Geminiviridae

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Geminiviridae
Good msv 3.jpg
Purified Maize streak virus (MSV) particles stained with uranyl acetate. Size bar indicates 50 nm.
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Monodnaviria
Kingdom: Shotokuvirae
Phylum: Cressdnaviricota
Class: Repensiviricetes
Order: Geplafuvirales
Family:Geminiviridae
Genera

See text

Geminiviridae is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. [1] [2] [3] Diseases associated with this family include: bright yellow mosaic, yellow mosaic, yellow mottle, leaf curling, stunting, streaks, reduced yields. [2] [4] They have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication (i.e. geminivirus genomes are ambisense). According to the Baltimore classification they are considered class II viruses. It is the largest known family of single stranded DNA viruses.

Contents

Mastrevirus and curtovirus transmission is via various leafhopper species (e.g. maize streak virus and other African streak viruses are transmitted by Cicadulina mbila ), the only known topocuvirus species, Tomato pseudo-curly top virus , is transmitted by the treehopper Micrutalis malleifera , and begomoviruses are transmitted by the whitefly species, Bemisia tabaci .

These viruses are responsible for a significant amount of crop damage worldwide. Epidemics of geminivirus diseases have arisen due to a number of factors, including the recombination of different geminiviruses coinfecting a plant, which enables novel, possibly virulent viruses to be developed. Other contributing factors include the transport of infected plant material to new locations, expansion of agriculture into new growing areas, and the expansion and migration of vectors that can spread the virus from one plant to another. [5]

Virology

The genome of ssDNA can either be a single component between 2500–3100 nucleotides, or, in the case of some begomoviruses, two similar-sized components each between 2600 and 2800 nucleotides. They have elongated, geminate capsids with two incomplete T=1 icosahedra joined at the missing vertex. The capsids range in size from 18–20 nm in diameter with a length of about 30 nm. Begomoviruses with two component (i.e. bipartite) genomes have these components separated into two different particles both of which must usually be transmitted together to initiate a new infection within a suitable host cell.

GenusType SpeciesStructureSymmetryCapsidGenomic arrangementGenomic segmentation
BecurtovirusBeet curly top Iran virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
BegomovirusBean golden yellow mosaic virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularSegmented
Capulavirus [6] Euphorbia caput-medusae latent virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
CurtovirusBeet curly top virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
EragrovirusEragrostis curvula streak virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
Grablovirus [7] Grapevine red blotch virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
MastrevirusMaize streak virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
TopocuvirusTomato pseudo-curly top virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite
TurncurtovirusTurnip curly top virusTwinned IcosahedralIncomplete T = 1Non-envelopedCircularMonopartite

Taxonomy

The following genera are recognized: [3]

Several additional genera have been proposed: Baminivirus, Nimivirus and Niminivirus. [8]

Replication

Drawing of geminiviruses Geminiviruses drawing.png
Drawing of geminiviruses

Geminivirus genomes encode only a few proteins; thus, they are dependent on host cell factors for replication: these include factors such as DNA polymerase—and probably repair polymerases—in order to amplify their genomes, as well as transcription factors. Geminiviruses replicate via a rolling circle mechanism like bacteriophages such as M13, and many plasmids. Replication occurs within the nucleus of an infected plant cell. First the single-stranded circular DNA is converted to a double-stranded circular intermediate. This step involves the use of cellular DNA repair enzymes to produce a complementary negative-sense strand, using the viral genomic or plus-sense DNA strand as a template. The next step is the rolling circle phase, where the viral strand is cleaved at a specific site situated within the origin of replication by the viral Rep protein in order to initiate replication. [9] This process in a eukaryotic nucleus can give rise to concatemeric double-stranded forms of replicative intermediate genomes, although double-stranded unit circles can be isolated from infected plants and cells. New single-stranded DNA forms of the virus genome (plus-sense) are probably formed by interaction of the coat protein with replicating DNA intermediates, as genomes lacking a CP gene do not form ssDNA. The ssDNA is packaged into germinate particles in the nucleus. It is not clear if these particles can then leave the nucleus and be transmitted to surrounding cells as virions, or whether ssDNA associated with coat protein and a movement protein is the form of the genome that gets trafficked from cell to cell via the plasmodesmata. [10]

