Geminiviridae


Geminiviridae

Chapter Contents

Posted March 2017

Geminiviridae: The Family

Geminiviridae: Member Taxa

Geminiviridae: Supporting Information

  • Authors - Corresponding author: Murilo Zerbini (zerbini@ufv.br)
  • Resources - Sequence alignments, tree files, Study Group Wiki
  • References - Literature cited

Citation

A summary of this ICTV Online (10th) Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

Zerbini, F.M., Briddon, R.W., Idris, A., Martin, D.P., Moriones, E., Navas-Castillo, J., Rivera-Bustamante, R., Roumagnac, P., Varsani, A., and ICTV Report Consortium. 2017, ICTV Virus Taxonomy Profile: GeminiviridaeJournal of General Virology, 98:131133.

Summary

The geminiviruses are a family of small, non-enveloped viruses with genomes comprising one or two single-stranded, circular DNAs of 2.5-5.2 kb in length. Geminiviruses are transmitted by various insects in four families of homopterans (whiteflies, leafhoppers, aphids and treehoppers). Members in the genus Begomovirus are transmitted by whiteflies, those in the genera Mastrevirus, Curtovirus, Becurtovirus and Turncurtovirus are transmitted by leafhoppers, one member of the genus Capulavirus is transmitted by an aphid, and the single member of the genus Topocuvirus is transmitted by a treehopper. The vectors of the only known members of genera Eragrovirus and Grablovirus remain unknown. Geminiviruses are important plant pathogens causing economically important diseases in most tropical and subtropical regions of the world.

Table 1.Geminiviridae. Characteristics of the family Geminiviridae.

Characteristic

Description

Typical member

bean golden yellow mosaic virus-[Dominican Republic:1987] (DNA-A L01635; DNA-B L01636), species Bean golden yellow mosaic virus, genus Begomovirus

Virion 

Twinned (geminate) incomplete icosahedra, T=1, 22x38 nm with a single coat protein

Genome

2.5-5.2 kb of single-stranded, circular DNA, mono- or bipartite

Replication

Complementary strand synthesized in the nucleus by host replication factors; double-stranded circular molecules serve as templates for both transcription and replication; replication employs a rolling-circle mechanism and also a recombination-dependent mechanism

Translation

From transcribed mRNAs

Host range

Plants (monocots and dicots)

Taxonomy

Nine genera collectively containing >360 species

Viruses classified into the nine genera show distinct host ranges, insect vectors and genome organizations:

Becurtovirus. This genus contains two recognised species, Beet curly top Iran virus and Spinach curly top Arizona virus (Varsani et al., 2014). Both are comprised of monopartite viruses transmitted by leafhoppers to dicot plants. Members of this genus are unusual in that instead of the TAATATTAC nonanucleotide found at the origin of virion strand replication (v-ori) in almost all other geminiviruses, they have a TAAGATTCC nonanucleotide.

Begomovirus. This genus consists of >320 recognised species, members of which infect dicot plants and are transmitted by whiteflies of the Bemisia tabaci cryptic species complex (Brown et al., 2015). The genome can be either bipartite (two circular ssDNA molecules, each about 2.6 kb) or monopartite (a single approximately 2.7 kb circular ssDNA molecule) (Rojas et al., 2005). Most monopartite begomoviruses are associated with circular DNA satellites of two types, alphasatellites and betasatellites (Zhou 2013). Begomoviruses usually induce severe symptoms in their hosts, including yellow mosaic, golden mosaic and leaf curl. Devastating pathogens include members of the species African cassava mosaic virus, Bean golden mosaic virus, Cotton leaf curl Kokhran virus and Tomato yellow leaf curl virus.

Capulavirus. This genus contains four species of viruses with monopartite genomes (Varsani et al., 2017), and members of one of them, Alfalfa leaf curl virus, are transmitted by an aphid (Roumagnac et al., 2015). A unique feature of capulavirus genomes is a complex arrangement of possible movement protein-encoding ORFs located in a 5' direction from the coat protein gene. All known capulaviruses have a TAATATTAC nonanucleotide at the v-ori.

Curtovirus. This genus contains three recognised species, including Beet curly top virus, whose members are economically important pathogens in North America and Iran (Chen and Gilbertson 2009) and have the widest host range of any geminivirus. Members infect dicot plants and are transmitted by leafhoppers.

