1
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Korshoj LE, Kielian T. Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601229. [PMID: 38979200 PMCID: PMC11230364 DOI: 10.1101/2024.06.28.601229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. We have developed an optimized bacterial single-cell RNA sequencing method, BaSSSh-seq, to study Staphylococcus aureus diversity during biofilm growth and transcriptional adaptations following immune cell exposure. We validated the ability of BaSSSh-seq to capture extensive transcriptional heterogeneity during biofilm compared to planktonic growth. Application of new computational tools revealed transcriptional regulatory networks across the heterogeneous biofilm subpopulations and identification of gene sets that were associated with a trajectory from planktonic to biofilm growth. BaSSSh-seq also detected alterations in biofilm metabolism, stress response, and virulence that were tailored to distinct immune cell populations. This work provides an innovative platform to explore biofilm dynamics at single-cell resolution, unlocking the potential for identifying biofilm adaptations to environmental signals and immune pressure.
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2
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Dailey HA, Medlock AE. Direct Spectroscopic Ferrochelatase Assay. Methods Mol Biol 2024; 2839:243-247. [PMID: 39008258 DOI: 10.1007/978-1-0716-4043-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Ferrochelatases (E.C. 4.99.1.1) catalyze the insertion of ferrous iron into either protoporphyrin IX to make protoheme IX or coproporphyrin III to make coproheme III. Ferrochelatase activity in extracts or purified protein can be measured via several assays. Here, we describe a rapid real-time direct spectroscopic ferrochelatase assay for both protoporphyrin and coproporphyrin ferrochelatases.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Augusta University/University of Georgia Medical Partnership, Athens, GA, USA.
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3
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Zhou Y, Chen J, Pu W, Cai N, Che B, Yang J, Wang M, Zhong S, Zuo X, Wang D, Wang Y, Zheng P, Sun J. Development of a growth-coupled selection platform for directed evolution of heme biosynthetic enzymes in Corynebacterium glutamicum. Front Bioeng Biotechnol 2023; 11:1236118. [PMID: 37654705 PMCID: PMC10465345 DOI: 10.3389/fbioe.2023.1236118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Heme is an important tetrapyrrole compound, and has been widely applied in food and medicine industries. Although microbial production of heme has been developed with metabolic engineering strategies during the past 20 years, the production levels are relatively low due to the multistep enzymatic processes and complicated regulatory mechanisms of microbes. Previous studies mainly adopted the strategies of strengthening precursor supply and product transportation to engineer microbes for improving heme biosynthesis. Few studies focused on the engineering and screening of efficient enzymes involved in heme biosynthesis. Herein, a growth-coupled, high-throughput selection platform based on the detoxification of Zinc-protoporphyrin IX (an analogue of heme) was developed and applied to directed evolution of coproporphyrin ferrochelatase, catalyzing the insertion of metal ions into porphyrin ring to generate heme or other tetrapyrrole compounds. A mutant with 3.03-fold increase in k cat/K M was selected. Finally, growth-coupled directed evolution of another three key enzymes involved in heme biosynthesis was tested by using this selection platform. The growth-coupled selection platform developed here can be a simple and effective strategy for directed evolution of the enzymes involved in the biosynthesis of heme or other tetrapyrrole compounds.
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Affiliation(s)
- Yingyu Zhou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ningyun Cai
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jinxing Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mengmeng Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shasha Zhong
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xingtao Zuo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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4
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Sebastiani F, Dali A, Alonso de Armiño DJ, Campagni L, Patil G, Becucci M, Hofbauer S, Estrin DA, Smulevich G. The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae. J Inorg Biochem 2023; 245:112243. [PMID: 37196412 DOI: 10.1016/j.jinorgbio.2023.112243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
This work focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The UV - vis and resonance Raman spectroscopies together with the molecular dynamics simulations clearly show that the wild-type coproheme-CO adduct is characterized by two CO conformers, one hydrogen-bonded to the distal H118 residue and the other showing a weak polar interaction with the distal cavity. Instead, upon conversion to heme b, i.e. after decarboxylation of propionates 2 and 4 and rotation by 90o of the porphyrin ring inside the cavity, CO probes a less polar environment. In the absence of the H118 residue, both coproheme and heme b complexes form only the non-H-bonded CO species. The unrotated MMD-CO adduct as observed in the H118F variant, confirms that decarboxylation of propionate 2 only, does not affect the heme cavity. The rupture of both the H-bonds involving propionates 2 and 4 destabilizes the porphyrin inside the cavity with the subsequent formation of a CO adduct in an open conformation. In addition, in this work we present data on CO binding to reversed heme b, obtained by hemin reconstitution of the H118A variant, and to heme d, obtained by addition of an excess of hydrogen peroxide. The results will be discussed and compared with those reported for the representatives of the firmicute clade.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Diego Javier Alonso de Armiño
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Lorenzo Campagni
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria.
| | - Dario A Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Departamento de Quimica Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, Sesto Fiorentino I-50019, Italy.
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5
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Falb N, Patil G, Furtmüller PG, Gabler T, Hofbauer S. Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis. Comput Struct Biotechnol J 2023; 21:3933-3945. [PMID: 37593721 PMCID: PMC10427985 DOI: 10.1016/j.csbj.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
The coproporphyrin dependent heme biosynthesis pathway is almost exclusively utilized by Gram-positive bacteria. This fact makes it a worthwhile topic for basic research, since a fundamental understanding of a metabolic pathway is necessary to translate the focus towards medical biotechnology, which is very relevant in this specific case, considering the need for new antibiotic targets to counteract the pathogenicity of Gram-positive superbugs. Over the years a lot of structural data on the set of enzymes acting in Gram-positive heme biosynthesis has accumulated in the Protein Database (www.pdb.org). One major challenge is to filter and analyze all available structural information in sufficient detail in order to be helpful and to draw conclusions. Here we pursued to give a holistic overview of structural information on enzymes involved in the coproporphyrin dependent heme biosynthesis pathway. There are many aspects to be extracted from experimentally determined structures regarding the reaction mechanisms, where the smallest variation of the position of an amino acid residue might be important, but also on a larger level regarding protein-protein interactions, where the focus has to be on surface characteristics and subunit (secondary) structural elements and oligomerization. This review delivers a status quo, highlights still missing information, and formulates future research endeavors in order to better understand prokaryotic heme biosynthesis.
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Affiliation(s)
- Nikolaus Falb
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
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6
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Zamarreño Beas J, Videira MAM, Karavaeva V, Lourenço FM, Almeida MR, Sousa F, Saraiva LM. In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase. Front Genet 2023; 14:1199357. [PMID: 37415606 PMCID: PMC10320005 DOI: 10.3389/fgene.2023.1199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
Intracellular heme formation and trafficking are fundamental processes in living organisms. Bacteria and archaea utilize three biogenesis pathways to produce iron protoporphyrin IX (heme b) that diverge after the formation of the common intermediate uroporphyrinogen III (uro'gen III). In this study, we identify and provide a detailed characterization of the enzymes involved in the transformation of uro'gen III into heme in Campylobacter jejuni, demonstrating that this bacterium utilizes the protoporphyrin-dependent (PPD) pathway. In general, limited knowledge exists regarding the mechanisms by which heme b reaches its target proteins after this final step. Specifically, the chaperones necessary for trafficking heme to prevent the cytotoxic effects associated with free heme remain largely unidentified. In C. jejuni, we identified a protein named CgdH2 that binds heme with a dissociation constant of 4.9 ± 1.0 µM, and this binding is impaired upon mutation of residues histidine 45 and 133. We demonstrate that C. jejuni CgdH2 establishes protein-protein interactions with ferrochelatase, suggesting its role in facilitating heme transfer from ferrochelatase to CgdH2. Furthermore, phylogenetic analysis reveals that C. jejuni CgdH2 is evolutionarily distinct from the currently known chaperones. Therefore, CgdH2 is the first protein identified as an acceptor of intracellularly formed heme, expanding our knowledge of the mechanisms underlying heme trafficking within bacterial cells.
