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Tremblay PL, Zhang T. Genetic tools for the electrotroph Sporomusa ovata and autotrophic biosynthesis. Appl Environ Microbiol 2024; 90:e0175723. [PMID: 38117058 PMCID: PMC10807461 DOI: 10.1128/aem.01757-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Sporomusa ovata is a Gram-negative acetogen of the Sporomusaceae family with a unique physiology. This anerobic bacterium is a core microbial catalyst for advanced CO2-based biotechnologies including gas fermentation, microbial electrosynthesis, and hybrid photosystem. Until now, no genetic tools exist for S. ovata, which is a critical obstacle to its optimization as an autotrophic chassis and the acquisition of knowledge about its metabolic capacities. Here, we developed an electroporation protocol for S. ovata. With this procedure, it became possible to introduce replicative plasmids such as pJIR751 and its derivatives into the acetogen. This system was then employed to demonstrate the feasibility of heterologous expression by introducing a functional β-glucuronidase enzyme under the promoters of different strengths in S. ovata. Next, a recombinant S. ovata strain producing the non-native product acetone both from an organic carbon substrate and from CO2 was constructed. Finally, a replicative plasmid capable of integrating itself on the chromosome of the acetogen was developed as a tool for genome editing, and gene deletion was demonstrated. These results indicate that S. ovata can be engineered and provides a first-generation genetic toolbox for the optimization of this biotechnological workhorse.IMPORTANCES. ovata harbors unique features that make it outperform most microbes for autotrophic biotechnologies such as a capacity to acquire electrons from different solid donors, a low H2 threshold, and efficient energy conservation mechanisms. The development of the first-generation genetic instruments described in this study is a key step toward understanding the molecular mechanisms involved in these outstanding metabolic and physiological characteristics. In addition, these tools enable the construction of recombinant S. ovata strains that can synthesize a wider range of products in an efficient manner.
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Affiliation(s)
- Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
- Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, China
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2
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Mok KC, Hallberg ZF, Procknow RR, Taga ME. Laboratory evolution of E. coli with a natural vitamin B 12 analog reveals roles for cobamide uptake and adenosylation in methionine synthase-dependent growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574217. [PMID: 38260444 PMCID: PMC10802341 DOI: 10.1101/2024.01.04.574217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The majority of bacteria use cobamides as cofactors for methionine synthesis or other diverse metabolic processes. Cobamides are a structurally diverse family of cofactors related to vitamin B12 (cobalamin), and most bacteria studied to date grow most robustly with particular cobamides. Because different environments contain varying abundances of distinct cobamides, bacteria are likely to encounter cobamides that do not function efficiently for their metabolism. Here, we performed a laboratory evolution of a cobamide-dependent strain of Escherichia coli with pseudocobalamin (pCbl), a cobamide that E. coli uses less effectively than cobalamin for MetH-dependent methionine synthesis, to identify genetic adaptations that lead to improved growth with less-preferred cobamides. After propagating and sequencing nine independent lines and validating the results by constructing targeted mutations, we found that increasing expression of the outer membrane cobamide transporter BtuB is beneficial during growth under cobamide-limiting conditions. Unexpectedly, we also found that overexpression of the cobamide adenosyltransferase BtuR confers a specific growth advantage in pCbl. Characterization of this phenotype revealed that BtuR and adenosylated cobamides contribute to optimal MetH-dependent growth. Together, these findings improve our understanding of how bacteria expand their cobamide-dependent metabolic potential.
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Affiliation(s)
- Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA U.S.A
| | - Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA U.S.A
| | - Rebecca R. Procknow
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA U.S.A
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA U.S.A
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3
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Abellon-Ruiz J, Jana K, Silale A, Frey AM, Baslé A, Trost M, Kleinekathöfer U, van den Berg B. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides. Nat Commun 2023; 14:4714. [PMID: 37543597 PMCID: PMC10404256 DOI: 10.1038/s41467-023-40427-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
Vitamin B12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B12 outer membrane transporters together with a conserved array of surface-exposed B12-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B12 with high affinities. Closing of the BtuG lid following B12 capture causes destabilisation of the bound B12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.
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Affiliation(s)
- Javier Abellon-Ruiz
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kalyanashis Jana
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew M Frey
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthias Trost
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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4
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Hallberg ZF, Seth EC, Thevasundaram K, Taga ME. Comparative Analysis of Corrinoid Profiles across Host-Associated and Environmental Samples. Biochemistry 2022; 61:2791-2796. [PMID: 36037062 DOI: 10.1021/acs.biochem.2c00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Vitamin B12 (the cyanated form of cobalamin cofactors) is best known for its essential role in human health. In addition to its function in human metabolism, cobalamin also plays important roles in microbial metabolism and can impact microbial community function. Cobalamin is a member of the structurally diverse family of cofactors known as cobamides that are produced exclusively by certain prokaryotes. Cobamides are considered shared nutrients in microbial communities because the majority of bacteria that possess cobamide-dependent enzymes cannot synthesize cobamides de novo. Furthermore, different microbes have evolved metabolic specificity for particular cobamides, and therefore, the availability of cobamides in the environment is important for cobamide-dependent microbes. Determining the cobamides present in an environment of interest is essential for understanding microbial metabolic interactions. By examining the abundances of different cobamides in diverse environments, including 10 obtained in this study, we find that, contrary to its preeminence in human metabolism, cobalamin is relatively rare in many microbial habitats. Comparison of cobamide profiles of mammalian gastrointestinal samples and wood-feeding insects reveals that host-associated cobamide abundances vary and that fecal cobamide profiles differ from those of their host gastrointestinal tracts. Environmental cobamide profiles obtained from aquatic, soil, and contaminated groundwater samples reveal that the cobamide compositions of environmental samples are highly variable. As the only commercially available cobamide, cobalamin is routinely supplied during microbial culturing efforts. However, these findings suggest that cobamides specific to a given microbiome may yield greater insight into nutrient utilization and physiological processes that occur in these habitats.
