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Fujishiro T, Ogawa S. The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis. Chem Sci 2021; 12:2172-2180. [PMID: 34163982 PMCID: PMC8179277 DOI: 10.1039/d0sc05439a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The class II chelatase CfbA catalyzes Ni2+ insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni2+ and Co2+ remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni2+, Ni-SHC, and Co2+ were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni2+-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co2+ than Ni2+. Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni2+ and Co2+ by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni2+ insertion catalytic mechanism was proposed: Ni2+ insertion to SHC is promoted by the support of an acetate side chain of SHC.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
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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. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 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] [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.
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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.
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Layer G. Heme biosynthesis in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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Optimization of hydrogenobyrinic acid biosynthesis in Escherichia coli using multi-level metabolic engineering strategies. Microb Cell Fact 2020; 19:118. [PMID: 32487216 PMCID: PMC7268678 DOI: 10.1186/s12934-020-01377-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hydrogenobyrinic acid is a key intermediate of the de-novo aerobic biosynthesis pathway of vitamin B12. The introduction of a heterologous de novo vitamin B12 biosynthesis pathway in Escherichia coli offers an alternative approach for its production. Although E. coli avoids major limitations that currently faced by industrial producers of vitamin B12, such as long growth cycles, the insufficient supply of hydrogenobyrinic acid restricts industrial vitamin B12 production. RESULTS By designing combinatorial ribosomal binding site libraries of the hemABCD genes in vivo, we found that their optimal relative translational initiation rates are 10:1:1:5. The transcriptional coordination of the uroporphyrinogen III biosynthetic module was realized by promoter engineering of the hemABCD operon. Knockdown of competitive heme and siroheme biosynthesis pathways by RBS engineering enhanced the hydrogenobyrinic acid titer to 20.54 and 15.85 mg L-1, respectively. Combined fine-tuning of the heme and siroheme biosynthetic pathways enhanced the hydrogenobyrinic acid titer to 22.57 mg L-1, representing a remarkable increase of 1356.13% compared with the original strain FH215-HBA. CONCLUSIONS Through multi-level metabolic engineering strategies, we achieved the metabolic balance of the uroporphyrinogen III biosynthesis pathway, eliminated toxicity due to by-product accumulation, and finally achieved a high HBA titer of 22.57 mg L-1 in E. coli. This lays the foundation for high-yield production of vitamin B12 in E. coli and will hopefully accelerate its industrial production.
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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.
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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
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Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. Microorganisms 2020; 8:microorganisms8020283. [PMID: 32093084 PMCID: PMC7074977 DOI: 10.3390/microorganisms8020283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light conditions, but cannot completely avoid this stress if environmental conditions suddenly change. R. capsulatus has a stronger pigmentation and faster switches to phototrophic growth than R. sphaeroides. However, its photooxidative stress response has not been investigated. Here, we compare both species by transcriptomics and proteomics, revealing that proteins involved in oxidation-reduction processes, DNA, and protein damage repair play pivotal roles. These functions are likely universal to many phototrophs. Furthermore, the alternative sigma factors RpoE and RpoHII are induced in both species, even though the genetic localization of the rpoE gene, the RpoE protein itself, and probably its regulon, are different. Despite sharing the same habitats, our findings also suggest individual strategies. The crtIB-tspO operon, encoding proteins for biosynthesis of carotenoid precursors and a regulator of photosynthesis, and cbiX, encoding a putative ferrochelatase, are induced in R. capsulatus. This specific response might support adaptation by maintaining high carotenoid-to-bacteriochlorophyll ratios and preventing the accumulation of porphyrin-derived photosensitizers.
