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Martínez Felices JM, Barreto YB, Thangaratnarajah C, Whittaker JJ, Alencar AM, Guskov A, Slotboom DJ. Cobalamin decyanation by the membrane transporter BtuM. Structure 2024; 32:1165-1173.e3. [PMID: 38733996 DOI: 10.1016/j.str.2024.04.014] [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: 06/20/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
BtuM is a bacterial cobalamin transporter that binds the transported substrate in the base-off state, with a cysteine residue providing the α-axial coordination of the central cobalt ion via a sulfur-cobalt bond. Binding leads to decyanation of cobalamin variants with a cyano group as the β-axial ligand. Here, we report the crystal structures of untagged BtuM bound to two variants of cobalamin, hydroxycobalamin and cyanocobalamin, and unveil the native residue responsible for the β-axial coordination, His28. This coordination had previously been obscured by non-native histidines of His-tagged BtuM. A model in which BtuM initially binds cobinamide reversibly with low affinity (KD = 4.0 μM), followed by the formation of a covalent bond (rate constant of 0.163 s-1), fits the kinetics data of substrate binding and decyanation of the cobalamin precursor cobinamide by BtuM. The covalent binding mode suggests a mechanism not used by any other transport protein.
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Affiliation(s)
- Jose M Martínez Felices
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Yan Borges Barreto
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands; Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Jacob J Whittaker
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Adriano M Alencar
- Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Albert Guskov
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Dirk J Slotboom
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands.
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2
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Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. ADVANCES IN GENETICS 2024; 111:237-310. [PMID: 38908901 DOI: 10.1016/bs.adgen.2024.04.001] [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: 06/24/2024]
Abstract
Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.
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Affiliation(s)
- Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñaki Odriozola
- Health Department of Basque Government, Donostia-San Sebastián, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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3
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Nijland M, Lefebvre SN, Thangaratnarajah C, Slotboom DJ. Bidirectional ATP-driven transport of cobalamin by the mycobacterial ABC transporter BacA. Nat Commun 2024; 15:2626. [PMID: 38521790 PMCID: PMC10960864 DOI: 10.1038/s41467-024-46917-1] [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: 10/13/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BacA is a mycobacterial ATP-binding cassette (ABC) transporter involved in the translocation of water-soluble compounds across the lipid bilayer. Whole-cell-based assays have shown that BacA imports cobalamin as well as unrelated hydrophilic compounds such as the antibiotic bleomycin and the antimicrobial peptide Bac7 into the cytoplasm. Surprisingly, there are indications that BacA also mediates the export of different antibacterial compounds, which is difficult to reconcile with the notion that ABC transporters generally operate in a strictly unidirectional manner. Here we resolve this conundrum by developing a fluorescence-based transport assay to monitor the transport of cobalamin across liposomal membranes. We find that BacA transports cobalamin in both the import and export direction. This highly unusual bidirectionality suggests that BacA is mechanistically distinct from other ABC transporters and facilitates ATP-driven diffusion, a function that may be important for the evolvability of specific transporters, and may bring competitive advantages to microbial communities.
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Affiliation(s)
- Mark Nijland
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Solène N Lefebvre
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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4
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Choi A, Dong K, Williams E, Pia L, Batagower J, Bending P, Shin I, Peters DI, Kaspar JR. Human saliva modifies growth, biofilm architecture, and competitive behaviors of oral streptococci. mSphere 2024; 9:e0077123. [PMID: 38319113 PMCID: PMC10900908 DOI: 10.1128/msphere.00771-23] [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: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example is the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions between S. mutans and several species of oral bacteria. However, these experiments were carried out in a medium without human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight Streptococcus species individually and found saliva to positively benefit growth rates while negatively influencing biofilm biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors of S. mutans in coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures of S. mutans and Streptococcus oralis with and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, with S. mutans upregulating carbohydrate uptake and utilization pathways while S. oralis upregulated genome features related to peptide uptake and glycan foraging. S. mutans also upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese leading to an advantage over its opponent. Our report highlights observable changes in microbial behaviors through leveraging environmental- and host-supplied resources over their competitors. IMPORTANCE Dental caries (tooth decay) is the most prevalent disease for both children and adults nationwide. Caries are initiated from demineralization of the enamel due to organic acid production through the metabolic activity of oral bacteria growing in biofilm communities attached to the tooth's surface. Mutans group streptococci are closely associated with caries development and initiation of the cariogenic cycle, which decreases the amount of acid-sensitive, health-associated commensal bacteria while selecting for aciduric and acidogenic species that then further drives the disease process. Defining the exchanges that occur between mutans group streptococci and oral commensals in a condition that closely mimics their natural environment is of critical need toward identifying factors that can influence odontopathogen establishment, persistence, and outgrowth. The goal of our research is to develop strategies, potentially through manipulation of microbial interactions characterized here, that prevent the emergence of mutans group streptococci while keeping the protective flora intact.
