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Ferousi C, Lindhoud S, Baymann F, Kartal B, Jetten MSM, Reimann J. Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria. Curr Opin Chem Biol 2017; 37:129-136. [DOI: 10.1016/j.cbpa.2017.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023]
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102
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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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103
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Elucidation of the biosynthesis of the methane catalyst coenzyme F 430. Nature 2017; 543:78-82. [PMID: 28225763 PMCID: PMC5337119 DOI: 10.1038/nature21427] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Methane biogenesis in methanogens is mediated by methyl-coenzyme M reductase, an enzyme that is also responsible for the utilisation of methane through anaerobic methane oxidation. The enzyme employs an ancillary factor called coenzyme F430, a nickel-containing modified tetrapyrrole that promotes catalysis through a novel methyl radical/Ni(II)-thiolate intermediate. However, the biosynthesis of coenzyme F430 from the common primogenitor uroporphyrinoge III, incorporating 11 steric centres into the macrocycle, has remained poorly understood although the pathway must involve chelation, amidation, macrocyclic ring reduction, lactamisation and carbocyclic ring formation. We have now identified the proteins that catalyse coenzyme F430 biosynthesis from sirohydrochlorin, termed CfbA-E, and shown their activity. The research completes our understanding of how nature is able to construct its repertoire of tetrapyrrole-based life pigments, permitting the development of recombinant systems to utilise these metalloprosthetic groups more widely.
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104
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Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc 2017; 139:1900-1911. [PMID: 27936663 PMCID: PMC5348300 DOI: 10.1021/jacs.6b11324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.
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Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - George H. Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Bennett R. Streit
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Garrett C. Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
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105
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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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106
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Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
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107
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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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108
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Radical new paradigm for heme degradation in Escherichia coli O157:H7. Proc Natl Acad Sci U S A 2016; 113:12138-12143. [PMID: 27791000 DOI: 10.1073/pnas.1603209113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All of the heme-degrading enzymes that have been characterized to date require molecular oxygen as a cosubstrate. Escherichia coli O157:H7 has been shown to express heme uptake and transport proteins, as well as use heme as an iron source. This enteric pathogen colonizes the anaerobic space of the lower intestine in mammals, yet no mechanism for anaerobic heme degradation has been reported. Herein we provide evidence for an oxygen-independent heme-degradation pathway. Specifically, we demonstrate that ChuW is a radical S-adenosylmethionine methyltransferase that catalyzes a radical-mediated mechanism facilitating iron liberation and the production of the tetrapyrrole product we termed "anaerobilin." We further demonstrate that anaerobilin can be used as a substrate by ChuY, an enzyme that is coexpressed with ChuW in vivo along with the heme uptake machinery. Our findings are discussed in terms of the competitive advantage this system provides for enteric bacteria, particularly those that inhabit an anaerobic niche in the intestines.
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109
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Hofbauer S, Dalla Sega M, Scheiblbrandner S, Jandova Z, Schaffner I, Mlynek G, Djinović-Carugo K, Battistuzzi G, Furtmüller PG, Oostenbrink C, Obinger C. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ. Biochemistry 2016; 55:5398-412. [PMID: 27599156 PMCID: PMC5041162 DOI: 10.1021/acs.biochem.6b00701] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of -205 ± 3 mV for LmHemQ and -207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 10(4) M(-1) s(-1)). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria.
