Alphasatellite: Difference between revisions
Content deleted Content added
m corrected authors list (CS1 maint) |
m undone authors list change |
||
| Line 72: | Line 72: | ||
}} |
}} |
||
'''''Alphasatellites''''' are single stranded [[Satellite (biology)|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.<ref name=Saunders1999>{{cite journal | |
'''''Alphasatellites''''' are single stranded [[Satellite (biology)|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.<ref name=Saunders1999>{{cite journal |author =Saunders K, Stanley J |title=A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses |journal=Virology |volume=264 |issue=1 |pages=142–52 |date=November 1999 |pmid=10544139 |doi=10.1006/viro.1999.9948 |url=http://linkinghub.elsevier.com/retrieve/pii/S0042-6822(99)99948-8}}</ref><ref name=Mansoor1999>{{cite journal |author =Mansoor S, Khan SH, Bashir A |title=Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan |journal=Virology |volume=259 |issue=1 |pages=190–9 |date=June 1999 |pmid=10364503 |doi=10.1006/viro.1999.9766 |url=http://linkinghub.elsevier.com/retrieve/pii/S0042-6822(99)99766-0|display-authors=etal}}</ref> 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.<ref name=Stanley2004>{{cite journal | |
These viruses were earlier known as DNA 1 components.<ref name=Stanley2004>{{cite journal |author =Stanley J |title=Subviral DNAs associated with geminivirus disease complexes |journal=Vet. Microbiol. |volume=98 |issue=2 |pages=121–9 |date=February 2004 |pmid=14741124 |url=http://linkinghub.elsevier.com/retrieve/pii/S0378113503003274 |doi=10.1016/j.vetmic.2003.10.005}}</ref> |
||
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. |
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. |
||
| Line 80: | Line 80: | ||
==Genome== |
==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.<ref name=Briddon2004>{{cite journal | |
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.<ref name=Briddon2004>{{cite journal |author =Briddon RW, Bull SE, Amin I |title=Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes |journal=Virology |volume=324 |issue=2 |pages=462–74 |date=July 2004 |pmid=15207631 |doi=10.1016/j.virol.2004.03.041 |url=http://linkinghub.elsevier.com/retrieve/pii/S0042682204002260|display-authors=etal}}</ref> |
||
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.<ref name=Xie2010>{{cite journal | |
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.<ref name=Xie2010>{{cite journal |author =Xie Y, Wu P, Liu P, Gong H, Zhou X |title=Characterization of alphasatellites associated with monopartite begomovirus/betasatellite complexes in Yunnan, China |journal=Virol. J. |volume=7 |issue= |pages=178 |year=2010 |pmid=20678232 |pmc=2922188 |doi=10.1186/1743-422X-7-178 |url=http://www.virologyj.com/content/7//178}}</ref> |
||
The open reading frame encodes a rolling circle replication initiator protein (Rep) similar to that found in the [[nanovirus]]es. The encoded protein is 32–37 kilo[[Atomic mass unit|Dalton]] in molecular weight with ~320 amino acids. It is highly conserved with 86.3–100.0% [[amino acid]] sequence identy between isolates. |
The open reading frame encodes a rolling circle replication initiator protein (Rep) similar to that found in the [[nanovirus]]es. The encoded protein is 32–37 kilo[[Atomic mass unit|Dalton]] 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 [[nucleotide]]s 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.<ref name="Xie2010"/> This portion of the genome appears to be redundant.<ref name=Shahid2009>{{cite journal | |
The adenine rich region is immediately downstream of the ''rep'' gene and is approximately 153–169 [[nucleotide]]s 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.<ref name="Xie2010"/> This portion of the genome appears to be redundant.<ref name=Shahid2009>{{cite journal |author =Shahid MS, Ali L, Andleeb S |title=The function of the a-rich region of the alphasatellite associated with the cotton leaf curl disease in Pakistan |journal=EurAsia J BioSci |volume=3 |pages=152–6 |year=2009 |url=http://ejobios.com/pdf/EJOB-9-12-3,19,152-156.pdf |format=PDF}}</ref> |
||
A putative second ORF in the genome of an alphasatellite virus has been described.<ref name=Romay2010>{{cite journal | |
A putative second ORF in the genome of an alphasatellite virus has been described.<ref name=Romay2010>{{cite journal |author =Romay G, Chirinos D, Geraud-Pouey F, Desbiez C |title=Association of an atypical alphasatellite with a bipartite New World begomovirus |journal=Arch. Virol. |volume=155 |issue=11 |pages=1843–7 |date=November 2010 |pmid=20665058 |doi=10.1007/s00705-010-0760-7 }}</ref> The significance of this finding (if any) is not known. |
||
Recombination occurs between alphasatellites.<ref name=Kumar2010>{{cite journal | |
Recombination occurs between alphasatellites.<ref name=Kumar2010>{{cite journal |author =Kumar J, Kumar A, Roy JK, Tuli R, Khan JA |title=Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba |journal=Virus Genes |volume=41 |issue=1 |pages=118–25 |date=August 2010 |pmid=20405195 |doi=10.1007/s11262-010-0482-7 }}</ref> |
||
==Virology== |
==Virology== |
||
