A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods

The TET/JBP Family of Nucleic Acid Base-Modifying 2-Oxoglutarate and Iron-Dependent Dioxygenases

The TET/JBP family of enzymes includes 2-oxoglutarate- and Fe(ii)-dependent dioxygenases that oxidize 5-methylpyrimidines in nucleic acids. They include euglenozoan JBP enzymes that catalyse the first step in the biosynthesis of the hypermodified thymine, base J, and metazoan TET enzymes that generate oxidized 5-methylcytosines (hydroxy-, formyl- and carboxymethylcytosine) in DNA. Recent studies suggest that these modified bases function as epigenetic marks and/or as potential intermediates for DNA demethylation during resetting of epigenetic 5mC marks upon zygote formation and in primordial germ cell development. Studies in mammalian models also point to an important role for these enzymes in haematopoiesis, tumour suppression, cell differentiation and neural behavioural adaptation. The TET/JBP family has undergone extensive gene expansion in fungi, such as mushrooms, in conjunction with a novel class of transposons and might play a role in genomic plasticity and speciation. Certain versions from stramenopiles and chlorophytes are likely to modify RNA and often show fusions to other RNA-modifying enzymatic domains. The ultimate origin of the TET/JBP family lies in bacteriophages where the enzymes are likely to catalyse formation of modified bases with key roles in DNA packaging and evasion of host restriction.

AlkB and Its Homologues – DNA Repair and Beyond

AlkB is an Fe(ii)/2-oxoglutarate-dependent dioxygenase that is part of the adaptive response to alkylating agents in Escherichia coli. AlkB hydroxylates a wide variety of alkylated DNA bases producing unstable intermediates which decompose to restore the non-alkylated bases. Homologues exist in other bacteria, metazoa (e.g. nine in humans), plants and viruses, but not in archaea, with many catalysing the same oxidative demethylation reactions as for AlkB. The mammalian enzymes Alkbh2 and Alkbh3 catalyse direct DNA repair, Alkbh5 and FTO (Alkbh9) are RNA demethylases, and Alkbh8 is used to synthesize a tRNA, while the remaining mammalian homologues have alternative functions. Alkbh1 is an apurinic/apyrimidinic lyase in addition to exhibiting demethylase activities, but no clear role for the Alkbh1 protein has emerged. Alkbh4 is involved in cell division and potentially demethylates actin, whereas the mitochondrial homologue Alkbh7 has a role in obesity; however, no enzymatic activity has been linked to Alkbh4 or Alkbh7. Here, we discuss AlkB as the ‘archetype’ of this class of hydroxylases, compare it to Alkbh2 and Alkbh3, and then briefly review the diverse (and largely unknown) functions of Alkbh1, Alkbh4, Alkbh6 and Alkbh7. Alkbh5, Alkbh8 and Alkbh9 (FTO) are described separately.

Inducible repair of alkylated DNA in microorganisms

Alkylating agents, which are widespread in the environment, also occur endogenously as primary and secondary metabolites. Such compounds have intrinsically extremely cytotoxic and frequently mutagenic effects, to which organisms have developed resistance by evolving multiple repair mechanisms to protect cellular DNA. One such defense against alkylation lesions is an inducible Adaptive (Ada) response. In Escherichia coli, the Ada response enhances cell resistance by the biosynthesis of four proteins: Ada, AlkA, AlkB, and AidB. The glycosidic bonds of the most cytotoxic lesion, N3-methyladenine (3meA), together with N3-methylguanine (3meG), O(2)-methylthymine (O(2)-meT), and O(2)-methylcytosine (O(2)-meC), are cleaved by AlkA DNA glycosylase. Lesions such as N1-methyladenine (1meA) and N3-methylcytosine (3meC) are removed from DNA and RNA by AlkB dioxygenase. Cytotoxic and mutagenic O(6)-methylguanine (O(6)meG) is repaired by Ada DNA methyltransferase, which transfers the methyl group onto its own cysteine residue from the methylated oxygen. We review (i) the individual Ada proteins Ada, AlkA, AlkB, AidB, and COG3826, with emphasis on the ubiquitous and versatile AlkB and its prokaryotic and eukaryotic homologs; (ii) the organization of the Ada regulon in several bacterial species; (iii) the mechanisms underlying activation of Ada transcription. In vivo and in silico analysis of various microorganisms shows the widespread existence and versatile organization of Ada regulon genes, including not only ada, alkA, alkB, and aidB but also COG3826, alkD, and other genes whose roles in repair of alkylated DNA remain to be elucidated. This review explores the comparative organization of Ada response and protein functions among bacterial species beyond the classical E. coli model.