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Mg-protoporphyrin IX monomethyl ester cyclase from Rhodobacter capsulatus: radical SAM-dependent synthesis of the isocyclic ring of bacteriochlorophylls. Biochem J 2020; 477:4635-4654. [DOI: 10.1042/bcj20200761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022]
Abstract
During bacteriochlorophyll a biosynthesis, the oxygen-independent conversion of Mg-protoporphyrin IX monomethyl ester (Mg-PME) to protochlorophyllide (Pchlide) is catalyzed by the anaerobic Mg-PME cyclase termed BchE. Bioinformatics analyses in combination with pigment studies of cobalamin-requiring Rhodobacter capsulatus mutants indicated an unusual radical S-adenosylmethionine (SAM) and cobalamin-dependent BchE catalysis. However, in vitro biosynthesis of the isocyclic ring moiety of bacteriochlorophyll using purified recombinant BchE has never been demonstrated. We established a spectroscopic in vitro activity assay which was subsequently validated by HPLC analyses and H218O isotope label transfer onto the carbonyl-group (C-131-oxo) of the isocyclic ring of Pchlide. The reaction product was further converted to chlorophyllide in the presence of light-dependent Pchlide reductase. BchE activity was stimulated by increasing concentrations of NADPH or SAM, and inhibited by S-adenosylhomocysteine. Subcellular fractionation experiments revealed that membrane-localized BchE requires an additional, heat-sensitive cytosolic component for activity. BchE catalysis was not sustained in chimeric experiments when a cytosolic extract from E. coli was used as a substitute. Size-fractionation of the soluble R. capsulatus fraction indicated that enzymatic activity relies on a specific component with an estimated molecular mass between 3 and 10 kDa. A structure guided site-directed mutagenesis approach was performed on the basis of a three-dimensional homology model of BchE. A newly established in vivo complementation assay was used to investigate 24 BchE mutant proteins. Potential ligands of the [4Fe-4S] cluster (Cys204, Cys208, Cys211), of SAM (Phe210, Glu308 and Lys320) and of the proposed cobalamin cofactor (Asp248, Glu249, Leu29, Thr71, Val97) were identified.
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Jasper J, Ramos JV, Trncik C, Jahn D, Einsle O, Layer G, Moser J. Chimeric Interaction of Nitrogenase-Like Reductases with the MoFe Protein of Nitrogenase. Chembiochem 2020; 21:1733-1741. [PMID: 31958206 PMCID: PMC7317204 DOI: 10.1002/cbic.201900759] [Citation(s) in RCA: 4] [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: 12/16/2019] [Revised: 01/17/2020] [Indexed: 11/24/2022]
Abstract
The engineering of transgenic organisms with the ability to fix nitrogen is an attractive possibility. However, oxygen sensitivity of nitrogenase, mainly conferred by the reductase component (NifH)2 , is an imminent problem. Nitrogenase-like enzymes involved in coenzyme F430 and chlorophyll biosynthesis utilize the highly homologous reductases (CfbC)2 and (ChlL)2 , respectively. Chimeric protein-protein interactions of these reductases with the catalytic component of nitrogenase (MoFe protein) did not support nitrogenase activity. Nucleotide-dependent association and dissociation of these complexes was investigated, but (CfbC)2 and wild-type (ChlL)2 showed no modulation of the binding affinity. By contrast, the interaction between the (ChlL)2 mutant Y127S and the MoFe protein was markedly increased in the presence of ATP (or ATP analogues) and reduced in the ADP state. Upon formation of the octameric (ChlL)2 MoFe(ChlL)2 complex, the ATPase activity of this variant is triggered, as seen in the homologous nitrogenase system. Thus, the described reductase(s) might be an attractive tool for further elucidation of the diverse functions of (NifH)2 and the rational design of a more robust reductase.
