1
|
Pérez-Castaño R, Aranda J, Widner FJ, Kieninger C, Deery E, Warren MJ, Orozco M, Elías-Arnanz M, Padmanabhan S, Kräutler B. The Rhodium Analogue of Coenzyme B 12 as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors. Angew Chem Int Ed Engl 2024; 63:e202401626. [PMID: 38416546 DOI: 10.1002/anie.202401626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Coenzyme B12 (AdoCbl; 5'-deoxy-5'-adenosylcobalamin), the quintessential biological organometallic radical catalyst, has a formerly unanticipated, yet extensive, role in photoregulation in bacteria. The light-responsive cobalt-corrin AdoCbl performs this nonenzymatic role by facilitating the assembly of CarH photoreceptors into DNA-binding tetramers in the dark, suppressing gene expression. Conversely, exposure to light triggers the decomposition of this AdoCbl-bound complex by a still elusive photochemical mechanism, activating gene expression. Here, we have examined AdoRhbl, the non-natural rhodium analogue of AdoCbl, as a photostable isostructural surrogate for AdoCbl. We show that AdoRhbl closely emulates AdoCbl in its uptake by bacterial cells and structural functionality as a regulatory ligand for CarH tetramerization, DNA binding, and repressor activity. Remarkably, we find AdoRhbl is photostable even when bound "base-off/His-on" to CarH in vitro and in vivo. Thus, AdoRhbl, an antivitamin B12, also represents an unprecedented anti-photoregulatory ligand, opening a pathway to precisely target biomimetic inhibition of AdoCbl-based photoregulation, with new possibilities for selective antibacterial applications. Computational biomolecular analysis of AdoRhbl binding to CarH yields detailed structural insights into this complex, which suggest that the adenosyl group of photoexcited AdoCbl bound to CarH may specifically undergo a concerted non-radical syn-1,2-elimination mechanism, an aspect not previously considered for this photoreceptor.
Collapse
Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Juan Aranda
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Florian J Widner
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona (Spain); the Joint BSC-IRB Research Program in Computational Biology, and Department of Biochemistry and Biomedicine, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física Blas Cabrera (IQF-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), 119 c/Serrano, 28006, Madrid, Spain
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| |
Collapse
|
2
|
Sayer AP, Llavero-Pasquina M, Geisler K, Holzer A, Bunbury F, Mendoza-Ochoa GI, Lawrence AD, Warren MJ, Mehrshahi P, Smith AG. Conserved cobalamin acquisition protein 1 is essential for vitamin B12 uptake in both Chlamydomonas and Phaeodactylum. Plant Physiol 2024; 194:698-714. [PMID: 37864825 PMCID: PMC10828217 DOI: 10.1093/plphys/kiad564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 10/23/2023]
Abstract
Microalgae play an essential role in global net primary productivity and global biogeochemical cycling. Despite their phototrophic lifestyle, over half of algal species depend for growth on acquiring an external supply of the corrinoid vitamin B12 (cobalamin), a micronutrient produced only by a subset of prokaryotic organisms. Previous studies have identified protein components involved in vitamin B12 uptake in bacterial species and humans. However, little is known about its uptake in algae. Here, we demonstrate the essential role of a protein, cobalamin acquisition protein 1 (CBA1), in B12 uptake in Phaeodactylum tricornutum using CRISPR-Cas9 to generate targeted knockouts and in Chlamydomonas reinhardtii by insertional mutagenesis. In both cases, CBA1 knockout lines could not take up exogenous vitamin B12. Complementation of the C. reinhardtii mutants with the wild-type CBA1 gene restored B12 uptake, and regulation of CBA1 expression via a riboswitch element enabled control of the phenotype. When visualized by confocal microscopy, a YFP-fusion with C. reinhardtii CBA1 showed association with membranes. Bioinformatics analysis found that CBA1-like sequences are present in all major eukaryotic phyla. In algal taxa, the majority that encoded CBA1 also had genes for B12-dependent enzymes, suggesting CBA1 plays a conserved role. Our results thus provide insight into the molecular basis of algal B12 acquisition, a process that likely underpins many interactions in aquatic microbial communities.
Collapse
Affiliation(s)
- Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Marcel Llavero-Pasquina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Katrin Geisler
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Gonzalo I Mendoza-Ochoa
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andrew D Lawrence
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| |
Collapse
|
3
|
Jackson LK, Dailey TA, Anderle B, Warren MJ, Bergonia HA, Dailey HA, Phillips JD. Exploiting Differences in Heme Biosynthesis between Bacterial Species to Screen for Novel Antimicrobials. Biomolecules 2023; 13:1485. [PMID: 37892169 PMCID: PMC10604556 DOI: 10.3390/biom13101485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The final three steps of heme biogenesis exhibit notable differences between di- and mono-derm bacteria. The former employs the protoporphyrin-dependent (PPD) pathway, while the latter utilizes the more recently uncovered coproporphyrin-dependent (CPD) pathway. In order to devise a rapid screen for potential inhibitors that differentiate the two pathways, the genes associated with the protoporphyrin pathway in an Escherichia coli YFP strain were replaced with those for the CPD pathway from Staphylococcus aureus (SA) through a sliding modular gene replacement recombineering strategy to generate the E. coli strain Sa-CPD-YFP. Potential inhibitors that differentially target the pathways were identified by screening compound libraries against the YFP-producing Sa-CPD-YFP strain in comparison to a CFP-producing E. coli strain. Using a mixed strain assay, inhibitors targeting either the CPD or PPD heme pathways were identified through a decrease in one fluorescent signal but not the other. An initial screen identified both azole and prodigiosin-derived compounds that were shown to specifically target the CPD pathway and which led to the accumulation of coproheme, indicating that the main target of inhibition would appear to be the coproheme decarboxylase (ChdC) enzyme. In silico modeling highlighted that these inhibitors are able to bind within the active site of ChdC.
Collapse
Affiliation(s)
- Laurie K. Jackson
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
| | - Tammy A. Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA (H.A.D.)
| | - Brenden Anderle
- WhiteTree Medical, 10437 S Jordan Gateway, South Jordan, UT 84095, USA;
| | - Martin J. Warren
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK;
| | - Hector A. Bergonia
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
| | - Harry A. Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA (H.A.D.)
| | - John D. Phillips
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
| |
Collapse
|
4
|
Beal DM, Liang M, Brown I, Budge JD, Burrows ER, Howland K, Lee P, Martin S, Morrell A, Nemoto-Smith E, Roobol J, Stanley M, Smales CM, Warren MJ. Modification of bacterial microcompartments with target biomolecules via post-translational SpyTagging. Mater Adv 2023; 4:2963-2970. [PMID: 37465645 PMCID: PMC10350929 DOI: 10.1039/d3ma00071k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelle-like structures formed within bacteria, often encapsulating enzymes and cellular processes, in particular, allowing toxic intermediates to be shielded from the general cellular environment. Outside of their biological role they are of interest, through surface modification, as potential drug carriers and polyvalent antigen display scaffolds. Here we use a post-translational modification approach, using copper free click chemistry, to attach a SpyTag to a target protein molecule for attachment to a specific SpyCatcher modified BMC shell protein. We demonstrate that a post-translationally SpyTagged material can react with a SpyCatcher modified BMC and show its presence on the surface of BMCs, enabling future investigation of these structures as polyvalent antigen display scaffolds for vaccine development. This post-translational 'click' methodology overcomes the necessity to genetically encode the SpyTag, avoids any potential reduction in expression yield and expands the scope of SpyTag/SpyCatcher vaccine scaffolds to form peptide epitope vaccines and small molecule delivery agents.