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Affiliation(s)
- Stefan Hofbauer
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , A-1030 Vienna, Austria
| | - Marco Dalla Sega
- 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
| | - Stefan Scheiblbrandner
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU-University of Natural Resources and Life Sciences , A-1190 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
| | - Irene Schaffner
- Department of Chemistry, Division of Biochemistry, VIBT-Vienna Institute of BioTechnology, BOKU-University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
| | - Georg Mlynek
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , A-1030 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
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology, University of Modena and Reggio Emilia , 41125 Modena, Italy
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, VIBT-Vienna Institute of BioTechnology, 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, Division of Biochemistry, VIBT-Vienna Institute of BioTechnology, BOKU-University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
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110
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The HemQ coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis. Biochem J 2016; 473:3997-4009. [PMID: 27597779 PMCID: PMC5095920 DOI: 10.1042/bcj20160696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/05/2016] [Indexed: 12/26/2022]
Abstract
Bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes, including cytochromes, peroxidases, globins, and catalase. Haem is synthesised via a series of tetrapyrrole intermediates, including non-metallated porphyrins, such as protoporphyrin IX, which is well known to generate reactive oxygen species in the presence of light and oxygen. Staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin III, a less reactive porphyrin. Here, we demonstrate, for the first time, that HemY of S. aureus is able to generate both protoporphyrin IX and coproporphyrin III, and that the terminal enzyme of this pathway, HemQ, can stimulate the generation of protoporphyrin IX (but not coproporphyrin III). Assays with hydrogen peroxide, horseradish peroxidase, superoxide dismutase, and catalase confirm that this stimulatory effect is mediated by superoxide. Structural modelling reveals that HemQ enzymes do not possess the structural attributes that are common to peroxidases that form compound I [FeIV==O]+, which taken together with the superoxide data leaves Fenton chemistry as a likely route for the superoxide-mediated stimulation of protoporphyrinogen IX oxidase activity of HemY. This generation of toxic free radicals could explain why HemQ enzymes have not been identified in organisms that synthesise haem via the classical protoporphyrin IX pathway. This work has implications for the divergent evolution of haem biosynthesis in ancestral microorganisms, and provides new structural and mechanistic insights into a recently discovered oxidative decarboxylase reaction.
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111
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Choby JE, Skaar EP. Heme Synthesis and Acquisition in Bacterial Pathogens. J Mol Biol 2016; 428:3408-28. [PMID: 27019298 PMCID: PMC5125930 DOI: 10.1016/j.jmb.2016.03.018] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA.
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112
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Differential Regulation of the Two Ferrochelatase Paralogues in Shewanella loihica PV-4 in Response to Environmental Stresses. Appl Environ Microbiol 2016; 82:5077-88. [PMID: 27287322 DOI: 10.1128/aem.00203-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Determining the function and regulation of paralogues is important in understanding microbial functional genomics and environmental adaptation. Heme homeostasis is crucial for the survival of environmental microorganisms. Most Shewanella species encode two paralogues of ferrochelatase, the terminal enzyme in the heme biosynthesis pathway. The function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, were investigated in Shewanella loihica PV-4. The disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), the precursor to heme, and decreased intracellular heme levels. hemH1 was constitutively expressed, and the expression of hemH2 increased when hemH1 was disrupted. The transcription of hemH1 was regulated by the housekeeping sigma factor RpoD and potentially regulated by OxyR, while hemH2 appeared to be regulated by the oxidative stress-associated sigma factor RpoE2. When an oxidative stress condition was mimicked by adding H2O2 to the medium or exposing the culture to light, PPIX accumulation was suppressed in the ΔhemH1 mutant. Consistently, transcriptome analysis indicated enhanced iron uptake and suppressed heme synthesis in the ΔhemH1 mutant. These data indicate that the two paralogues are functional in the heme synthesis pathway but regulated by environmental conditions, providing insights into the understanding of bacterial response to environmental stresses and a great potential to commercially produce porphyrin compounds. IMPORTANCE Shewanella is capable of utilizing a variety of electron acceptors for anaerobic respiration because of the existence of multiple c-type cytochromes in which heme is an essential component. The cytochrome-mediated electron transfer across cellular membranes could potentially be used for biotechnological purposes, such as electricity generation in microbial fuel cells and dye decolorization. However, the mechanism underlying the regulation of biosynthesis of heme and cytochromes is poorly understood. Our study has demonstrated that two ferrochelatase genes involved in heme biosynthesis are differentially regulated in response to environmental stresses, including light and reactive oxygen species. This is an excellent example showing how bacteria have evolved to maintain cellular heme homeostasis. More interestingly, the high yields of extracellular protoporphyrin IX by the Shewanella loihica PV-4 mutants could be utilized for commercial production of this valuable chemical via bacterial fermentation.