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Affiliation(s)
- Jan Jasper
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - José V. Ramos
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Christian Trncik
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Dieter Jahn
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - Oliver Einsle
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Gunhild Layer
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Jürgen Moser
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
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Kessi J, Hörtensteiner S. Inhibition of bacteriochlorophyll biosynthesis in the purple phototrophic bacteria Rhodospirillumrubrum and Rhodobacter capsulatus grown in the presence of a toxic concentration of selenite. BMC Microbiol 2018; 18:81. [PMID: 30064359 PMCID: PMC6069883 DOI: 10.1186/s12866-018-1209-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 06/27/2018] [Indexed: 11/21/2022] Open
Abstract
Background In many works, the chemical composition of bacterially-produced elemental selenium nanoparticles (Se0-nanoparticles) was investigated using electron dispersive X-ray analysis. The results suggest that these particles should be associated with organic compounds. However, a complete analysis of their chemical composition is still missing. Aiming at identifying organic compounds associated with the Se0-nanoparticles produced by the purple phototrophic bacteria Rhodospirillum rubrum and Rhodobacter capsulatus (α group of the proteobacteria), we used MALDI-TOF spectrometry.Results This technic revealed that numerous signals obtained from particles produced by both species of bacteria were from metabolites of the photosynthetic system. Furthermore, not only bacteriochlorophyll a, bacteriopheophytin a, and bacteriopheophorbide a, which are known to accumulate in stationary phase cultures of these bacteria grown phototrophically in the absence of selenite, were identified. The particles were also associated with intermediary metabolites of the bacteriochlorophyll a biosynthesis pathway such as protoporphyrin IX, protoporphyrin IX monomethyl ester, bacteriochlorophyllide a and, most likely, Mg-protoporphyrin IX-monomethyl ester, as well as with oxidation products of the substrates of protochlorophyllide reductase and chlorin reductase.Conclusion Accumulation of intermediary metabolites of the bacteriochlorophyll biosynthesis pathway in these purple phototrophic bacteria was attributed to inhibition of oxygen-sensitive enzymes involved in this pathway. Consistent with this interpretation it has been reported that these bacteria reduce selenite intracellularly, that they contain high levels of glutathione and that the reduction of selenite with glutathione is a very fast reaction accompanied by the production of reactive oxygen species. As many enzymes involved in the biosynthesis of bacteriochlorophyll contain [Fe-S] clusters in their active site, which are known to be degraded in the presence of reactive oxygen species as well as in the presence of molecular oxygen, we concluded that the substrates of these enzymes accumulate in cells during selenite reduction.Association of metabolites of bacteriochlorophyll biosynthesis and degradation with the Se0-nanoparticles produced by Rhodospirillum rubrum and Rhodobacter capsulatus is proposed to result from coating of the nanoparticles with the intracytoplasmic membrane of these bacteria, where the photochemical apparatus is concentrated.
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Affiliation(s)
- Janine Kessi
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
- Kirschenweg 10, Würenlingen, 5303 Switzerland
| | - Stefan Hörtensteiner
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
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Fang L, Ge H, Huang X, Liu Y, Lu M, Wang J, Chen W, Xu W, Wang Y. Trophic Mode-Dependent Proteomic Analysis Reveals Functional Significance of Light-Independent Chlorophyll Synthesis in Synechocystis sp. PCC 6803. MOLECULAR PLANT 2017; 10:73-85. [PMID: 27585879 DOI: 10.1016/j.molp.2016.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/03/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The photosynthetic model organism Synechocystis sp. PCC 6803 can grow in different trophic modes, depending on the availability of light and exogenous organic carbon source. However, how the protein profile changes to facilitate the cells differentially propagate in different modes has not been comprehensively investigated. Using isobaric labeling-based quantitative proteomics, we simultaneously identified and quantified 45% Synechocystis proteome across four different trophic modes, i.e., autotrophic, heterotrophic, photoheterotrophic, and mixotrophic modes. Among the 155 proteins that are differentially expressed across four trophic modes, proteins involved in nitrogen assimilation and light-independent chlorophyll synthesis are dramatically upregulated in the mixotrophic mode, concomitant with a dramatic increase of PII phosphorylation that senses carbon and nitrogen assimilation status. Moreover, functional study using a mutant defective in light-independent chlorophyll synthesis revealed that this pathway is important for chlorophyll accumulation under a cycled light/dark illumination regime, a condition mimicking day/night cycles in certain natural habitats. Collectively, these results provide the most comprehensive information on trophic mode-dependent protein expression in cyanobacterium, and reveal the functional significance of light-independent chlorophyll synthesis in trophic growth.
