Alphasatellite

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Alphasatellitidae
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Family:Alphasatellitidae

Alphasatellites are a single-stranded DNA family of satellite viruses that depend on the presence of another virus (helper viruses) to replicate their genomes. As such, they have minimal genomes with very low genomic redundancy. The genome is a single circular single strand DNA molecule. [1] The first alphasatellites were described in 1999 and were associated with cotton leaf curl disease and Ageratum yellow vein disease. [2] [3] As begomoviruses are being characterised at the molecular level an increasing number of alphasatellites are being described.

Contents

These viruses were earlier known as DNA 1 components. [4]

These viruses are generally found in the Old World. A number have been isolated from the New World but their association with their host viruses is still being studied.

Genome

The genome is between 1300 and 1400 nucleotides in length and has three conserved features: a hairpin structure, a single open reading frame (ORF) and an adenine rich region. [5]

The hairpin structure has a loop that includes the nonanucleotide, TAGTATTAC, which is common to nanoviruses and differs from the TAATATTAC sequence of geminiviruses by one nucleotide. In both geminiviruses and nanoviruses this sequence contains the origin of replication (ori) and is nicked by the rolling circle replication initiator protein to initiate viral DNA replication. On the basis of the hairpin structures alphasatellites can be divided into 5 clades. [6]

The open reading frame encodes a rolling circle replication initiator protein (Rep) similar to that found in the nanoviruses. The encoded protein is 32–37 kiloDalton in molecular weight with ~320 amino acids. It is highly conserved with 86.3–100.0% amino acid sequence identity between isolates.[ citation needed ]

The adenine rich region is immediately downstream of the rep gene and is approximately 153–169 nucleotides in length with an adenine content of between 52.3–58.4%. Phylogenectic analysis of this region shows that they can be divided into three clades which correspond to those found on phylogenetic analysis of the entire genome. [6] This portion of the genome appears to be redundant. [7]

A putative second ORF in the genome of an alphasatellite virus has been described. [8] The significance of this finding (if any) is not known.

Recombination occurs between alphasatellites. [9]

Virology

There are no distinctive virions because the viral genomes are encapsidated within the coat protein of the helper virus.[ citation needed ]

Alphasatellites associated with the begomoviruses require a begomovirus for movement in plants and insect transmission but are capable of self replication in host plants. They do not appear to cause disease in plants or to alter the course of infection by the begomovirus. They may be able to reduce the severity of an infection by the begomoviruses. [10] [11]

Alphasatellites have also been described in association with Nanoviridae . These tend to be slightly shorter (1100–1300 nucleotides) but to encode proteins in addition to the rep gene. Because of the multiple component genome of the Nanoviridae these were not initially recognised as distinct genomes. [12] [13] [14]

Alphasatellites may be the target of RNA silencing. [15]

Taxonomy

Alphasatellites are grouped together in the family Alphasatellitidae. This family has three subfamilies, 18 genera, and 85 species. The following subfamilies and genera are recognized (-satellitinae denotes subfamily and -satellite denotes genus): [16]

Evolution

Given the similarities between the rep proteins of the alphasatellites and the nanoviruses, it is likely that the alphasatellites evolved from the nanoviruses. [6]

Uses

These viruses have been used in the development of viral gene silencing studies. [17]

Related Research Articles

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A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. After invading a host cell's cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backwards). The new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. Many retroviruses cause serious diseases in humans, other mammals, and birds.

<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.

<span class="mw-page-title-main">Viral protein</span>

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<i>Geminiviridae</i> Family of viruses

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. Diseases associated with this family include: bright yellow mosaic, yellow mosaic, yellow mottle, leaf curling, stunting, streaks, reduced yields. They have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication. According to the Baltimore classification they are considered class II viruses. It is the largest known family of single stranded DNA viruses.

<span class="mw-page-title-main">Arenavirus</span> Family of RNA viruses

An arenavirus is a bi- or trisegmented ambisense RNA virus that is a member of the family Arenaviridae. These viruses infect rodents and occasionally humans. A class of novel, highly divergent arenaviruses, properly known as reptarenaviruses, have also been discovered which infect snakes to produce inclusion body disease. At least eight arenaviruses are known to cause human disease. The diseases derived from arenaviruses range in severity. Aseptic meningitis, a severe human disease that causes inflammation covering the brain and spinal cord, can arise from the lymphocytic choriomeningitis virus. Hemorrhagic fever syndromes, including Lassa fever, are derived from infections such as Guanarito virus, Junin virus, Lassa virus, Lujo virus, Machupo virus, Sabia virus, or Whitewater Arroyo virus. Because of the epidemiological association with rodents, some arenaviruses and bunyaviruses are designated as roboviruses.