These viruses tend to be introduced into and initially infect differentiated plant cells, via the piercing mouthparts of the vector insect: however, these cells generally lack the host enzymes necessary for DNA replication, making it difficult for the virus to replicate. To overcome this block geminiviruses can induce plant cells to reenter the cell cycle from a quiescent state so that viral replication can occur. [11]

Virus Rep protein

The only protein encoded in the viral genome that is essential for geminiviral DNA replication is the geminiviral replication protein Rep. [12] Rep initiates rolling circle replication of the viral DNA and interacts with other host proteins that are components of the replication machinery.

Host RAD54 and DNA polymerases

Host protein RAD54 modulates geminiviral DNA replication. [13] RAD54 protein acts in DNA recombination and repair and appears to be necessary for rolling circle replication of the viral DNA. Also, replication of the geminivirus DNA is mediated by the host plant DNA polymerases alpha and delta. [14]

GenusHost detailsTissue tropismEntry detailsRelease detailsReplication siteAssembly siteTransmission
Becurtovirus SpinachPhloem; sieve; phloem-limitedViral movement; mechanical inoculationBuddingNucleusNucleusViral movement; contact
Begomovirus Dicotyledonous plantsPhloem; sieve; phloem-limitedViral movement; mechanical inoculationBuddingNucleusNucleusBemisia tabaci whiteflies
Capulavirus Dicotyledonous plantsNoneViral movement; mechanical inoculationBuddingNucleusNucleusAphid
Curtovirus Dicotyledonous plantsPhloem-limitedViral movement; mechanical inoculationBuddingNucleusNucleusBeet leefhopper
Eragrovirus PlantsNoneViral movement; mechanical inoculationBuddingNucleusNucleusTreehopper; leafhopper
Grablovirus Vitis vinifera (grapevine)NoneViral movement; mechanical inoculationBuddingNucleusNucleusTreehopper
Mastrevirus Monocots [15] NoneViral movement; mechanical inoculationBuddingNucleusNucleusLeafhopper
Topocuvirus Dicotyledonous plantsNoneCell receptor endocytosisBuddingNucleusNucleusLeafhopper
Turncurtovirus TurnipNoneCell receptor endocytosisBuddingNucleusNucleusLeafhopper

Evolution

These viruses may have evolved from a phytoplasma plasmid. [16] Geminiviruses are capable of horizontal gene transfer of genetic information to the plant host. [17]

Related Research Articles

<span class="mw-page-title-main">DNA virus</span> Virus that has DNA as its genetic material

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

<i>Hepadnaviridae</i> Family of viruses

Hepadnaviridae is a family of viruses. Humans, apes, and birds serve as natural hosts. There are currently 18 species in this family, divided among 5 genera. Its best-known member is hepatitis B virus. Diseases associated with this family include: liver infections, such as hepatitis, hepatocellular carcinomas, and cirrhosis. It is the sole accepted family in the order Blubervirales.

<i>Nanoviridae</i> Family of viruses

Nanoviridae is a family of viruses. Plants serve as natural hosts. There are currently 12 species in this family, divided among 2 genera and one unassigned species. Diseases associated with this family include: stunting.

<span class="mw-page-title-main">Viral replication</span> Formation of biological viruses during the infection process

Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and packaging these copies, the virus continues infecting new hosts. Replication between viruses is greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm.

<span class="mw-page-title-main">Rolling circle replication</span> DNA synthesis technique

Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. Some eukaryotic viruses also replicate their DNA or RNA via the rolling circle mechanism.

Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.

Mungbean yellow mosaic virus (MYMV) is a plant pathogenic virus of the family Geminiviridae. Of the various viral diseases inflicting legume crops, Mungbean Yellow Mosaic disease is one of the most destructive and widely distributed. The disease has been reported from various countries.