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Affiliation(s)
- Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Ye Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Min Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.
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Layer G, Krausze J, Moser J. Reduction of Chemically Stable Multibonds: Nitrogenase-Like Biosynthesis of Tetrapyrroles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:147-161. [DOI: 10.1007/5584_2016_175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Lange C, Kiesel S, Peters S, Virus S, Scheer H, Jahn D, Moser J. Broadened Substrate Specificity of 3-Hydroxyethyl Bacteriochlorophyllide a Dehydrogenase (BchC) Indicates a New Route for the Biosynthesis of Bacteriochlorophyll a. J Biol Chem 2015; 290:19697-709. [PMID: 26088139 PMCID: PMC4528133 DOI: 10.1074/jbc.m115.660555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/18/2015] [Indexed: 11/06/2022] Open
Abstract
Bacteriochlorophyll a biosynthesis requires formation of a 3-hydroxyethyl group on pyrrole ring A that gets subsequently converted into a 3-acetyl group by 3-vinyl bacteriochlorophyllide a hydratase (BchF) followed by 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC). Heterologous overproduction of Chlorobaculum tepidum BchF revealed an integral transmembrane protein that was efficiently isolated by detergent solubilization. Recombinant C. tepidum BchC was purified as a soluble protein-NAD(+) complex. Substrate recognition of BchC was investigated using six artificial substrate molecules. Modification of the isocyclic E ring, omission of the central magnesium ion, zinc as an alternative metal ion, and a non-reduced B ring system were tolerated by BchC. According to this broadened in vitro activity, the chlorin 3-hydroxyethyl chlorophyllide a was newly identified as a natural substrate of BchC in a reconstituted pathway consisting of dark-operative protochlorophyllide oxidoreductase, BchF, and BchC. The established reaction sequence would allow for an additional new branching point for the synthesis of bacteriochlorophyll a. Biochemical and site-directed mutagenesis analyses revealed, in contrast to theoretical predictions, a zinc-independent BchC catalysis that requires NAD(+) as a cofactor. Based on these results, we are designating a new medium-chain dehydrogenase/reductase family (MDR057 BchC) as theoretically proposed from a recent bioinformatics analysis.
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Affiliation(s)
- Christiane Lange
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Svenja Kiesel
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Sabine Peters
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Simone Virus
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Hugo Scheer
- Department Biology I, Botany, Ludwig-Maximilians-Universität München, Menzingerstrasse 67, D-80638 München, Germany
| | - Dieter Jahn
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Jürgen Moser
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
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Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments. Life (Basel) 2015; 5:1172-203. [PMID: 25830590 PMCID: PMC4500134 DOI: 10.3390/life5021172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 01/10/2023] Open
Abstract
Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions. Another mechanism adaptive to hypoxic conditions is mediated by the transcriptional regulator ChlR that senses low oxygen and subsequently activates the transcription of genes encoding enzymes that work under low-oxygen tension. In diazotrophic cyanobacteria, this multilayered regulation also contributes in Chl biosynthesis by supporting energy production for nitrogen fixation that also requires low-oxygen conditions. We will also discuss the evolutionary implications of cyanobacterial tetrapyrrole biosynthesis and regulation, because low oxygen-type enzymes also appear to be evolutionarily older than oxygen-dependent enzymes.