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Affiliation(s)
- Allen Choi
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Kevin Dong
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Emily Williams
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Lindsey Pia
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Jordan Batagower
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Paige Bending
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Iris Shin
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Daniel I Peters
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Justin R Kaspar
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
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Luo W, Yin Z, Zhang M, Huang X, Yin J. Dietary Lactobacillus delbrueckii Affects Ileal Bacterial Composition and Circadian Rhythms in Pigs. Animals (Basel) 2024; 14:412. [PMID: 38338054 PMCID: PMC10854795 DOI: 10.3390/ani14030412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Intestinal bacteria, synchronized with diet and feeding time, exhibit circadian rhythms and anticipate host gut function; however the effect of dietary probiotics on gut bacterial diurnal rhythms remains obscure. In this study, bacteria were sequenced at 6 Zeitgeber times (ZT) from a pig model of ileal T-shaped fistula to test ileal bacterial composition and circadian rhythms after Lactobacillus delbrueckii administration. The results showed that dietary L. delbrueckii enhanced ileal bacterial α-diversity at Zeitgeber time (ZT) 16, evidenced by an increased Simpson index compared with control pigs. At the phylum level, Firmicutes was identified as the largest phyla represented in pigs, but dietary L. delbrueckii only increased the abundance of Tenericutes at ZT16. At the genus level, 11/100 genera (i.e., Lactobacillus, Enterococcus, Leptotrichia, Pediococcus, Bifidobacte, Cellulosilyticum, Desulfomicrobium, Sharpea, Eubacterium, Propionivibrio, and Aerococcus) were markedly differentiated in L. delbrueckii-fed pigs and the effect was rhythmicity-dependent. Meanwhile, dietary L. delbrueckii affected six pathways of bacterial functions, such as membrane transport, metabolism of cofactors and vitamins, cell motility, the endocrine system, signaling molecules and interaction, and the nervous system. Cosinor analysis was conducted to test bacterial circadian rhythm in pigs, while no significant circadian rhythm in bacterial α-diversity and phyla composition was observed. Lactobacillus, Terrisporobacter, and Weissella exhibited significant rhythmic fluctuation in the control pigs, which was disturbed by probiotic exposure. In addition, dietary L. delbrueckii affected circadian rhythms in ileal Romboutsia, Erysipelatoclostridium, Cellulosilyticum, and Eubacterium abundances. Dietary L. delbrueckii affected both ileal bacterial composition and circadian rhythms, which might further regulate gut function and host metabolism in pigs.
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Affiliation(s)
- Wenxin Luo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.L.); (Z.Y.); (M.Z.); (X.H.)
- Hunan Biological and Electromechanical Polytechnic, Changsha 410125, China
| | - Zhangzheng Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.L.); (Z.Y.); (M.Z.); (X.H.)
| | - Mingliang Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.L.); (Z.Y.); (M.Z.); (X.H.)
| | - Xingguo Huang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.L.); (Z.Y.); (M.Z.); (X.H.)
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.L.); (Z.Y.); (M.Z.); (X.H.)
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6
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Diamanti E, Souza PCT, Setyawati I, Bousis S, Monjas L, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Commun Biol 2023; 6:1182. [PMID: 37985798 PMCID: PMC10662466 DOI: 10.1038/s42003-023-05555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes. Here, we report on the identification of a promising class of inhibitors of the ECF transporters. We used coarse-grained molecular dynamics simulations on Lactobacillus delbrueckii ECF-FolT2 and ECF-PanT to profile the binding mode and mechanism of inhibition of this novel chemotype. The results corroborate the postulated mechanism of transport and pave the way for further drug-discovery efforts.
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Affiliation(s)
- Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
- Laboratoire de Biologie et Modélisation de la Cellule (UMR 5239, Inserm, U1293) and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 and CNRS, 46 Allée d'Italie, 69007, Lyon, France
| | - Inda Setyawati
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
- Department of Biochemistry, Bogor Agricultural University, Dramaga, 16680, Bogor, Indonesia
| | - Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Leticia Monjas
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lotteke J Y M Swier
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Aleksei Tsarenko
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Weronika K Stanek
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Manuel Jäger
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Siewert J Marrink
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands.