<span class="mw-page-title-main">HHV Infected Cell Polypeptide 0</span> Protein

Human Herpes Virus (HHV) Infected Cell Polypeptide 0 (ICP0) is a protein, encoded by the DNA of herpes viruses. It is produced by herpes viruses during the earliest stage of infection, when the virus has recently entered the host cell; this stage is known as the immediate-early or α ("alpha") phase of viral gene expression. During these early stages of infection, ICP0 protein is synthesized and transported to the nucleus of the infected host cell. Here, ICP0 promotes transcription from viral genes, disrupts structures in the nucleus known as nuclear dots or promyelocytic leukemia (PML) nuclear bodies, and alters the expression of host and viral genes in combination with a neuron specific protein. At later stages of cellular infection, ICP0 relocates to the cell cytoplasm to be incorporated into new virion particles.

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<i>Begomovirus</i> Genus of viruses

Begomovirus is a genus of viruses, in the family Geminiviridae. They are plant viruses that as a group have a very wide host range, infecting dicotyledonous plants. Worldwide they are responsible for a considerable amount of economic damage to many important crops such as tomatoes, beans, squash, cassava and cotton. There are 445 species in this genus.

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Cotton leaf curl viruses (CLCuV) are a number of plant pathogenic virus species of the family Geminiviridae.

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.

Gyrovirus is a genus of viruses, in the family Anelloviridae. Until 2011, chicken anemia virus was the only Gyrovirus identified, but since then gyroviruses have also been identified in humans. Diseases associated with this genus include: chicken infectious anemia, which is associated with depletion of cortical thymocytes and erythroblastoid cells.

Idaeovirus is a genus of positive-sense ssRNA viruses that contains two species: Raspberry bushy dwarf virus (RBDV) and Privet idaeovirus. RBDV has two host-dependent clades: one for raspberries; the other for grapevines. Infections are a significant agricultural burden, resulting in decreased yield and quality of crops. RBDV has a synergistic relation with Raspberry leaf mottle virus, with co-infection greatly amplifying the concentration of virions in infected plants. The virus is transmitted via pollination with RBDV-infected pollen grains that first infect the stigma before causing systemic infection.

<span class="mw-page-title-main">Agnoprotein</span> Viral protein found in some polyomaviruses

Agnoprotein is a protein expressed by some members of the polyomavirus family from a gene called the agnogene. Polyomaviruses in which it occurs include two human polyomaviruses associated with disease, BK virus and JC virus, as well as the simian polyomavirus SV40.

<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>Avian metaavulavirus 2</i> Species of virus

Avian metaavulavirus 2, formerly Avian paramyxovirus 2, is a species of virus belonging to the family Paramyxoviridae and genus Metaavulavirus. The virus is a negative strand RNA virus containing a monopartite genome. Avian metaavulavirus 2 is one of nine species belonging to the genus Metaavulavirus. The most common serotype of Avulavirinae is serotype 1, the cause of Newcastle disease (ND). Avian metaavulavirus 2 has been known to cause disease, specifically mild respiratory infections in domestic poultry, including turkeys and chickens, and has many economic effects on egg production and poultry industries. The virus was first isolated from a strain in Yucaipa, California in 1956. Since then, other isolates of the virus have been isolated worldwide.

<i>Pepper leaf curl virus</i> Species of virus

Pepper leaf curl virus(PepLCV) is a DNA virus from the genus Begomovirus and the family Geminiviridae. PepLCV causes severe disease especially in pepper (Capsicum spp.). It can be found in tropical and subtropical regions such as Thailand and India, but has also been detected in countries such as the United States and Nigeria. This virus is transmitted by an insect vector from the family Aleyrodidae and order Hemiptera, the whitefly Bemisia tabaci. The primary host for PepLCV are several Capsicum spp.. PepLCV has been responsible for several epidemics and causes severe economic losses. It is the focus of research trying to understand the genetic basis of resistance. Currently, a source of resistance to the virus has been identified in the Bhut Jolokia pepper.

Chilli leaf curl virus(ChiLCV) is a DNA virus from the genus Begomovirus and the family Geminiviridae. ChiLCV causes severe disease especially in pepper (Capsicum spp.), but also affects other crops such as tomato (Solanum lycopersicum). It can be found in tropical and subtropical regions primarily in India, but has also been detected in countries such as Indonesia and Sri Lanka. This virus is transmitted by an insect vector from the family Aleyrodidae and order Hemiptera, the whitefly Bemisia tabaci. The primary host for ChiLCV are several Capsicum spp., but host species also include tomato and amaranth. ChiLCV has been responsible for several epidemics and causes severe economic losses. It is the focus of research trying to understand the genetic basis of resistance. Currently, a few sources of resistance have been discovered and used to breed resistant varieties.