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Kiesel S, Wätzlich D, Lange C, Reijerse E, Bröcker MJ, Rüdiger W, Lubitz W, Scheer H, Moser J, Jahn D. Iron-sulfur cluster-dependent catalysis of chlorophyllide a oxidoreductase from Roseobacter denitrificans. J Biol Chem 2015; 290:1141-54. [PMID: 25422320 PMCID: PMC4294481 DOI: 10.1074/jbc.m114.617761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/18/2014] [Indexed: 11/06/2022] Open
Abstract
Bacteriochlorophyll a biosynthesis requires the stereo- and regiospecific two electron reduction of the C7-C8 double bond of chlorophyllide a by the nitrogenase-like multisubunit metalloenzyme, chlorophyllide a oxidoreductase (COR). ATP-dependent COR catalysis requires interaction of the protein subcomplex (BchX)2 with the catalytic (BchY/BchZ)2 protein to facilitate substrate reduction via two redox active iron-sulfur centers. The ternary COR enzyme holocomplex comprising subunits BchX, BchY, and BchZ from the purple bacterium Roseobacter denitrificans was trapped in the presence of the ATP transition state analog ADP·AlF4(-). Electron paramagnetic resonance experiments revealed a [4Fe-4S] cluster of subcomplex (BchX)2. A second [4Fe-4S] cluster was identified on (BchY/BchZ)2. Mutagenesis experiments indicated that the latter is ligated by four cysteines, which is in contrast to the three cysteine/one aspartate ligation pattern of the closely related dark-operative protochlorophyllide a oxidoreductase (DPOR). In subsequent mutagenesis experiments a DPOR-like aspartate ligation pattern was implemented for the catalytic [4Fe-4S] cluster of COR. Artificial cluster formation for this inactive COR variant was demonstrated spectroscopically. A series of chemically modified substrate molecules with altered substituents on the individual pyrrole rings and the isocyclic ring were tested as COR substrates. The COR enzyme was still able to reduce the B ring of substrates carrying modified substituents on ring systems A, C, and E. However, substrates with a modification of the distantly located propionate side chain were not accepted. A tentative substrate binding mode was concluded in analogy to the related DPOR system.
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Affiliation(s)
- Svenja Kiesel
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Denise Wätzlich
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Christiane Lange
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Edward Reijerse
- Max-Planck-Institute for Chemical Energy Conversion, D-45470 Mülheim, Germany
| | - Markus J Bröcker
- Department of Molecular Biophysics and Biochemistry, Yale University New Haven, Connecticut 06520, and
| | - Wolfhart Rüdiger
- Department Biology I, Botany, Ludwig-Maximilians-Universität München, D-80638 München, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, D-45470 Mülheim, Germany
| | - Hugo Scheer
- Department Biology I, Botany, Ludwig-Maximilians-Universität München, D-80638 München, Germany
| | - Jürgen Moser
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany,
| | - Dieter Jahn
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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Hu Y, Ribbe MW. Nitrogenase and homologs. J Biol Inorg Chem 2014; 20:435-45. [PMID: 25491285 DOI: 10.1007/s00775-014-1225-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/24/2014] [Indexed: 11/24/2022]
Abstract
Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, 2230 McGaugh Hall, University of California, Irvine, CA, 92697-3900, USA,
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Yamamoto H, Kato M, Yamanashi K, Fujita Y. Reconstitution of a sequential reaction of two nitrogenase-like enzymes in the bacteriochlorophyll biosynthetic pathway of Rhodobacter capsulatus. Biochem Biophys Res Commun 2014; 448:200-5. [PMID: 24769479 DOI: 10.1016/j.bbrc.2014.04.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
Abstract
The parental structure of bacteriochlorophyll a, bacteriochlorin, is formed by a sequential operation of two nitrogenase-like enzymes, dark-operative protochlorophyllide oxidoreductase (DPOR) and chlorophyllide a oxidoreductase (COR). Both DPOR and COR consist of two components, Fe protein and MoFe protein cognates. Here we determined kinetic parameters of COR and established the reconstitution system for the formation of bacteriochlorin (3-vinyl bacteriochlorophyllide a) from porphyrin (protochlorophyllide) with purified components of DPOR and COR from Rhodobacter capsulatus. This reconstitution system confirmed the recent finding that COR catalyzes 8-vinyl reduction of 8-vinyl chlorophyllide a in addition to the known activity of C7C8 double bond reduction, and provides a promising model to investigate how two nitrogenase-like enzymes are coordinated in bacteriochlorophyll biosynthesis.