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Affiliation(s)
- Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Erica C Seth
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kersh Thevasundaram
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
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5
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Cobalamin Riboswitches Are Broadly Sensitive to Corrinoid Cofactors to Enable an Efficient Gene Regulatory Strategy. mBio 2022; 13:e0112122. [PMID: 35993747 PMCID: PMC9600662 DOI: 10.1128/mbio.01121-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In bacteria, many essential metabolic processes are controlled by riboswitches, gene regulatory RNAs that directly bind and detect metabolites. Highly specific effector binding enables riboswitches to respond to a single biologically relevant metabolite. Cobalamin riboswitches are a potential exception because over a dozen chemically similar but functionally distinct cobalamin variants (corrinoid cofactors) exist in nature. Here, we measured cobalamin riboswitch activity in vivo using a Bacillus subtilis fluorescent reporter system and found, among 38 tested riboswitches, a subset responded to corrinoids promiscuously, while others were semiselective. Analyses of chimeric riboswitches and structural models indicate, unlike other riboswitch classes, cobalamin riboswitches indirectly differentiate among corrinoids by sensing differences in their structural conformation. This regulatory strategy aligns riboswitch-corrinoid specificity with cellular corrinoid requirements in a B. subtilis model. Thus, bacteria can employ broadly sensitive riboswitches to cope with the chemical diversity of essential metabolites. IMPORTANCE Some bacterial mRNAs contain a region called a riboswitch which controls gene expression by binding to a metabolite in the cell. Typically, riboswitches sense and respond to a limited range of cellular metabolites, often just one type. In this work, we found the cobalamin (vitamin B12) riboswitch class is an exception, capable of sensing and responding to multiple variants of B12-collectively called corrinoids. We found cobalamin riboswitches vary in corrinoid specificity with some riboswitches responding to each of the corrinoids we tested, while others responding only to a subset of corrinoids. Our results suggest the latter class of riboswitches sense intrinsic conformational differences among corrinoids in order to support the corrinoid-specific needs of the cell. These findings provide insight into how bacteria sense and respond to an exceptionally diverse, often essential set of enzyme cofactors.
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6
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Mathur Y, Vartak AR, Hazra AB. Guardian of cobamide diversity: Probing the role of CobT in lower ligand activation in the biosynthesis of vitamin B 12 and other cobamide cofactors. Methods Enzymol 2022; 668:25-59. [PMID: 35589196 DOI: 10.1016/bs.mie.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Enzymes catalyze a wide variety of reactions with exquisite precision under crowded conditions within cellular environments. When encountered with a choice of small molecules in their vicinity, even though most enzymes continue to be specific about the substrate they pick, some others are able to accept a range of substrates and subsequently produce a variety of products. The biosynthesis of Vitamin B12, an essential nutrient required by humans involves a multi-substrate α-phosphoribosyltransferase enzyme CobT that activates the lower ligand of B12. Vitamin B12 is a member of the cobamide family of cofactors which share a common tetrapyrrolic corrin scaffold with a centrally coordinated cobalt ion, and an upper and a lower ligand. The structural difference between B12 and other cobamides mainly arises from variations in the lower ligand, which is attached to the activated corrin ring by CobT and other downstream enzymes. In this chapter, we describe the steps involved in identifying and reconstituting the activity of new CobT homologs by deriving lessons from those previously characterized. We then highlight biochemical techniques to study the unique properties of these homologs. Finally, we describe a pairwise substrate competition assay to rank CobT substrate preference, a general method that can be applied for the study of other multi-substrate enzymes. Overall, the analysis with CobT provides insights into the range of cobamides that can be synthesized by an organism or a community, complementing efforts to predict cobamide diversity from complex metagenomic data.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Aniket R Vartak
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India; Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, India.
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7
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Availability of vitamin B 12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. THE ISME JOURNAL 2022; 16:2002-2014. [PMID: 35585186 PMCID: PMC9296465 DOI: 10.1038/s41396-022-01250-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 01/22/2023]
Abstract
Genome analyses predict that the cofactor cobalamin (vitamin B12, called B12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B12 supply and interacts with producers. B12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5’6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate α-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B12 and α-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B12. Surprisingly, Prochlorococcus, known to produce pseudo-B12 and not B12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B12 supply in the subtropical Pacific. These findings show that availability of B12 and α-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B12-dependent enzymatic reactions on a community level.
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8
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Ma AT, Kantner DS, Beld J. Cobamide remodeling. VITAMINS AND HORMONES 2022; 119:43-63. [PMID: 35337629 DOI: 10.1016/bs.vh.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cobamides are a family of structurally-diverse cofactors which includes vitamin B12 and over a dozen natural analogs. Within the nucleotide loop structure, cobamide analogs have variable lower ligands that fall into three categories: benzimidazoles, purines, and phenols. The range of cobamide analogs that can be utilized by an organism is dependent on the specificity of its cobamide-dependent enzymes, and most bacteria are able to utilize multiple analogs but not all. Some bacteria have pathways for cobamide remodeling, a process in which imported cobamides are converted into compatible analogs. Here we discuss cobamide analog diversity and three pathways for cobamide remodeling, mediated by amidohydrolase CbiZ, phosphodiesterase CbiR, and some homologs of cobamide synthase CobS. Remodeling proteins exhibit varying degrees of specificity for cobamide substrates, reflecting different strategies to ensure that imported cobamides can be utilized.
