Role of the precorrin 6‐X reductase gene in cobamide biosynthesis in Methanococcus maripaludis

Kim, Wonduck; Major, Tiffany A.; Whitman, William B.

doi:10.1155/2005/903614

Cited by 8 publications

(6 citation statements)

References 30 publications

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“…To confirm de novo cobalamin production in M. smegmatis, we generated an unmarked, in-frame deletion of cobK (Figure S1A, C-E). Homologs of this gene, which encodes a putative precorrin-6x reductase required for corrin ring synthesis (5,11,20), have been shown in other organisms to be required for corrin ring synthesis (21)(22)(23). To ensure that all phenotypes reflected the consequences of the specific gene deletions and/or disruptions, and were not confounded by off-site mutations, the parental strain on May 10, 2021 by guest http://jb.asm.org/ Downloaded from and derivative mutants were subjected to whole-genome sequencing.…”

Section: The De Novo Cobalamin Biosynthesis Pathway Is Functional In M Smegmatismentioning

confidence: 99%

De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis

et al. 2021

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Cobalamin is an essential co-factor in all domains of life, yet its biosynthesis is restricted to some bacteria and archaea. Mycobacterium smegmatis, an environmental saprophyte frequently used as surrogate for the obligate human pathogen, M. tuberculosis, carries approximately 30 genes predicted to be involved in de novo cobalamin biosynthesis. M. smegmatis also encodes multiple cobalamin-dependent enzymes, including MetH, a methionine synthase which catalyzes the final reaction in methionine biosynthesis. In addition to metH, M. smegmatis possesses a cobalamin-independent methionine synthase, metE, suggesting that enzyme use – MetH or MetE – is regulated by cobalamin availability. Consistent with this notion, we previously described a cobalamin-sensing riboswitch controlling metE expression in M. tuberculosis. Here, we apply a targeted mass spectrometry-based approach to confirm de novo cobalamin biosynthesis in M. smegmatis during aerobic growth in vitro. We also demonstrate that M. smegmatis can transport and assimilate exogenous cyanocobalamin (CNCbl; a.k.a. vitamin B12) and its precursor, dicyanocobinamide ((CN)2Cbi). However, the uptake of CNCbl and (CN)2Cbi in this organism is restricted and seems dependent on the conditional essentiality of the cobalamin-dependent methionine synthase. Using gene and protein expression analyses combined with single-cell growth kinetics and live-cell time-lapse microscopy, we show that transcription and translation of metE are strongly attenuated by endogenous cobalamin. These results support the inference that metH essentiality in M. smegmatis results from riboswitch-mediated repression of MetE expression. Moreover, differences observed in cobalamin-dependent metabolism between M. smegmatis and M. tuberculosis provide some insight into the selective pressures which might have shaped mycobacterial metabolism for pathogenicity. IMPORTANCE Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis as human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remain poorly understood. Using the non-pathogenic saprophyte, M. smegmatis, we investigated the production of cobalamin, transport and assimilation of cobalamin precursors, and the role of cobalamin in regulating methionine biosynthesis. We confirm constitutive de novo cobalamin biosynthesis in M. smegmatis, in contrast with M. tuberculosis, which appears to lack de novo cobalamin biosynthetic capacity. We also show that uptake of cyanocobalamin (vitamin B12) and its precursors is restricted in M. smegmatis, apparently depending on the co-factor requirements of the cobalamin-dependent methionine synthase. These observations establish M. smegmatis as informative foil to elucidate key metabolic adaptations enabling mycobacterial pathogenicity.

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Section: The De Novo Cobalamin Biosynthesis Pathway Is Functional In M Smegmatismentioning

confidence: 99%

De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis

et al. 2021

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“…N. brevis genome (SI Appendix, Dataset S2). A near-complete pathway for cobalamin (B 12 ) synthesis was also identified in the genome, missing only precorrin-6X reductase (cbiJ-cobK), which is also lacking in nearly all known cobalamin-producing archaea (34) except Methanococcus (35). Proteins within each of these pathways were detected in the proteome.…”

Section: Resultsmentioning

confidence: 99%

Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Santoro

Dupont

Richter

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

265

239

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Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.nitrification | marine metagenomics | genome streamlining | archaea

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“…They carry the genes for 19 of the 20 steps required, including cbiX, the gene for the second and characteristic step for the anaerobic pathway. Although Leptospirillum groups II and III lack the genes cbiJ and cobK, this function could be complemented at very low levels by alternative nonspecific reactions as in Methanococcus maripaludis (37). It is possible that both organisms could also produce cobalamin through the aerobic pathway; most of the steps are shared between pathways, and they contain cobB, the aerobic alternative to cbiA.…”

Section: Comparative Genomics (I) Energy Metabolism (A) Electron Trmentioning

confidence: 99%

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “ Leptospirillum rubarum ” (Group II) and “ Leptospirillum ferrodiazotrophum ” (Group III) Bacteria in Acid Mine Drainage Biofilms

Goltsman

Denef

Singer

et al. 2009

Appl Environ Microbiol

167

155

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We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic ironoxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyldependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.To understand how microorganisms contribute to biogeochemical cycling, it is necessary to determine the roles of uncultivated as well as cultivated groups and to establish how these roles vary during ecological succession and when environmental conditions change. Shotgun genomic sequencing (metagenomics) has opened new opportunities for cultureindependent studies of microbial communities. Examples include investigations of acid mine drainage (AMD) biofilm communities (4, 43, 75), symbiosis in a marine worm involving sulfur-oxidizing and sulfate-reducing bacteria (85), and enhanced biological phosphorous removal by sludge communities (32). From these genomic data sets, it has been possible to reconstruct aspects of the metabolism of individual organisms (32) and coexisting community members (29, 75) and to identify which organisms contribute community-essential functions (75). An interesting question relates to how differences in metabolic potential between organisms from the same lineage allow them to occupy distinct niches. Identification of potentially adaptive traits in closely related organisms is also important from an evolutionary perspective.Genomic data do not...

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Role of the precorrin 6‐X reductase gene in cobamide biosynthesis in Methanococcus maripaludis

Cited by 8 publications

References 30 publications

De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis

De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis

Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “ Leptospirillum rubarum ” (Group II) and “ Leptospirillum ferrodiazotrophum ” (Group III) Bacteria in Acid Mine Drainage Biofilms

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