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Affiliation(s)
- Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Mina Kato
- School of Agricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Kaori Yamanashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex. Proc Natl Acad Sci U S A 2013; 110:2094-8. [PMID: 23341615 DOI: 10.1073/pnas.1218303110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photosynthesis uses chlorophylls for the conversion of light into chemical energy, the driving force of life on Earth. During chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase (DPOR), a nitrogenase-like metalloenzyme, catalyzes the chemically challenging two-electron reduction of the fully conjugated ring system of protochlorophyllide a. The reduction of the C-17=C-18 double bond results in the characteristic ring architecture of all chlorophylls, thereby altering the absorption properties of the molecule and providing the basis for light-capturing and energy-transduction processes of photosynthesis. We report the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP·AlF(3)-stabilized) transition state complex between the DPOR components L(2) and (NB)(2) from the marine cyanobacterium Prochlorococcus marinus. Our analysis permits a thorough investigation of the dynamic interplay between L(2) and (NB)(2). Upon complex formation, substantial ATP-dependent conformational rearrangements of L(2) trigger the protein-protein interactions with (NB)(2) as well as the electron transduction via redox-active [4Fe-4S] clusters. We also present the identification of artificial "small-molecule substrates" of DPOR in correlation with those of nitrogenase. The catalytic differences and similarities between DPOR and nitrogenase have broad implications for the energy transduction mechanism of related multiprotein complexes that are involved in the reduction of chemically stable double and/or triple bonds.
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Comparative and Functional Genomics of Anoxygenic Green Bacteria from the Taxa Chlorobi, Chloroflexi, and Acidobacteria. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_3] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Yamamoto H, Kurumiya S, Ohashi R, Fujita Y. Functional evaluation of a nitrogenase-like protochlorophyllide reductase encoded by the chloroplast DNA of Physcomitrella patens in the cyanobacterium Leptolyngbya boryana. PLANT & CELL PHYSIOLOGY 2011; 52:1983-1993. [PMID: 21949030 DOI: 10.1093/pcp/pcr132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR) is a nitrogenase-like enzyme consisting of the two components, L-protein (a ChlL dimer) and NB-protein (a ChlN-ChlB heterotetramer), to catalyze Pchlide reduction in Chl biosynthesis. While nitrogenase is distributed only among certain prokaryotes, the probable structural genes for DPOR are encoded by chloroplast DNA in lower plants. Here we show functional evaluation of DPOR encoded by chloroplast DNA in a moss Physcomitrella patens by the complementation analysis of the cyanobacterium Leptolyngbya boryana and the heterologous reconstitution of the moss L-protein and the cyanobacterial NB-protein. Two shuttle vectors to overexpress chlL and chlN-chlB from P. patens were introduced into the cyanobacterial chlL- and chlB-lacking mutants, respectively. Both transformants restored the ability to perform Chl biosynthesis in the dark, indicating that the chloroplast-encoded DPOR components form an active complex with the cyanobacterial components. The L-protein of P. patens was purified from the cyanobacterial transformant, and DPOR activity was reconstituted in a heterologous combination with the cyanobacterial NB-protein. The specific activity of the L-protein from P. patens was determined to be 118 nmol min(-1) mg (-1), which is even higher than that of the cyanobacterial L-protein (76 nmol min(-1) mg (-1)). Upon exposure to air, the activity of the L-protein from P. patens decayed with a half-life of 30 s, which was eight times faster than that of the cyanobacterial L-protein (240 s). These results suggested that the chloroplast-encoded L-protein functions as efficiently as the cyanobacterial L-protein but is more oxygen labile than the cyanobacterial L-protein.