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Affiliation(s)
- Jordi Zamarreño Beas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Val Karavaeva
- Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Frederico M. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mafalda R. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipa Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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7
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Cheng YY, Chen Z, Cao X, Ross TD, Falbel TG, Burton BM, Venturelli OS. Programming bacteria for multiplexed DNA detection. Nat Commun 2023; 14:2001. [PMID: 37037805 PMCID: PMC10086068 DOI: 10.1038/s41467-023-37582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
DNA is a universal and programmable signal of living organisms. Here we develop cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA-sensing mechanism and simple detection procedure could enable programmable DNA sensing for a wide range of applications.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhengyi Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler D Ross
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Ushimaru R, Lyu J, Abe I. Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad016. [PMID: 37422437 PMCID: PMC10548856 DOI: 10.1093/jimb/kuad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities potentially beneficial for the producing organisms and for human use. The unique properties of tetrapyrrole natural products derive from their extensively modified and highly conjugated macrocyclic core structures. Most of these various tetrapyrrole natural products biosynthetically originate from a branching point precursor, uroporphyrinogen III, which contains propionate and acetate side chains on its macrocycle. Over the past few decades, many modification enzymes with unique catalytic activities, and the diverse enzymatic chemistries employed to cleave the propionate side chains from the macrocycles, have been identified. In this review, we highlight the tetrapyrrole biosynthetic enzymes required for the propionate side chain removal processes and discuss their various chemical mechanisms. ONE-SENTENCE SUMMARY This mini-review describes various enzymes involved in the propionate side chain cleavages during the biosynthesis of tetrapyrrole cofactors and secondary metabolites.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jiaqi Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Sebastiani F, Baroni C, Patil G, Dali A, Becucci M, Hofbauer S, Smulevich G. The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of C. diphtheriae Coproheme Decarboxylase. Biomolecules 2023; 13:235. [PMID: 36830604 PMCID: PMC9953210 DOI: 10.3390/biom13020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Monoderm bacteria accumulate heme b via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H2O2, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen Corynebacterium diphtheriae ChdC complexed with coproheme and heme b. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Chiara Baroni
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Gaurav Patil
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
- INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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10
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Ma J, Zhang C, Dang K, Liao Y, Feng X, Zhou P. Spherical pneumonia caused by Ralstonia mannitolilytica: a case report and literature review. BMC Pulm Med 2023; 23:20. [PMID: 36647091 PMCID: PMC9841942 DOI: 10.1186/s12890-023-02316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Spherical pneumonia is an extremely rare condition that is difficult to diagnose. It is a specific type of lung infection that often manifests as a round or round-like mass on chest imaging. Spherical pneumonia is easily misdiagnosed as a pulmonary tumor; therefore, awareness of this disease must be strengthened. CASE PRESENTATION The patient was a 29-year-old female who had persistent cough and sputum for approximately 1 month and fever for 5 days. Chest computed tomography (CT) at our hospital revealed a mass in the lower lobe of the right lung near the hilar region, with obstructive pulmonary atelectasis and obstructive pneumonia. Although lung cancer was suspected, Ralstonia mannitolilytica was detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, and no cancer cells or Mycobacterium tuberculosis were detected. Finally, the patient was diagnosed with spherical pneumonia caused by R. mannitolilytica. Anti-infective treatment, symptomatic treatment, and administration of a traditional Chinese medicine decoction were performed based on the syndrome differentiation. After 10 days of treatment, chest CT revealed few lesions in the lower lobe of the right lung, which were significantly reduced compared with those in the past. CONCLUSIONS Spherical pneumonia caused by R. mannitolilytica has not yet been reported and differential diagnosis is key in clinical diagnosis. When spherical pneumonia is difficult to diagnose, mNGS may be a better alternative.
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Affiliation(s)
- Jianli Ma
- grid.411304.30000 0001 0376 205XClinical Medical School, Chengdu University of Traditional Chinese Medicine, No 39 Shi-Er-Qiao Road, Jin Niu District, Chengdu, 610072 Sichuan Province People’s Republic of China
| | - Chuantao Zhang
- grid.415440.0Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province People’s Republic of China
| | - Kaijie Dang
- grid.411304.30000 0001 0376 205XClinical Medical School, Chengdu University of Traditional Chinese Medicine, No 39 Shi-Er-Qiao Road, Jin Niu District, Chengdu, 610072 Sichuan Province People’s Republic of China
| | - Yichao Liao
- grid.411304.30000 0001 0376 205XClinical Medical School, Chengdu University of Traditional Chinese Medicine, No 39 Shi-Er-Qiao Road, Jin Niu District, Chengdu, 610072 Sichuan Province People’s Republic of China
| | - Xue Feng
- grid.411304.30000 0001 0376 205XClinical Medical School, Chengdu University of Traditional Chinese Medicine, No 39 Shi-Er-Qiao Road, Jin Niu District, Chengdu, 610072 Sichuan Province People’s Republic of China
| | - Pengcheng Zhou
- grid.415440.0Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province People’s Republic of China
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11
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Dali A, Gabler T, Sebastiani F, Destinger A, Furtmüller PG, Pfanzagl V, Becucci M, Smulevich G, Hofbauer S. Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation. Protein Sci 2023; 32:e4534. [PMID: 36479958 PMCID: PMC9794026 DOI: 10.1002/pro.4534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Alina Destinger
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vera Pfanzagl
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy,INSTM Research Unit of FirenzeSesto Fiorentino (Fi)Italy
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
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12
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Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
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13
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Tobuse AJ, Ang CW, Yeong KY. Modern vaccine development via reverse vaccinology to combat antimicrobial resistance. Life Sci 2022; 302:120660. [PMID: 35642852 DOI: 10.1016/j.lfs.2022.120660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
With the continuous evolution of bacteria, the global antimicrobial resistance health threat is causing millions of deaths yearly. While depending on antibiotics as a primary treatment has its merits, there are no effective alternatives thus far in the pharmaceutical market against some drug-resistant bacteria. In recent years, vaccinology has become a key topic in scientific research. Combining with the growth of technology, vaccine research is seeing a new light where the process is made faster and more efficient. Although less discussed, bacterial vaccine is a feasible strategy to combat antimicrobial resistance. Some vaccines have shown promising results with good efficacy against numerous multidrug-resistant strains of bacteria. In this review, we aim to discuss the findings from studies utilizing reverse vaccinology for vaccine development against some multidrug-resistant bacteria, as well as provide a summary of multi-year bacterial vaccine studies in clinical trials. The advantages of reverse vaccinology in the generation of new bacterial vaccines are also highlighted. Meanwhile, the limitations and future prospects of bacterial vaccine concludes this review.
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Affiliation(s)
- Asuka Joy Tobuse
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Chee Wei Ang
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Keng Yoon Yeong
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia.