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Choi A, Dong K, Williams E, Pia L, Batagower J, Bending P, Shin I, Peters DI, Kaspar JR. Human Saliva Modifies Growth, Biofilm Architecture and Competitive Behaviors of Oral Streptococci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554151. [PMID: 37662325 PMCID: PMC10473590 DOI: 10.1101/2023.08.21.554151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example are the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions between S. mutans and several species of oral bacteria. However, these experiments were carried out in a medium that was absent of human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight streptococci species individually, and found saliva to positively benefit growth rates while negatively influencing biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors of S. mutans in coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures of S. mutans and Streptococcus oralis with and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, with S. mutans upregulating carbohydrate uptake and utilization pathways while S. oralis upregulated genome features related to peptide uptake and glycan foraging. S. mutans also upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese to give it an advantage over its opponent. Our report highlights observable changes in microbial behaviors via leveraging environmental- and host-supplied resources over their competitors.
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Affiliation(s)
- Allen Choi
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Kevin Dong
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Emily Williams
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Lindsey Pia
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Jordan Batagower
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Paige Bending
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Iris Shin
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Daniel I Peters
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Justin R Kaspar
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
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8
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Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
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Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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9
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Mateos G, Martínez-Bonilla A, Martínez JM, Amils R. Vitamin B 12 Auxotrophy in Isolates from the Deep Subsurface of the Iberian Pyrite Belt. Genes (Basel) 2023; 14:1339. [PMID: 37510244 PMCID: PMC10378866 DOI: 10.3390/genes14071339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Vitamin B12 is an enzymatic cofactor that is essential for both eukaryotes and prokaryotes. The development of life in extreme environments depends on cofactors such as vitamin B12 as well. The genomes of twelve microorganisms isolated from the deep subsurface of the Iberian Pyrite Belt have been analyzed in search of enzymatic activities that require vitamin B12 or are involved in its synthesis and import. Results have revealed that vitamin B12 is needed by these microorganisms for several essential enzymes such as ribonucleotide reductase, methionine synthase and epoxyqueosine reductase. Isolate Desulfosporosinus sp. DEEP is the only analyzed genome that holds a set core of proteins that could lead to the production of vitamin B12. The rest are dependent on obtaining it from the subsurface oligotrophic environment in which they grow. Sought proteins involved in the import of vitamin B12 are not widespread in the sample. The dependence found in the genomes of these microorganisms is supported by the production of vitamin B12 by microorganisms such as Desulfosporosinus sp. DEEP, showing that the operation of deep subsurface biogeochemical cycles is dependent on cofactors such as vitamin B12.
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Affiliation(s)
- Guillermo Mateos
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Adrián Martínez-Bonilla
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José M Martínez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Astrobiología (CAB-INTA), 28850 Torrejón de Ardoz, Spain
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10
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Dutra J, Gomes R, Yupanqui García GJ, Romero-Cale DX, Santos Cardoso M, Waldow V, Groposo C, Akamine RN, Sousa M, Figueiredo H, Azevedo V, Góes-Neto A. Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 2023; 11:e14642. [PMID: 36655046 PMCID: PMC9841911 DOI: 10.7717/peerj.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.
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Affiliation(s)
- Joyce Dutra
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rosimeire Gomes
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glen Jasper Yupanqui García
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana Santos Cardoso
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rubens N. Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maira Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique Figueiredo
- Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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11
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Nijland M, Martínez Felices JM, Slotboom DJ, Thangaratnarajah C. Membrane transport of cobalamin. VITAMINS AND HORMONES 2022; 119:121-148. [PMID: 35337617 DOI: 10.1016/bs.vh.2022.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A wide variety of organisms encode cobalamin-dependent enzymes catalyzing essential metabolic reactions, but the cofactor cobalamin (vitamin B12) is only synthesized by a subset of bacteria and archaea. The biosynthesis of cobalamin is complex and energetically costly, making cobalamin variants and precursors metabolically valuable. Auxotrophs for these molecules have evolved uptake mechanisms to compensate for the lack of a synthesis pathway. Bacterial transport of cobalamin involves the passage over one or two lipidic membranes in Gram-positive and -negative bacteria, respectively. In higher eukaryotes, a complex system of carriers, receptors and transporters facilitates the delivery of the essential molecule to the tissues. Biochemical and genetic approaches have identified different transporter families involved in cobalamin transport. The majority of the characterized cobalamin transporters are active transport systems that belong to the ATP-binding cassette (ABC) superfamily of transporters. In this chapter, we describe the different cobalamin transport systems characterized to date that are present in bacteria and humans, as well as yet-to-be-identified transporters.