Collapse
Affiliation(s)
- David M Beal
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Mingzhi Liang
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Ian Brown
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - James D Budge
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Kevin Howland
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Phoebe Lee
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Andrew Morrell
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Joanne Roobol
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Maria Stanley
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co Dublin A94 X099 Ireland
| | - Martin J Warren
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- Quadram Institute Bioscience Norwich UK
- Norwich Medical School, University of East Anglia Norwich UK
| |
Collapse
|
5
|
Young TR, Deery E, Foster AW, Martini MA, Osman D, Warren MJ, Robinson NJ. Two Distinct Thermodynamic Gradients for Cellular Metalation of Vitamin B 12. JACS Au 2023; 3:1472-1483. [PMID: 37234125 PMCID: PMC10206600 DOI: 10.1021/jacsau.3c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The acquisition of CoII by the corrin component of vitamin B12 follows one of two distinct pathways, referred to as early or late CoII insertion. The late insertion pathway exploits a CoII metallochaperone (CobW) from the COG0523 family of G3E GTPases, while the early insertion pathway does not. This provides an opportunity to contrast the thermodynamics of metalation in a metallochaperone-requiring and a metallochaperone-independent pathway. In the metallochaperone-independent route, sirohydrochlorin (SHC) associates with the CbiK chelatase to form CoII-SHC. CoII-buffered enzymatic assays indicate that SHC binding enhances the thermodynamic gradient for CoII transfer from the cytosol to CbiK. In the metallochaperone-dependent pathway, hydrogenobyrinic acid a,c-diamide (HBAD) associates with the CobNST chelatase to form CoII-HBAD. Here, CoII-buffered enzymatic assays indicate that CoII transfer from the cytosol to HBAD-CobNST must somehow traverse a highly unfavorable thermodynamic gradient for CoII binding. Notably, there is a favorable gradient for CoII transfer from the cytosol to the MgIIGTP-CobW metallochaperone, but further transfer of CoII from the GTP-bound metallochaperone to the HBAD-CobNST chelatase complex is thermodynamically unfavorable. However, after nucleotide hydrolysis, CoII transfer from the chaperone to the chelatase complex is calculated to become favorable. These data reveal that the CobW metallochaperone can overcome an unfavorable thermodynamic gradient for CoII transfer from the cytosol to the chelatase by coupling this process to GTP hydrolysis.
Collapse
Affiliation(s)
- Tessa R. Young
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Evelyne Deery
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
| | - Andrew W. Foster
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Maria Alessandra Martini
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Inorganic Spectroscopy, Max Planck Institute
for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Deenah Osman
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
- Quadram
Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, U.K.
| | - Nigel J. Robinson
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| |
Collapse
|
6
|
Niklewicz A, Smith AD, Smith A, Holzer A, Klein A, McCaddon A, Molloy AM, Wolffenbuttel BHR, Nexo E, McNulty H, Refsum H, Gueant JL, Dib MJ, Ward M, Murphy M, Green R, Ahmadi KR, Hannibal L, Warren MJ, Owen PJ. The importance of vitamin B 12 for individuals choosing plant-based diets. Eur J Nutr 2023; 62:1551-1559. [PMID: 36469110 PMCID: PMC10030528 DOI: 10.1007/s00394-022-03025-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/05/2022] [Indexed: 12/09/2022]
Abstract
Vitamin B12 is an essential nutrient that is not made by plants; consequently, unfortified plant-based foods are not a reliable supply. Recent estimates suggest high rates of vitamin B12 deficiency among the vegetarian and vegan populations, particularly in pregnant women or women of child-bearing age who, for ethical and health reasons, are shifting towards higher consumption of plant-based foods in ever-increasing numbers. Vitamin B12 plays crucial metabolic roles across the life-course and in particular during pregnancy and in early development (first 1000 days of life). Evidence now implicates vitamin B12 deficiency with increased risk to a range of neuro, vascular, immune, and inflammatory disorders. However, the current UK recommended nutrient intake for vitamin B12 does not adequately consider the vitamin B12 deficit for those choosing a plant-based diet, including vegetarianism and in particular veganism, representing a hidden hunger. We provide a cautionary note on the importance of preventing vitamin B12 deficits for those individuals choosing a plant-based diet and the health professionals advising them.
Collapse
Affiliation(s)
- Ali Niklewicz
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7XH, UK
| | - A David Smith
- OPTIMA, Department of Pharmacology, University of Oxford, Oxford, UK
| | - Alison Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Andrew Klein
- Department of Anaesthesia and Intensive Care, Royal Papworth Hospital, Cambridge, UK
| | - Andrew McCaddon
- Faculty of Social and Life Sciences, Wrexham Glyndwr University, Wrexham, UK
| | - Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Ebba Nexo
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Helga Refsum
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jean-Louis Gueant
- Department of Hepato-Gastroenterology, University Regional Hospital of Nancy, and Inserm UMRS 1256 N-GERE (Nutrition-Genetics-Environmental Risks)-University of Lorraine, 54000, Nancy, France
| | - Marie-Joe Dib
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Michelle Murphy
- Facultat de Medicina I Ciències de La Salut, Unitat de Medicina Preventiva I Salut Pública, Universitat Rovira I Virgili, Reus, IISPV, CIBEROBN, Tarragona, Spain
| | - Ralph Green
- School of Medicine, University of California, Davis, CA, USA
| | - Kourosh R Ahmadi
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7XH, UK
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Paediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, 79106, Freiburg, Germany.
| | - Martin J Warren
- Norwich Research Park, Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - P Julian Owen
- Consultant Orthopaedic Surgeon, Department of Trauma & Orthopaedics, Addenbrooke's, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | | |
Collapse
|
7
|
Kieninger C, Deery E, Lawrence AD, Warren MJ, Krautler B. Hydrogenobinamide and nibinamide - Metal-free ligand and Ni(II)-analogue of the vitamin B 12 precursor cobinamide. J PORPHYR PHTHALOCYA 2023. [DOI: 10.1142/s1088424623500463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
8
|
Wiedemair M, Kieninger C, Wurst K, Podewitz M, Deery E, Paxhia MD, Warren MJ, Kräutler B. Solution, Crystal and in‐Silico Structures of the Organometallic Vitamin B12‐Derivative Acetylcobalamin and of its Novel Rhodium‐Analogue Acetylrhodibalamin. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Markus Wiedemair
- University of Innsbruck: Universitat Innsbruck Institute of Organic Chemistry Innrain 80/82 6020 Innsbruck AUSTRIA
| | - Christoph Kieninger
- University of Innsbruck: Universitat Innsbruck Institute of Organic Chemistry Innrain 80/82 6020 Innsbruck AUSTRIA
| | - Klaus Wurst
- University of Innsbruck: Universitat Innsbruck Institute of General, Inorganic and Theoretical Chemistry Innrain 80/82 6020 Innsbruck AUSTRIA
| | - Maren Podewitz
- TU Wien: Technische Universitat Wien Institute of Materials Chemistry Lehargasse 4 A-1060 Vienna AUSTRIA
| | - Evelyne Deery
- University of Kent at Canterbury: University of Kent School of Biosciences UNITED KINGDOM
| | - Michael D Paxhia
- Quadram Institute Bioscience Food Innovation and Health Programme UNITED KINGDOM
| | - Martin J Warren
- University of Kent School of Biosciences School of Biosciences UNITED KINGDOM
| | - Bernhard Kräutler
- University of Innsbruck: Universitat Innsbruck Institute of Organic Chemistry Innrain 80/82 A-6020 Innsbruck AUSTRIA
| |
Collapse
|
9
|
Bunbury F, Deery E, Sayer AP, Bhardwaj V, Harrison EL, Warren MJ, Smith AG. Exploring the onset of B 12 -based mutualisms using a recently evolved Chlamydomonas auxotroph and B 12 -producing bacteria. Environ Microbiol 2022; 24:3134-3147. [PMID: 35593514 PMCID: PMC9545926 DOI: 10.1111/1462-2920.16035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 12/01/2022]
Abstract
Cobalamin (vitamin B12 ) is a cofactor for essential metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonize the algal phycosphere, forming stable communities that gain preferential access to photosynthate and in return provide compounds such as B12 . Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12 -dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12 -independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesize that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12 -dependent algae.