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14
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Hunter GA, Ferreira GC. Metal ion coordination sites in ferrochelatase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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An active site at work – the role of key residues in C. diphteriae coproheme decarboxylase. J Inorg Biochem 2022; 229:111718. [DOI: 10.1016/j.jinorgbio.2022.111718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 01/01/2022] [Indexed: 12/12/2022]
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16
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17
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Wang C, Dou X, Li J, Wu J, Cheng Y, An N. Composition and Diversity of the Ocular Surface Microbiota in Patients With Blepharitis in Northwestern China. Front Med (Lausanne) 2021; 8:768849. [PMID: 34950683 PMCID: PMC8688757 DOI: 10.3389/fmed.2021.768849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/17/2021] [Indexed: 12/27/2022] Open
Abstract
Purpose: To investigate the composition and diversity of the microbiota on the ocular surface of patients with blepharitis in northwestern China via 16S rDNA amplicon sequencing. Methods: Thirty-seven patients with blepharitis divided into groups of anterior, posterior and mixed blepharitis and twenty healthy controls from northwestern China were enrolled in the study. Samples were collected from the eyelid margin and conjunctival sac of each participant. The V3–V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences in taxonomy and diversity among different groups were compared. Results: The composition of the ocular surface microbiota of patients with blepharitis was similar to that of healthy subjects, but there were differences in the relative abundance of each bacterium. At the phylum level, the abundances of Actinobacteria, Cyanobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, and Atribacteria were significantly higher in the blepharitis group than in the healthy control group, while the relative abundance of Firmicutes was significantly lower (p < 0.05, Mann-Whitney U). At the genus level, the abundances of Lactobacillus, Ralstonia, Bacteroides, Akkermansia, Bifidobacterium, Escherichia-Shigella, Faecalibacterium, and Brevibacterium were significantly higher in the blepharitis group than in the healthy control group, while the relative abundances of Bacillus, Staphylococcus, Streptococcus, and Acinetobacter were significantly lower in the blepharitis group (p < 0.05, Mann-Whitney U). The microbiota of anterior blepharitis was similar to that of mixed blepharitis but different from that of posterior blepharitis. Lactobacillus and Bifidobacterium are biomarkers of posterior blepharitis, and Ralstonia is a biomarker of mixed blepharitis. There was no significant difference in the ocular surface microbiota between the eyelid margin and conjunctival sac with or without blepharitis. Conclusion: The ocular surface microbiota of patients with blepharitis varied among different study groups, according to 16S rDNA amplicon sequencing analysis. The reason might be due to the participants being from different environments and having different lifestyles. Lactobacillus, Bifidobacterium, Akkermansia, Ralstonia, and Bacteroides may play important roles in the pathogenesis of blepharitis.
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Affiliation(s)
- Changhao Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Xiuhong Dou
- College of Life Science, Northwest University, Xi'an, China
| | - Jian Li
- College of Life Science, Northwest University, Xi'an, China
| | - Jie Wu
- Department of Ophthalmology, Xi'an No.1 Hospital, First Affiliated Hospital of Northwest University, Xi'an, China.,Shaanxi Key Laboratory of Ophthalmology, Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Yan Cheng
- Department of Ophthalmology, Xi'an No.1 Hospital, First Affiliated Hospital of Northwest University, Xi'an, China.,Shaanxi Key Laboratory of Ophthalmology, Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Na An
- Department of Ophthalmology, Xi'an No.1 Hospital, First Affiliated Hospital of Northwest University, Xi'an, China.,Shaanxi Key Laboratory of Ophthalmology, Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Shaanxi Institute of Ophthalmology, Xi'an, China
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18
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Gabler T, Sebastiani F, Helm J, Dali A, Obinger C, Furtmüller PG, Smulevich G, Hofbauer S. Substrate specificity and complex stability of coproporphyrin ferrochelatase is governed by hydrogen-bonding interactions of the four propionate groups. FEBS J 2021; 289:1680-1699. [PMID: 34719106 DOI: 10.1111/febs.16257] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022]
Abstract
Coproporpyhrin III is the substrate of coproporphyrin ferrochelatases (CpfCs). These enzymes catalyse the insertion of ferrous iron into the porphyrin ring. This is the penultimate step within the coproporphyrin-dependent haeme biosynthesis pathway. This pathway was discovered in 2015 and is mainly utilised by monoderm bacteria. Prior to this discovery, monoderm bacteria were believed to utilise the protoporphyrin-dependent pathway, analogously to diderm bacteria, where the substrate for the respective ferrochelatase is protoporphyrin IX, which has two propionate groups at positions 6 and 7 and two vinyl groups at positions 2 and 4. In this work, we describe for the first time the interactions of the four-propionate substrate, coproporphyrin III, and the four-propionate product, iron coproporphyrin III (coproheme), with the CpfC from Listeria monocytogenes and pin down differences with respect to the protoporphyrin IX and haeme b complexes in the wild-type (WT) enzyme. We further created seven LmCpfC variants aiming at altering substrate and product coordination. The WT enzyme and all the variants were comparatively studied by spectroscopic, thermodynamic and kinetic means to investigate in detail the H-bonding interactions, which govern complex stability and substrate specificity. We identified a tyrosine residue (Y124 in LmCpfC), coordinating the propionate at position 2, which is conserved in monoderm CpfCs, to be highly important for binding and stabilisation. Importantly, we also describe a tyrosine-serine-threonine triad, which coordinates the propionate at position 4. The study of the triad variants indicates structural differences between the coproporphyrin III and the coproheme complexes. ENZYME: EC 4.99.1.9.
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Affiliation(s)
- Thomas Gabler
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Federico Sebastiani
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy
| | - Johannes Helm
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrea Dali
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy.,INSTM Research Unit of Firenze, Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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19
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Seif Y, Palsson BØ. Path to improving the life cycle and quality of genome-scale models of metabolism. Cell Syst 2021; 12:842-859. [PMID: 34555324 PMCID: PMC8480436 DOI: 10.1016/j.cels.2021.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 02/17/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
Abstract
Genome-scale models of metabolism (GEMs) are key computational tools for the systems-level study of metabolic networks. Here, we describe the "GEM life cycle," which we subdivide into four stages: inception, maturation, specialization, and amalgamation. We show how different types of GEM reconstruction workflows fit in each stage and proceed to highlight two fundamental bottlenecks for GEM quality improvement: GEM maturation and content removal. We identify common characteristics contributing to increasing quality of maturing GEMs drawing from past independent GEM maturation efforts. We then shed some much-needed light on the latent and unrecognized but pervasive issue of content removal, demonstrating the substantial effects of model pruning on its solution space. Finally, we propose a novel framework for content removal and associated confidence-level assignment which will help guide future GEM development efforts, reduce duplication of effort across groups, potentially aid automated reconstruction platforms, and boost the reproducibility of model development.
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Affiliation(s)
- Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Bernhard Ørn Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
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20
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Sebastiani F, Michlits H, Lier B, Becucci M, Furtmüller PG, Oostenbrink C, Obinger C, Hofbauer S, Smulevich G. Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C. diphtheriae. Biophys J 2021; 120:3600-3614. [PMID: 34339636 PMCID: PMC8456308 DOI: 10.1016/j.bpj.2021.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 02/06/2023] Open
Abstract
Monoderm bacteria utilize coproheme decarboxylases (ChdCs) to generate heme b by a stepwise decarboxylation of two propionate groups of iron coproporphyrin III (coproheme), forming two vinyl groups. This work focuses on actinobacterial ChdC from Corynebacterium diphtheriae (CdChdC) to elucidate the hydrogen peroxide-mediated decarboxylation of coproheme via monovinyl monopropionyl deuteroheme (MMD) to heme b, with the principal aim being to understand the reorientation mechanism of MMD during turnover. Wild-type CdChdC and variants, namely H118A, H118F, and A207E, were studied by resonance Raman and ultraviolet-visible spectroscopy, mass spectrometry, and molecular dynamics simulations. As actinobacterial ChdCs use a histidine (H118) as a distal base, we studied the H118A and H118F variants to elucidate the effect of 1) the elimination of the proton acceptor and 2) steric constraints within the active site. The A207E variant mimics the proximal H-bonding network found in chlorite dismutases. This mutation potentially increases the rigidity of the proximal site and might impair the rotation of the reaction intermediate MMD. We found that both wild-type CdChdC and the variant H118A convert coproheme mainly to heme b upon titration with H2O2. Interestingly, the variant A207E mostly accumulates MMD along with small amounts of heme b, whereas H118F is unable to produce heme b and accumulates only MMD. Together with molecular dynamics simulations, the spectroscopic data provide insight into the reaction mechanism and the mode of reorientation of MMD, i.e., a rotation in the active site versus a release and rebinding.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino (FI), Italy
| | - Hanna Michlits
- Department of Chemistry, Institute of Biochemistry, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bettina Lier
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino (FI), Italy
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, Sesto Fiorentino, Italy.