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Affiliation(s)
- Mark Nijland
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
| | - Jose M Martínez Felices
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
| | - Dirk J Slotboom
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands.
| | - Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
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12
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Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MC, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185:345-360.e28. [PMID: 35063075 PMCID: PMC9985924 DOI: 10.1016/j.cell.2021.12.025] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/01/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023]
Abstract
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.
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Affiliation(s)
- Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David M. Bianchi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler M. Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo C.R. Melo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nataliya Safronova
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - James P. Sáenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | | | - Kim S. Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | | | | | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NSF Center for the Physics of Living Cells, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.
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13
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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. MICROBIOME 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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14
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Microbial Plankton Community Structure and Function Responses to Vitamin B 12 and B 1 Amendments in an Upwelling System. Appl Environ Microbiol 2021; 87:e0152521. [PMID: 34495690 PMCID: PMC8552899 DOI: 10.1128/aem.01525-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B12 and B1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B1 and B12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B12 and B1 uptake, and Pelagibacterales expressed genes involved in vitamin B1 uptake. Interestingly, the relative expression of vitamin B12 and B1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass. IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B12 and B1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B12 and B1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.
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15
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Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM. Proc Natl Acad Sci U S A 2021; 118:2105014118. [PMID: 34408021 DOI: 10.1073/pnas.2105014118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Energy-coupling factor (ECF)-type transporters are small, asymmetric membrane protein complexes (∼115 kDa) that consist of a membrane-embedded, substrate-binding protein (S component) and a tripartite ATP-hydrolyzing module (ECF module). They import micronutrients into bacterial cells and have been proposed to use a highly unusual transport mechanism, in which the substrate is dragged across the membrane by a toppling motion of the S component. However, it remains unclear how the lipid bilayer could accommodate such a movement. Here, we used cryogenic electron microscopy at 200 kV to determine structures of a folate-specific ECF transporter in lipid nanodiscs and detergent micelles at 2.7- and 3.4-Å resolution, respectively. The structures reveal an irregularly shaped bilayer environment around the membrane-embedded complex and suggest that toppling of the S component is facilitated by protein-induced membrane deformations. In this way, structural remodeling of the lipid bilayer environment is exploited to guide the transport process.
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16
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Elevator-type mechanisms of membrane transport. Biochem Soc Trans 2021; 48:1227-1241. [PMID: 32369548 PMCID: PMC7329351 DOI: 10.1042/bst20200290] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
Membrane transporters are integral membrane proteins that mediate the passage of solutes across lipid bilayers. These proteins undergo conformational transitions between outward- and inward-facing states, which lead to alternating access of the substrate-binding site to the aqueous environment on either side of the membrane. Dozens of different transporter families have evolved, providing a wide variety of structural solutions to achieve alternating access. A sub-set of structurally diverse transporters operate by mechanisms that are collectively named 'elevator-type'. These transporters have one common characteristic: they contain a distinct protein domain that slides across the membrane as a rigid body, and in doing so it 'drags" the transported substrate along. Analysis of the global conformational changes that take place in membrane transporters using elevator-type mechanisms reveals that elevator-type movements can be achieved in more than one way. Molecular dynamics simulations and experimental data help to understand how lipid bilayer properties may affect elevator movements and vice versa.
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17
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Setyawati I, Stanek WK, Majsnerowska M, Swier LJYM, Pardon E, Steyaert J, Guskov A, Slotboom DJ. In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters. eLife 2020; 9:64389. [PMID: 33350937 PMCID: PMC7755397 DOI: 10.7554/elife.64389] [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] [Received: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023] Open
Abstract
Energy-coupling factor (ECF) transporters mediate import of micronutrients in prokaryotes. They consist of an integral membrane S-component (that binds substrate) and ECF module (that powers transport by ATP hydrolysis). It has been proposed that different S-components compete for docking onto the same ECF module, but a minimal liposome-reconstituted system, required to substantiate this idea, is lacking. Here, we co-reconstituted ECF transporters for folate (ECF-FolT2) and pantothenate (ECF-PanT) into proteoliposomes, and assayed for crosstalk during active transport. The kinetics of transport showed that exchange of S-components is part of the transport mechanism. Competition experiments suggest much slower substrate association with FolT2 than with PanT. Comparison of a crystal structure of ECF-PanT with previously determined structures of ECF-FolT2 revealed larger conformational changes upon binding of folate than pantothenate, which could explain the kinetic differences. Our work shows that a minimal in vitro system with two reconstituted transporters recapitulates intricate kinetics behaviour observed in vivo.
