The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli

Abstract

The enteric bacterium Escherichia coli synthesizes cobalamin (coenzyme B 12 ) only when provided with the complex intermediate cobinamide. Three cobalamin biosynthetic genes have been cloned from Escherichia coli K-12, and their nucleotide sequences have been determined. The three genes form an operon (cob) under the control of several promoters and are induced by cobinamide, a precursor of cobalamin. The cob operon of E. coli comprises the cobU gene, encoding the bifunctional cobinamide kinase-guanylyltransferase; the cobS gene, encoding cobalamin synthetase; and the cobT gene, encoding dimethylbenzimidazole phosphoribosyltransferase. The physiological roles of these sequences were verified by the isolation of Tn10 insertion mutations in the cobS and cobT genes. All genes were named after their Salmonella typhimurium homologs and are located at the corresponding positions on the E. coli genetic map. Although the nucleotide sequences of the Salmonella cob genes and the E. coli cob genes are homologous, they are too divergent to have been derived from an operon present in their most recent common ancestor. On the basis of comparisons of G؉C content, codon usage bias, dinucleotide frequencies, and patterns of synonymous and nonsynonymous substitutions, we conclude that the cob operon was introduced into the Salmonella genome from an exogenous source. The cob operon of E. coli may be related to cobalamin synthetic genes now found among non-Salmonella enteric bacteria.Although commonly touted as one of the largest and oldest of the cofactors participating in modern biochemistry (20,23,59,60), the physiological importance of cobalamin (coenzyme B 12 ), especially among enteric bacteria, has remained enigmatic (58, 63). Cobalamin is derived from uroporphyrinogen III, a precursor in the synthesis of heme, siroheme, and chlorophylls as well as cobamides (Fig. 1). The conversion of uroporphyrinogen III to the complex intermediate cobinamide is referred to as part I of the biosynthetic pathway (hereafter designated CobI). Part II of the pathway (CobII) entails the biosynthesis of dimethylbenzimidazole (DMB) from probable flavin precursors (11,27,39). The covalent linkage of cobinamide, DMB, and a phosphoribosyl group donated by nicotinate mononucleotide is achieved by part III of the pathway (CobIII). Although most enteric bacteria can synthesize cobalamin de novo under either aerobic or anaerobic conditions (38), Escherichia coli synthesizes cobalamin only when provided with the complex intermediate cobinamide (38, 66); therefore, E. coli performs only parts II and III of the cobalamin biosynthetic pathway.The cobalamin biosynthetic genes in the closely related enteric bacterium Salmonella typhimurium have been characterized, and most constitute a large, 20-gene operon located at min 41 on the genetic map (28, 29, 52). It has been proposed that these genes are not ancestral to the Salmonella chromosome but have been introduced by horizontal transfer at or following the divergence of the salmonellae from Escherichia speci...

Global Gene Expression Profiling in Escherichia coliK12

“…Other studies in Salmonella typhimurium establish that the arcA gene product activates the expression of the cob operon required for cobalamin synthesis (53). Therefore, it is again unclear whether or not the increases in the cobU and cobT genes reported in Table II are the result of direct or indirect effects of IHF.…”

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

“…Although this enzyme is a phosphoribosyltransferase, it does not utilize PRPP as a substrate. Rather, the 5-phosphoribosyl moiety is detached from the nicotinamide mononucleotide and is added to the 5,6-dimethylbenzimidazole, and thus one N-glycoside bond is replaced by a second N-glycoside bond (293,294). A variant of this enzyme (EC 2.4.2.55) has been characterized from the bacterium Sporomusa ovata.…”

Effect of mutations in the transmethylase and dehydrogenase/chelatase domains of sirohaem synthase (CysG) on sirohaem and cobalamin biosynthesis

“…it contains the CobII and CobIII genes [36]. However, the closely related enteric species Salmonella typhimurium possesses all the genes for cobalamin biosynthesis de no o, although cobalamin synthesis is attained only under anaerobic conditions [37].…”