Bioinformatic mapping of AlkB homology domains in viruses.
BACKGROUND
AlkB-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.


RESULTS
Profile-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.


CONCLUSIONS
The 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.
Bratlie
Marit S
MS
Department of Cancer Research and Molecular Medicine, Faculty of Medicine, MTFS, Norwegian University of Science and Technology, N-7489 Trondheim, Norway. marit.bratlie@ntnu.no <marit.bratlie@ntnu.no>
Drabløs
Finn
F
D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry; D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry; D004249:DNA Damage; D019175:DNA Methylation; D004260:DNA Repair; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D016679:Genome, Viral; D023281:Genomics; D006801:Humans; D008745:Methylation; D006899:Mixed Function Oxygenases / Q000737:chemistry*; D008969:Molecular Sequence Data; D010100:Oxygen / Q000737:chemistry; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
D029968:Escherichia coli Proteins; C036386:3-methylcytosine; C008407:1-methyladenine; D012313:RNA; D003596:Cytosine; D006899:Mixed Function Oxygenases; C466427:AlkB protein, E coli; D000225:Adenine; D010100:Oxygen