Abstract
BackgroundAlkB-like proteins are members of the 2-oxoglutarate- and Fe(II)-dependent oxygenase superfamily. In Escherichia coli the protein protects RNA and DNA against damage from methylating agents. 1-methyladenine and 3-methylcytosine are repaired by oxidative demethylation and direct reversal of the methylated base back to its unmethylated form. Genes for AlkB homologues are widespread in nature, and Eukaryotes often have several genes coding for AlkB-like proteins. Similar domains have also been observed in certain plant viruses. The function of the viral domain is unknown, but it has been suggested that it may be involved in protecting the virus against the post-transcriptional gene silencing (PTGS) system found in plants. We wanted to do a phylogenomic mapping of viral AlkB-like domains as a basis for analysing functional aspects of these domains, because this could have some relevance for understanding possible alternative roles of AlkB homologues e.g. in Eukaryotes.ResultsProfile-based searches of protein sequence libraries showed that AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, but mainly in a subgroup of the Flexiviridae family. Sequence analysis indicated that the AlkB domains probably are functionally conserved, and that they most likely have been integrated relatively recently into several viral genomes at geographically distinct locations. This pattern seems to be more consistent with increased environmental pressure, e.g. from methylating pesticides, than with interaction with the PTGS system.ConclusionsThe AlkB domain found in viral genomes is most likely a conventional DNA/RNA repair domain that protects the viral RNA genome against methylating compounds from the environment.
Highlights
Introduction ofAlkB domain in plant virus is probably a recent event The observed distribution of AlkB domains could most be explained by assuming that an ancestral AlkB domain was integrated into the genome of the last common ancestor of the Flexiviridae 2 subfamily
Similarity of viral AlkB domains to other AlkB sequences The results described above may indicate that the AlkB domains have been integrated into the replicase polyprotein relatively recently
In Bamboo mosaic virus, which belongs to Flexiviridae, the residues H68, D122, R125 and Y213 have been identified as putative active site residues with similarity to the Sindbis virus-like methyltransferase [17], and it has been demonstrated that this region of the Bamboo mosaic virus has methyltransferase activity, as it catalyses the transfer of a methyl group from S-adenosylmethionine (AdoMet) to GTP or guanylylimidodiphosphate (GIDP)
Summary
Introduction ofAlkB domain in plant virus is probably a recent event The observed distribution of AlkB domains could most be explained by assuming that an ancestral AlkB domain was integrated into the genome of the last common ancestor of the Flexiviridae 2 subfamily. Subsequent http://www.biomedcentral.com/1471-2164/6/1 virus generations derived from this common ancestor would contain an AlkB domain, except in those cases where the domain was lost again. This scenario could include subsequent transfer to a small number of other virus families e.g. by recombination. The AlkB protein of E. coli, and probably most of its homologues, is involved in repair of alkylation damage in DNA and RNA. It repairs 1-methyladenine and 3-methylcytosine by oxidative demethylation and direct reversal of the methylated base back to its unmethylated form. Very few residues are totally conserved across these structures, basically just the residues involved in coordination of the Fe(II) ion and the 2-oxoglutarate
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