Alphasatellite
Encyclopedia
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. 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.
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.
(ORF) and an adenine
rich region.
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.
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 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. This portion of the genome appears to be redundant.
A putative second ORF in the genome of an alphasatellite virus has been described. The significance of this finding (if any) is not known.
Recombination occurs between alphasatellites.
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.
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.
Alphasatellites may be the target of RNA silencing.
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. Proposals for their consistent naming have also been proposed.
These viruses were earlier known as DNA 1 components.
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 frameOpen reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
(ORF) and an adenine
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
rich region.
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.
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
Atomic mass unit
The unified atomic mass unit or dalton is a unit that is used for indicating mass on an atomic or molecular scale. It is defined as one twelfth of the rest mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state, and has a value of...
in molecular weight with ~320 amino acids. It is highly conserved with 86.3-100.0% amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequence identy between isolates.
The adenine rich region is immediately downstream of the rep gene and is approximately 153-169 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
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. This portion of the genome appears to be redundant.
A putative second ORF in the genome of an alphasatellite virus has been described. The significance of this finding (if any) is not known.
Recombination occurs between alphasatellites.
Virology
There are no distinctive virons because the viral genomes are encapsidated within the coat protein of the helper virus.Alphasatellites associated with the begomovirus
Begomovirus
The genus Begomovirus contains more than 200 species and belongs to the taxonomic family Geminiviridae. They are plant viruses that as a group have a very wide host range, infecting dicotyledonous plants...
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.
Alphasatellites have also been described in association with the Nanoviridae
Nanoviridae
The Nanoviridae are a family of viruses, including the following genera:*Genus Nanovirus; type species: Subterranean clover stunt virus*Genus Babuvirus; type species: Banana bunchy top virus-Virus structure and genome:...
. 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.
Alphasatellites may be the target of RNA silencing.
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. Proposals for their consistent naming have also been proposed.