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113
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Transcriptomic analysis for elucidating the physiological effects of 5-aminolevulinic acid accumulation on Corynebacterium glutamicum. Microbiol Res 2016; 192:292-299. [PMID: 27664748 DOI: 10.1016/j.micres.2016.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/10/2016] [Accepted: 08/03/2016] [Indexed: 11/22/2022]
Abstract
5-Aminolevulinic acid (ALA), the committed intermediate of the heme biosynthetic pathway, attracts close attention among researchers because of its potential applications to cancer treatment and agriculture. Overexpression of heterologous hemA and hemL, which encode glutamyl-tRNA reductase and glutamate-1-semialdehyde aminotransferase, respectively, in Corynebacterium glutamicum produces ALA, although whether ALA accumulation causes unintended effects on the host is unknown. Here we used an integrated systems approach to compare global transcriptional changes induced by the expression of hemA and hemL. Metabolic pathway such as glycolysis was inhibited, but tricarboxylic acid cycle, pentose phosphate pathway, and respiratory metabolism were stimulated. Moreover, the transcriptional levels of certain genes involved in heme biosynthesis were up-regulated, and the data implicate the two-component system (TCS) HrrSA was involved in the regulation of heme synthesis. With these understandings, it is proposed that ALA accumulation stimulates heme synthesis pathway and respiratory metabolism. Our study illuminates the physiological effects of overexpressing hemA and hemL on the phenotype of C. glutamicum and contributes important insights into the regulatory mechanisms of the heme biosynthetic pathways.
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114
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Ahmed FH, Mohamed AE, Carr PD, Lee BM, Condic-Jurkic K, O'Mara ML, Jackson CJ. Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Sci 2016; 25:1692-709. [PMID: 27364382 DOI: 10.1002/pro.2975] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/29/2016] [Indexed: 12/12/2022]
Abstract
Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.
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Affiliation(s)
- F Hafna Ahmed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - A Elaaf Mohamed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Paul D Carr
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Brendon M Lee
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
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115
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Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 2016; 17:473. [PMID: 27342196 PMCID: PMC4921024 DOI: 10.1186/s12864-016-2782-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Background Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. Results Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. Conclusions Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Computation Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Claudia Lerma-Ortiz
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jeffrey D Mullen
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer J Thiaville
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
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116
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Dennis ML, Pitcher NP, Lee MD, DeBono AJ, Wang ZC, Harjani JR, Rahmani R, Cleary B, Peat TS, Baell JB, Swarbrick JD. Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. J Med Chem 2016; 59:5248-63. [PMID: 27094768 DOI: 10.1021/acs.jmedchem.6b00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a member of the folate biosynthesis pathway found in prokaryotes and lower eukaryotes that catalyzes the pyrophosphoryl transfer from the ATP cofactor to a 6-hydroxymethyl-7,8-dihydropterin substrate. We report the chemical synthesis of a series of S-functionalized 8-mercaptoguanine (8MG) analogues as substrate site inhibitors of HPPK and quantify binding against the E. coli and S. aureus enzymes (EcHPPK and SaHPPK). The results demonstrate that analogues incorporating acetophenone-based substituents have comparable affinities for both enzymes. Preferential binding of benzyl-substituted 8MG derivatives to SaHPPK was reconciled when a cryptic pocket unique to SaHPPK was revealed by X-ray crystallography. Differential chemical shift perturbation analysis confirmed this to be a common mode of binding for this series to SaHPPK. One compound (41) displayed binding affinities of 120 nM and 1.76 μM for SaHPPK and EcHPPK, respectively, and represents a lead for the development of more potent and selective inhibitors of SaHPPK.