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Affiliation(s)
- Amy T Ma
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States.
| | - Daniel S Kantner
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Joris Beld
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
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9
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Abstract
Cobamides are a family of enzyme cofactors that are required by organisms in all domains of life. Over a dozen cobamides exist in nature although only cobalamin (vitamin B12), the cobamide required by humans, has been studied extensively. Cobamides are exclusively produced by a subset of prokaryotes. Importantly, the bacteria and archaea that synthesize cobamides de novo typically produce a single type of cobamide, and furthermore, organisms that use cobamides are selective for certain cobamides. Therefore, a detailed understanding of the cobamide-dependent metabolism of an organism or microbial community of interest requires experiments performed with a variety of cobamides. A notable challenge is that cobalamin is the only cobamide that is commercially available at present. In this chapter, we describe methods to extract, purify, and quantify various cobamides from bacteria for use in laboratory experiments.
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Affiliation(s)
- Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, United States.
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10
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Kremp F, Müller V. Methanol and methyl group conversion in acetogenic bacteria: biochemistry, physiology and application. FEMS Microbiol Rev 2021; 45:5903270. [PMID: 32901799 DOI: 10.1093/femsre/fuaa040] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/29/2020] [Indexed: 12/24/2022] Open
Abstract
The production of bulk chemicals mostly depends on exhausting petroleum sources and leads to emission of greenhouse gases. Within the last decades the urgent need for alternative sources has increased and the development of bio-based processes received new attention. To avoid the competition between the use of sugars as food or fuel, other feedstocks with high availability and low cost are needed, which brought acetogenic bacteria into focus. This group of anaerobic organisms uses mixtures of CO2, CO and H2 for the production of mostly acetate and ethanol. Also methanol, a cheap and abundant bulk chemical produced from methane, is a suitable substrate for acetogenic bacteria. In methylotrophic acetogens the methyl group is transferred to the Wood-Ljungdahl pathway, a pathway to reduce CO2 to acetate via a series of C1-intermediates bound to tetrahydrofolic acid. Here we describe the biochemistry and bioenergetics of methanol conversion in the biotechnologically interesting group of anaerobic, acetogenic bacteria. Further, the bioenergetics of biochemical production from methanol is discussed.
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Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
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11
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Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. Int J Mol Sci 2021; 22:ijms22094522. [PMID: 33926061 PMCID: PMC8123684 DOI: 10.3390/ijms22094522] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Many microbial producers of coenzyme B12 family cofactors together with their metabolically interdependent pathways are comprehensively studied and successfully used both in natural ecosystems dominated by auxotrophs, including bacteria and mammals, and in the safe industrial production of vitamin B12. Metabolic reconstruction for genomic and metagenomic data and functional genomics continue to mine the microbial and genetic resources for biosynthesis of the vital vitamin B12. Availability of metabolic engineering techniques and usage of affordable and renewable sources allowed improving bioprocess of vitamins, providing a positive impact on both economics and environment. The commercial production of vitamin B12 is mainly achieved through the use of the two major industrial strains, Propionobacterium shermanii and Pseudomonas denitrificans, that involves about 30 enzymatic steps in the biosynthesis of cobalamin and completely replaces chemical synthesis. However, there are still unresolved issues in cobalamin biosynthesis that need to be elucidated for future bioprocess improvements. In the present work, we review the current state of development and challenges for cobalamin (vitamin B12) biosynthesis, describing the major and novel prospective strains, and the studies of environmental factors and genetic tools effecting on the fermentation process are reported.
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Affiliation(s)
- Larissa Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
- Correspondence:
| | - Liudmila Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Maksim Marchenok
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Oksana Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
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12
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Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila. mBio 2020; 11:mBio.02507-20. [PMID: 33293380 PMCID: PMC7733943 DOI: 10.1128/mbio.02507-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.
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13
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Uebanso T, Shimohata T, Mawatari K, Takahashi A. Functional Roles of B‐Vitamins in the Gut and Gut Microbiome. Mol Nutr Food Res 2020; 64:e2000426. [DOI: 10.1002/mnfr.202000426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
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14
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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15
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Sokolovskaya OM, Plessl T, Bailey H, Mackinnon S, Baumgartner MR, Yue WW, Froese DS, Taga ME. Naturally occurring cobalamin (B 12) analogs can function as cofactors for human methylmalonyl-CoA mutase. Biochimie 2020; 183:35-43. [PMID: 32659443 DOI: 10.1016/j.biochi.2020.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Cobalamin, commonly known as vitamin B12, is an essential micronutrient for humans because of its role as an enzyme cofactor. Cobalamin is one of over a dozen structurally related compounds - cobamides - that are found in certain foods and are produced by microorganisms in the human gut. Very little is known about how different cobamides affect B12-dependent metabolism in human cells. Here, we test in vitro how diverse cobamide cofactors affect the function of methylmalonyl-CoA mutase (MMUT), one of two cobalamin-dependent enzymes in humans. We find that, although cobalamin is the most effective cofactor for MMUT, multiple cobamides support MMUT function with differences in binding affinity (Kd), binding kinetics (kon), and concentration dependence during catalysis (KM, app). Additionally, we find that six disease-associated MMUT variants that cause cobalamin-responsive impairments in enzymatic activity also respond to other cobamides, with the extent of catalytic rescue dependent on the identity of the cobamide. Our studies challenge the exclusive focus on cobalamin in the context of human physiology, indicate that diverse cobamides can support the function of a human enzyme, and suggest future directions that will improve our understanding of the roles of different cobamides in human biology.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Henry Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK
| | - Sabrina Mackinnon
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA.