Collapse
Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Vaibhav Bhardwaj
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ellen L Harrison
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| |
Collapse
|
10
|
Scott AF, Deery E, Lawrence AD, Warren MJ. Plasmodium falciparum hydroxymethylbilane synthase does not house any cosynthase activity within the haem biosynthetic pathway. Microbiology (Reading) 2021; 167. [PMID: 34661520 PMCID: PMC8698207 DOI: 10.1099/mic.0.001095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Uroporphyrinogen III, the universal progenitor of macrocyclic, modified tetrapyrroles, is produced from aminolaevulinic acid (ALA) by a conserved pathway involving three enzymes: porphobilinogen synthase (PBGS), hydroxymethylbilane synthase (HmbS) and uroporphyrinogen III synthase (UroS). The gene encoding uroporphyrinogen III synthase has not yet been identified in Plasmodium falciparum, but it has been suggested that this activity is housed inside a bifunctional hybroxymethylbilane synthase (HmbS). Additionally, an unknown protein encoded by PF3D7_1247600 has also been predicted to possess UroS activity. In this study it is demonstrated that neither of these proteins possess UroS activity and the real UroS remains to be identified. This was demonstrated by the failure of codon-optimized genes to complement a defined Escherichia coli hemD− mutant (SASZ31) deficient in UroS activity. Furthermore, HPLC analysis of the oxidized reaction product from recombinant, purified P. falciparum HmbS showed that only uroporphyrin I could be detected (corresponding to hydroxymethylbilane production). No uroporphyrin III was detected, showing that P. falciparum HmbS does not have UroS activity and can only catalyze the formation of hydroxymethylbilane from porphobilinogen.
Collapse
Affiliation(s)
- Alan F. Scott
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
- Present address: School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
- *Correspondence: Alan F. Scott,
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Andrew D. Lawrence
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Martin J. Warren
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| |
Collapse
|
11
|
Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. Biochim Biophys Acta Mol Cell Res 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
Collapse
Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
| |
Collapse
|
12
|
Kräutler B, Widner FJ, Kieninger C, Wurst K, Deery E, Lawrence AD, Warren MJ. Synthesis, Spectral Characterization and Crystal Structure of Chlororhodibalamin: A Synthesis Platform for Rhodium Analogues of Vitamin B12 and for Rh-Based Antivitamins B12. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1707288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractChlororhodibalamin (ClRhbl), a rhodium analogue of vitamin B12 (cyanocobalamin), was prepared in 84% yield by metalation of the metal-free B12 ligand hydrogenobalamin using the RhI-complex [Rh(CO)2Cl]2. ClRhbl was identified and characterized by UV/Vis, circular dichroism, high-resolution mass and heteronuclear NMR spectra. The RhIII-corrin ClRhbl features the ‘base-on’ architecture of vitamin B12. X-ray analysis of single crystals of ClRhbl have revealed its detailed 3D-geometry and close structural similarity to the CoIII-analogue chlorocobalamin (ClCbl). ClRhbl is a versatile starting material for the preparation of other rhodibalamins, among them the organometallic derivatives adenosylrhodibalamin and methylrhodibalamin, the Rh analogues of the important coenzyme and cofactor forms of B12, adenosylcobalamin and methylcobalamin.
Collapse
Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck
| | - Florian J. Widner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck
| | - Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck
| | | | | | - Martin J. Warren
- School of Biosciences, University of Kent
- Quadram Institute Bioscience
| |
Collapse
|
13
|
Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B
12
by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B
12
Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | - Klaus Wurst
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maria Stanley
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | - Evelyne Deery
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Martin J. Warren
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
- Quadram Institute Bioscience Norwich Science Park Norwich NR4 7UQ UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| |
Collapse
|
14
|
Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B 12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B 12 Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020; 59:20129-20136. [PMID: 32686888 PMCID: PMC7693184 DOI: 10.1002/anie.202008407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/18/2022]
Abstract
The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition-metal analogue of vitamin B12 . Described here is Nibl, synthesized by incorporation of a NiII ion into the metal-free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal-free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X-ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII . The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four-coordinate base-off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.
Collapse
Affiliation(s)
- Christoph Kieninger
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | - Klaus Wurst
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maria Stanley
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | - Evelyne Deery
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Martin J. Warren
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
- Quadram Institute BioscienceNorwich Science ParkNorwichNR4 7UQUK
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| |
Collapse
|
15
|
Abstract
Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.
Collapse
Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| |
Collapse
|
16
|
Juodeikis R, Lee MJ, Mayer M, Mantell J, Brown IR, Verkade P, Woolfson DN, Prentice MB, Frank S, Warren MJ. Effect of metabolosome encapsulation peptides on enzyme activity, coaggregation, incorporation, and bacterial microcompartment formation. Microbiologyopen 2020; 9:e1010. [PMID: 32053746 PMCID: PMC7221423 DOI: 10.1002/mbo3.1010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/21/2023] Open
Abstract
Metabolosomes, catabolic bacterial microcompartments (BMCs), are proteinaceous organelles that are associated with the breakdown of metabolites such as propanediol and ethanolamine. They are composed of an outer multicomponent protein shell that encases a specific metabolic pathway. Protein cargo found within BMCs is directed by the presence of an encapsulation peptide that appears to trigger aggregation before the formation of the outer shell. We investigated the effect of three distinct encapsulation peptides on foreign cargo in a recombinant BMC system. Our data demonstrate that these peptides cause variations in enzyme activity and protein aggregation. We observed that the level of protein aggregation generally correlates with the size of metabolosomes, while in the absence of cargo BMCs self‐assemble into smaller compartments. The results agree with a flexible model for BMC formation based around the ability of the BMC shell to associate with an aggregate formed due to the interaction of encapsulation peptides.
Collapse
Affiliation(s)
- Rokas Juodeikis
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Matthew J Lee
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Matthias Mayer
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Bristol, UK.,Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Ian R Brown
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK.,Wolfson Bioimaging Facility, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Chemistry, University of Bristol, Bristol, UK
| | | | - Stefanie Frank
- Department of Biochemical Engineering, University College London, London, UK
| | - Martin J Warren
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| |
Collapse
|
17
|
Kieninger C, Baker JA, Podewitz M, Wurst K, Jockusch S, Lawrence AD, Deery E, Gruber K, Liedl KR, Warren MJ, Kräutler B. Zinc Substitution of Cobalt in Vitamin B 12: Zincobyric acid and Zincobalamin as Luminescent Structural B 12‐Mimics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | - Joseph A. Baker
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | | | | | - Evelyne Deery
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | - Karl Gruber
- Institute for Molecular Biosciences University of Graz Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | | | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| |
Collapse
|
18
|
Kieninger C, Baker JA, Podewitz M, Wurst K, Jockusch S, Lawrence AD, Deery E, Gruber K, Liedl KR, Warren MJ, Kräutler B. Zinc Substitution of Cobalt in Vitamin B 12 : Zincobyric acid and Zincobalamin as Luminescent Structural B 12 -Mimics. Angew Chem Int Ed Engl 2019; 58:14568-14572. [PMID: 31420932 PMCID: PMC6790578 DOI: 10.1002/anie.201908428] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Indexed: 11/14/2022]
Abstract
Replacing the central cobalt ion of vitamin B12 by other metals has been a long-held aspiration within the B12 -field. Herein, we describe the synthesis from hydrogenobyric acid of zincobyric acid (Znby) and zincobalamin (Znbl), the Zn-analogues of the natural cobalt-corrins cobyric acid and vitamin B12 , respectively. The solution structures of Znby and Znbl were studied by NMR-spectroscopy. Single crystals of Znby were produced, providing the first X-ray crystallographic structure of a zinc corrin. The structures of Znby and of computationally generated Znbl were found to resemble the corresponding CoII -corrins, making such Zn-corrins potentially useful for investigations of B12 -dependent processes. The singlet excited state of Znby had a short life-time, limited by rapid intersystem crossing to the triplet state. Znby allowed the unprecedented observation of a corrin triplet (ET =190 kJ mol-1 ) and was found to be an excellent photo-sensitizer for 1 O2 (ΦΔ =0.70).
