Cobalamin (CBL), along with chlorophyll, haem, sirohaem and coenzyme F430, constitute a class of the most structurally complex cofactors synthesized by bacteria. The distinctive feature of these cofactors is their tetrapyrrole-derived framework with a centrally chelated metal ion (cobalt, magnesium, iron, or nickel). Methylcobalamin and Ado-CBL, two derivatives of vitamin B12 (cyanocobalamin) with different upper axial ligands, are essential cofactors for several important enzymes which catalyze a variety of transmethylation and rearrangement reactions. Among the most prominent vitamin B12-dependent enzymes in bacteria and archaea are the methionine synthase isozyme MetH from enteric bacteria; the ribonucleotide reductase isozyme NrdJ from deeply rooted eubacteria and archaea; diol dehydratases and ethanolamine ammonia lyase from enteric bacteria involved in anaerobic glycerol, 1,2-propanediol and ethanolamine fermentation; glutamate and methylmalonyl-CoA mutases from clostridia and streptomycetes; and various CBL-dependent methyltransferases from methane-producing archaea (1, 2, 3, 4, 5).

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Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009 Feb 10;10:78.
PMID: 19208259

Most prokaryotic organisms, as well as animals (including humans) and protists have enzymes that require CBL as cofactor, whereas plants and fungi are thought not to use it. Among the CBL-utilizing organisms, only some bacterial and archaeal species are able to synthesize CBL de novo (6). To our knowledge, there are two distinct routes of the CBL biosynthesis in bacteria (Fig. 1): the well-studied oxygen-dependent (aerobic) pathway studied in Pseudomonas denitrificans and the oxygen-independent (anaerobic) pathway which was partially resolved in Salmonella typhimurium, Bacillus megaterium and Propionibacterium shermanii (7).
The biosynthesis of Ado-CBL from Uro`III, the last common precursor of various tetrapyrrolic cofactors, requires about twenty five enzymes (6) and can be divided into two major parts. The first part, the corrin-ring synthesis, is different in the anaerobic and aerobic pathways: the former starts with the insertion of cobalt into precorrin-2, whereas in the latter this chelation reaction occurs only after the corrin ring synthesis. The second part of the Ado-CBL pathway is common for both anaerobic and aerobic routes and involves adenosylation of CR, attachment of the aminopropanol arm, and assembly of the nucleotide loop which bridges the lower ligand DMB and CR (4). The corresponding CBL genes from S. typhimurium and P. denitrificans have different traditional names, mainly using prefixes cbi and cob, respectively (Fig. 1). For example, S. typhimurium has two separate genes, cbiE and cbiT, that encode precorrin methyltransferase and decarboxylase, respectively, whereas in P. denitrificans these functions are encoded by one gene cobL. For consistency, we use the S. typhimurium names whenever possible. In particular, we assign gene names to experimentally uncharacterized genes using analysis of orthology.
The anaerobic and aerobic pathways contain several pathway-specific enzymes. Firstly, the cobalt insertion is performed by the ATP-dependent aerobic cobalt chelatase of P. denitrificans which consists of CobN, CobS, and CobT subunits, and two distinct, ATP-independent, single-subunit cobalt chelatases, CbiK from S. typhimurium and CbiX from B. megaterium, which are associated with the anaerobic pathway (8, 9, 10). Secondly, as the majority of the intermediates of the anaerobic, but not aerobic, pathway have the cobalt ion inserted into the macrocycle, the pathways could use enzymes with different substrate specifities. CobG from P. denitrificans requires molecular oxygen to oxidize precorrin 3A and is specific for the aerobic pathway (11). The respective CR oxidation of anaerobic route is likely mediated via the complexed cobalt ion, which can assume different valence states. In summary, CbiD, CbiG and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT and CobW are unique to the aerobic pathway of P. denitrificans.
In most bacteria, cobalt and other heavy-metal ions are mainly accumulated by the fast and unspecific CorA transport system (12). An additional cobalt transporter, a part of the cobalt-dependent nitrile hydratase gene cluster, was identified in Rhodococcus rhodochrous and, together with some nickel-specific transporters, belongs to the HoxN family of chemiosmotic transporters (13). Further, the ATP-dependent transport system CbiMNQO, encoded by CBL biosynthetic operon in S. typhimurium, likely mediates high-affinity transport of cobalt ions for the B12 synthesis (14). Vitamin B12, cobinamide, and other corrinoids are actively transported in enteric bacteria using the TonB-dependent outer membrane receptor BtuB in the complex with the ABC transport system BtuFCD (15).
Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B12) biosynthetic pathway in available prokaryotic genomes. Here we found a highly conserved RNA secondary structure, the regulatory B12-element, which is widely distributed in the upstream regions of cobalamin biosynthetic/transport genes in Eubacteria. In addition, the binding signal (CBL-box) for a hypothetical B12 regulator was identified in some Archaea. Search for B12-elements and CBL-boxes and positional analysis identified a large number of new candidate B12-regulated genes in various prokaryotes. Among new-assigned functions associated with the cobalamin biosynthesis there are several new types of cobalt transporters, ChlI and ChlD subunits of the CobN-dependent cobaltochelatase complex, cobalt reductase BluB, adenosyltransferase PduO, several new proteins linked to the lower ligand assembly pathway, L-threonine kinase PduX, and a large number of other hypothetical proteins. Most missing genes detected within the cobalamin biosynthetic pathways of various bacteria were identified as nonorthologous substitutes. The variable parts of the cobalamin metabolism appear to be the cobalt transport and insertion, the CobG/CbiG- and CobF/CbiD-catalyzed reactions, and the lower ligand synthesis pathway. The most interesting result of analysis of B12-elements is that B12-independent isozymes of the methionine synthase and ribonucleotide reductase are regulated by B12-elements in bacteria that have both B12-dependent and B12-independent isozymes. Moreover, B12 regulons of various bacteria are thought to include enzymes from known B12-dependent or alternative pathways.
CbiZ Adenosylcobinamide amidohydrolase (EC 3.5.1.90)= CobX in Rodionov et al paper 2003
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2003)Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem. 278: 41148-59.

Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. (2003)Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA. 9: 1084-97.

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