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Affiliation(s)
- Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Biochemistry Department, Bogor Agricultural University, Bogor, Indonesia
| | - Weronika K Stanek
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Maria Majsnerowska
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Lotteke J Y M Swier
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Albert Guskov
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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18
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Turner ME, Huynh K, Carroll RK, Ahn SJ, Rice KC. Characterization of the Streptococcus mutans SMU.1703c-SMU.1702c Operon Reveals Its Role in Riboflavin Import and Response to Acid Stress. J Bacteriol 2020; 203:e00293-20. [PMID: 33077636 PMCID: PMC7950412 DOI: 10.1128/jb.00293-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/15/2020] [Indexed: 11/20/2022] Open
Abstract
Streptococcus mutans utilizes numerous metabolite transporters to obtain essential nutrients in the "feast or famine" environment of the human mouth. S. mutans and most other streptococci are considered auxotrophic for several essential vitamins including riboflavin (vitamin B2), which is used to generate key cofactors and to perform numerous cellular redox reactions. Despite the well-known contributions of this vitamin to central metabolism, little is known about how S. mutans obtains and metabolizes B2 The uncharacterized protein SMU.1703c displays high sequence homology to the riboflavin transporter RibU. Deletion of SMU.1703c hindered S. mutans growth in complex and defined medium in the absence of saturating levels of exogenous riboflavin, whereas deletion of cotranscribed SMU.1702c alone had no apparent effect on growth. Expression of SMU.1703c in a Bacillus subtilis riboflavin auxotroph functionally complemented growth in nonsaturating riboflavin conditions. S. mutans was also able to grow on flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN) in an SMU.1703c-dependent manner. Deletion of SMU.1703c and/or SMU.1702c impacted S. mutans acid stress tolerance, as all mutants showed improved growth at pH 5.5 compared to that of the wild type when medium was supplemented with saturating riboflavin. Cooccurrence of SMU.1703c and SMU.1702c, a hypothetical PAP2 family acid phosphatase gene, appears unique to the streptococci and may suggest a connection of SMU.1702c to the acquisition or metabolism of flavins within this genus. Identification of SMU.1703c as a RibU-like riboflavin transporter furthers our understanding of how S. mutans acquires essential micronutrients within the oral cavity and how this pathogen successfully competes within nutrient-starved oral biofilms.IMPORTANCE Dental caries form when acid produced by oral bacteria erodes tooth enamel. This process is driven by the fermentative metabolism of cariogenic bacteria, most notably Streptococcus mutans Nutrient acquisition is key in the competitive oral cavity, and many organisms have evolved various strategies to procure carbon sources or necessary biomolecules. B vitamins, such as riboflavin, which many oral streptococci must scavenge from the oral environment, are necessary for survival within the competitive oral cavity. However, the primary mechanism and proteins involved in this process remain uncharacterized. This study is important because it identifies a key step in S. mutans riboflavin acquisition and cofactor generation, which may enable the development of novel anticaries treatment strategies via selective targeting of metabolite transporters.
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Affiliation(s)
- Matthew E Turner
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Khanh Huynh
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Sang-Joon Ahn
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
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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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20
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Ford RC, Hellmich UA. What monomeric nucleotide binding domains can teach us about dimeric ABC proteins. FEBS Lett 2020; 594:3857-3875. [PMID: 32880928 DOI: 10.1002/1873-3468.13921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.
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Affiliation(s)
- Robert C Ford
- Faculty of Biology Medicine and Health, The University of Manchester, UK
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt, Germany
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Slotboom DJ, Ettema TW, Nijland M, Thangaratnarajah C. Bacterial multi-solute transporters. FEBS Lett 2020; 594:3898-3907. [PMID: 32810294 DOI: 10.1002/1873-3468.13912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
Bacterial membrane proteins of the SbmA/BacA family are multi-solute transporters that mediate the uptake of structurally diverse hydrophilic molecules, including aminoglycoside antibiotics and antimicrobial peptides. Some family members are full-length ATP-binding cassette (ABC) transporters, whereas other members are truncated homologues that lack the nucleotide-binding domains and thus mediate ATP-independent transport. A recent cryo-EM structure of the ABC transporter Rv1819c from Mycobacterium tuberculosis has shed light on the structural basis for multi-solute transport and has provided insight into the mechanism of transport. Here, we discuss how the protein architecture makes SbmA/BacA family transporters prone to inadvertent import of antibiotics and speculate on the question which physiological processes may benefit from multi-solute transport.