Collapse
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | | | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | | | | | - Evelyne Deery
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | - Karl Gruber
- Institute for Molecular BiosciencesUniversity ofGrazAustria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | | | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| |
Collapse
|
19
|
Kieninger C, Deery E, Lawrence AD, Podewitz M, Wurst K, Nemoto-Smith E, Widner FJ, Baker JA, Jockusch S, Kreutz CR, Liedl KR, Gruber K, Warren MJ, Kräutler B. The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B 12 Cofactors for Catalysis. Angew Chem Int Ed Engl 2019; 58:10756-10760. [PMID: 31115943 PMCID: PMC6771967 DOI: 10.1002/anie.201904713] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 11/09/2022]
Abstract
The B12 cofactors instill a natural curiosity regarding the primordial selection and evolution of their corrin ligand. Surprisingly, this important natural macrocycle has evaded molecular scrutiny, and its specific role in predisposing the incarcerated cobalt ion for organometallic catalysis has remained obscure. Herein, we report the biosynthesis of the cobalt-free B12 corrin moiety, hydrogenobyric acid (Hby), a compound crafted through pathway redesign. Detailed insights from single-crystal X-ray and solution structures of Hby have revealed a distorted helical cavity, redefining the pattern for binding cobalt ions. Consequently, the corrin ligand coordinates cobalt ions in desymmetrized "entatic" states, thereby promoting the activation of B12 -cofactors for their challenging chemical transitions. The availability of Hby also provides a route to the synthesis of transition metal analogues of B12 .
Collapse
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | | | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Emi Nemoto-Smith
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Florian J Widner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Joseph A Baker
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | | | - Christoph R Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Karl Gruber
- Institute for Molecular Biosciences, University of Graz, Austria
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| |
Collapse
|
20
|
Kieninger C, Deery E, Lawrence AD, Podewitz M, Wurst K, Nemoto‐Smith E, Widner FJ, Baker JA, Jockusch S, Kreutz CR, Liedl KR, Gruber K, Warren MJ, Kräutler B. Die Hydrogenobyrsäure‐Struktur enthüllt den Corrin‐Liganden als entatisches Zustandsmodul zur Steigerung der Katalyseaktivität von B
12
‐Cofaktoren. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Evelyne Deery
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Andrew D. Lawrence
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Emi Nemoto‐Smith
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Florian J. Widner
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Joseph A. Baker
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | | | - Christoph R. Kreutz
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Karl Gruber
- Institute for Molecular BiosciencesUniversity of Graz Österreich
| | - Martin J. Warren
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| |
Collapse
|
21
|
Osman D, Martini MA, Foster AW, Chen J, Scott AJP, Morton RJ, Steed JW, Lurie-Luke E, Huggins TG, Lawrence AD, Deery E, Warren MJ, Chivers PT, Robinson NJ. Bacterial sensors define intracellular free energies for correct enzyme metalation. Nat Chem Biol 2019; 15:241-249. [PMID: 30692683 PMCID: PMC6420079 DOI: 10.1038/s41589-018-0211-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/04/2018] [Indexed: 01/06/2023]
Abstract
There is a challenge for metalloenzymes to acquire their correct metals because some inorganic elements form more stable complexes with proteins than do others. These preferences can be overcome provided some metals are more available than others. However, while the total amount of cellular metal can be readily measured, the available levels of each metal have been more difficult to define. Metal-sensing transcriptional regulators are tuned to the intracellular availabilities of their cognate ions. Here we have determined the standard free energy for metal complex formation to which each sensor, in a set of bacterial metal sensors, is attuned: The less competitive the metal, the less favorable the free energy and hence greater availability to which the cognate allosteric mechanism is tuned. Comparing these free energies with values derived from the metal affinities of a metalloprotein reveals the mechanism of correct metalation exemplified here by a cobalt-chelatase for vitamin B12.
Collapse
Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | | | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, OH, USA
| | | | - Richard J Morton
- Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle-upon-Tyne, UK
| | | | | | | | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Peter T Chivers
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
| |
Collapse
|
22
|
Lee MJ, Mantell J, Brown IR, Fletcher JM, Verkade P, Pickersgill RW, Woolfson DN, Frank S, Warren MJ. De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments. Nat Commun 2018; 9:3413. [PMID: 30143644 PMCID: PMC6109187 DOI: 10.1038/s41467-018-05922-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/31/2018] [Indexed: 01/05/2023] Open
Abstract
Bacterial microcompartments, BMCs, are proteinaceous organelles that encase a specific metabolic pathway within a semi-permeable protein shell. Short encapsulation peptides can direct cargo proteins to the lumen of the compartments. However, the fusion of such peptides to non-native proteins does not guarantee encapsulation and often causes aggregation. Here, we report an approach for targeting recombinant proteins to BMCs that utilizes specific de novo coiled-coil protein–protein interactions. Attachment of one coiled-coil module to PduA (a component of the BMC shell) allows targeting of a fluorescent protein fused to a cognate coiled-coil partner. This interaction takes place on the outer surface of the BMC. The redesign of PduA to generate an N-terminus on the luminal side of the BMC results in intact compartments to which proteins can still be targeted via the designed coiled-coil system. This study provides a strategy to display proteins on the surface or within the lumen of the BMCs. Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.
Collapse
Affiliation(s)
- Matthew J Lee
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Ian R Brown
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 6BT, UK.
| | - Martin J Warren
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| |
Collapse
|
23
|
Videira MAM, Lobo SAL, Silva LSO, Palmer DJ, Warren MJ, Prieto M, Coutinho A, Sousa FL, Fernandes F, Saraiva LM. Staphylococcus aureushaem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG. Mol Microbiol 2018; 109:385-400. [DOI: 10.1111/mmi.14060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - Susana A. L. Lobo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - Liliana S. O. Silva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - David J. Palmer
- School of Biosciences; University of Kent, Giles Lane; Canterbury UK
| | - Martin J. Warren
- School of Biosciences; University of Kent, Giles Lane; Canterbury UK
| | - Manuel Prieto
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
| | - Ana Coutinho
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
| | - Filipa L. Sousa
- Department of Ecogenomics and Systems Biology; University of Vienna; Vienna Austria
| | - Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
- Research Unit on Applied Molecular Biosciences−Rede de Química e Tecnologia (UCIBIO-REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica Portugal
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| |
Collapse
|
24
|
Lawrence AD, Nemoto-Smith E, Deery E, Baker JA, Schroeder S, Brown DG, Tullet JMA, Howard MJ, Brown IR, Smith AG, Boshoff HI, Barry CE, Warren MJ. Construction of Fluorescent Analogs to Follow the Uptake and Distribution of Cobalamin (Vitamin B 12) in Bacteria, Worms, and Plants. Cell Chem Biol 2018; 25:941-951.e6. [PMID: 29779954 DOI: 10.1016/j.chembiol.2018.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/25/2022]
Abstract
Vitamin B12 is made by only certain prokaryotes yet is required by a number of eukaryotes such as mammals, fish, birds, worms, and Protista, including algae. There is still much to learn about how this nutrient is trafficked across the domains of life. Herein, we describe ways to make a number of different corrin analogs with fluorescent groups attached to the main tetrapyrrole-derived ring. A further range of analogs were also constructed by attaching similar fluorescent groups to the ribose ring of cobalamin, thereby generating a range of complete and incomplete corrinoids to follow uptake in bacteria, worms, and plants. By using these fluorescent derivatives we were able to demonstrate that Mycobacterium tuberculosis is able to acquire both cobyric acid and cobalamin analogs, that Caenorhabditis elegans takes up only the complete corrinoid, and that seedlings of higher plants such as Lepidium sativum are also able to transport B12.