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Affiliation(s)
- Matthew L Dennis
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Noel P Pitcher
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Aaron J DeBono
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Zhong-Chang Wang
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, People's Republic of China
| | - Jitendra R Harjani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Raphaël Rahmani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Ben Cleary
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - James D Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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117
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Acharya G, Kaur G, Subramanian S. Evolutionary relationships between heme-binding ferredoxin α + β barrels. BMC Bioinformatics 2016; 17:168. [PMID: 27089923 PMCID: PMC4835899 DOI: 10.1186/s12859-016-1033-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions. RESULTS We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels. CONCLUSIONS Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies.
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Affiliation(s)
- Giriraj Acharya
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
| | - Gurmeet Kaur
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
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118
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Prunetti L, El Yacoubi B, Schiavon CR, Kirkpatrick E, Huang L, Bailly M, El Badawi-Sidhu M, Harrison K, Gregory JF, Fiehn O, Hanson AD, de Crécy-Lagard V. Evidence that COG0325 proteins are involved in PLP homeostasis. MICROBIOLOGY-SGM 2016; 162:694-706. [PMID: 26872910 DOI: 10.1099/mic.0.000255] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pyridoxal 5'-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.
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Affiliation(s)
- Laurence Prunetti
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Cara R Schiavon
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ericka Kirkpatrick
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lili Huang
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, USA
| | - Marc Bailly
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Mona El Badawi-Sidhu
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, CA, USA
| | - Katherine Harrison
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jesse F Gregory
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, CA, USA
| | - Andrew D Hanson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
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119
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From chlorite dismutase towards HemQ - the role of the proximal H-bonding network in haeme binding. Biosci Rep 2016; 36:BSR20150330. [PMID: 26858461 PMCID: PMC4793301 DOI: 10.1042/bsr20150330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.
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120
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Celis AI, Streit BR, Moraski GC, Kant R, Lash TD, Lukat-Rodgers GS, Rodgers KR, DuBois JL. Unusual Peroxide-Dependent, Heme-Transforming Reaction Catalyzed by HemQ. Biochemistry 2015; 54:4022-32. [PMID: 26083961 DOI: 10.1021/acs.biochem.5b00492] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A recently proposed pathway for heme b biosynthesis, common to diverse bacteria, has the conversion of two of the four propionates on coproheme III to vinyl groups as its final step. This reaction is catalyzed in a cofactor-independent, H2O2-dependent manner by the enzyme HemQ. Using the HemQ from Staphylococcus aureus (SaHemQ), the initial decarboxylation step was observed to rapidly and obligately yield the three-propionate harderoheme isomer III as the intermediate, while the slower second decarboxylation appeared to control the overall rate. Both synthetic harderoheme isomers III and IV reacted when bound to HemQ, the former more slowly than the latter. While H2O2 is the assumed biological oxidant, either H2O2 or peracetic acid yielded the same intermediates and products, though amounts significantly greater than the expected 2 equiv were required in both cases and peracetic acid reacted faster. The ability of peracetic acid to substitute for H2O2 suggests that, despite the lack of catalytic residues conventionally present in heme peroxidase active sites, reaction pathways involving high-valent iron intermediates cannot be ruled out.
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Affiliation(s)
- Arianna I Celis
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
| | - Bennett R Streit
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
| | - Garrett C Moraski
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
| | - Ravi Kant
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
| | - Timothy D Lash
- ‡Department of Chemistry, Illinois State University, Normal, Illinois 61790-4160, United States
| | - Gudrun S Lukat-Rodgers
- §Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102-6050, United States
| | - Kenton R Rodgers
- §Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102-6050, United States
| | - Jennifer L DuBois
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
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121
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Lobo SAL, Scott A, Videira MAM, Winpenny D, Gardner M, Palmer MJ, Schroeder S, Lawrence AD, Parkinson T, Warren MJ, Saraiva LM. Staphylococcus aureushaem biosynthesis: characterisation of the enzymes involved in final steps of the pathway. Mol Microbiol 2015; 97:472-87. [DOI: 10.1111/mmi.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Susana A. L. Lobo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
| | - Alan Scott
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
| | - David Winpenny
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Mark Gardner
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Mike J. Palmer
- Pfizer Global Research and Development; Sandwich Kent UK
| | - Susanne Schroeder
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Andrew D. Lawrence
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | | | - Martin J. Warren
- School of Biosciences; University of Kent; Giles Lane Canterbury Kent CT2 7NJ UK
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa, Avenida da República (EAN); 2780-157 Oeiras Portugal
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122
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Celis AI, DuBois JL. Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys 2015; 574:3-17. [PMID: 25778630 PMCID: PMC4414885 DOI: 10.1016/j.abb.2015.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.