Tomato yellow leaf curl virus (TYLCV) is a DNA virus from the genus Begomovirus and the family Geminiviridae. TYLCV causes the most destructive disease of tomato, and it can be found in tropical and subtropical regions causing severe economic losses. This virus is transmitted by an insect vector from the family Aleyrodidae and order Hemiptera, the whitefly Bemisia tabaci, commonly known as the silverleaf whitefly or the sweet potato whitefly. The primary host for TYLCV is the tomato plant, and other plant hosts where TYLCV infection has been found include eggplants, potatoes, tobacco, beans, and peppers. Due to the rapid spread of TYLCV in the last few decades, there is an increased focus in research trying to understand and control this damaging pathogen. Some interesting findings include the virus being sexually transmitted from infected males to non-infected females, and an evidence that TYLCV is transovarially transmitted to offspring for two generations.

Anelloviridae is a family of viruses. They are classified as vertebrate viruses and have a non-enveloped capsid, which is round with isometric, icosahedral symmetry and has a triangulation number of 3.

Plectrovirus is a genus of viruses, in the family Plectroviridae. Bacteria in the phylum Mycoplasmatota serve as natural hosts, making these viruses bacteriophages. Acholeplasma virus L51 is the only species in the genus.

Ipomovirus is a genus of positive-strand RNA viruses in the family Potyviridae. Member viruses infect plants and are transmitted by whiteflies. The name of the genus is derived from Ipomoea – the generic name of sweet potato. There are seven species in this genus.

Yingchengvirus is a genus of double stranded DNA viruses that infect haloarchaea. The genus was previously named Betasphaerolipovirus.

<span class="mw-page-title-main">Positive-strand RNA virus</span> Class of viruses in the Baltimore classification

Positive-strand RNA viruses are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome.

<i>Genomoviridae</i> Family of viruses

Genomoviridae is a family of single stranded DNA viruses that mainly infect fungi. The genomes of this family are small. The genomes are circular single-stranded DNA and encode rolling-circle replication initiation proteins (Rep) and unique capsid proteins. In Rep-based phylogenies, genomoviruses form a sister clade to plant viruses of the family Geminiviridae. Ten genera are recognized in this family.

<i>Riboviria</i> Realm of viruses

Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.

<i>Sweet potato leaf curl virus</i> Species of virus

Sweet potato leaf curl virus is commonly abbreviated SPLCV. Select isolates are referred to as SPLCV followed by an abbreviation of where they were isolated. For example, the Brazilian isolate is referred to as SPLCV-Br.

In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:

<i>Ground squirrel hepatitis virus</i> Species of virus

Ground squirrel hepatitis virus, abbreviated GSHV, is a partially double-stranded DNA virus that is closely related to human Hepatitis B virus (HBV) and Woodchuck hepatitis virus (WHV). It is a member of the family of viruses Hepadnaviridae and the genus Orthohepadnavirus. Like the other members of its family, GSHV has high degree of species and tissue specificity. It was discovered in Beechey ground squirrels, Spermophilus beecheyi, but also infects Arctic ground squirrels, Spermophilus parryi. Commonalities between GSHV and HBV include morphology, DNA polymerase activity in genome repair, cross-reacting viral antigens, and the resulting persistent infection with viral antigen in the blood (antigenemia). As a result, GSHV is used as an experimental model for HBV.

<i>Monodnaviria</i> Realm of viruses

Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family Parvoviridae. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in which the coding portion of the genome is flanked by telomeres at each end that form hairpin loops. During RHR, these hairpin loops repeatedly unfold and refold to change the direction of DNA replication so that replication progresses in a continuous manner back and forth across the genome. RHR is initiated and terminated by an endonuclease encoded by parvoviruses that is variously called NS1 or Rep, and RHR is similar to rolling circle replication, which is used by ssDNA viruses that have circular genomes.

