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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
Bacteria encounter chemically similar nutrients in their environment that impact their growth in distinct ways. Among such nutrients are cobamides, the structurally diverse family of cofactors related to vitamin B12 (cobalamin), which function as cofactors for diverse metabolic processes. Given that different environments contain varying abundances of different cobamides, bacteria are likely to encounter cobamides that enable them to grow robustly as well as those 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 mutations that increase expression of the outer membrane cobamide transporter BtuB are 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 the latter 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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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B 12. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580003. [PMID: 38405713 PMCID: PMC10888822 DOI: 10.1101/2024.02.12.580003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Alexa M. Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zoila I. Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Ella T. Sieradzki
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, 94550 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | - Jillian F. Banfield
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Hans K. Carlson
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Mary K. Firestone
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12. THE ISME JOURNAL 2024; 18:wrae094. [PMID: 38832716 PMCID: PMC11287211 DOI: 10.1093/ismejo/wrae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ella T Sieradzki
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jennifer Pett-Ridge
- Physical & Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
| | - Jillian F Banfield
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, United States
- Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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Benjdia A, Berteau O. B 12-dependent radical SAM enzymes: Ever expanding structural and mechanistic diversity. Curr Opin Struct Biol 2023; 83:102725. [PMID: 37931378 DOI: 10.1016/j.sbi.2023.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
In the last decade, B12-dependent radical SAM enzymes have emerged as central biocatalysts in the biosynthesis of a myriad of natural products. Notably, these enzymes have been shown to catalyze carbon-carbon bond formation on unactivated carbon atoms leading to unusual methylations. Recently, structural studies have revealed unprecedented insights into the complex chemistry catalyzed by these enzymes. In this review, we cover recent advances in our understanding of B12-dependent radical SAM enzymes from a mechanistic and structural perspective. We discuss the unanticipated diversity of these enzymes which suggests evolutionary links between various biosynthetic and metabolic pathways from antibiotic to RiPP and methane biosynthesis.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
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Green MA, Alvarez-Aponte ZI, Trotter VV, Taga ME. Draft Genome Sequence of Pedococcus sp. Strain 5OH_020, Isolated from California Grassland Soil. Microbiol Resour Announc 2023:e0002523. [PMID: 37154712 DOI: 10.1128/mra.00025-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus.
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Affiliation(s)
- Myka A Green
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Zoila I Alvarez-Aponte
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
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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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