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16
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Flexible Cobamide Metabolism in Clostridioides ( Clostridium) difficile 630 Δ erm. J Bacteriol 2020; 202:JB.00584-19. [PMID: 31685533 DOI: 10.1128/jb.00584-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/26/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridioides (Clostridium) difficile is an opportunistic pathogen known for its ability to colonize the human gut under conditions of dysbiosis. Several aspects of its carbon and amino acid metabolism have been investigated, but its cobamide (vitamin B12 and related cofactors) metabolism remains largely unexplored. C. difficile has seven predicted cobamide-dependent pathways encoded in its genome in addition to a nearly complete cobamide biosynthesis pathway and a cobamide uptake system. To address the importance of cobamides to C. difficile, we studied C. difficile 630 Δerm and mutant derivatives under cobamide-dependent conditions in vitro Our results show that C. difficile can use a surprisingly diverse array of cobamides for methionine and deoxyribonucleotide synthesis and can use alternative metabolites or enzymes, respectively, to bypass these cobamide-dependent processes. C. difficile 630 Δerm produces the cobamide pseudocobalamin when provided the early precursor 5-aminolevulinic acid or the late intermediate cobinamide (Cbi) and produces other cobamides if provided an alternative lower ligand. The ability of C. difficile 630 Δerm to take up cobamides and Cbi at micromolar or lower concentrations requires the transporter BtuFCD. Genomic analysis revealed genetic variations in the btuFCD loci of different C. difficile strains, which may result in differences in the ability to take up cobamides and Cbi. These results together demonstrate that, like other aspects of its physiology, cobamide metabolism in C. difficile is versatile.IMPORTANCE The ability of the opportunistic pathogen Clostridioides difficile to cause disease is closely linked to its propensity to adapt to conditions created by dysbiosis of the human gut microbiota. The cobamide (vitamin B12) metabolism of C. difficile has been underexplored, although it has seven metabolic pathways that are predicted to require cobamide-dependent enzymes. Here, we show that C. difficile cobamide metabolism is versatile, as it can use a surprisingly wide variety of cobamides and has alternative functions that can bypass some of its cobamide requirements. Furthermore, C. difficile does not synthesize cobamides de novo but produces them when given cobamide precursors. A better understanding of C. difficile cobamide metabolism may lead to new strategies to treat and prevent C. difficile-associated disease.
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17
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Ma AT, Tyrell B, Beld J. Specificity of cobamide remodeling, uptake and utilization in Vibrio cholerae. Mol Microbiol 2019; 113:89-102. [PMID: 31609521 DOI: 10.1111/mmi.14402] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2019] [Indexed: 12/11/2022]
Abstract
Cobamides are a group of compounds including vitamin B12 that can vary at the lower base position of the nucleotide loop. They are synthesized de novo by only a subset of prokaryotes, but some organisms encode partial biosynthesis pathways for converting one variant to another (remodeling) or completing biosynthesis from an intermediate (corrinoid salvaging). Here, we explore the cobamide specificity in Vibrio cholerae through examination of three natural variants representing major cobamide groups: commercially available cobalamin, and isolated pseudocobalamin and p-cresolylcobamide. We show that BtuB, the outer membrane corrinoid transporter, mediates the uptake of all three variants and the intermediate cobinamide. Our previous work suggested that V. cholerae could convert pseudocobalamin produced by cyanobacteria into cobalamin. In this work, cobamide specificity in V. cholerae is demonstrated by remodeling of pseudocobalamin and salvaging of cobinamide to produce cobalamin. Cobamide remodeling in V. cholerae is distinct from the canonical pathway requiring amidohydrolase CbiZ, and heterologous expression of V. cholerae CobS was sufficient for remodeling. Furthermore, function of V. cholerae cobamide-dependent methionine synthase MetH was robustly supported by cobalamin and p-cresolylcobamide, but not pseudocobalamin. Notably, the inability of V. cholerae to produce and utilize pseudocobalamin contrasts with enteric bacteria like Salmonella.
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Affiliation(s)
- Amy T Ma
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Breanna Tyrell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
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18
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Gude S, Taga ME. Multi-faceted approaches to discovering and predicting microbial nutritional interactions. Curr Opin Biotechnol 2019; 62:58-64. [PMID: 31597114 DOI: 10.1016/j.copbio.2019.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/07/2023]
Abstract
Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B12 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches.
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Affiliation(s)
- Sebastian Gude
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA.