References

  1. ↑ Zerbini, FM; Briddon, RW; Idris, A; Martin, DP; Moriones, E; Navas-Castillo, J; Rivera-Bustamante, R; Roumagnac, P; Varsani, A; ICTV Report Consortium (February 2017). "ICTV Virus Taxonomy Profile: Geminiviridae". The Journal of General Virology. 98 (2): 131–133. doi:10.1099/jgv.0.000738. PMC   5802298 . PMID   28284245.
  2. 1 2 "Geminiviridae". ICTV Online (10th) Report.
  3. 1 2 "Virus Taxonomy: 2020 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 13 May 2021.
  4. ↑ "Viral Zone". ExPASy. Retrieved 15 June 2015.
  5. ↑ Gray and Banerjee; Banerjee, N (1999). "Mechanisms of Arthropod Transmission of Plant and Animal Viruses". Microbiol Mol Biol Rev. 63 (1): 128–148. doi:10.1128/MMBR.63.1.128-148.1999. PMC   98959 . PMID   10066833.
  6. ↑ "Genus: Capulavirus - Geminiviridae - ssDNA Viruses - International Committee on Taxonomy of Viruses (ICTV)". International Committee on Taxonomy of Viruses (ICTV). Retrieved 18 August 2017.[ dead link ]
  7. ↑ "Genus: Grablovirus - Geminiviridae - ssDNA Viruses - International Committee on Taxonomy of Viruses (ICTV)". International Committee on Taxonomy of Viruses (ICTV). Archived from the original on 22 October 2020. Retrieved 18 August 2017.
  8. ↑ Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (November 2012). "High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage". J Virol. 86 (22): 12161–75. doi:10.1128/JVI.00869-12. PMC   3486453 . PMID   22933275.
  9. ↑ Chasan R (1995). "Geminiviruses: A Twin Approach to Replication" (PDF). Plant Cell. 7 (6): 659–661. doi:10.1105/tpc.7.6.659. PMC   1464598 .
  10. ↑ Gutierrez C (2000). "NEW EMBO MEMBERS' REVIEW: DNA replication and cell cycle in plants: learning from geminiviruses". The EMBO Journal. 19 (5): 792–799. doi:10.1093/emboj/19.5.792. PMC   305619 . PMID   10698921.
  11. ↑ Hanley Bowdoin lab Archived 11 February 2007 at the Wayback Machine
  12. ↑ Rizvi I, Choudhury NR, Tuteja N (February 2015). "Insights into the functional characteristics of geminivirus rolling-circle replication initiator protein and its interaction with host factors affecting viral DNA replication". Arch Virol. 160 (2): 375–87. doi:10.1007/s00705-014-2297-7. PMID   25449306.
  13. ↑ Kaliappan K, Choudhury NR, Suyal G, Mukherjee SK (March 2012). "A novel role for RAD54: this host protein modulates geminiviral DNA replication". FASEB J. 26 (3): 1142–60. doi: 10.1096/fj.11-188508 . PMID   22171001.
  14. ↑ Wu M, Wei H, Tan H, Pan S, Liu Q, Bejarano ER, Lozano-Durán R (May 2021). "Plant DNA polymerases α and δ mediate replication of geminiviruses". Nat Commun. 12 (1): 2780. doi:10.1038/s41467-021-23013-2. PMC   8119979 . PMID   33986276.
  15. ↑ "Mastrevirus ~ ViralZone".
  16. ↑ Krupovic M, Ravantti JJ, Bamford DH (2009). "Geminiviruses: a tale of a plasmid becoming a virus". BMC Evol Biol. 9 (1): 112. Bibcode:2009BMCEE...9..112K. doi: 10.1186/1471-2148-9-112 . PMC   2702318 . PMID   19460138.
  17. ↑ Catoni, Marco; Noris, Emanuela; Vaira, Anna Maria; Jonesman, Thomas; Matić, Slavica; Soleimani, Reihaneh; Behjatnia, Seyed Ali Akbar; Vinals, Nestor; Paszkowski, Jerzy; Accotto, Gian Paolo (13 December 2018). "Virus-mediated export of chromosomal DNA in plants". Nature Communications. 9 (1): 5308. Bibcode:2018NatCo...9.5308C. doi:10.1038/s41467-018-07775-w. ISSN   2041-1723. PMC   6293997 . PMID   30546019.
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