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Affiliation(s)
- Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Thijs W Ettema
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mark Nijland
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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22
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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: 88] [Impact Index Per Article: 22.0] [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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23
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Hillman ET, Kozik AJ, Hooker CA, Burnett JL, Heo Y, Kiesel VA, Nevins CJ, Oshiro JM, Robins MM, Thakkar RD, Wu ST, Lindemann SR. Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. Microb Genom 2020; 6:mgen000399. [PMID: 32589566 PMCID: PMC7478625 DOI: 10.1099/mgen.0.000399] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.
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Affiliation(s)
- Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
| | - Ariangela J. Kozik
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Present address: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - John L. Burnett
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Yoojung Heo
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Violet A. Kiesel
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Clayton J. Nevins
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
- Present address: Department of Soil and Water Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Jordan M.K.I. Oshiro
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Melissa M. Robins
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Riya D. Thakkar
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sophie Tongyu Wu
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen R. Lindemann
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
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24
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Jochim A, Adolf L, Belikova D, Schilling NA, Setyawati I, Chin D, Meyers S, Verhamme P, Heinrichs DE, Slotboom DJ, Heilbronner S. An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis. eLife 2020; 9:e57322. [PMID: 32515736 PMCID: PMC7299338 DOI: 10.7554/elife.57322] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/09/2020] [Indexed: 01/03/2023] Open
Abstract
Energy-coupling factor type transporters (ECF) represent trace nutrient acquisition systems. Substrate binding components of ECF-transporters are membrane proteins with extraordinary affinity, allowing them to scavenge trace amounts of ligand. A number of molecules have been described as substrates of ECF-transporters, but an involvement in iron-acquisition is unknown. Host-induced iron limitation during infection represents an effective mechanism to limit bacterial proliferation. We identified the iron-regulated ECF-transporter Lha in the opportunistic bacterial pathogen Staphylococcus lugdunensis and show that the transporter is specific for heme. The recombinant substrate-specific subunit LhaS accepted heme from diverse host-derived hemoproteins. Using isogenic mutants and recombinant expression of Lha, we demonstrate that its function is independent of the canonical heme acquisition system Isd and allows proliferation on human cells as sources of nutrient iron. Our findings reveal a unique strategy of nutritional heme acquisition and provide the first example of an ECF-transporter involved in overcoming host-induced nutritional limitation.
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Affiliation(s)
- Angelika Jochim
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | - Lea Adolf
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | - Darya Belikova
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | | | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Denny Chin
- Department of Microbiology and Immunology, University of Western OntarioLondonCanada
| | | | | | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western OntarioLondonCanada
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
- German Centre for Infection Research (DZIF), Partner Site TübingenTübingenGermany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight InfectionsTübingenGermany
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25
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Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nat Commun 2020; 11:1763. [PMID: 32273501 PMCID: PMC7145868 DOI: 10.1038/s41467-020-15554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/13/2020] [Indexed: 01/12/2023] Open
Abstract
Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity measurements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters.
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26
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Rempel S, Gati C, Nijland M, Thangaratnarajah C, Karyolaimos A, de Gier JW, Guskov A, Slotboom DJ. A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds. Nature 2020; 580:409-412. [DOI: 10.1038/s41586-020-2072-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 01/08/2020] [Indexed: 01/10/2023]
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Abstract
Energy-coupling factor (ECF)-type ATP-binding cassette (ABC) transporters catalyze membrane transport of micronutrients in prokaryotes. Crystal structures and biochemical characterization have revealed that ECF transporters are mechanistically distinct from other ABC transport systems. Notably, ECF transporters make use of small integral membrane subunits (S-components) that are predicted to topple over in the membrane when carrying the bound substrate from the extracellular side of the bilayer to the cytosol. Here, we review the phylogenetic diversity of ECF transporters as well as recent structural and biochemical advancements that have led to the postulation of conceptually different mechanistic models. These models can be described as power stroke and thermal ratchet. Structural data indicate that the lipid composition and bilayer structure are likely to have great impact on the transport function. We argue that study of ECF transporters could lead to generic insight into membrane protein structure, dynamics, and interaction.