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19
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Puentes Jácome LA, Wang PH, Molenda O, Li YXJJ, Islam MA, Edwards EA. Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides-Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11364-11374. [PMID: 31441646 DOI: 10.1021/acs.est.9b02339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichloroethene (TCE) bioremediation has been demonstrated at field sites using microbial cultures harboring TCE-respiring Dehalococcoides whose growth is cobalamin (vitamin B12)-dependent. Bioaugmentation cultures grown ex situ with ample exogenous vitamins and at neutral pH may become vitamin-limited or inhibited by acidic pH once injected into field sites, resulting in incomplete TCE dechlorination and accumulation of vinyl chloride (VC). Here, we report growth of the Dehalococcoides-containing bioaugmentation culture KB-1 in a TCE-amended mineral medium devoid of vitamins and in a VC-amended mineral medium at low pH (6.0 and 5.5). In these cultures, Acetobacterium, which can synthesize 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, and Sporomusa are dominant acetogens. At neutral pH, Acetobacterium supports complete TCE dechlorination by Dehalococcoides at millimolar levels with a substantial increase in cobalamin (∼20-fold). Sustained dechlorination of VC to ethene was achieved at pH as low as 5.5. Below pH 5.0, dechlorination was not stimulated by DMB supplementation but was restored by raising pH to neutral. Cell-extract assays revealed that vinyl chloride reductase activity declines significantly below pH 6.0 and is undetectable below pH 5.0. This study highlights the importance of cobamide-producing populations and pH in microbial dechlorinating communities for successful bioremediation at field sites.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Yi Xuan Jine-Jine Li
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - M Ahsanul Islam
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
- Department of Cell and Systems Biology , University of Toronto , Toronto , Ontario M5S 3G5 , Canada
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20
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Sokolovskaya OM, Mok KC, Park JD, Tran JLA, Quanstrom KA, Taga ME. Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme. mBio 2019; 10:e01303-19. [PMID: 31551329 PMCID: PMC6759758 DOI: 10.1128/mbio.01303-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/23/2019] [Indexed: 12/25/2022] Open
Abstract
Cobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl coenzyme A (CoA) mutase (MCM). The in vitro binding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCM in vitro largely correlate with in vivo cobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria.IMPORTANCE Cobamides, including vitamin B12, are enzyme cofactors used by organisms in all domains of life. Cobamides are structurally diverse, and microbial growth and metabolism vary based on cobamide structure. Understanding cobamide preference in microorganisms is important given that cobamides are widely used and appear to mediate microbial interactions in host-associated and aquatic environments. Until now, the biochemical basis for cobamide preferences was largely unknown. In this study, we analyzed the effects of the structural diversity of cobamides on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). We found that very small changes in cobamide structure could dramatically affect the binding affinity of cobamides to MCM. Strikingly, cobamide-dependent growth of a model bacterium, Sinorhizobium meliloti, largely correlated with the cofactor binding selectivity of S. meliloti MCM, emphasizing the importance of cobamide-dependent enzyme selectivity in bacterial growth and cobamide-mediated microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
- Department of Chemistry, University of California Berkeley, Berkeley, California, USA
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jong Duk Park
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jennifer L A Tran
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Kathryn A Quanstrom
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
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21
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Schubert T, von Reuß SH, Kunze C, Paetz C, Kruse S, Brand-Schön P, Nelly AM, Nüske J, Diekert G. Guided cobamide biosynthesis for heterologous production of reductive dehalogenases. Microb Biotechnol 2018; 12:346-359. [PMID: 30549216 PMCID: PMC6389850 DOI: 10.1111/1751-7915.13339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 12/01/2022] Open
Abstract
Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide‐respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB‐2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5‐dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3‐chloro‐4‐hydroxy‐phenylacetate‐converting enzyme RdhA6 and the 3,5‐dichlorophenol‐dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceAY51) appeared to be non‐selective towards different Cbas. However, the functional production of the 1,2‐dichloroethane‐dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6‐dimethylbenzimidazolyl‐Cba, but substantially enhanced in cells that incorporated 5‐methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.
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Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Stephan H von Reuß
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Cindy Kunze
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Christian Paetz
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Stefan Kruse
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Peggy Brand-Schön
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Anita Mac Nelly
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Jörg Nüske
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
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22
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Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. ISME JOURNAL 2018; 13:789-804. [PMID: 30429574 PMCID: PMC6461909 DOI: 10.1038/s41396-018-0304-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/14/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022]
Abstract
The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.
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23
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Stability of vitamin B12 with the protection of whey proteins and their effects on the gut microbiome. Food Chem 2018; 276:298-306. [PMID: 30409598 DOI: 10.1016/j.foodchem.2018.10.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 09/28/2018] [Accepted: 10/06/2018] [Indexed: 01/17/2023]
Abstract
Cobalamin degrades in the presence of light and heat, which causes spectral changes and loss of coenzyme activity. In the presence of beta-lactoglobulin or alpha-lactalbumin, the thermal- and photostabilities of adenosylcobalamin (ADCBL) and cyanocobalamin (CNCBL) are increased by 10-30%. Similarly, the stabilities of ADCBL and CNCBL are increased in the presence of whey proteins by 19.7% and 2.2%, respectively, when tested in gastric juice for 2 h. Due to the limited absorption of cobalamin during digestion, excess cobalamin can enter the colon and modulate the gut microbiome. In a colonic model in vitro, supplementation with cobalamin and whey enhanced the proportions of Firmicutes and Bacteroidetes spp. and reduced those of Proteobacteria spp., which includes pathogens such as Escherichia and Shigella spp., and Pseudomonas spp. Thus, while complex formation could improve the stability and bioavailability of cobalamin, these complexes might also mediate gut microecology to influence human nutrition and health.
