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Alphasatellite

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Alphasatellitidae
Virus classification Edit this classification
(unranked): Virus
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.

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

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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

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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

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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

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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

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

References

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  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. ^ a b c 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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