargonium species, of the fresh weight of the plant tissue. CCFV was first dis- causing disease in association with other viruses. The inci- covered in the Mount Kosiusko alpine region of Australia dence of NTNV in Narcissus cultivars and HCRSV in Hibis- in Cardamine lilacina, a wild perennial Brassica. It has also cus primarily reflects distribution of infected nursery stock. been shown to infect Arabidopsis and other Brassica species. Numerous small RNA viruses have been reported to nat- urally infect cucurbits, causing significant disease problems. Table 1. List of species in the genus Carmovirus Several of these viruses are recognized tombusviruses, while Sequenced species others—such as MNSV, CLSV, and CSBV—have been iden- Carnation mottle (CarMV) tified as carmoviruses based on sequence and genome or- Cardamine chlorotic fleck (CCFV) ganization properties. MNSV occurs worldwide in green- Cowpea mottle (CPMoV) Melon necrotic spot (MNSV) house cucurbits and is both soil and seed transmitted, while Saguaro cactus (SCV) CSBV has been primarily restricted to infrequent outbreaks Turnip crinkle (TCV) around the Mediterranean. All three viruses have been re- Classified species ported to be transmitted in association with the fungus Ol- Ahlum water-borne (AWBV) pidium bornovanus. Bean mild mosaic (BMMV) Several carmoviruses have been discovered in natural le- Cucumber leaf spot (CLSV) guminous hosts, with GMoV being potentially the most im- Cucumber soil-borne (CSBV) portant, causing serious disease losses in legumes in Africa. Galinsoga mosaic (GaMV) BMMV has been reported to be a latent virus widely distrib- Hibiscus chlorotic ringspot (HCRSV) uted in bean cultivars in El Salvador, and BMoV has been Pelargonium flower break (PFBV) found in Vigna species in Asia. Beetle vectors have been Weddel water-borne (WWBV) identified for these viruses, but seed transmission may also Tentative species be an important factor in their distribution. Blackgram mottle (BMoV) TCV is neither common nor widespread in nature in spite Elderberry latent (ELV) of the fact that it is reportedly beetle transmitted. It has a Glycine mottle (GMoV) Narcissus tip necrosis (NTNV) relatively wide experimental host range in some 20 plant Plaintain 6 (PIV-6) families, including experimentally useful Arabidopsis and Squash necrosis (SqNV) Brassica species, in which it accumulates to extremely high Tephrosia symptomless (TeSV) Carmoviruses (Tombusviridae) 245 Other carmoviruses have been isolated worldwide from bly” for this virus identified two possible sites based on natural hosts with little apparent disease and are presum- the identification of RNA fragments in the rp-complex pro- ably of little agricultural concern. These include TeSV from tected from RNase digestion by CP. Further in vivo studies legumes in Kenya, GMoV from glycine in Australia, SCV narrowed the assembly origin site to a bulged hairpin loop from saguaro cactus in Arizona, GaMV from potato weed in of 28 nt within a 180 nt region at the 3’ end of the CP gene. Australia and PIV-6 from plantain weed in England. The in- frequent isolation of these genetically similar viruses in
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