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24
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Yan J, Bi M, Bourdon AK, Farmer AT, Wang PH, Molenda O, Quaile AT, Jiang N, Yang Y, Yin Y, Şimşir B, Campagna SR, Edwards EA, Löffler FE. Purinyl-cobamide is a native prosthetic group of reductive dehalogenases. Nat Chem Biol 2017; 14:8-14. [PMID: 29106396 PMCID: PMC6081238 DOI: 10.1038/nchembio.2512] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/02/2017] [Indexed: 01/21/2023]
Abstract
Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense. Cobamides featuring different lower bases are not functionally equivalent, and purinyl-Cba elicits different physiological responses in corrinoid-auxotrophic, organohalide-respiring bacteria. Given that cobamide-dependent enzymes catalyze key steps in essential metabolic pathways, the discovery of a novel cobamide structure and the realization that lower bases can effectively modulate enzyme activities generate opportunities to manipulate functionalities of microbiomes.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, P.R. China.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Meng Bi
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Yi Yang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Burcu Şimşir
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
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25
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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions. mSystems 2017; 2:mSystems00038-17. [PMID: 29104938 PMCID: PMC5663940 DOI: 10.1128/msystems.00038-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022] Open
Abstract
Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems. Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.
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26
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Frank SA. Receptor uptake arrays for vitamin B 12, siderophores, and glycans shape bacterial communities. Ecol Evol 2017; 7:10175-10195. [PMID: 29238546 PMCID: PMC5723603 DOI: 10.1002/ece3.3544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/20/2017] [Accepted: 09/28/2017] [Indexed: 01/15/2023] Open
Abstract
Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.
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Affiliation(s)
- Steven A. Frank
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
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Schubert T. The organohalide-respiring bacterium Sulfurospirillum multivorans: a natural source for unusual cobamides. World J Microbiol Biotechnol 2017; 33:93. [DOI: 10.1007/s11274-017-2258-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/01/2017] [Indexed: 01/27/2023]
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28
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Abreu NA, Taga ME. Decoding molecular interactions in microbial communities. FEMS Microbiol Rev 2016; 40:648-63. [PMID: 27417261 DOI: 10.1093/femsre/fuw019] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 12/21/2022] Open
Abstract
Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia.
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Affiliation(s)
- Nicole A Abreu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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29
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Yan J, Şimşir B, Farmer AT, Bi M, Yang Y, Campagna SR, Löffler FE. The corrinoid cofactor of reductive dehalogenases affects dechlorination rates and extents in organohalide-respiring Dehalococcoides mccartyi. ISME JOURNAL 2015; 10:1092-101. [PMID: 26555247 DOI: 10.1038/ismej.2015.197] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/09/2015] [Accepted: 09/22/2015] [Indexed: 12/20/2022]
Abstract
Corrinoid auxotrophic organohalide-respiring Dehalococcoides mccartyi (Dhc) strains are keystone bacteria for reductive dechlorination of toxic and carcinogenic chloroorganic contaminants. We demonstrate that the lower base attached to the essential corrinoid cofactor of reductive dehalogenase (RDase) enzyme systems modulates dechlorination activity and affects the vinyl chloride (VC) RDases BvcA and VcrA differently. Amendment of 5,6-dimethylbenzimidazolyl-cobamide (DMB-Cba) to Dhc strain BAV1 and strain GT cultures supported cis-1,2-dichloroethene-to-ethene reductive dechlorination at rates of 107.0 (±12.0) μM and 67.4 (±1.4) μM Cl(-) released per day, respectively. Strain BAV1, expressing the BvcA RDase, reductively dechlorinated VC to ethene, although at up to fivefold lower rates in cultures amended with cobamides carrying 5-methylbenzimidazole (5-MeBza), 5-methoxybenzimidazole (5-OMeBza) or benzimidazole (Bza) as the lower base. In contrast, strain GT harboring the VcrA RDase failed to grow and dechlorinate VC to ethene in medium amended with 5-OMeBza-Cba or Bza-Cba. The amendment with DMB to inactive strain GT cultures restored the VC-to-ethene-dechlorinating phenotype and intracellular DMB-Cba was produced, demonstrating cobamide uptake and remodeling. The distinct responses of Dhc strains with BvcA versus VcrA RDases to different cobamides implicate that the lower base exerts control over Dhc reductive dechlorination rates and extents (that is, detoxification), and therefore the dynamics of Dhc strains with discrete reductive dechlorination capabilities. These findings emphasize that the role of the corrinoid/lower base synthesizing community must be understood to predict strain-specific Dhc activity and achieve efficacious contaminated site cleanup.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Burcu Şimşir
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Meng Bi
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Yi Yang
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
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30
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Denman SE, Martinez Fernandez G, Shinkai T, Mitsumori M, McSweeney CS. Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog. Front Microbiol 2015; 6:1087. [PMID: 26528253 PMCID: PMC4602129 DOI: 10.3389/fmicb.2015.01087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/22/2015] [Indexed: 12/29/2022] Open
Abstract
Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population and functional shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of H2-consuming Prevotella and Selenomonas spp. Metagenomic analysis of propionate production pathways was dominated by genomic content from these species. Reductive acetogenic marker gene libraries and metagenomics analysis indicate that reductive acetogenic species do not play a major role in the BCM treated rumen.
