Alphasatellite
Alphasatellites are single stranded viruses that are dependent on another 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 identy 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.
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.[16]
References
- ^ Saunders K & Stanley J (1999). A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses. Virology 264: 142–152.
- ^ Mansoor S, Khan SH, Bashir A, Saeed M, Zafar Y, Malik KA, Briddon R, Stanley J, Markham PG (1999) Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan. Virology 259(1):190-199
- ^ Stanley J (2004) Subviral DNAs associated with geminivirus disease complexes. Vet Microbiol 4;98(2):121-129
- ^ Briddon RW, Bull SE, Amin I, Mansoor S, Bedford ID, Rishi N, Siwatch SS, Zafar Y, Abdel-Salam AM, Markham PG (2004) Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes. Virology ;324(2):462-474
- ^ 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
- ^ 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. EurAsia J BioSci 3: 152-156
- ^ Romay G, Chirinos D, Geraud-Pouey F, Desbiez C (2010) Association of an atypical alphasatellite with a bipartite New World begomovirus. Arch Virol 155(11):1843-1847
- ^ Kumar J, Kumar A, Roy JK, Tuli R, Khan JA (2010) Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba. Virus Genes 41(1):118-125
- ^ Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK (2011) An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol 92(Pt 3):706-717
- ^ Nawaz-Ul-Rehman MS, Nahid N, Mansoor S, Briddon RW, Fauquet CM (2010) Post-transcriptional gene silencing suppressor activity of two non-pathogenic alphasatellites associated with a begomovirus. Virology 405(2):300-308
- ^ Katul L, Maiss E, Vetten HJ (1995) Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene. J. Gen. Virol. 76: 475–479
- ^ Katul L, Timchenko T, Gronenborn B, Vetten HJ (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: 3101–3109
- ^ Sano Y, Wada M, Hashimoto Y, Matsumoto T, Kojima M, 1998. Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome. J Gen Virol 79, 3111–3118
- ^ Amin I, Hussain K, Akbergenov R, Yadav JS, Qazi J, Mansoor S, Hohn T, Fauquet CM, Briddon RW (2011) Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex. Mol Plant Microbe Interact 24(8):973-983
- ^ Briddon RW, Brown JK, Moriones E, Stanley J, Zerbini M, Zhou X, Fauquet CM (2008) Recommendations for the classification and nomenclature of the DNA-beta satellites of begomoviruses. Arch Virol 153(4):763-781
- ^ Huang CJ, Zhang T, Li FF, Zhang XY, Zhou XP (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