Eragrovirus. This genus has only one recognised species, Eragrostis curvula streak virus, members of which gave monopartite genomes (Varsani et al., 2014). All known isolates have been found infecting the monocot plant Eragrostis curvula (weeping love grass) in the Kwa-Zulu Natal region of South Africa (Varsani et al., 2009). Like the becurtoviruses, eragroviruses have a TAAGATTCC nonanucleotide sequence at the v-ori.

Grablovirus. This genus contains only one species, Grapevine red blotch virus (Varsani et al., 2017), members of which infect grapevines and have been found in Canada, South Korea and the USA.

Mastrevirus. These monopartite viruses infect mostly monocots and some dicots, and are transmitted by different species of leafhoppers (Muhire et al., 2013). Of the 32 recognized species in this genus, Maize streak virus, members of which causes a severe disease of maize in Africa  (Shepherd et al., 2010), and Wheat dwarf virus, members of which causes a disease of wheat across northern Europe, the Middle East and Asia (Kvarnheden et al., 2002), are the best studied. Recently a mastrevirus in the species Wheat dwarf India virus has been shown to associate with alphasatellites and betasatellites (Kumar et al., 2014).

Topocuvirus. A member of the single recognized species in this genus, Tomato pseudo-curly top virus, is transmitted by a treehopper (Briddon et al., 1996). The virus genome is similar to those of curtoviruses.

Turncurtovirus. Turnip curly top virus is currently the only recognized species within this genus (Varsani et al., 2014). All known 20 isolates belonging to this monopartite, leafhopper-transmitted species have been recovered from the dicot plants Brassica rapa or Raphanus sativus originating from Iran (Kamali et al., 2016, Razavinejad et al., 2013).

Virion

Morphology

Virions are typically twinned ("geminate"). For maize streak virus (MSV, genus Mastrevirus), cryo-electron microscopy has shown that virions are about 22×38 nm in size, consisting of two incomplete icosahedra (T=1) containing a total of 110 coat protein subunits organized as 22 pentameric capsomers (Zhang et al., 2001) (Figure 1.Geminiviridae).

Figure 1.Geminiviridae. (Left) Cryo-electron microscopic reconstruction of maize streak virus (MSV) viewed along a two-fold axis of symmetry. The bar represents 10 nm. (Right) Purified particles of MSV stained with uranyl acetate showing typical twinned quasi-isometric subunits. The bar represents 50 nm. (From (Zhang et al., 2001); courtesy of R. McKenna).

Physicochemical and physical properties

The virion S20,w is approximately 70S (Goodman et al., 1980).

Nucleic acid

Twinned virions contain a single copy of circular ssDNA, ranging in size from 2.5 to 3.2 kb. Hence, for viruses with bipartite genomes, two virions containing different genomic components are required for infection and the total genome size is about 5.2 kb (Von Arnim et al., 1993, Hamilton et al., 1983). Half-size defective components and ssDNA satellites are also encapsidated (Zhou 2013).

Proteins

Virions contain a single structural protein (CP; Mr about 28–34×103). No other proteins have been found associated with virions (Zhang et al., 2001, Goodman et al., 1980).

Genome organization and replication

Viruses in the genera Becurtovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus and Turncurtovirus have a single genomic component, whereas those in the genus Begomovirus have either one or two components.

Replication occurs through double-stranded replicative intermediates by both recombination-dependent and rolling circle mechanisms (Stenger et al., 1991, Preiss and Jeske 2003). Complementary-sense DNA synthesis on the virion-sense (encapsidated) strand to produce dsDNA depends solely on host factors (Saunders et al., 1992). Virus ssDNA synthesis is initiated by cleavage of the virion-sense strand by the virus-encoded replication-associated protein (Rep) immediately downstream of the 3' thymidine residue in a conserved TA(A,G)TATT/AC sequence located in the loop of a potential stem-loop structure within the intergenic region (IR) (Laufs et al., 1995, Fontes et al., 1994). Large amounts of heterogenous sub- and extra-genome length geminivirus DNA (hDNA) are generated during rolling-circle replication, and most of the viral DNA that accumulates within infected cells is likely produced from this hDNA by recombination-dependent mechanisms that rely on host DNA double-stranded break repair complexes (Preiss and Jeske 2003). Geminiviruses do not encode a DNA polymerase, and consequently rely entirely on host factors that must be recruited during the early stages of replication.