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Affiliation(s)
- Stuart E Denman
- CSIRO, Agriculture Flagship, Queensland Bioscience Precinct St. Lucia, QLD, Australia
| | | | - Takumi Shinkai
- National Institute of Livestock and Grassland Science Tsukuba, Japan
| | - Makoto Mitsumori
- National Institute of Livestock and Grassland Science Tsukuba, Japan
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31
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Visser M, Pieterse MM, Pinkse MWH, Nijsse B, Verhaert PDEM, de Vos WM, Schaap PJ, Stams AJM. Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis. Environ Microbiol 2015; 18:2843-55. [PMID: 26147498 DOI: 10.1111/1462-2920.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/19/2015] [Accepted: 06/26/2015] [Indexed: 01/06/2023]
Abstract
The Sporomusa genus comprises anaerobic spore-forming acetogenic bacteria that stain Gram-negative. Sporomusa species typically grow with one-carbon substrates and N-methylated compounds. In the degradation of these compounds methyltransferases are involved. In addition, Sporomusa species can grow autotrophically with H2 and CO2 , and use a variety of sugars for acetogenic growth. Here we describe a genome analysis of Sporomusa strain An4 and a proteome analysis of cells grown under five different conditions. Comparison of the genomes of Sporomusa strain An4 and Sporomusa ovata strain H1 indicated that An4 is a S. ovata strain. Proteome analysis showed a high abundance of several methyltransferases, predominantly trimethylamine methyltransferases, during growth with betaine, whereas trimethylamine is one of the main end-products of betaine degradation. In methanol degradation methyltransferases are also involved. In methanol-utilizing methanogens, two methyltransferases catalyse methanol conversion, methyltransferase 1 composed of subunits MtaB and MtaC and methyltransferase 2, also called MtaA. The two methyltransferase 1 subunits MtaB and MtaC were highly abundant when strain An4 was grown with methanol. However, instead of MtaA a methyltetrahydrofolate methyltransferase was synthesized. We propose a novel methanol degradation pathway in Sporomusa strain An4 that uses a methyltetrahydrofolate methyltransferase instead of MtaA.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Mervin M Pieterse
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Martijn W H Pinkse
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter D E M Verhaert
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Department of Veterinary Biosciences, Helsinki University, Helsinki, Finland.,Department of Bacteriology and Immunology, Helsinki University, Helsinki, Finland
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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32
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Crofts TS, Hazra AB, Tran JLA, Sokolovskaya OM, Osadchiy V, Ad O, Pelton J, Bauer S, Taga ME. Regiospecific Formation of Cobamide Isomers Is Directed by CobT. Biochemistry 2014; 53:7805-15. [DOI: 10.1021/bi501147d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Terence S. Crofts
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Amrita B. Hazra
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Jennifer LA Tran
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Olga M. Sokolovskaya
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Vadim Osadchiy
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Omer Ad
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Jeffrey Pelton
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Stefan Bauer
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Michiko E. Taga
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
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33
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Crofts TS, Men Y, Alvarez-Cohen L, Taga ME. A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples. Front Microbiol 2014; 5:592. [PMID: 25431570 PMCID: PMC4230183 DOI: 10.3389/fmicb.2014.00592] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/20/2014] [Indexed: 12/13/2022] Open
Abstract
Cobamides are a family of enzyme cofactors that include vitamin B12 (cobalamin) and are produced solely by prokaryotes. Structural variability in the lower axial ligand has been observed in cobamides produced by diverse organisms. Of the three classes of lower ligands, the benzimidazoles are uniquely found in cobamides, whereas the purine and phenolic bases have additional biological functions. Many organisms acquire cobamides by salvaging and remodeling cobamides or their precursors from the environment. These processes require free benzimidazoles for incorporation as lower ligands, though the presence of benzimidazoles in the environment has not been previously investigated. Here, we report a new purification method and bioassay to measure the total free benzimidazole content of samples from microbial communities and laboratory media components. The bioassay relies on the “calcofluor-bright” phenotype of a bluB mutant of the model cobalamin-producing bacterium Sinorhizobium meliloti. The concentrations of individual benzimidazoles in these samples were measured by liquid chromatography-tandem mass spectrometry. Several benzimidazoles were detected in subpicomolar to subnanomolar concentrations in host-associated and environmental samples. In addition, benzimidazoles were found to be common contaminants of laboratory media components. These results suggest that benzimidazoles present in the environment and in laboratory media have the potential to influence microbial metabolic activities.
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Affiliation(s)
- Terence S Crofts
- Department of Plant and Microbial Biology, University of California at Berkeley Berkeley, CA, USA
| | - Yujie Men
- Department of Civil and Environmental Engineering, University of California at Berkeley Berkeley, CA, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California at Berkeley Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California at Berkeley Berkeley, CA, USA
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34
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Abstract
The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities.
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Affiliation(s)
- Patrick H Degnan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA.
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35
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Seth EC, Taga ME. Nutrient cross-feeding in the microbial world. Front Microbiol 2014; 5:350. [PMID: 25071756 PMCID: PMC4086397 DOI: 10.3389/fmicb.2014.00350] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/23/2014] [Indexed: 12/25/2022] Open
Abstract
The stability and function of a microbial community depends on nutritional interactions among community members such as the cross-feeding of essential small molecules synthesized by a subset of the population. In this review, we describe examples of microbe–microbe and microbe–host cofactor cross-feeding, a type of interaction that influences the forms of metabolism carried out within a community. Cofactor cross-feeding can contribute to both the health and nutrition of a host organism, the virulence and persistence of pathogens, and the composition and function of environmental communities. By examining the impact of shared cofactors on microbes from pure culture to natural communities, we stand to gain a better understanding of the interactions that link microbes together, which may ultimately be a key to developing strategies for manipulating microbial communities with human health, agricultural, and environmental implications.