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21
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Klimka A, Mertins S, Nicolai AK, Rummler LM, Higgins PG, Günther SD, Tosetti B, Krut O, Krönke M. Epitope-specific immunity against Staphylococcus aureus coproporphyrinogen III oxidase. NPJ Vaccines 2021; 6:11. [PMID: 33462229 PMCID: PMC7813823 DOI: 10.1038/s41541-020-00268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus represents a serious infectious threat to global public health and a vaccine against S. aureus represents an unmet medical need. We here characterise two S. aureus vaccine candidates, coproporphyrinogen III oxidase (CgoX) and triose phosphate isomerase (TPI), which fulfil essential housekeeping functions in heme synthesis and glycolysis, respectively. Immunisation with rCgoX and rTPI elicited protective immunity against S. aureus bacteremia. Two monoclonal antibodies (mAb), CgoX-D3 and TPI-H8, raised against CgoX and TPI, efficiently provided protection against S. aureus infection. MAb-CgoX-D3 recognised a linear epitope spanning 12 amino acids (aa), whereas TPI-H8 recognised a larger discontinuous epitope. The CgoX-D3 epitope conjugated to BSA elicited a strong, protective immune response against S. aureus infection. The CgoX-D3 epitope is highly conserved in clinical S. aureus isolates, indicating its potential wide usability against S. aureus infection. These data suggest that immunofocusing through epitope-based immunisation constitutes a strategy for the development of a S. aureus vaccine with greater efficacy and better safety profile.
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Affiliation(s)
- Alexander Klimka
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Sonja Mertins
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Anne Kristin Nicolai
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Liza Marie Rummler
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Saskia Diana Günther
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany.,Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Bettina Tosetti
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany.,Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Oleg Krut
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany.,Paul-Ehrlich Institute, Langen, Germany
| | - Martin Krönke
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany. .,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany. .,Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), Cologne, Germany.
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22
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Guiberson ER, Weiss A, Ryan DJ, Monteith AJ, Sharman K, Gutierrez DB, Perry WJ, Caprioli RM, Skaar EP, Spraggins JM. Spatially Targeted Proteomics of the Host-Pathogen Interface during Staphylococcal Abscess Formation. ACS Infect Dis 2021; 7:101-113. [PMID: 33270421 DOI: 10.1021/acsinfecdis.0c00647] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Staphylococcus aureus is a common cause of invasive and life-threatening infections that are often multidrug resistant. To develop novel treatment approaches, a detailed understanding of the complex host-pathogen interactions during infection is essential. This is particularly true for the molecular processes that govern the formation of tissue abscesses, as these heterogeneous structures are important contributors to staphylococcal pathogenicity. To fully characterize the developmental process leading to mature abscesses, temporal and spatial analytical approaches are required. Spatially targeted proteomic technologies such as micro-liquid extraction surface analysis offer insight into complex biological systems including detection of bacterial proteins and their abundance in the host environment. By analyzing the proteomic constituents of different abscess regions across the course of infection, we defined the immune response and bacterial contribution to abscess development through spatial and temporal proteomic assessment. The information gathered was mapped to biochemical pathways to characterize the metabolic processes and immune strategies employed by the host. These data provide insights into the physiological state of bacteria within abscesses and elucidate pathogenic processes at the host-pathogen interface.
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Affiliation(s)
- Emma R. Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Daniel J. Ryan
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Andrew J. Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - William J. Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
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23
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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: 36] [Impact Index Per Article: 9.0] [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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24
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Understanding molecular enzymology of porphyrin-binding α + β barrel proteins - One fold, multiple functions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140536. [PMID: 32891739 PMCID: PMC7611857 DOI: 10.1016/j.bbapap.2020.140536] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022]
Abstract
There is a high functional diversity within the structural superfamily of porphyrin-binding dimeric α + β barrel proteins. In this review we aim to analyze structural constraints of chlorite dismutases, dye-decolorizing peroxidases and coproheme decarboxylases in detail. We identify regions of structural variations within the highly conserved fold, which are most likely crucial for functional specificities. The loop linking the two ferredoxin-like domains within one subunit can be of different sequence lengths and can adopt various structural conformations, consequently defining the shape of the substrate channels and the respective active site architectures. The redox cofactor, heme b or coproheme, is oriented differently in either of the analyzed enzymes. By thoroughly dissecting available structures and discussing all available results in the context of the respective functional mechanisms of each of these redox-active enzymes, we highlight unsolved mechanistic questions in order to spark future research in this field.
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25
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The uroS and yifB Genes Conserved among Tetrapyrrole Synthesizing-Deficient Bacteroidales Are Involved in Bacteroides fragilis Heme Assimilation and Survival in Experimental Intra-abdominal Infection and Intestinal Colonization. Infect Immun 2020; 88:IAI.00103-20. [PMID: 32457103 DOI: 10.1128/iai.00103-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/15/2020] [Indexed: 01/01/2023] Open
Abstract
The human intestinal anaerobic commensal and opportunistic pathogen Bacteroides fragilis does not synthesize the tetrapyrrole protoporphyrin IX in order to form heme that is required for growth stimulation and survival in vivo Consequently, B. fragilis acquires essential heme from host tissues during extraintestinal infection. The absence of several genes necessary for de novo heme biosynthesis is a common characteristic of many anaerobic bacteria; however, the uroS gene, encoding a uroporphyrinogen III synthase for an early step of heme biosynthesis, is conserved among the heme-requiring Bacteroidales that inhabit the mammalian gastrointestinal tract. In this study, we show that the ability of B. fragilis to utilize heme or protoporphyrin IX for growth was greatly reduced in a ΔuroS mutant. This growth defect appears to be linked to the suppression of reverse chelatase and ferrochelatase activities in the absence of uroS In addition, this ΔuroS suppressive effect was enhanced by the deletion of the yifB gene, which encodes an Mg2+-chelatase protein belonging to the ATPases associated with various cellular activities (AAA+) superfamily of proteins. Furthermore, the ΔuroS mutant and the ΔuroS ΔyifB double mutant had a severe survival defect compared to the parent strain in competitive infection assays using animal models of intra-abdominal infection and intestinal colonization. This shows that the presence of the uroS and yifB genes in B. fragilis seems to be linked to pathophysiological and nutritional competitive fitness for survival in host tissues. Genetic complementation studies and enzyme kinetics assays indicate that B. fragilis UroS is functionally different from canonical bacterial UroS proteins. Taken together, these findings show that heme assimilation and metabolism in the anaerobe B. fragilis have diverged from those of aerobic and facultative anaerobic pathogenic bacteria.
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26
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Hofbauer S, Helm J, Obinger C, Djinović-Carugo K, Furtmüller PG. Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase. FEBS J 2020; 287:2779-2796. [PMID: 31794133 PMCID: PMC7340540 DOI: 10.1111/febs.15164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 12/02/2019] [Indexed: 01/24/2023]
Abstract
Coproporphyrin ferrochelatases (CpfCs, EC 4.99.1.9) insert ferrous iron into coproporphyrin III yielding coproheme. CpfCs are utilized by prokaryotic, mainly monoderm (Gram-positive) bacteria within the recently detected coproporphyrin-dependent (CPD) heme biosynthesis pathway. Here, we present a comprehensive study on CpfC from Listeria monocytogenes (LmCpfC) including the first crystal structure of a coproheme-bound CpfC. Comparison of crystal structures of apo-LmCpfC and coproheme-LmCpfC allowed identification of structural rearrangements and of amino acids involved in tetrapyrrole macrocycle and Fe2+ binding. Differential scanning calorimetry of apo-, coproporphyrin III-, and coproheme-LmCpfC underline the pronounced noncovalent interaction of both coproporphyrin and coproheme with the protein (ΔTm = 11 °C compared to apo-LmCpfC), which includes the propionates (p2, p4, p6, p7) and the amino acids Arg29, Arg45, Tyr46, Ser53, and Tyr124. Furthermore, the thermodynamics and kinetics of coproporphyrin III and coproheme binding to apo-LmCpfC is presented as well as the kinetics of insertion of ferrous iron into coproporphyrin III-LmCpfC that immediately leads to formation of ferric coproheme-LmCpfC (kcat /KM = 4.7 × 105 m-1 ·s-1 ). We compare the crystal structure of coproheme-LmCpfC with available structures of CpfCs with artificial tetrapyrrole macrocycles and discuss our data on substrate binding, iron insertion and substrate release in the context of the CPD heme biosynthesis pathway. ENZYME: EC 4.99.1.9 DATABASE: pdb-codes of structural data in this work: 6RWV, 6SV3.
