Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkBReport as inadecuate

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BMC Genomics

, 4:48

First Online: 10 December 2003Received: 16 September 2003Accepted: 10 December 2003


BackgroundCombination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe oxygenase superfamily.

ResultsIn this article, we report identification and sequence analysis of five human members of the 2OG-Fe oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family and specifically to the lineage that groups together hABH2 and hABH3 rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes.

ConclusionsWe hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes.

Keywordsphylogenomics bioinformatics dealkylation demethylation dioxygenases List of abbreviations usedhABHhuman AlkB homolog

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-4-48 contains supplementary material, which is available to authorized users.

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Author: Michal A Kurowski - Ashok S Bhagwat - Grzegorz Papaj - Janusz M Bujnicki


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