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J. Biol. Chem., Vol. 278, Issue 42, 41148-41159, October 17, 2003

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Comparative Genomics of the Vitamin B₁₂ Metabolism and Regulation in Prokaryotes^*,

Dmitry A. Rodionov   ¶, Alexey G. Vitreschak  ||, Andrey A. Mironov   and Mikhail S. Gelfand  

From the State Scientific Center GosNIIGenetika, Moscow 113545, Russia, the ^||Institute for Problems of Information Transmission, Moscow 101447, Russia, and Integrated Genomics-Moscow, P.O. Box 348, Moscow 117333, Russia

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. A search for B12 elements and CBL-boxes and positional analysis identified a large number of new candidate B₁₂-regulated genes in various prokaryotes. Among newly 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.

Received for publication, June 3, 2003

^* This work was supported in part by Howard Hughes Medical Institute Grant 55000309 and Ludwig Institute for Cancer Research Grant CRDF RBO-1268. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains an additional table.

^¶ To whom correspondence should be addressed. Fax: 7-095-315-05-01; E-mail: rodionov{at}genetika.ru.

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