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Affiliation(s)
- Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Helm
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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27
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Michlits H, Lier B, Pfanzagl V, Djinović-Carugo K, Furtmüller PG, Oostenbrink C, Obinger C, Hofbauer S. Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation. ACS Catal 2020; 10:5405-5418. [PMID: 32440366 PMCID: PMC7235987 DOI: 10.1021/acscatal.0c00411] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/08/2020] [Indexed: 11/29/2022]
Abstract
![]()
Coproheme
decarboxylases (ChdCs) catalyze the final step in heme b biosynthesis of monoderm and some diderm bacteria. In
this reaction, coproheme is converted to heme b via
monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation
steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme
depend on hydrogen peroxide and the presence of a catalytic tyrosine.
Here we demonstrate that ChdCs from Actinobacteria are unique in using
a histidine (H118 in ChdC from Corynebacterium diphtheriae, CdChdC) as a distal base in addition to the redox-active
tyrosine (Y135). We present the X-ray crystal structures of coproheme-CdChdC and MMD-CdChdC, which clearly show
(i) differences in the active site architecture between Firmicutes
and Actinobacteria and (ii) rotation of the redox-active reaction
intermediate (MMD) after formation of the vinyl group at position
2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen
peroxide (kapp = (4.90 ± 1.25) ×
104 M–1 s–1). The resulting
Compound I is rapidly converted to a catalytically active Compound
I* (oxoiron(IV) Y135•) that initiates the radical
decarboxylation reactions. As a consequence of the more efficient
Compound I formation, actinobacterial ChdCs exhibit a higher catalytic
efficiency in comparison to representatives from Firmicutes. On the
basis of the kinetic data of wild-type CdChdC and
the variants H118A, Y135A, and H118A/Y135A together with high-resolution
crystal structures and molecular dynamics simulations, we present
a molecular mechanism for the hydrogen peroxide dependent conversion
of coproheme via MMD to heme b and discuss differences
between ChdCs from Actinobacteria and Firmicutes.
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Affiliation(s)
- Hanna Michlits
- Department of Chemistry, Institute of Biochemistry, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Bettina Lier
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department for Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Paul G. Furtmüller
- Department of Chemistry, Institute of Biochemistry, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, BOKU−University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
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28
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Celis AI, Choby JE, Kentro J, Skaar EP, DuBois JL. Control of Metabolite Flux during the Final Steps of Heme b Biosynthesis in Gram-Positive Bacteria. Biochemistry 2019; 58:5259-5270. [PMID: 31241911 PMCID: PMC7160669 DOI: 10.1021/acs.biochem.9b00140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The pathway for assembling heme ends with a unique set of enzymes in Gram-positive bacteria. Substrates for these reactions include coproporphyrin III, Fe(II), and H2O2, which are highly reactive and toxic. Because these bacteria lack membranous compartments, we hypothesized that metabolite flux may occur via a transient protein-protein interaction between the final two pathway enzymes, coproporphyrin ferrochelatase (CpfC) and coproheme decarboxylase (ChdC). This hypothesis was tested using enzymes from the pathogen Staphylococcus aureus and a corresponding ΔchdC knockout strain. The ultraviolet-visible spectral features of coproporphyrin III served as an in vitro indicator of a protein-protein interaction. A CpfC-ChdC KD of 17 ± 7 μM was determined, consistent with transient complexation and supported by the observation that the catalytic competence of both enzymes was moderately suppressed in the stable complex. The ΔchdC S. aureus was transformed with plasmids containing single-amino acid mutants in the active site gate of ChdC. The porphyrin content and growth phenotypes of these mutants showed that K129 and Y133 promote the ChdC-CpfC interaction and revealed the importance of E120. Understanding the nature of interactions between these enzymes and those further upstream in the heme biosynthesis pathway could provide new means of specifically targeting pathogenic Gram-positive bacteria such as S. aureus.
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Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States
| | - Jacob E. Choby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2561, United States,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States,Graduate Program in Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - James Kentro
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2561, United States,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States,Corresponding Author Address: 221 Chemistry and Biochemistry Building, Bozeman, MT 59715. Phone: 406-994-2844.
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29
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Celis AI, DuBois JL. Making and breaking heme. Curr Opin Struct Biol 2019; 59:19-28. [PMID: 30802830 PMCID: PMC6706330 DOI: 10.1016/j.sbi.2019.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 10/27/2022]
Abstract
Mechanisms for making and breaking the heme b cofactor (heme) are more diverse than previously expected. Biosynthetic pathways have diverged at least twice along taxonomic lines, reflecting differences in membrane organization and O2 utilization among major groups of organisms. At least three families of heme degradases are now known, again differing in whether and how O2 is used by the organism and possibly the purpose for turning over the tetrapyrrole. Understanding these enzymes and pathways offers a handle for antimicrobial development and for monitoring heme use in organismal and ecological systems.
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Affiliation(s)
- Arianna I Celis
- Montana State University, 103 Chemistry and Biochemistry, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Montana State University, 103 Chemistry and Biochemistry, Bozeman, MT 59717, United States.
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30
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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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31
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Milazzo L, Gabler T, Pühringer D, Jandova Z, Maresch D, Michlits H, Pfanzagl V, Djinović-Carugo K, Oostenbrink C, Furtmüller PG, Obinger C, Smulevich G, Hofbauer S. Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b. ACS Catal 2019; 9:6766-6782. [PMID: 31423350 PMCID: PMC6691569 DOI: 10.1021/acscatal.9b00963] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/20/2019] [Indexed: 12/24/2022]
Abstract
Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme. Here we present the crystal structures of coproheme-loaded ChdC from Listeria monocytogenes (LmChdC) and the three-propionate intermediate, for which the propionate at position 2 (p2) has been converted to a vinyl group and is rotated by 90° compared to the coproheme complex structure. Single, double, and triple mutants of LmChdC, in which H-bonding interactions to propionates 2, 4, 6, and 7 were eliminated, allowed us to obtain the assignment of the coproheme propionates by resonance Raman spectroscopy and to follow the H2O2-mediated conversion of coproheme to heme b. Substitution of H2O2 by chlorite allowed us to monitor compound I formation in the inactive Y147H variant which lacks the catalytically essential Y147. This residue was demonstrated to be oxidized during turnover by using the spin-trap 2-methyl-2-nitrosopropane. Based on these findings and the data derived from molecular dynamics simulations of cofactor structures in distinct poses, we propose a reaction mechanism for the stepwise decarboxylation of coproheme that includes a 90° rotation of the intermediate three-propionate redox cofactor.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Zuzana Jandova
- Department
of Material Sciences and Process Engineering, Institute of Molecular
Modeling and Simulation, BOKU−University
of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Daniel Maresch
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Chris Oostenbrink
- Department
of Material Sciences and Process Engineering, Institute of Molecular
Modeling and Simulation, BOKU−University
of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Stefan Hofbauer
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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32
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Dai J, Liu Y, Liu S, Li S, Gao N, Wang J, Zhou J, Qiu D. Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins. BMC Microbiol 2019; 19:173. [PMID: 31362704 PMCID: PMC6664582 DOI: 10.1186/s12866-019-1549-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 01/31/2023] Open
Abstract
