Alphasatellite

Alphasatellite
Virus classification
Group: Group II (ssDNA)
Species

Begomovirus group

Ageratum leaf curl Cameroon alphasatellite
Ageratum leaf curl Pakistan alphasatellite
Ageratum yellow vein alphasatellite
Ageratum yellow vein India alphasatellite
Ageratum yellow vein Kenya alphasatellite
Ageratum yellow vein Pakistan alphasatellite
Ageratum yellow vein Singapore alphasatellite
Chilli leaf curl Multan alphasatellite
Cleome leaf crumple alphasatellite
Cotton leaf curl alphasatellite
Cotton leaf curl Burewala alphasatellite
Cotton leaf curl Dabwali alphasatellite
Cotton leaf curl Gezira alphasatellite
Cotton leaf curl India alphasatellite
Cotton leaf curl Multan alphasatellite
Cotton leaf curl Pakistan alphasatellite
Croton yellow vein mosaic alphasatellite
Euphorbia yellow mosaic alphasatellite
Gossypium darwinii symptomless alphasatellite
Gossypium mustelinium symptomless alphasatellite
Hollyhock crumple alphasatellite
Hollyhock yellow vein virus-associated symptomless alphasatellite
Hibiscus leaf curl alphasatellite
Malvastrum yellow mosaic alphasatellite
Malvastrum yellow mosaic Cameroon alphasatellite
Malvastrum yellow mosaic Hainan alphasatellite
Milk vetch dwarf alphasatellite
Melon chlorotic mosaic alphasatellite
Mimosa yellow leaf curl alphasatellite
Okra leaf curl alphasatellite
Okra leaf curl Barombi alphasatellite
Okra leaf curl Burkina Faso alphasatellite
Okra leaf curl Mali alphasatellite
Okra leaf curl Tiko alphasatellite
Potato leaf curl alphasatellite
Sida leaf curl alphasatellite
Sida yellow vein alphasatellite
Sida yellow vein Vietnam alphasatellite
Tobacco curly shoot alphasatellite
Tobacco curly shoot China alphasatellite
Tomato leaf curl alphasatellite
Tomato leaf curl Cameroon alphasatellite
Tobacco leaf curl China alphasatellite
Tobacco leaf curl Pakistan alphasatellite
Tomato yellow leaf curl China alphasatellite
Tomato yellow leaf curl DNA2
Tomato yellow leaf curl Thailand alphasatellite
Tomato yellow leaf curl Yunnan alphasatellite
Verbesina encelioides leaf curl alphasatellite
Vernonia yellow vein Fujian alphasatellite

Nanoviridae group

Banana bunchy top alphasatellite
Banana bunchy top Taiwan alphasatellite
Banana bunchy top S1 alphasatellite
Banana bunchy top Vietnam alphasatellite
Banana bunchy top Y alphasatellite
Coconut foliar decay alphasatellite
Faba bean necrotic yellows alphasatellite
Milk vetch dwarf alphasatellite
Subterranean clover stunt alphasatellite

Alphasatellites are single stranded satellite DNA that are dependent on a virus for transmission. The genome is a single circular single strand DNA molecule. The first alphasatellites were described in 1999 and were associated with cotton leaf curl disease and Ageratum yellow vein disease.[1][2] 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.[3]

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.[4]

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.[5]

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.

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.[5] This portion of the genome appears to be redundant.[6]

A putative second ORF in the genome of an alphasatellite virus has been described.[7] The significance of this finding (if any) is not known.

Recombination occurs between alphasatellites.[8]

Virology

There are no distinctive virons because the viral genomes are encapsidated within the coat protein of the helper virus.

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.[9][10]

Alphasatellites have also been described in association with the 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.[11][12][13]

Alphasatellites may be the target of RNA silencing.[14]

Taxonomy

There is no formal type member.

At present alphasatellites are not organised into genera or higher taxa. A division between those associated with the Begomoviruses and those with associated with Nanoviridae seems logical at present.

It is recommended that strains with 80%+ identity be classified into a species.[15] Proposals for their consistent naming have also been proposed.

A family - Alphasatellitidae - has been proposed for this group of viruses.[16] Within this family are two subfamilies - Geminialphasatellitinae and Nanoalphasatellitinae. These subfamilies contain four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites respectively.

Evolution

Given the similarities between the rep proteins of the alphasatellites and the nanoviruses, it is likely that the alphasatellites evolved from the nanoviruses.[5] Further work in this area is needed to clarify this.

Uses

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

See also

  • Betasatellite

References

  1. ↑ 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.
  2. ↑ 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.
  3. ↑ 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.
  4. ↑ 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.
  5. 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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". J. Gen. Virol. 92 (Pt 3): 706–17. doi:10.1099/vir.0.025288-0. PMID 21084498.
  10. ↑ 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.
  11. ↑ Katul L, Maiss E, Vetten HJ (February 1995). "Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene". J. Gen. Virol. 76 (Pt 2): 475–9. doi:10.1099/0022-1317-76-2-475. PMID 7844570.
  12. ↑ 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". J. Gen. Virol. 79 (Pt 12): 3101–9. doi:10.1099/0022-1317-79-12-3101. PMID 9880028.
  13. ↑ 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". J. Gen. Virol. 79 (Pt 12): 3111–8. doi:10.1099/0022-1317-79-12-3111. PMID 9880029.
  14. ↑ 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.
  15. ↑ Briddon RW, Brown JK, Moriones E, et al. (2008). "Recommendations for the classification and nomenclature of the DNA-beta satellites of begomoviruses". Arch. Virol. 153 (4): 763–81. doi:10.1007/s00705-007-0013-6. PMID 18247103.
  16. ↑ Briddon RW, Martin DP, Roumagnac P, Navas-Castillo J, Fiallo-Olivé E, Moriones E, Lett JM, Zerbini FM, Varsani A (2018). "Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites". Arch Virol. doi:10.1007/s00705-018-3854-2.
  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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