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Fujishiro T, Shimada Y, Nakamura R, Ooi M. Structure of sirohydrochlorin ferrochelatase SirB: the last of the structures of the class II chelatase family. Dalton Trans 2019; 48:6083-6090. [PMID: 30778451 DOI: 10.1039/c8dt04727h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structure of Bacillus subtilis SirB, which catalyses the insertion of Fe2+ into the substrate sirohydrochlorin (SHC) in siroheme biosynthesis, is reported herein as the last of the structures of class II chelatases. The structure of SirB with Co2+ showed that the active site of SirB is located at the N-terminal domain with metal-binding amino acid residues His10, Glu43, and His76, which was also predicted for CbiX, but is distinct from the C-terminal active sites of CbiK and HemH. The biosynthetic model reactions using SirB, Co2+ and uroporphyrin I or protoporphyrin IX as a SHC analogue revealed that SirB showed chelatase activity for uroporphyrin I, but not for protoporphyrin IX. Simulations of tetrapyrroles docking to SirB provided an insight into its tetrapyrrole substrate recognition: SHC and uroporphyrin I were suitably bound beside the Co2+ ion-binding site at the active site cavity; protoporphyrin IX was also docked to the active site but its orientation was different from those of the other two tetrapyrroles. Summarizing the present data, it was proposed that the key structural features for substrate recognition of SirB could be the hydrophobic area at the active site as well as the substituents of the tetrapyrroles.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
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Videira MAM, Lobo SAL, Sousa FL, Saraiva LM. Identification of the sirohaem biosynthesis pathway in Staphylococcus aureus. FEBS J 2019; 287:1537-1553. [PMID: 31605669 DOI: 10.1111/febs.15091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 10/09/2019] [Indexed: 11/27/2022]
Abstract
Sirohaem is a modified tetrapyrrole and a key prosthetic group of several enzymes involved in nitrogen and sulfur metabolisms. This work shows that Staphylococcus aureus produces sirohaem through a pathway formed by three independent enzymes. Of the two putative sirohaem synthases encoded in the S. aureus genome and annotated as cysG, one is herein shown to be a uroporphyrinogen III methyltransferase that converts uroporphyrinogen III to precorrin-2, and was renamed as UroM. The second cysG gene encodes a precorrin-2 dehydrogenase that converts precorrin-2 to sirohydrochlorin, and was designated as P2D. The last step was found to be performed by the gene nirR that, in fact, codes for a protein with sirohydrochlorin ferrochelatase activity, labelled as ShfC. Additionally, site-directed mutagenesis studies of S. aureus ShfC revealed that residues H22 and H87, which are predicted by homology modelling to be located at the active site, control the ferrochelatase activity. Within bacteria, sirohaem synthesis may occur via one, two or three enzymes, and we propose to name the correspondent pathways as Types 1, 2 and 3, respectively. A phylogenetic analysis revealed that Type 1 is the most used pathway in Gammaproteobacteria and Streptomycetales, Type 2 predominates in Fibrobacteres and Vibrionales, and Type 3 predominates in Firmicutes of the Bacillales order. Altogether, we concluded that the current distribution of sirohaem pathways within bacteria, which changes at the genus or species level and within taxa, seems to be the result of evolutionary multiple fusion/fission events.
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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.,Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Filipa L Sousa
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Peng J, Wang H, Lu J, Hui W, Wang Y, Shang X. Identifying term relations cross different gene ontology categories. BMC Bioinformatics 2017; 18:573. [PMID: 29297309 PMCID: PMC5751813 DOI: 10.1186/s12859-017-1959-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecular function, biological process and cellular component. For better biological reasoning, identifying the biological relationships between terms in different categories are important. However, the existing measurements to calculate similarity between terms in different categories are either developed by using the GO data only or only take part of combined gene co-function network information. Results We propose an iterative ranking-based method called CroGO2 to measure the cross-categories GO term similarities by incorporating level information of GO terms with both direct and indirect interactions in the gene co-function network. Conclusions The evaluation test shows that CroGO2 performs better than the existing methods. A genome-specific term association network for yeast is also generated by connecting terms with the high confidence score. The linkages in the term association network could be supported by the literature. Given a gene set, the related terms identified by using the association network have overlap with the related terms identified by GO enrichment analysis.
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Affiliation(s)
- Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Honggang Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Junya Lu
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Weiwei Hui
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
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Gumpert H, Kubicek-Sutherland JZ, Porse A, Karami N, Munck C, Linkevicius M, Adlerberth I, Wold AE, Andersson DI, Sommer MOA. Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment. Front Microbiol 2017; 8:1852. [PMID: 29018426 PMCID: PMC5622998 DOI: 10.3389/fmicb.2017.01852] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.
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Affiliation(s)
- Heidi Gumpert
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | | | - Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Marius Linkevicius
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes. Biosystems 2017; 155:20-28. [DOI: 10.1016/j.biosystems.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023]
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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: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [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.
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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
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Streit BR, Celis AI, Shisler K, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Reactions of Ferrous Coproheme Decarboxylase (HemQ) with O 2 and H 2O 2 Yield Ferric Heme b. Biochemistry 2016; 56:189-201. [PMID: 27982566 DOI: 10.1021/acs.biochem.6b00958] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently discovered pathway for the biosynthesis of heme b ends in an unusual reaction catalyzed by coproheme decarboxylase (HemQ), where the Fe(II)-containing coproheme acts as both substrate and cofactor. Because both O2 and H2O2 are available as cellular oxidants, pathways for the reaction involving either can be proposed. Analysis of reaction kinetics and products showed that, under aerobic conditions, the ferrous coproheme-decarboxylase complex is rapidly and selectively oxidized by O2 to the ferric state. The subsequent second-order reaction between the ferric complex and H2O2 is slow, pH-dependent, and further decelerated by D2O2 (average kinetic isotope effect of 2.2). The observation of rapid reactivity with peracetic acid suggested the possible involvement of Compound I (ferryl porphyrin cation radical), consistent with coproheme and harderoheme reduction potentials in the range of heme proteins that heterolytically cleave H2O2. Resonance Raman spectroscopy nonetheless indicated a remarkably weak Fe-His interaction; how the active site structure may support heterolytic H2O2 cleavage is therefore unclear. From a cellular perspective, the use of H2O2 as an oxidant in a catalase-positive organism is intriguing, as is the unusual generation of heme b in the Fe(III) rather than Fe(II) state as the end product of heme synthesis.
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Affiliation(s)
- Bennett R Streit
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
| | - Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
| | - Kenton R Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
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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] [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.
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Affiliation(s)
- David J Palmer
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
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