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Affiliation(s)
- S Rempel
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - W K Stanek
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - D J Slotboom
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , , .,Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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29
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Finkenwirth F, Sippach M, Pecina SN, Gäde M, Ruta J, Ricke A, Bondarenko E, Klare JP, Zinke M, Lange S, Lange A, Steinhoff HJ, Eitinger T. Dynamic interactions of CbiN and CbiM trigger activity of a cobalt energy-coupling-factor transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183114. [PMID: 31666178 DOI: 10.1016/j.bbamem.2019.183114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Energy-coupling factor (ECF) transporters for uptake of vitamins and transition-metal ions into prokaryotic cells share a common architecture consisting of a substrate-specific integral membrane protein (S), a transmembrane coupling protein (T) and two cytoplasmic ATP-binding-cassette-family ATPases. S components rotate within the membrane to expose their binding pockets alternately to the exterior and the cytoplasm. In contrast to vitamin transporters, metal-specific systems rely on additional proteins with essential but poorly understood functions. CbiN, a membrane protein composed of two transmembrane helices tethered by an extracytoplasmic loop of 37 amino-acid residues represents the auxiliary component that temporarily interacts with the CbiMQO2 Co2+ transporter. CbiN was previously shown to induce significant Co2+ transport activity in the absence of CbiQO2 in cells producing the S component CbiM plus CbiN or a Cbi(MN) fusion. Here we analyzed the mode of interaction between the two protein domains. Any deletion in the CbiN loop abolished transport activity. In silico predicted protein-protein contacts between segments of the CbiN loop and loops in CbiM were confirmed by cysteine-scanning mutagenesis and crosslinking. Likewise, an ordered structure of the CbiN loop was observed by electron paramagnetic resonance analysis after site-directed spin labeling. The N-terminal loop of CbiM containing three of four metal ligands was partially immobilized in wild-type Cbi(MN) but completely immobile in inactive variants with CbiN loop deletions. Decreased dynamics of the inactive form was also detected by solid-state nuclear magnetic resonance of isotope-labeled protein in proteoliposomes. In conclusion, CbiM-CbiN loop-loop interactions facilitate metal insertion into the binding pocket.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Michael Sippach
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Sinah N Pecina
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Mario Gäde
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Julia Ruta
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Adrian Ricke
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Elena Bondarenko
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Johann P Klare
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Maximilian Zinke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | | | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany.
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30
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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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31
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Finkenwirth F, Eitinger T. ECF-type ABC transporters for uptake of vitamins and transition metal ions into prokaryotic cells. Res Microbiol 2019; 170:358-365. [PMID: 31283960 DOI: 10.1016/j.resmic.2019.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/15/2022]
Abstract
Energy-coupling factor (ECF) transporters mediate the uptake of micronutrients in prokaryotes. They consist of two ATP-binding-cassette family ATPases, a transmembrane coupling protein (T component) and a substrate-binding membrane protein (S component). ECF transporters for Co2+ and Ni2+ ions have one or two additional proteins with extracytoplasmic regions but poorly understood function. Homologs of T components with a predicted localization in plastids are widespread in plants but their physiological role is unclear. S components in eukaryotes are very rare and restricted to biotin-specific variants. Apart from a potential contribution to the export of flavins to serve the assembly of extracytoplasmic electron transfer chains, ECF transporters function as importers.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.