Collapse
Affiliation(s)
- Andrew D Lawrence
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Emi Nemoto-Smith
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Joseph A Baker
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Susanne Schroeder
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - David G Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | | | - Mark J Howard
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Ian R Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Helena I Boshoff
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Clifton E Barry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| |
Collapse
|
25
|
Uddin I, Frank S, Warren MJ, Pickersgill RW. A Generic Self-Assembly Process in Microcompartments and Synthetic Protein Nanotubes. Small 2018; 14:e1704020. [PMID: 29573556 DOI: 10.1002/smll.201704020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/26/2018] [Indexed: 06/08/2023]
Abstract
Bacterial microcompartments enclose a biochemical pathway and reactive intermediate within a protein envelope formed by the shell proteins. Herein, the orientation of the propanediol-utilization (Pdu) microcompartment shell protein PduA in bacterial microcompartments and in synthetic nanotubes, and the orientation of PduB in synthetic nanotubes are revealed. When produced individually, PduA hexamers and PduB trimers, tessellate to form flat sheets in the crystal, or they can self-assemble to form synthetic protein nanotubes in solution. Modelling the orientation of PduA in the 20 nm nanotube so as to preserve the shape complementarity and key interactions seen in the crystal structure suggests that the concave surface of the PduA hexamer faces out. This orientation is confirmed experimentally in synthetic nanotubes and in the bacterial microcompartment produced in vivo. The PduB nanotubes described here have a larger diameter, 63 nm, with the concave surface of the trimer again facing out. The conserved concave surface out characteristic of these nano-structures reveals a generic assembly process that causes the interface between adjacent subunits to bend in a common direction that optimizes shape complementarity and minimizes steric clashes. This understanding underpins engineering strategies for the biotechnological application of protein nanotubes.
Collapse
Affiliation(s)
- Ismail Uddin
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4AA, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4AA, UK
| |
Collapse
|
26
|
Abstract
The biosynthesis of B12, involving up to 30 different enzyme-mediated steps, only occurs in bacteria. Thus, most eukaryotes require an external source of B12, and yet the vitamin appears to have only two functions in eukaryotes: as a cofactor for the enzymes methionine synthase and methylmalonylCoA mutase. These two functions are crucial for normal health in humans, and in particular, the formation of methionine is essential for providing methyl groups for over 100 methylation processes. Interference with the methionine synthase reaction not only depletes the body of methyl groups but also leads to the accumulation of homocysteine, a risk factor for many diseases. The syndrome pernicious anemia, characterized by lack of intrinsic factor, leads to a severe, sometimes fatal form of B12 deficiency. However, there is no sharp cutoff for B12 deficiency; rather, there is a continuous inverse relationship between serum B12 and a variety of undesirable outcomes, including neural tube defects, stroke, and dementia. The brain is particularly vulnerable; in children, inadequate B12 stunts brain and intellectual development. Suboptimal B12 status (serum B12<300pmol/L) is very common, occurring in 30%-60% of the population, in particular in pregnant women and in less-developed countries. Thus, many tens of millions of people in the world may suffer harm from having a poor B12 status. Public health steps are urgently needed to correct this inadequacy.
Collapse
Affiliation(s)
- A David Smith
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Helga Refsum
- Department of Nutrition, University of Oslo, Oslo, Norway
| |
Collapse
|
27
|
Lee MJ, Mantell J, Hodgson L, Alibhai D, Fletcher JM, Brown IR, Frank S, Xue WF, Verkade P, Woolfson DN, Warren MJ. Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm. Nat Chem Biol 2017; 14:142-147. [DOI: 10.1038/nchembio.2535] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
|
28
|
Huber I, Palmer DJ, Ludwig KN, Brown IR, Warren MJ, Frunzke J. Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum. ACS Synth Biol 2017; 6:2145-2156. [PMID: 28826205 DOI: 10.1021/acssynbio.7b00167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bacterial microcompartments have significant potential in the area of industrial biotechnology for the production of small molecules, especially involving metabolic pathways with toxic or volatile intermediates. Corynebacterium glutamicum is an established industrial workhorse for the production of amino acids and has been investigated for the production of diamines, dicarboxylic acids, polymers and biobased fuels. Herein, we describe components for the establishment of bacterial microcompartments as production chambers in C. glutamicum. Within this study, we optimized genetic clusters for the expression of the shell components of the Citrobacter freundii propanediol utilization (Pdu) bacterial compartment, thereby facilitating heterologous compartment production in C. glutamicum. Upon induction, transmission electron microscopy images of thin sections from these strains revealed microcompartment-like structures within the cytosol. Furthermore, we demonstrate that it is possible to target eYFP to the empty microcompartments through C-terminal fusions with synthetic scaffold interaction partners (PDZ, SH3 and GBD) as well as with a non-native C-terminal targeting peptide from AdhDH (Klebsiella pneumonia). Thus, we show that it is possible to target proteins to compartments where N-terminal targeting is not possible. The overproduction of PduA alone leads to the construction of filamentous structures within the cytosol and eYFP molecules are localized to these structures when they are N-terminally fused to the P18 and D18 encapsulation peptides from PduP and PduD, respectively. In the future, these nanotube-like structures might be used as scaffolds for directed cellular organization and pathway enhancement.
Collapse
Affiliation(s)
- Isabel Huber
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - David J. Palmer
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Kira N. Ludwig
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ian R. Brown
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Julia Frunzke
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
29
|
Moore SJ, Sowa ST, Schuchardt C, Deery E, Lawrence AD, Ramos JV, Billig S, Birkemeyer C, Chivers PT, Howard MJ, Rigby SEJ, Layer G, Warren MJ. Erratum: Corrigendum: Elucidation of the biosynthesis of the methane catalyst coenzyme F430. Nature 2017; 545:116. [DOI: 10.1038/nature22317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
30
|
Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev 2017; 81:e00048-16. [PMID: 28123057 PMCID: PMC5312243 DOI: 10.1128/mmbr.00048-16] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
Collapse
Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Tamara A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Mark R O'Brian
- Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Martin J Warren
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| |
Collapse
|
31
|
Liang M, Frank S, Lünsdorf H, Warren MJ, Prentice MB. Bacterial microcompartment-directed polyphosphate kinase promotes stable polyphosphate accumulation inE. coli. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600415] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Mingzhi Liang
- Department of Microbiology; University College Cork; Cork Ireland
- School of Biosciences; University of Kent; Canterbury Kent UK
| | - Stefanie Frank
- Department of Biochemical Engineering; University College London; London UK
| | - Heinrich Lünsdorf
- Central Facility for Microscopy; Helmholtz Center of Infection Research; Braunschweig Germany
| | | | - Michael B. Prentice
- Department of Microbiology; University College Cork; Cork Ireland
- Department of Pathology; University College Cork; Cork Ireland
- APC Microbiome Institute; University College Cork; Cork Ireland
| |
Collapse
|
32
|
Lobo SAL, Videira MAM, Pacheco I, Wass MN, Warren MJ, Teixeira M, Matias PM, Romão CV, Saraiva LM. Desulfovibrio vulgaris CbiK P cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues. Environ Microbiol 2016; 19:106-118. [PMID: 27486032 DOI: 10.1111/1462-2920.13479] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/27/2016] [Indexed: 11/26/2022]
Abstract
The sulfate-reducing bacteria of the Desulfovibrio genus make three distinct modified tetrapyrroles, haem, sirohaem and adenosylcobamide, where sirohydrochlorin acts as the last common biosynthetic intermediate along the branched tetrapyrrole pathway. Intriguingly, D. vulgaris encodes two sirohydrochlorin chelatases, CbiKP and CbiKC , that insert cobalt/iron into the tetrapyrrole macrocycle but are thought to be distinctly located in the periplasm and cytoplasm respectively. Fusing GFP onto the C-terminus of CbiKP confirmed that the protein is transported to the periplasm. The structure-function relationship of CbiKP was studied by constructing eleven site-directed mutants and determining their chelatase activities, oligomeric status and haem binding abilities. Residues His154 and His216 were identified as essential for metal-chelation of sirohydrochlorin. The tetrameric form of the protein is stabilized by Arg54 and Glu76, which form hydrogen bonds between two subunits. His96 is responsible for the binding of two haem groups within the main central cavity of the tetramer. Unexpectedly, CbiKP is shown to bind two additional haem groups through interaction with His103. Thus, although still retaining cobaltochelatase activity, the presence of His96 and His103 in CbiKP , which are absent from all other known bacterial cobaltochelatases, has evolved CbiKP a new function as a haem binding protein permitting it to act as a potential haem chaperone or transporter.