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Affiliation(s)
- Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
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123
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Schaffner I, Hofbauer S, Krutzler M, Pirker KF, Bellei M, Stadlmayr G, Mlynek G, Djinovic-Carugo K, Battistuzzi G, Furtmüller PG, Daims H, Obinger C. Dimeric chlorite dismutase from the nitrogen-fixing cyanobacterium Cyanothece sp. PCC7425. Mol Microbiol 2015; 96:1053-68. [PMID: 25732258 PMCID: PMC4973843 DOI: 10.1111/mmi.12989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2015] [Indexed: 11/28/2022]
Abstract
It is demonstrated that cyanobacteria (both azotrophic and non-azotrophic) contain heme b oxidoreductases that can convert chlorite to chloride and molecular oxygen (incorrectly denominated chlorite 'dismutase', Cld). Beside the water-splitting manganese complex of photosystem II, this metalloenzyme is the second known enzyme that catalyses the formation of a covalent oxygen-oxygen bond. All cyanobacterial Clds have a truncated N-terminus and are dimeric (i.e. clade 2) proteins. As model protein, Cld from Cyanothece sp. PCC7425 (CCld) was recombinantly produced in Escherichia coli and shown to efficiently degrade chlorite with an activity optimum at pH 5.0 [kcat 1144 ± 23.8 s(-1), KM 162 ± 10.0 μM, catalytic efficiency (7.1 ± 0.6) × 10(6) M(-1) s(-1)]. The resting ferric high-spin axially symmetric heme enzyme has a standard reduction potential of the Fe(III)/Fe(II) couple of -126 ± 1.9 mV at pH 7.0. Cyanide mediates the formation of a low-spin complex with k(on) = (1.6 ± 0.1) × 10(5) M(-1) s(-1) and k(off) = 1.4 ± 2.9 s(-1) (KD ∼ 8.6 μM). Both, thermal and chemical unfolding follows a non-two-state unfolding pathway with the first transition being related to the release of the prosthetic group. The obtained data are discussed with respect to known structure-function relationships of Clds. We ask for the physiological substrate and putative function of these O2 -producing proteins in (nitrogen-fixing) cyanobacteria.
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Affiliation(s)
- Irene Schaffner
- 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.,Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Michael Krutzler
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Katharina F Pirker
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Marzia Bellei
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Gerhard Stadlmayr
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Georg Mlynek
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
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124
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Dailey HA, Gerdes S. HemQ: An iron-coproporphyrin oxidative decarboxylase for protoheme synthesis in Firmicutes and Actinobacteria. Arch Biochem Biophys 2015; 574:27-35. [PMID: 25711532 DOI: 10.1016/j.abb.2015.02.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 02/05/2023]
Abstract
Genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some Archaea. It is now known that among the Firmicutes and Actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. These proteins, named HemQ, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme III into protoheme IX. As purified, HemQs do not contain bound heme, but readily bind exogeneously supplied heme with low micromolar affinity. The heme-bound form of HemQ has low peroxidase activity and in the presence of peroxide the bound heme may be destroyed. Thus, it is possible that HemQ may serve a dual role as a decarboxylase in heme biosynthesis and a regulatory protein in heme homeostasis.
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Affiliation(s)
- Harry A Dailey
- Biomedical and Health Sciences Institute, Department of Microbiology and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Svetlana Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
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