Background Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, are investigated in S. oneidensis MR-1. Result In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1ΔhemH1ΔhemH2, which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1ΔhemH1 mutant to compensate for the loss of hemH1. The periplasmic glutathione peroxidase gene pgpD, located in the same operon with hemH2, and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX. Electronic supplementary material The online version of this article (10.1186/s12866-019-1549-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaqi Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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33
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Choby JE, Skaar EP. Staphylococcus aureus Coproporphyrinogen III Oxidase Is Required for Aerobic and Anaerobic Heme Synthesis. mSphere 2019; 4:e00235-19. [PMID: 31292227 PMCID: PMC6620371 DOI: 10.1128/msphere.00235-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 11/20/2022] Open
Abstract
The virulence of the human pathogen Staphylococcus aureus is supported by many heme-dependent proteins, including key enzymes of cellular respiration. Therefore, synthesis of heme is a critical component of staphylococcal physiology. S. aureus generates heme via the coproporphyrin-dependent pathway, conserved across members of the Firmicutes and Actinobacteria In this work, we genetically investigate the oxidation of coproporphyrinogen to coproporphyrin in this heme synthesis pathway. The coproporphyrinogen III oxidase CgoX has previously been identified as the oxygen-dependent enzyme responsible for this conversion under aerobic conditions. However, because S. aureus uses heme during anaerobic nitrate respiration, we hypothesized that coproporphyrin production is able to proceed in the absence of oxygen. Therefore, we tested the contribution to anaerobic heme synthesis of CgoX and two other proteins previously identified as potential oxygen-independent coproporphyrinogen dehydrogenases, NWMN_1486 and NWMN_1636. We have found that CgoX alone is responsible for aerobic and anaerobic coproporphyrin synthesis from coproporphyrinogen and is required for aerobic and anaerobic heme-dependent growth. This work provides an explanation for how S. aureus heme synthesis proceeds under both aerobic and anaerobic conditions.IMPORTANCE Heme is a critical molecule required for aerobic and anaerobic respiration by organisms across kingdoms. The human pathogen Staphylococcus aureus has served as a model organism for the study of heme synthesis and heme-dependent physiology and, like many species of the phyla Firmicutes and Actinobacteria, generates heme through a coproporphyrin intermediate. A critical step in terminal heme synthesis is the production of coproporphyrin by the CgoX enzyme, which was presumed to be oxygen dependent. However, S. aureus also requires heme during anaerobic growth; therefore, the synthesis of coproporphyrin by an oxygen-independent mechanism is required. Here, we identify CgoX as the enzyme performing the oxygen-dependent and -independent synthesis of coproporphyrin from coproporphyrinogen, resolving a key outstanding question in the coproporphyrin-dependent heme synthesis pathway.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Graduate Program in Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Milazzo L, Gabler T, Pfanzagl V, Michlits H, Furtmüller PG, Obinger C, Hofbauer S, Smulevich G. The hydrogen bonding network of coproheme in coproheme decarboxylase from Listeria monocytogenes: Effect on structure and catalysis. J Inorg Biochem 2019; 195:61-70. [PMID: 30925402 PMCID: PMC6517287 DOI: 10.1016/j.jinorgbio.2019.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 11/29/2022]
Abstract
Coproheme decarboxylase (ChdC) catalyzes the oxidative decarboxylation of coproheme to heme b, i.e. the last step in the recently described coproporphyrin-dependent pathway. Coproheme decarboxylation from Listeria monocytogenes is a robust enzymatic reaction of low catalytic efficiency. Coproheme acts as both substrate and redox cofactor activated by H2O2. It fully depends on the catalytic Y147 close to the propionyl group at position 2. In the present study we have investigated the effect of disruption of the comprehensive and conserved hydrogen bonding network between the four propionates and heme cavity residues on (i) the conformational stability of the heme cavity, (ii) the electronic configuration of the ferric redox cofactor/substrate, (iii) the binding of carbon monoxide and, (iv) the decarboxylation reaction mediated by addition of H2O2. Nine single, double and triple mutants of ChdC from Listeria monocytogenes were produced in E. coli. The respective coproheme- and heme b-complexed proteins were studied by UV–Vis, resonance Raman, circular dichroism spectroscopy, and mass spectrometry. Interactions of propionates 2 and 4 with residues in the hydrophobic cavity are crucial for maintenance of the heme cavity architecture, for the mobile distal glutamine to interact with carbon monoxide, and to keep the heme cavity in a closed conformation during turnover. By contrast, the impact of substitution of residues interacting with solvent exposed propionates 6 and 7 was negligible. Except for Y147A and K151A all mutant ChdCs exhibited a wild-type-like catalytic activity. The findings are discussed with respect to the structure-function relationships of ChdCs.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, (Fi), Italy
| | - Thomas Gabler
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, (Fi), Italy.
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Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J Biol Macromol 2019; 127:585-593. [PMID: 30660563 DOI: 10.1016/j.ijbiomac.2019.01.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/16/2022]
Abstract
A homology model of ferrochelatase (HemH), the heme biosynthesis terminal step enzyme from Salmonella Typhi was generated to understand the mechanism of metal insertion into protoporphyrin IX for heme biosynthesis. The overall fold of membrane associated ferrochelatase (StFc) from S. Typhi is similar to human and Yeast ferrochelatase than Bacillus subtilis, and Bacillus anthracis. An insertion of 16 amino acid residues in helical switch having hydrophobic patch proposed to interact with membrane lipids and in opening and closing of heme binding cleft. The sequence analysis and the docking study revealed that the protoporphyrin binding site in StFc has a crucial replacement of Tyr/Met to Leu13 unique in comparison to other known structures, where Tyr13 observed in B. subtilis/B. anthracis while Met76 in human/yeast play important role in holding protoporphyrin in optimal orientation for metalation. A sitting-a-top (SAT) complex mechanism for metalation is proposed with His194 and Glu264 lie at the bottom and Leu13 on the top of the porphyrin ring. In addition, an entry and exit mechanism is also proposed for protoporphyrin binding into cavity by opening and closing of helical switch using molecular dynamics simulation studies of Apo and heme complexed model structure of S. Typhi HemH.
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Affiliation(s)
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rohit Bansal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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Biochemical characterization of protoporphyrinogen dehydrogenase and protoporphyrin ferrochelatase of Vibrio vulnificus and the critical complex formation between these enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2674-2687. [PMID: 30251658 DOI: 10.1016/j.bbagen.2018.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/28/2018] [Accepted: 08/13/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Protoporphyrin IX (PPn), an intermediate in the heme biosynthesis reaction, generates singlet oxygen upon exposure to UV light. It has been proposed that PPn is channeled directly to ferrochelatase within a protoporphyrinogen dehydrogenase (PgdH1)-protoporphyrin ferrochelatase (PpfC) complex as a way to avoid this damaging side reaction. However, the PgdH1-PpfC complex has not been characterized, and the question of how heme affects the activities of PgdH1 has not been addressed. METHODS Protein interactions were explored through pull-down assays and western blotting, and the importance of this complex in vivo was examined using inter-species combinations of the two proteins. The purified PgdH1-PpfC complex was characterized kinetically and used for heme binding studies. RESULTS In Vibrio vulnificus, PgdH1 and PpfC formed an 8:8 heterohexadecameric complex that was important for maintaining PPn at low levels. PpfC catalyzed PPn efficiently whether or not it was part of the complex. Notably, heme was a noncompetitive inhibitor of V. vulnificus PgdH1, but a competitive inhibitor of the human protoporphyrinogen oxidase PgoX. CONCLUSION The PdgH1-PpfC complex is important for protective channeling of PPn and for efficient catalysis of free PPn. The production of PPn by PgdH1 is regulated by feedback inhibition by heme. GENERAL SIGNIFICANCE Both proteobacteria and eukaryotes have evolved mechanisms to prevent the harmful accumulation of the heme biosynthesis intermediate PPn. The data presented here suggest two previously unknown mechanisms: the channeling of PPn through the PgdH1-PpfC complex, and the direct inhibition of PgdH1 activity (PgoX activity as well) by heme.