Collapse
Affiliation(s)
- Susana A L Lobo
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Marco A M Videira
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Isabel Pacheco
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Mark N Wass
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| |
Collapse
|
33
|
Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Total Synthesis, Structure, and Biological Activity of Adenosylrhodibalamin, the Non-Natural Rhodium Homologue of Coenzyme B12. Angew Chem Int Ed Engl 2016; 55:11281-6. [PMID: 27355790 PMCID: PMC5103170 DOI: 10.1002/anie.201603738] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/12/2022]
Abstract
B12 is unique among the vitamins as it is biosynthesized only by certain prokaryotes. The complexity of its synthesis relates to its distinctive cobalt corrin structure, which is essential for B12 biochemistry and renders coenzyme B12 (AdoCbl) so intriguingly suitable for enzymatic radical reactions. However, why is cobalt so fit for its role in B12 -dependent enzymes? To address this question, we considered the substitution of cobalt in AdoCbl with rhodium to generate the rhodium analogue 5'-deoxy-5'-adenosylrhodibalamin (AdoRbl). AdoRbl was prepared by de novo total synthesis involving both biological and chemical steps. AdoRbl was found to be inactive in vivo in microbial bioassays for methionine synthase and acted as an in vitro inhibitor of an AdoCbl-dependent diol dehydratase. Solution NMR studies of AdoRbl revealed a structure similar to that of AdoCbl. However, the crystal structure of AdoRbl revealed a conspicuously better fit of the corrin ligand for Rh(III) than for Co(III) , challenging the current views concerning the evolution of corrins.
Collapse
Affiliation(s)
- Florian J Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.,Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Dana Heldt
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften, Universität Graz, Austria
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck, Austria
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.
| |
Collapse
|
34
|
Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Totalsynthese, Struktur und biologische Aktivität von Adenosylrhodibalamin, dem unnatürlichen Rhodiumhomologen von Coenzym B12. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603738] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Florian J. Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
- Plant and Microbial Biology Department; University of California; Berkeley USA
| | - Andrew D. Lawrence
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Evelyne Deery
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Dana Heldt
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Stefanie Frank
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften; Universität Graz; Österreich
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie; Universität Innsbruck; Österreich
| | - Martin J. Warren
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
| |
Collapse
|
35
|
Bag S, Prentice MB, Liang M, Warren MJ, Roy Choudhury K. Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions. BMC Bioinformatics 2016; 17:234. [PMID: 27296169 PMCID: PMC4904361 DOI: 10.1186/s12859-016-1107-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Background Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most current approaches for structure determination improve cryo-ET resolution either by some form of sub-tomogram averaging or template matching, respectively precluding detection of shapes that vary across objects or are a priori unknown. Various macromolecular structures possess polyhedral structure. We propose a classification method for polyhedral shapes from incomplete individual cryo-ET reconstructions, based on topological features of an extracted polyhedral graph (PG). Results We outline a pipeline for extracting PG from 3-D cryo-ET reconstructions. For classification, we construct a reference library of regular polyhedra. Using geometric simulation, we construct a non-parametric estimate of the distribution of possible incomplete PGs. In studies with simulated data, a Bayes classifier constructed using these distributions has an average test set misclassification error of < 5 % with upto 30 % of the object missing, suggesting accurate polyhedral shape classification is possible from individual incomplete cryo-ET reconstructions. We also demonstrate how the method can be made robust to mis-specification of the PG using an SVM based classifier. The methodology is applied to cryo-ET reconstructions of 30 micro-compartments isolated from E. coli bacteria. Conclusions The predicted shapes aren’t unique, but all belong to the non-symmetric Johnson solid family, illustrating the potential of this approach to study variation in polyhedral macromolecular structures. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1107-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sukantadev Bag
- Statistics Department, University College Cork, Cork, Ireland
| | | | - Mingzhi Liang
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Kingshuk Roy Choudhury
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27705, USA.
| |
Collapse
|
36
|
Lee MJ, Brown IR, Juodeikis R, Frank S, Warren MJ. Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli. Metab Eng 2016; 36:48-56. [PMID: 26969252 PMCID: PMC4909751 DOI: 10.1016/j.ymben.2016.02.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/05/2016] [Accepted: 02/22/2016] [Indexed: 01/01/2023]
Abstract
Bacterial microcompartments (BMCs) enhance the breakdown of metabolites such as 1,2-propanediol (1,2-PD) to propionic acid. The encapsulation of proteins within the BMC is mediated by the presence of targeting sequences. In an attempt to redesign the Pdu BMC into a 1,2-PD synthesising factory using glycerol as the starting material we added N-terminal targeting peptides to glycerol dehydrogenase, dihydroxyacetone kinase, methylglyoxal synthase and 1,2-propanediol oxidoreductase to allow their inclusion into an empty BMC. 1,2-PD producing strains containing the fused enzymes exhibit a 245% increase in product formation in comparison to un-tagged enzymes, irrespective of the presence of BMCs. Tagging of enzymes with targeting peptides results in the formation of dense protein aggregates within the cell that are shown by immuno-labelling to contain the vast majority of tagged proteins. It can therefore be concluded that these protein inclusions are metabolically active and facilitate the significant increase in product formation. Fusion of BMC targeting peptides to enzymes has a variable effect on activity. Tagged enzymes for 1,2-propanediol synthesis are localised to a BMC. BMC-targeted proteins localised within the BMC are protected from proteases. TEM reveals tagged enzymes form large intracellular protein aggregates. Strains with enzyme aggregates are shown to have enhanced 1,2-propanediol production.