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32
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Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL. Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. Front Microbiol 2019; 10:1316. [PMID: 31275260 PMCID: PMC6593275 DOI: 10.3389/fmicb.2019.01316] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/27/2019] [Indexed: 01/05/2023] Open
Abstract
The human gut microbiome harbors a diverse array of metabolic pathways contributing to its development and homeostasis via a complex web of diet-dependent metabolic interactions within the microbial community and host. Genomics-based reconstruction and predictive modeling of these interactions would provide a framework for diagnostics and treatment of dysbiosis-related syndromes via rational selection of therapeutic prebiotics and dietary nutrients. Of particular interest are micronutrients, such as B-group vitamins, precursors of indispensable metabolic cofactors, that are produced de novo by some gut bacteria (prototrophs) but must be provided exogenously in the diet for many other bacterial species (auxotrophs) as well as for the mammalian host. Cross-feeding of B vitamins between prototrophic and auxotrophic species is expected to strongly contribute to the homeostasis of microbial communities in the distal gut given the efficient absorption of dietary vitamins in the upper gastrointestinal tract. To confidently estimate the balance of microbiome micronutrient biosynthetic capabilities and requirements using available genomic data, we have performed a subsystems-based reconstruction of biogenesis, salvage and uptake for eight B vitamins (B1, B2, B3, B5, B6, B7, B9, and B12) and queuosine (essential factor in tRNA modification) over a reference set of 2,228 bacterial genomes representing 690 cultured species of the human gastrointestinal microbiota. This allowed us to classify the studied organisms with respect to their pathway variants and infer their prototrophic vs. auxotrophic phenotypes. In addition to canonical vitamin pathways, several conserved partial pathways were identified pointing to alternative routes of syntrophic metabolism and expanding a microbial vitamin "menu" by several pathway intermediates (vitamers) such as thiazole, quinolinate, dethiobiotin, pantoate. A cross-species comparison was applied to assess the extent of conservation of vitamin phenotypes at distinct taxonomic levels (from strains to families). The obtained reference collection combined with 16S rRNA gene-based phylogenetic profiles was used to deduce phenotype profiles of the human gut microbiota across in two large cohorts. This analysis provided the first estimate of B-vitamin requirements, production and sharing capabilities in the human gut microbiome establishing predictive phenotype profiling as a new approach to classification of microbiome samples. Future expansion of our reference genomic collection of metabolic phenotypes will allow further improvement in coverage and accuracy of predictive phenotype profiling of the human microbiome.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Matvei S. Khoroshkin
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Stanislav N. Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Department of Physics, P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Semen A. Leyn
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Scott N. Peterson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | | | - Andrei L. Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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Chen L, Gu Q, Li P, Chen S, Li Y. Genomic analysis of Lactobacillus reuteri WHH1689 reveals its probiotic properties and stress resistance. Food Sci Nutr 2019; 7:844-857. [PMID: 30847163 PMCID: PMC6392878 DOI: 10.1002/fsn3.934] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 02/06/2023] Open
Abstract
Lactobacillus reuteri (L. reuteri) WHH1689, which was isolated from Chinese traditional highland barley wine, exhibited high survival period at room temperature in drinkable probiotic yogurt. This article aimed to indicate the genes involved in probiotic function of WHH1689 and reveal potential stress resistance based on genomic analysis. Analysis of comparative genome with closely related L. reuteri strains identified special stress adaptation. MUMmer and ACT softwares were applied for collinear analysis, and OrthoMCL program was used for sequence alignment involved in distribution of protein cluster. We identified genes coding for carbohydrate transport and enzymes, carbon metabolism pathway, gastrointestinal tract resistance, adhesive ability, and folic acid biosynthesis, etc. Genome sequence and comparative genome analysis of L. reuteri WHH1689 demonstrated specific genes for genetic adaptation and stress resistance. Tolerance, adhesion, and folate test indicated the strain had multiple probiotics. L. reuteri WHH1689 has the potential to be a probiotic candidate in dairy foods.
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Affiliation(s)
- Lin Chen
- Key Laboratory for Food Microbial Technology of Zhejiang ProvinceCollege of Food Science and BiotechnologyZhejiang Gongshang UniversityHangzhouChina
- Research and Develop DepartmentHangzhou Wahaha Group Co. Ltd.HangzhouChina
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang ProvinceCollege of Food Science and BiotechnologyZhejiang Gongshang UniversityHangzhouChina
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang ProvinceCollege of Food Science and BiotechnologyZhejiang Gongshang UniversityHangzhouChina
| | - Su Chen
- Research and Develop DepartmentHangzhou Wahaha Group Co. Ltd.HangzhouChina
| | - Yanjun Li
- Research and Develop DepartmentHangzhou Wahaha Group Co. Ltd.HangzhouChina
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34
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Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM. Nat Commun 2018; 9:3038. [PMID: 30072686 PMCID: PMC6072759 DOI: 10.1038/s41467-018-05441-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/04/2018] [Indexed: 01/11/2023] Open
Abstract
Uptake of vitamin B12 is essential for many prokaryotes, but in most cases the membrane proteins involved are yet to be identified. We present the biochemical characterization and high-resolution crystal structure of BtuM, a predicted bacterial vitamin B12 uptake system. BtuM binds vitamin B12 in its base-off conformation, with a cysteine residue as axial ligand of the corrin cobalt ion. Spectroscopic analysis indicates that the unusual thiolate coordination allows for decyanation of vitamin B12. Chemical modification of the substrate is a property other characterized vitamin B12-transport proteins do not exhibit. Uptake of vitamin B12 is essential for many prokaryotes, but in most cases the membrane proteins involved are yet to be identified. Here, the authors use X-ray crystallography and spectroscopy to characterize BtuM, a predicted bacterial substrate-modifying vitamin B12 transporter.
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