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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] [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
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Geeraerts Z, Celis AI, Mayfield JA, Lorenz M, Rodgers KR, DuBois JL, Lukat-Rodgers GS. Distinguishing Active Site Characteristics of Chlorite Dismutases with Their Cyanide Complexes. Biochemistry 2018; 57:1501-1516. [PMID: 29406727 PMCID: PMC5849076 DOI: 10.1021/acs.biochem.7b01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
O2-evolving chlorite dismutases (Clds) efficiently convert chlorite (ClO2-) to O2 and Cl-. Dechloromonas aromatica Cld ( DaCld) is a highly active chlorite-decomposing homopentameric enzyme, typical of Clds found in perchlorate- and chlorate-respiring bacteria. The Gram-negative, human pathogen Klebsiella pneumoniae contains a homodimeric Cld ( KpCld) that also decomposes ClO2-, albeit with an activity 10-fold lower and a turnover number lower than those of DaCld. The interactions between the distal pocket and heme ligand of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their cyanide complexes for insight into active site characteristics that are deterministic for chlorite decomposition. At 4.7 × 10-9 M, the KD for the KpCld-CN- complex is 2 orders of magnitude smaller than that of DaCld-CN- and indicates an affinity for CN- that is greater than that of most heme proteins. The difference in CN- affinity between Kp- and DaClds is predominantly due to differences in koff. The kinetics of binding of cyanide to DaCld, DaCld(R183Q), and KpCld between pH 4 and 8.5 corroborate the importance of distal Arg183 and a p Ka of ∼7 in stabilizing complexes of anionic ligands, including the substrate. The Fe-C stretching and FeCN bending modes of the DaCld-CN- (νFe-C, 441 cm-1; δFeCN, 396 cm-1) and KpCld-CN- (νFe-C, 441 cm-1; δFeCN, 356 cm-1) complexes reveal differences in their FeCN angle, which suggest different distal pocket interactions with their bound cyanide. Conformational differences in their catalytic sites are also reported by the single ferrous KpCld carbonyl complex, which is in contrast to the two conformers observed for DaCld-CO.
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Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Jeffery A. Mayfield
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Megan Lorenz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
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McClary JS, Boehm AB. Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions. Front Microbiol 2018; 9:249. [PMID: 29599752 PMCID: PMC5863498 DOI: 10.3389/fmicb.2018.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
The transcriptional response of Staphylococcus aureus strain Newman to sunlight exposure was investigated under both oxic and anoxic conditions using RNA sequencing to gain insight into potential mechanisms of inactivation. S. aureus is a pathogenic bacterium detected at recreational beaches which can cause gastrointestinal illness and skin infections, and is of increasing public health concern. To investigate the S. aureus photostress response in oligotrophic seawater, S. aureus cultures were suspended in seawater and exposed to full spectrum simulated sunlight. Experiments were performed under oxic or anoxic conditions to gain insight into the effects of oxygen-mediated and non-oxygen-mediated inactivation mechanisms. Transcript abundance was measured after 6 h of sunlight exposure using RNA sequencing and was compared to transcript abundance in paired dark control experiments. Culturable S. aureus decayed following biphasic inactivation kinetics with initial decay rate constants of 0.1 and 0.03 m2 kJ−1 in oxic and anoxic conditions, respectively. RNA sequencing revealed that 71 genes had different transcript abundance in the oxic sunlit experiments compared to dark controls, and 18 genes had different transcript abundance in the anoxic sunlit experiments compared to dark controls. The majority of genes showed reduced transcript abundance in the sunlit experiments under both conditions. Three genes (ebpS, NWMN_0867, and NWMN_1608) were found to have the same transcriptional response to sunlight between both oxic and anoxic conditions. In the oxic condition, transcripts associated with porphyrin metabolism, nitrate metabolism, and membrane transport functions were increased in abundance during sunlight exposure. Results suggest that S. aureus responds differently to oxygen-dependent and oxygen-independent photostress, and that endogenous photosensitizers play an important role during oxygen-dependent indirect photoinactivation.
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Affiliation(s)
- Jill S McClary
- Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Alexandria B Boehm
- Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
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Choby JE, Grunenwald CM, Celis AI, Gerdes SY, DuBois JL, Skaar EP. Staphylococcus aureus HemX Modulates Glutamyl-tRNA Reductase Abundance To Regulate Heme Biosynthesis. mBio 2018; 9:e02287-17. [PMID: 29437922 PMCID: PMC5801465 DOI: 10.1128/mbio.02287-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is responsible for a significant amount of devastating disease. Its ability to colonize the host and cause infection is supported by a variety of proteins that are dependent on the cofactor heme. Heme is a porphyrin used broadly across kingdoms and is synthesized de novo from common cellular precursors and iron. While heme is critical to bacterial physiology, it is also toxic in high concentrations, requiring that organisms encode regulatory processes to control heme homeostasis. In this work, we describe a posttranscriptional regulatory strategy in S. aureus heme biosynthesis. The first committed enzyme in the S. aureus heme biosynthetic pathway, glutamyl-tRNA reductase (GtrR), is regulated by heme abundance and the integral membrane protein HemX. GtrR abundance increases dramatically in response to heme deficiency, suggesting a mechanism by which S. aureus responds to the need to increase heme synthesis. Additionally, HemX is required to maintain low levels of GtrR in heme-proficient cells, and inactivation of hemX leads to increased heme synthesis. Excess heme synthesis in a ΔhemX mutant activates the staphylococcal heme stress response, suggesting that regulation of heme synthesis is critical to reduce self-imposed heme toxicity. Analysis of diverse organisms indicates that HemX is widely conserved among heme-synthesizing bacteria, suggesting that HemX is a common factor involved in the regulation of GtrR abundance. Together, this work demonstrates that S. aureus regulates heme synthesis by modulating GtrR abundance in response to heme deficiency and through the activity of the broadly conserved HemX.IMPORTANCEStaphylococcus aureus is a leading cause of skin and soft tissue infections, endocarditis, bacteremia, and osteomyelitis, making it a critical health care concern. Development of new antimicrobials against S. aureus requires knowledge of the physiology that supports this organism's pathogenesis. One component of staphylococcal physiology that contributes to growth and virulence is heme. Heme is a widely utilized cofactor that enables diverse chemical reactions across many enzyme families. S. aureus relies on many critical heme-dependent proteins and is sensitive to excess heme toxicity, suggesting S. aureus must maintain proper intracellular heme homeostasis. Because S. aureus provides heme for heme-dependent enzymes via synthesis from common precursors, we hypothesized that regulation of heme synthesis is one mechanism to maintain heme homeostasis. In this study, we identify that S. aureus posttranscriptionally regulates heme synthesis by restraining abundance of the first heme biosynthetic enzyme, GtrR, via heme and the broadly conserved membrane protein HemX.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Graduate Program in Microbiology & Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Caroline M Grunenwald
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Pfanzagl V, Holcik L, Maresch D, Gorgone G, Michlits H, Furtmüller PG, Hofbauer S. Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments. Arch Biochem Biophys 2018; 640:27-36. [PMID: 29331688 DOI: 10.1016/j.abb.2018.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 01/08/2023]
Abstract
Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity. Based on available biochemical data and phylogenetic analyses a sequence motif (-Y-P-M/F-X-K/R-) is defined for ChdCs. We show for the first time that in diderm bacteria an active coproheme decarboxylase is present and that the archaeal ChdC homolog from Sulfolobus solfataricus is inactive and its physiological role remains elusive. This shows the limitation of phylogenetic prediction of an enzymatic activity, since the identified sequence motif is equally conserved across all previously defined clades.
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Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Laurenz Holcik
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulia Gorgone
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron-binding site. Biochem J 2017; 474:3513-3522. [PMID: 28864672 PMCID: PMC5633918 DOI: 10.1042/bcj20170362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022]
Abstract
The majority of characterised ferrochelatase enzymes catalyse the final step of classical haem synthesis, inserting ferrous iron into protoporphyrin IX. However, for the recently discovered coproporphyrin-dependent pathway, ferrochelatase catalyses the penultimate reaction where ferrous iron is inserted into coproporphyrin III. Ferrochelatase enzymes from the bacterial phyla Firmicutes and Actinobacteria have previously been shown to insert iron into coproporphyrin, and those from Bacillus subtilis and Staphylococcus aureus are known to be inhibited by elevated iron concentrations. The work herein reports a Km (coproporphyrin III) for S. aureus ferrochelatase of 1.5 µM and it is shown that elevating the iron concentration increases the Km for coproporphyrin III, providing a potential explanation for the observed iron-mediated substrate inhibition. Together, structural modelling, site-directed mutagenesis, and kinetic analyses confirm residue Glu271 as being essential for the binding of iron to the inhibitory regulatory site on S. aureus ferrochelatase, providing a molecular explanation for the observed substrate inhibition patterns. This work therefore has implications for how haem biosynthesis in S. aureus is regulated by iron availability.