Collapse
Affiliation(s)
- Matthew J Lee
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Ian R Brown
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Rokas Juodeikis
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
| |
Collapse
|
37
|
Lobo SAL, Scott A, Videira MAM, Winpenny D, Gardner M, Palmer MJ, Schroeder S, Lawrence AD, Parkinson T, Warren MJ, Saraiva LM. Staphylococcus aureushaem biosynthesis: characterisation of the enzymes involved in final steps of the pathway. Mol Microbiol 2015; 97:472-87. [DOI: 10.1111/mmi.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Susana A. L. Lobo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
| | - Alan Scott
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
| | - David Winpenny
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Mark Gardner
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Mike J. Palmer
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Susanne Schroeder
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Andrew D. Lawrence
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | | | - Martin J. Warren
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
| |
Collapse
|
38
|
Bali S, Palmer DJ, Schroeder S, Ferguson SJ, Warren MJ. Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1. Cell Mol Life Sci 2014; 71:2837-63. [PMID: 24515122 DOI: 10.1007/s00018-014-1563-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/19/2013] [Accepted: 01/10/2014] [Indexed: 02/05/2023]
Abstract
Hemes (a, b, c, and o) and heme d 1 belong to the group of modified tetrapyrroles, which also includes chlorophylls, cobalamins, coenzyme F430, and siroheme. These compounds are found throughout all domains of life and are involved in a variety of essential biological processes ranging from photosynthesis to methanogenesis. The biosynthesis of heme b has been well studied in many organisms, but in sulfate-reducing bacteria and archaea, the pathway has remained a mystery, as many of the enzymes involved in these characterized steps are absent. The heme pathway in most organisms proceeds from the cyclic precursor of all modified tetrapyrroles uroporphyrinogen III, to coproporphyrinogen III, which is followed by oxidation of the ring and finally iron insertion. Sulfate-reducing bacteria and some archaea lack the genetic information necessary to convert uroporphyrinogen III to heme along the "classical" route and instead use an "alternative" pathway. Biosynthesis of the isobacteriochlorin heme d 1, a cofactor of the dissimilatory nitrite reductase cytochrome cd 1, has also been a subject of much research, although the biosynthetic pathway and its intermediates have evaded discovery for quite some time. This review focuses on the recent advances in the understanding of these two pathways and their surprisingly close relationship via the unlikely intermediate siroheme, which is also a cofactor of sulfite and nitrite reductases in many organisms. The evolutionary questions raised by this discovery will also be discussed along with the potential regulation required by organisms with overlapping tetrapyrrole biosynthesis pathways.
Collapse
Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | | | | | | | | |
Collapse
|
39
|
Lawrence AD, Frank S, Newnham S, Lee MJ, Brown IR, Xue WF, Rowe ML, Mulvihill DP, Prentice MB, Howard MJ, Warren MJ. Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synth Biol 2014; 3:454-465. [PMID: 24933391 DOI: 10.1021/sb4001118] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Targeting of proteins to bacterial microcompartments (BMCs) is mediated by an 18-amino-acid peptide sequence. Herein, we report the solution structure of the N-terminal targeting peptide (P18) of PduP, the aldehyde dehydrogenase associated with the 1,2-propanediol utilization metabolosome from Citrobacter freundii. The solution structure reveals the peptide to have a well-defined helical conformation along its whole length. Saturation transfer difference and transferred NOE NMR has highlighted the observed interaction surface on the peptide with its main interacting shell protein, PduK. By tagging both a pyruvate decarboxylase and an alcohol dehydrogenase with targeting peptides, it has been possible to direct these enzymes to empty BMCs in vivo and to generate an ethanol bioreactor. Not only are the purified, redesigned BMCs able to transform pyruvate into ethanol efficiently, but the strains containing the modified BMCs produce elevated levels of alcohol.
Collapse
Affiliation(s)
- Andrew D. Lawrence
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Stefanie Frank
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Sarah Newnham
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Matthew J. Lee
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Ian R. Brown
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Wei-Feng Xue
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Michelle L. Rowe
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Daniel P. Mulvihill
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | | | - Mark J. Howard
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| |
Collapse
|
40
|
Lobo SA, Lawrence AD, Romão CV, Warren MJ, Teixeira M, Saraiva LM. Characterisation of Desulfovibrio vulgaris haem b synthase, a radical SAM family member. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2014; 1844:1238-47. [DOI: 10.1016/j.bbapap.2014.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 11/27/2022]
|
41
|
Palmer DJ, Schroeder S, Lawrence AD, Deery E, Lobo SA, Saraiva LM, McLean KJ, Munro AW, Ferguson SJ, Pickersgill RW, Brown DG, Warren MJ. The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Mol Microbiol 2014; 93:247-61. [PMID: 24865947 PMCID: PMC4145669 DOI: 10.1111/mmi.12656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2014] [Indexed: 11/28/2022]
Abstract
Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe-coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B-product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.
Collapse
Affiliation(s)
- David J Palmer
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Pang A, Frank S, Brown I, Warren MJ, Pickersgill RW. Structural insights into higher order assembly and function of the bacterial microcompartment protein PduA. J Biol Chem 2014; 289:22377-84. [PMID: 24873823 PMCID: PMC4139245 DOI: 10.1074/jbc.m114.569285] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bacterial microcompartments are large proteinaceous assemblies that are found in the cytoplasm of some bacteria. These structures consist of proteins constituting a shell that houses a number of enzymes involved in specific metabolic processes. The 1,2-propanediol-utilizing microcompartment is assembled from seven different types of shell proteins, one of which is PduA. It is one of the more abundant components of the shell and intriguingly can form nanotubule-like structures when expressed on its own in the cytoplasm of Escherichia coli. We propose a model that accounts for the size and appearance of these PduA structures and underpin our model using a combinatorial approach. Making strategic mutations at Lys-26, Val-51, and Arg-79, we targeted residues predicted to be important for PduA assembly. We present the effect of the amino acid residue substitution on the phenotype of the PduA higher order assemblies (transmission electron microscopy) and the crystal structure of the K26D mutant with one glycerol molecule bound to the central pore. Our results support the view that the hexamer-hexamer interactions seen in PduA crystals persist in the cytoplasmic structures and reveal the profound influence of the two key amino acids, Lys-26 and Arg-79, on tiling, not only in the crystal lattice but also in the bacterial cytoplasm. Understanding and controlling PduA assemblies is valuable in order to inform manipulation for synthetic biology and biotechnological applications.
Collapse
Affiliation(s)
- Allan Pang
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom and
| | - Stefanie Frank
- the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Ian Brown
- the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Martin J Warren
- the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Richard W Pickersgill
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom and
| |
Collapse
|
43
|
Bali S, Rollauer S, Roversi P, Raux-Deery E, Lea SM, Warren MJ, Ferguson SJ. Identification and characterization of the 'missing' terminal enzyme for siroheme biosynthesis in α-proteobacteria. Mol Microbiol 2014; 92:153-63. [PMID: 24673795 PMCID: PMC4063343 DOI: 10.1111/mmi.12542] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2014] [Indexed: 11/27/2022]
Abstract
It has recently been shown that the biosynthetic route for both the d1 -haem cofactor of dissimilatory cd1 nitrite reductases and haem, via the novel alternative-haem-synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. In many denitrifiers (which require d1 -haem), the pathway to make siroheme remained to be identified. Here we identify and characterize a sirohydrochlorin-ferrochelatase from Paracoccus pantotrophus that catalyses the last step of siroheme synthesis. It is encoded by a gene annotated as cbiX that was previously assumed to be encoding a cobaltochelatase, acting on sirohydrochlorin. Expressing this chelatase from a plasmid restored the wild-type phenotype of an Escherichia coli mutant-strain lacking sirohydrochlorin-ferrochelatase activity, showing that this chelatase can act in the in vivo siroheme synthesis. A ΔcbiX mutant in P. denitrificans was unable to respire anaerobically on nitrate, proving the role of siroheme as a precursor to another cofactor. We report the 1.9 Å crystal structure of this ferrochelatase. In vivo analysis of single amino acid variants of this chelatase suggests that two histidines, His127 and His187, are essential for siroheme synthesis. This CbiX can generally be identified in α-proteobacteria as the terminal enzyme of siroheme biosynthesis.