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Affiliation(s)
- Erica C Seth
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
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36
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Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl Environ Microbiol 2014; 80:2133-41. [PMID: 24463969 DOI: 10.1128/aem.03477-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Corrinoids are essential cofactors of reductive dehalogenases in Dehalococcoides mccartyi, an important bacterium in bioremediation, yet sequenced D. mccartyi strains do not possess the complete pathway for de novo corrinoid biosynthesis. Pelosinus sp. and Desulfovibrio sp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growing D. mccartyi strain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)- and lactate-amended medium in cocultures with Desulfovibrio vulgaris Hildenborough (DvH) or Pelosinus fermentans R7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.
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37
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Degnan PH, Barry NA, Mok KC, Taga ME, Goodman AL. Human gut microbes use multiple transporters to distinguish vitamin B₁₂ analogs and compete in the gut. Cell Host Microbe 2014; 15:47-57. [PMID: 24439897 PMCID: PMC3923405 DOI: 10.1016/j.chom.2013.12.007] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/13/2013] [Accepted: 12/18/2013] [Indexed: 12/20/2022]
Abstract
Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B₁₂ transporters that in at least two cases confer a competitive advantage in the presence of distinct B₁₂ analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host.
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Affiliation(s)
- Patrick H Degnan
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA
| | - Natasha A Barry
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA
| | - Kenny C Mok
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA.
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38
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Keller S, Ruetz M, Kunze C, Kräutler B, Diekert G, Schubert T. Exogenous 5,6-dimethylbenzimidazole caused production of a non-functional tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans. Environ Microbiol 2013; 16:3361-9. [PMID: 24433392 DOI: 10.1111/1462-2920.12268] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/09/2013] [Accepted: 08/26/2013] [Indexed: 11/26/2022]
Abstract
Corrinoid-dependent reductive dehalogenation is mediated by phylogenetically diverse anaerobic bacteria that either synthesize corrinoids de novo or are dependent on corrinoid salvaging from the environment. The tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram-negative Epsilonproteobacterium Sulfurospirillum multivorans harbours a norpseudo-B12 as corrinoid cofactor. Norpseudo-B12 differs from coenzyme B12 in the nucleotide loop structure. Adenine instead of 5,6-dimethylbenzimidazole (DMB) serves as lower ligand base of the central cobalt ion, and the nucleotide loop of norpseudo-B12 lacks a methyl group at position 176. In this study, S. multivorans was grown anaerobically with PCE in the presence of DMB. At a DMB concentration of 25 μM, the adenine moiety in the nucleotide loop of norpseudo-B12 was quantitatively replaced by DMB. The formation of the DMB-containing nor-B12 severely affected PCE-dependent growth and the PceA activity. In DMB-treated cells processing of the cytoplasmic PceA precursor was impeded, a result pointing to retarded cofactor incorporation. PceA enriched from cells cultivated with DMB contained nor-B12 . Nor-B12 purified from cells grown in the presence of DMB mediated the abiotic reductive dehalogenation of trichloroacetate to dichloroacetate at a 25-fold lower rate in comparison with norpseudo-B12 , a fact underpinning the relevance of norpseudo-B12 as efficient catalyst for reductive dehalogenation in general.
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Affiliation(s)
- Sebastian Keller
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
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39
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Hazra AB, Tran JLA, Crofts TS, Taga ME. Analysis of substrate specificity in CobT homologs reveals widespread preference for DMB, the lower axial ligand of vitamin B(12). ACTA ACUST UNITED AC 2013; 20:1275-85. [PMID: 24055005 DOI: 10.1016/j.chembiol.2013.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/02/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Cobamides such as vitamin B12 (cobalamin) are produced exclusively by prokaryotes and used by many other organisms as cofactors for diverse metabolic processes. Cobamides are cobalt-containing tetrapyrroles with upper and lower axial ligands. The structure of the lower ligand varies in cobamides produced by different bacteria. We investigated the biochemical basis of this structural variability by exploring the reactivity of homologs of CobT, the enzyme responsible for activating lower ligand bases for incorporation into cobamides. Our results show that CobT enzymes can activate a range of lower ligand substrates, and the majority of the enzymes tested preferentially attach 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin. This suggests that many bacteria that synthesize cobamides other than cobalamin in pure culture may produce cobalamin in mixed communities by attaching DMB when it is available in the environment.
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Affiliation(s)
- Amrita B Hazra
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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40
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Crofts TS, Seth EC, Hazra AB, Taga ME. Cobamide structure depends on both lower ligand availability and CobT substrate specificity. ACTA ACUST UNITED AC 2013; 20:1265-74. [PMID: 24055007 DOI: 10.1016/j.chembiol.2013.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/01/2013] [Accepted: 08/05/2013] [Indexed: 11/16/2022]
Abstract
Cobamides are members of the vitamin B12 family of cofactors that function in a variety of metabolic processes and are synthesized only by prokaryotes. Cobamides produced by different organisms vary in the structure of the lower axial ligand. Here we explore the molecular factors that control specificity in the incorporation of lower ligand bases into cobamides. We find that the cobT gene product, which activates lower ligand bases for attachment, limits the range of lower ligand bases that can be incorporated by bacteria. Furthermore, we demonstrate that the substrate specificity of CobT can be predictably altered by changing two active site residues. These results demonstrate that sequence variations in cobT homologs contribute to cobamide structural diversity. This analysis could open new routes to engineering specific cobamide production and understanding cobamide-dependent processes.
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Affiliation(s)
- Terence S Crofts
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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