<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.

References

  1. ↑ Silva, Jorge Miguel; Pratas, Diogo; Caetano, Tânia; Matos, Sérgio (2022-08-11). "The complexity landscape of viral genomes". GigaScience. 11: giac079. doi:10.1093/gigascience/giac079. ISSN   2047-217X. PMC   9366995 . PMID   35950839.
  2. ↑ Saunders K, Stanley J (November 1999). "A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses". Virology. 264 (1): 142–52. doi: 10.1006/viro.1999.9948 . PMID   10544139.
  3. ↑ Mansoor S, Khan SH, Bashir A, et al. (June 1999). "Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan". Virology. 259 (1): 190–9. doi: 10.1006/viro.1999.9766 . PMID   10364503.
  4. ↑ Stanley J (February 2004). "Subviral DNAs associated with geminivirus disease complexes". Vet. Microbiol. 98 (2): 121–9. doi:10.1016/j.vetmic.2003.10.005. PMID   14741124.
  5. ↑ Briddon RW, Bull SE, Amin I, et al. (July 2004). "Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes". Virology. 324 (2): 462–74. doi: 10.1016/j.virol.2004.03.041 . PMID   15207631.
  6. 1 2 3 Xie Y, Wu P, Liu P, Gong H, Zhou X (2010). "Characterization of alphasatellites associated with monopartite begomovirus/betasatellite complexes in Yunnan, China". Virol. J. 7: 178. doi:10.1186/1743-422X-7-178. PMC   2922188 . PMID   20678232.
  7. ↑ Shahid MS, Ali L, Andleeb S (2009). "The function of the a-rich region of the alphasatellite associated with the cotton leaf curl disease in Pakistan" (PDF). EurAsia J BioSci. 3: 152–6. Archived from the original (PDF) on 2014-03-08. Retrieved 2014-03-08.
  8. ↑ Romay G, Chirinos D, Geraud-Pouey F, Desbiez C (November 2010). "Association of an atypical alphasatellite with a bipartite New World begomovirus". Arch. Virol. 155 (11): 1843–7. doi:10.1007/s00705-010-0760-7. PMID   20665058. S2CID   20039085.
  9. ↑ Kumar J, Kumar A, Roy JK, Tuli R, Khan JA (August 2010). "Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba". Virus Genes. 41 (1): 118–25. doi:10.1007/s11262-010-0482-7. PMID   20405195. S2CID   6790138.
  10. ↑ Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK (March 2011). "An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation" (pdf). J. Gen. Virol. 92 (Pt 3): 706–17. doi: 10.1099/vir.0.025288-0 . PMID   21084498.
  11. ↑ Nawaz-Ul-Rehman MS, Nahid N, Mansoor S, Briddon RW, Fauquet CM (September 2010). "Post-transcriptional gene silencing suppressor activity of two non-pathogenic alphasatellites associated with a begomovirus". Virology. 405 (2): 300–8. doi: 10.1016/j.virol.2010.06.024 . PMID   20598726.
  12. ↑ Katul L, Maiss E, Vetten HJ (February 1995). "Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene" (pdf). J. Gen. Virol. 76 (Pt 2): 475–9. doi: 10.1099/0022-1317-76-2-475 . PMID   7844570.
  13. ↑ Katul L, Timchenko T, Gronenborn B, Vetten HJ (December 1998). "Ten distinct circular ssDNA components, four of which encode putative replication-associated proteins, are associated with the faba bean necrotic yellows virus genome" (pdf). J. Gen. Virol. 79 (Pt 12): 3101–9. doi: 10.1099/0022-1317-79-12-3101 . PMID   9880028.
  14. ↑ Sano Y, Wada M, Hashimoto Y, Matsumoto T, Kojima M (December 1998). "Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome" (pdf). J. Gen. Virol. 79 (Pt 12): 3111–8. doi: 10.1099/0022-1317-79-12-3111 . PMID   9880029.
  15. ↑ Amin I, Hussain K, Akbergenov R, et al. (August 2011). "Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex". Mol. Plant Microbe Interact. 24 (8): 973–83. doi: 10.1094/MPMI-01-11-0001 . PMID   21751853.
  16. ↑ "Virus Taxonomy: 2022 Release". International Committee on Taxonomy of Viruses (ICTV). March 2023. Retrieved 14 August 2023.
  17. ↑ Huang CJ, Zhang T, Li FF, Zhang XY, Zhou XP (February 2011). "Development and application of an efficient virus-induced gene silencing system in Nicotiana tabacum using geminivirus alphasatellite". J Zhejiang Univ Sci B. 12 (2): 83–92. doi:10.1631/jzus.B1000157. PMC   3030953 . PMID   21265040.
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