Collapse
Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
| | - Sarah Rollauer
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | - Pietro Roversi
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | - Martin J Warren
- School of Biosciences, University of KentCanterbury, Kent, CT2 7NJ, UK
| | - Stuart J Ferguson
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
| |
Collapse
|
44
|
Moore SJ, Mayer MJ, Biedendieck R, Deery E, Warren MJ. Towards a cell factory for vitamin B12 production in Bacillus megaterium: bypassing of the cobalamin riboswitch control elements. N Biotechnol 2014; 31:553-61. [PMID: 24657453 DOI: 10.1016/j.nbt.2014.03.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 12/27/2022]
Abstract
Bacillus megaterium is a bacterium that has been used in the past for the industrial production of vitamin B12 (cobalamin), the anti-pernicious anaemia factor. Cobalamin is a modified tetrapyrrole with a cobalt ion coordinated within its macrocycle. More recently, B. megaterium has been developed as a host for the high-yield production of recombinant proteins using a xylose inducible promoter system. Herein, we revisit cobalamin production in B. megaterium DSM319. We have investigated the importance of cobalt for optimum growth and cobalamin production. The cobaltochelatase (CbiX(L)) is encoded within a 14-gene cobalamin biosynthetic (cbi) operon, whose gene-products oversee the transformation of uroporphyrinogen III into adenosylcobyrinic acid a,c-diamide, a key precursor of cobalamin synthesis. The production of CbiX(L) in response to exogenous cobalt was monitored. The metal was found to stimulate cobalamin biosynthesis and decrease the levels of CbiX(L). From this we were able to show that the entire cbi operon is transcriptionally regulated by a B12-riboswitch, with a switch-off point at approximately 5 nM cobalamin. To bypass the effects of the B12-riboswitch the cbi operon was cloned without these regulatory elements. Growth of these strains on minimal media supplemented with glycerol as a carbon source resulted in significant increases in cobalamin production (up to 200 μg L(-1)). In addition, a range of partially amidated intermediates up to adenosylcobyric acid was detected. These findings outline a potential way to develop B. megaterium as a cell factory for cobalamin production using cheap raw materials.
Collapse
Affiliation(s)
- Simon J Moore
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Matthias J Mayer
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Rebekka Biedendieck
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Evelyne Deery
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
| |
Collapse
|
45
|
Azim N, Deery E, Warren MJ, Wolfenden BAA, Erskine P, Cooper JB, Coker A, Wood SP, Akhtar M. Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution. ACTA ACUST UNITED AC 2014; 70:744-51. [PMID: 24598743 PMCID: PMC3949521 DOI: 10.1107/s139900471303294x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
Collapse
Affiliation(s)
- N Azim
- School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan
| | - E Deery
- School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England
| | - M J Warren
- School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England
| | - B A A Wolfenden
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - P Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J B Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - A Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S P Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - M Akhtar
- School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan
| |
Collapse
|
46
|
Azim N, Deery E, Warren MJ, Erskine P, Cooper JB, Wood SP, Akhtar M. Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:906-8. [PMID: 23908040 PMCID: PMC3729171 DOI: 10.1107/s1744309113018526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/04/2013] [Indexed: 11/24/2022]
Abstract
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. PBGD from B. megaterium was expressed and the enzyme was crystallized in a form which diffracts synchrotron radiation to high resolution. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.
Collapse
Affiliation(s)
- N Azim
- School of Biological Sciences, University of Punjab, New Campus, Lahore 54590, Pakistan
| | | | | | | | | | | | | |
Collapse
|
47
|
Collins HF, Biedendieck R, Leech HK, Gray M, Escalante-Semerena JC, McLean KJ, Munro AW, Rigby SEJ, Warren MJ, Lawrence AD. Bacillus megaterium has both a functional BluB protein required for DMB synthesis and a related flavoprotein that forms a stable radical species. PLoS One 2013; 8:e55708. [PMID: 23457476 PMCID: PMC3573010 DOI: 10.1371/journal.pone.0055708] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/29/2012] [Indexed: 01/05/2023] Open
Abstract
Despite the extensive study of the biosynthesis of the complex molecule B12 (cobalamin), the mechanism by which the lower ligand 5,6-dimethylbenzimidazole (DMB) is formed has remained something of a mystery. However, recent work has identified and characterized a DMB-synthase (BluB) responsible for the oxygen-dependent, single enzyme conversion of FMN to DMB. In this work, we have identified BluB homologs from the aerobic purple, nonsulfur, photosynthetic bacterium Rhodobacter capsulatus and the aerobic soil bacterium Bacillus megaterium and have demonstrated DMB synthesis by the use of a novel complementation assay in which a B12 deficient strain, substituted with the precursor cobinamide is recovered either by the addition of DMB or by the recombinant expression of a bluB gene. The DMB-synthetic activity of the purified recombinant BluB enzymes was further confirmed in vitro by providing the enzyme with FMNH2 and oxygen and observing the formation of DMB by HPLC. The formation of a 4a-peroxyflavin intermediate, the first step in the oxygen dependent mechanism of DMB biosynthesis, is reported here and is the first intermediate in the enzyme catalysed reaction to be demonstrated experimentally to date. The identification and characterization of an FMN-binding protein found on the cobI operon of B. megaterium, CbiY, is also detailed, revealing an FMN-containing enzyme which is able to stabilize a blue flavin semiquinone upon reduction with a 1-electron donor.
Collapse
Affiliation(s)
- Hannah F. Collins
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Rebekka Biedendieck
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Helen K. Leech
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Michael Gray
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Kirsty J. McLean
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Andrew W. Munro
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Martin J. Warren
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Andrew D. Lawrence
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| |
Collapse
|
48
|
Moore SJ, Biedendieck R, Lawrence AD, Deery E, Howard MJ, Rigby SEJ, Warren MJ. Characterization of the enzyme CbiH60 involved in anaerobic ring contraction of the cobalamin (vitamin B12) biosynthetic pathway. J Biol Chem 2013; 288:297-305. [PMID: 23155054 PMCID: PMC3537027 DOI: 10.1074/jbc.m112.422535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/12/2012] [Indexed: 11/06/2022] Open
Abstract
The anaerobic pathway for the biosynthesis of cobalamin (vitamin B(12)) has remained poorly characterized because of the sensitivity of the pathway intermediates to oxygen and the low activity of enzymes. One of the major bottlenecks in the anaerobic pathway is the ring contraction step, which has not been observed previously with a purified enzyme system. The Gram-positive aerobic bacterium Bacillus megaterium has a complete anaerobic pathway that contains an unusual ring contraction enzyme, CbiH(60), that harbors a C-terminal extension with sequence similarity to the nitrite/sulfite reductase family. To improve solubility, the enzyme was homologously produced in the host B. megaterium DSM319. CbiH(60) was characterized by electron paramagnetic resonance and shown to contain a [4Fe-4S] center. Assays with purified recombinant CbiH(60) demonstrate that the enzyme converts both cobalt-precorrin-3 and cobalt factor III into the ring-contracted product cobalt-precorrin-4 in high yields, with the latter transformation dependent upon DTT and an intact Fe-S center. Furthermore, the ring contraction process was shown not to involve a change in the oxidation state of the central cobalt ion of the macrocycle.
Collapse
Affiliation(s)
- Simon J. Moore
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Rebekka Biedendieck
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
- the Institute of Microbiology, Technische Universität Braunschweig, Braunschweig D-38106, Germany, and
| | - Andrew D. Lawrence
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Evelyne Deery
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Mark J. Howard
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Stephen E. J. Rigby
- the Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Martin J. Warren
- From the School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| |
Collapse
|
49
|
Frank S, Lawrence AD, Prentice MB, Warren MJ. Bacterial microcompartments moving into a synthetic biological world. J Biotechnol 2013; 163:273-9. [DOI: 10.1016/j.jbiotec.2012.09.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 01/22/2023]
|
50
|
Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A, Waterman J, Wilson KS, Brown D, Geeves MA, Howard MJ, Pickersgill RW, Warren MJ. An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nat Chem Biol 2012; 8:933-40. [PMID: 23042036 PMCID: PMC3480714 DOI: 10.1038/nchembio.1086] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022]
Abstract
The biosynthesis of many vitamins and coenzymes has often proved difficult to elucidate due to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B12) pathway in E. coli, and by His-tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly-bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalysed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, has been identified, which can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.
Collapse
Affiliation(s)
- Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|