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Geeraerts Z, Rodgers KR, DuBois JL, Lukat-Rodgers GS. Active Sites of O 2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations. Biochemistry 2017; 56:4509-4524. [PMID: 28758386 DOI: 10.1021/acs.biochem.7b00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O2-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO2- to O2 and Cl-. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate- and chlorate-respiring bacteria. The Cld from the Gram-negative human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their fluorides, chlorides, and hydroxides. Cooperative binding of Cl- to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(FeIII-F) bands at 385 and 390 cm-1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond donation to the F- ligand, indicating that atoms directly coordinated to heme iron are accessible to distal H-bond donation. New vibrational frequency correlations between either ν(FeIII-F) or ν(FeIII-OH) and ν(FeII-His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe-X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.
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Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Kenton R 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
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
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Influence of IS 256 on Genome Variability and Formation of Small-Colony Variants in Staphylococcus aureus. Antimicrob Agents Chemother 2017; 61:AAC.00144-17. [PMID: 28584147 DOI: 10.1128/aac.00144-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/30/2017] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus has acquired resistance to nearly all antibiotics used in clinical practice. Whereas some resistance mechanisms are conferred by uptake of resistance genes, others evolve by mutation. In this study, IS256 has been shown to play a role, e.g., in S. aureus strains displaying intermediate resistance to vancomycin (VISA). To characterize the IS256 insertion sites in the genomes of two closely related sequence type 247 (ST247) VISA strains, all insertions were mapped in both VISA and a susceptible control strain. The results showed that the three ST247 strains contained the highest number so far of IS256 insertions for all sequenced S. aureus strains. Furthermore, in contrast to the case with the other IS elements in these genomes, the IS256 insertion sites were not identical in the closely related strains, indicating a high transposition frequency of IS256 When IS256 was introduced into a laboratory strain which was then cultured in the presence of antibiotics, it was possible to isolate small-colony variants (SCVs) that possessed IS256 insertions in guaA and hemY that displayed increased resistance to vancomycin and aminoglycosides, respectively. For these clones, a very rapid reversion to the wild type that resembled the fast reversion of clinical SCVs was observed. The reversion was caused by excision of IS256 in a small number of fast-growing clones that quickly outcompeted the SCVs in broth cultures. In conclusion, the presence of IS256 confers a strong genomic plasticity that is useful for adaptation to antibiotic stress.
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Antibacterial photosensitization through activation of coproporphyrinogen oxidase. Proc Natl Acad Sci U S A 2017; 114:E6652-E6659. [PMID: 28739897 DOI: 10.1073/pnas.1700469114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-positive bacteria cause the majority of skin and soft tissue infections (SSTIs), resulting in the most common reason for clinic visits in the United States. Recently, it was discovered that Gram-positive pathogens use a unique heme biosynthesis pathway, which implicates this pathway as a target for development of antibacterial therapies. We report here the identification of a small-molecule activator of coproporphyrinogen oxidase (CgoX) from Gram-positive bacteria, an enzyme essential for heme biosynthesis. Activation of CgoX induces accumulation of coproporphyrin III and leads to photosensitization of Gram-positive pathogens. In combination with light, CgoX activation reduces bacterial burden in murine models of SSTI. Thus, small-molecule activation of CgoX represents an effective strategy for the development of light-based antimicrobial therapies.
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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: 207] [Impact Index Per Article: 29.6] [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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Neumann W, Gulati A, Nolan EM. Metal homeostasis in infectious disease: recent advances in bacterial metallophores and the human metal-withholding response. Curr Opin Chem Biol 2016; 37:10-18. [PMID: 27992799 DOI: 10.1016/j.cbpa.2016.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 09/14/2016] [Indexed: 10/20/2022]
Abstract
A tug-of-war between the mammalian host and bacterial pathogen for nutrients, including first-row transition metals (e.g. Mn, Fe, Zn), occurs during infection. Here we present recent advances about three metal-chelating metabolites that bacterial pathogens deploy when invading the host: staphylopine, staphyloferrin B, and enterobactin. These highlights provide new insights into the mechanisms of bacterial metal acquisition and regulation, as well as the contributions of host-defense proteins during the human innate immune response. The studies also underscore that the chemical composition of the microenvironment at an infection site can influence bacterial pathogenesis and the innate immune system.
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Affiliation(s)
- Wilma Neumann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anmol Gulati
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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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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Hofbauer S, Mlynek G, Milazzo L, Pühringer D, Maresch D, Schaffner I, Furtmüller PG, Smulevich G, Djinović-Carugo K, Obinger C. Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-lessons from the first crystal structure and kinetic studies. FEBS J 2016; 283:4386-4401. [PMID: 27758026 PMCID: PMC5157759 DOI: 10.1111/febs.13930] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/11/2016] [Accepted: 10/17/2016] [Indexed: 11/30/2022]
Abstract
Heme biosynthesis in Gram-positive bacteria follows a recently described coproporphyrin-dependent pathway with HemQ catalyzing the decarboxylation of coproheme to heme b. Here we present the first crystal structure of a HemQ (homopentameric coproheme-HemQ from Listeria monocytogenes) at 1.69 Å resolution and the conversion of coproheme to heme b followed by UV-vis and resonance Raman spectroscopy as well as mass spectrometry. The ferric five-coordinated coproheme iron of HemQ is weakly bound by a neutral proximal histidine H174. In the crystal structure of the resting state, the distal Q187 (conserved in Firmicutes HemQ) is H-bonded with propionate p2 and the hydrophobic distal cavity lacks solvent water molecules. Two H2 O2 molecules are shown to be necessary for decarboxylation of the propionates p2 and p4, thereby forming the corresponding vinyl groups of heme b. The overall reaction is relatively slow (kcat /KM = 1.8 × 102 m-1 ·s-1 at pH 7.0) and occurs in a stepwise manner with a three-propionate intermediate. We present the noncovalent interactions between coproheme and the protein and propose a two-step reaction mechanism. Furthermore, the structure of coproheme-HemQ is compared to that of the phylogenetically related heme b-containing chlorite dismutases. DATABASE Structural data are available in the PDB under the accession number 5LOQ.
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Affiliation(s)
- Stefan Hofbauer
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria
| | - Georg Mlynek
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria
| | - Lisa Milazzo
- Dipartimento di Chimica 'Ugo Schiff', Università di Firenze, Sesto Fiorentino (FI), Italy
| | - Dominic Pühringer
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria.,Division of Biochemistry, Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Irene Schaffner
- Division of Biochemistry, Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul G Furtmüller
- Division of Biochemistry, Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica 'Ugo Schiff', Università di Firenze, Sesto Fiorentino (FI), Italy
| | - Kristina Djinović-Carugo
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Christian Obinger
- Division of Biochemistry, Department of Chemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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50
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Wang B, Wen X, Xi Z. Molecular Simulations Bring New Insights into Protoporphyrinogen IX Oxidase/Protoporphyrinogen IX Interaction Modes. Mol Inform 2016; 35:476-482. [DOI: 10.1002/minf.201600008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/27/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Baifan Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University; Collaborative Innovation Center of Chemical Science and Engineering; Tianjin 300071 P. R. China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University; Collaborative Innovation Center of Chemical Science and Engineering; Tianjin 300071 P. R. China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University; Collaborative Innovation Center of Chemical Science and Engineering; Tianjin 300071 P. R. China
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