| Line 96: | Line 96: | ||
There are no distinctive virons because the viral genomes are encapsidated within the coat protein of the helper virus. |
There are no distinctive virons because the viral genomes are encapsidated within the coat protein of the helper virus. |
||
Alphasatellites associated with the [[begomovirus]]es 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.<ref name=Idris2011>{{cite journal | |
Alphasatellites associated with the [[begomovirus]]es 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.<ref name=Idris2011>{{cite journal |author =Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK |title=An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation |journal=J. Gen. Virol. |volume=92 |issue=Pt 3 |pages=706–17 |date=March 2011 |pmid=21084498 |doi=10.1099/vir.0.025288-0 |url=http://vir.sgmjournals.org/cgi/pmidlookup?view=long&pmid=21084498}}</ref><ref name=Nawaz-Ul-Rehman2010>{{cite journal |author =Nawaz-Ul-Rehman MS, Nahid N, Mansoor S, Briddon RW, Fauquet CM |title=Post-transcriptional gene silencing suppressor activity of two non-pathogenic alphasatellites associated with a begomovirus |journal=Virology |volume=405 |issue=2 |pages=300–8 |date=September 2010 |pmid=20598726 |doi=10.1016/j.virol.2010.06.024 |url=http://linkinghub.elsevier.com/retrieve/pii/S0042-6822(10)00406-X}}</ref> |
||
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.<ref name=Katul1995>{{cite journal | |
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.<ref name=Katul1995>{{cite journal |author =Katul L, Maiss E, Vetten HJ |title=Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene |journal=J. Gen. Virol. |volume=76 |issue=Pt 2 |pages=475–9 |date=February 1995 |pmid=7844570 |url=http://vir.sgmjournals.org/cgi/pmidlookup?view=long&pmid=7844570 |doi=10.1099/0022-1317-76-2-475}}</ref><ref name=Katul1998>{{cite journal |author =Katul L, Timchenko T, Gronenborn B, Vetten HJ |title=Ten distinct circular ssDNA components, four of which encode putative replication-associated proteins, are associated with the faba bean necrotic yellows virus genome |journal=J. Gen. Virol. |volume=79 |issue=Pt 12 |pages=3101–9 |date=December 1998 |pmid=9880028 |url=http://vir.sgmjournals.org/cgi/pmidlookup?view=long&pmid=9880028}}</ref><ref name=Sano1998>{{cite journal |author =Sano Y, Wada M, Hashimoto Y, Matsumoto T, Kojima M |title=Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome |journal=J. Gen. Virol. |volume=79 |issue=Pt 12 |pages=3111–8 |date=December 1998 |pmid=9880029 |url=http://vir.sgmjournals.org/cgi/pmidlookup?view=long&pmid=9880029}}</ref> |
||
Alphasatellites may be the target of RNA silencing.<ref name=Amin2011>{{cite journal | |
Alphasatellites may be the target of RNA silencing.<ref name=Amin2011>{{cite journal |author =Amin I, Hussain K, Akbergenov R |title=Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex |journal=Mol. Plant Microbe Interact. |volume=24 |issue=8 |pages=973–83 |date=August 2011 |pmid=21751853 |doi=10.1094/MPMI-01-11-0001 |url=http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-01-11-0001|display-authors=etal}}</ref> |
||
==Taxonomy== |
==Taxonomy== |
||
| Line 108: | Line 108: | ||
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. |
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.<ref name=Briddon2008>{{cite journal | |
It is recommended that strains with 80%+ identity be classified into a species.<ref name=Briddon2008>{{cite journal |author =Briddon RW, Brown JK, Moriones E |title=Recommendations for the classification and nomenclature of the DNA-beta satellites of begomoviruses |journal=Arch. Virol. |volume=153 |issue=4 |pages=763–81 |year=2008 |pmid=18247103 |doi=10.1007/s00705-007-0013-6 |display-authors=etal}}</ref> Proposals for their consistent naming have also been proposed. |
||
==Evolution== |
==Evolution== |
||
| Line 116: | Line 116: | ||
==Uses== |
==Uses== |
||
These viruses have been used in the development of viral gene silencing studies.<ref name=Huang2011>{{cite journal | |
These viruses have been used in the development of viral gene silencing studies.<ref name=Huang2011>{{cite journal |author =Huang CJ, Zhang T, Li FF, Zhang XY, Zhou XP |title=Development and application of an efficient virus-induced gene silencing system in Nicotiana tabacum using geminivirus alphasatellite |journal=J Zhejiang Univ Sci B |volume=12 |issue=2 |pages=83–92 |date=February 2011 |pmid=21265040 |pmc=3030953 |doi=10.1631/jzus.B1000157 |url=http://www.zju.edu.cn/jzus/article.php?doi=10.1631/jzus.B1000157}}</ref> |
||
==See also== |
==See also== |
||
Revision as of 18:53, 14 May 2016
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 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]
See also
References
- ^ 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.
- ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
- ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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. PMID 9880028.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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. PMID 9880029.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link)