In all cases, coding regions in both virion-sense and complementary-sense strands diverge from an intergenic region, and transcription is bi-directional, with independently controlled transcripts initiating within the intergenic region (IR) (Sunter and Bisaro 1989). Geminiviruses use multiple overlapping transcripts to control gene expression; those in the genera Mastrevirus and, probably, also Becurtovirus, Capulavirus and Grablovirus additionally use transcript splicing (Schalk et al., 1989).

Genus demarcation criteria 

These include host range (monocots or dicots), type of vector (leafhoppers, treehoppers, whiteflies, aphids), genome organization (mono- or bipartite), and phylogenetic relationships.

Derivation of names

Becurto: from the type species Beet curly top Iran virus.

Begomo: from the type species Bean golden yellow mosaic virus (previously Bean golden mosaic virus).

Capula: from the type species Euphorbia caput-medusae latent virus.

Curto: from the type species Beet curly top virus.

Eragro: from the type species Eragrostis curvula streak virus.

Gemini: from Latin meaning "twin", describing the characteristic twinned (geminate) particle morphology.

Grablo: from the type species Grapevine red blotch virus.

Mastre: from the type species Maize streak virus.

Topocu: from the type species Tomato pseudo-curly top virus.

Turncurto: from the type species Turnip curly top virus.

Phylogenetic relationships

Phylogenetic analysis of complete genome sequences (DNA-A sequences in the case of bipartite begomoviruses) from isolates of representative species shows that geminiviruses cluster according to the current taxonomic classification into nine genera (Figure 2.Geminiviridae). In addition, they cluster according to geographic distribution, at least within the begomoviruses, probably reflecting their evolutionary divergence as a consequence of isolation due to the inability of their insect vectors to fly over long distances (Rocha et al., 2013). Despite frequent inter-species recombination events and the increasing worldwide movement of infected plants, it is remarkable that this geographical distribution is still apparent. The begomoviruses further display a clear subdivision into four phylogenetic groups: Old World, New World, and the so-called "legumoviruses" and "sweepoviruses" (Ilyas et al., 2009, Trenado et al., 2011). Old World begomoviruses can be either mono- or bipartite, contain an AV2/V2 ORF, and are often associated with both alphasatellites and betasatellites. New World begomoviruses are mostly bipartite (with one exception), do not contain an AV2/V2 ORF, and can be associated with alphasatellites (but so far no association with betasatellites has been shown). Legumoviruses and sweepoviruses are associated, respectively, with legume hosts and with sweet potato. They can be mono- or bipartite and their clustering is not related to geographical location.

Figure 2.Geminiviridae. A. Unrooted, neighbor-joining phylogenetic tree of the full genome sequences (or DNA-A sequences for bipartite geminiviruses) of representative isolates in the various genera in the family Geminiviridae. This tree is presented as a guide to describe relative similarities between the geminivirus groups, as it is not possible credibly to align all of the representative genomes from various recognised genera and novel divergent geminivirus isolates, as inter-species and inter-genus recombination has played a major part in the diversification of the represented virus isolates. B. Maximum-likelihood phylogenetic tree (applying the LG+I+G amino acid substitution model) inferred from Rep sequences of representative isolates of the various genera in the family Geminiviridae. Numbers associated with branches indicate percentage aLRT support for these branches. The tree is rooted with Rep sequences of members of the family Genomoviridae (not shown). Branches with <80% support were collapsed. (OW) and (NW) stand for Old World and New World, respectively.

Similarity with other taxa

Members of the plant virus families Geminiviridae and Nanoviridae have circular ssDNA genomes and replicate by a rolling circle mechanism. All these viruses have highly conserved sequences, either TA(A,G)TATTAC (geminiviruses) or TAGTATTAC (nanoviruses) in the loop of a putative stem-loop structure within the IR, in which a nick is introduced during the initiation of replication. Interestingly, the majority of alphasatellites that associate with begomoviruses have the nanovirus-like sequence TAGTATTAC, consistent with them having evolved from components of nanoviruses. Similar structures are found in members of the animal virus family Circoviridae as well as the genus Anellovirus, both of which also have small circular ssDNA genomes. It is speculated that geminiviruses derive from prokaryotic episomal replicons, based on conservation of motifs in proteins that function in rolling circle replication initiation.

In addition to the nine currently existing genera, two additional genera are likely be created in the near future to accommodate two species that are currently classified in the family but are unassigned to a genus: Citrus chlorotic dwarf virus and Mulberry mosaic dwarf virus. Viruses of these species have genome organizations which are distinct from those of the viruses in the currently existing genera.