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Affiliation(s)
- Haruki Yamamoto
- School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Abstract
Nitrogenase-like dark operative protochlorophyllide oxidoreductase (DPOR) is involved in the two-electron reduction of protochlorophyllide to form chlorophyllide during chlorophyll biosynthesis. Formation of bacteriochlorophyll additionally requires a structurally related enzyme system which is termed chlorophyllide oxidoreductase (COR). During DPOR catalysis, the homodimeric subunit ChlL(2) transfers electrons to the corresponding heterotetrameric catalytic subunit (ChlN/ChlB)(2). Analogously, subunit BchX(2) of the COR enzymes delivers electrons to subunit (BchY/BchZ)(2). The ChlL(2) protein is a dynamic switch protein triggering the ATP-dependent transfer of electrons via a [4Fe-4S] cluster onto a second [4Fe-4S] cluster located on subunit (ChlN/ChlB)(2). This initial electron transfer step of DPOR catalysis clearly resembles nitrogenase catalysis. However, the subsequent substrate reduction process was proposed to be unrelated since no molybdenum-containing cofactor or a P-cluster equivalent is employed. To investigate the transient interaction of both subcomplexes ChlL(2) and (ChlN/ChlB)(2) and the resulting electron transfer processes, the ternary DPOR enzyme holocomplex was trapped as an octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex after incubation with non-hydrolyzable ATP analogs. Electron paramagnetic resonance spectroscopic experiments of various DPOR complexes in combination with circular dichroism spectroscopic experiments of the ChlL(2) protein revealed a detailed redox catalytic cycle for nucleotide-dependent DPOR catalysis.
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Affiliation(s)
- Jürgen Moser
- Institut für Mikrobiologie, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
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15
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Moser J, Bröcker MJ. Methods for nitrogenase-like dark operative protochlorophyllide oxidoreductase. Methods Mol Biol 2011; 766:129-143. [PMID: 21833865 DOI: 10.1007/978-1-61779-194-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nitrogenase-like dark operative protochlorophyllide oxidoreductase (DPOR) is involved in the biosynthesis of chlorophylls and bacteriochlorophylls in gymnosperms, ferns, algae, and photosynthetic bacteria. During protochlorophyllide (Pchlide) reduction, the homodimeric subunit ChlL(2) of DPOR transfers electrons on the corresponding heterotetrameric catalytic subunit (ChlN/ChlB)(2). Although DPOR shares significant amino acid sequence homology to the nitrogenase system, only the initial catalytic steps of DPOR resemble nitrogenase catalysis. Investigation of the cyanobacterial DPOR from Prochlorococcus marinus indicated that subcomplex ChlL(2) is functioning as an ATP-dependent switch protein, triggering the transient interaction of ChlL(2) and (ChlN/ChlB)(2). This dynamic subunit interplay is responsible for the transfer of a single electron from the [4Fe-4S] cluster of ChlL(2) onto a second [4Fe-4S] cluster located on (ChlN/ChlB)(2). However, the second part of DPOR catalysis is unrelated to nitrogenase catalysis, since no molybdenum-containing cofactor or a P-cluster equivalent is employed. Instead, two consecutive electron transfer steps are mediated via the [4Fe-4S] cluster of (ChlN/ChlB)(2), resulting in the reduction of the conjugated ring system of the substrate molecule Pchlide (Figs. 5.1a and 5.2).
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Affiliation(s)
- Jürgen Moser
- Institut für Mikrobiologie, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
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Kondo T, Nomata J, Fujita Y, Itoh S. EPR study of 1Asp-3Cys ligated 4Fe-4S iron-sulfur cluster in NB-protein (BchN-BchB) of a dark-operative protochlorophyllide reductase complex. FEBS Lett 2010; 585:214-8. [PMID: 21126521 DOI: 10.1016/j.febslet.2010.11.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/23/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
Abstract
Dark-operative protochlorophyllide oxidoreductase, a nitrogenase-like enzyme, contains two [4Fe-4S] clusters, one in the L-protein ((BchL)(2)) and the other in the NB-protein ((BchN-BchB)(2)). The reduced NB-cluster in the NB-protein, which is ligated by 1Asp/3Cys residues, showed a broad S=3/2 electron paramagnetic resonance signal that is rather rare in [4Fe-4S] clusters. A 4Cys-ligated NB-cluster in the mutated variant BchB-D36C protein, in which the Asp36 was replaced by a Cys, gave a rhombic normal S=1/2 signal and lost the catalytic activity. The results suggest that Asp36 contributes to the low redox potential necessary to reduce protochlorophyllide.
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Affiliation(s)
- Toru Kondo
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan.
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Reinbothe C, El Bakkouri M, Buhr F, Muraki N, Nomata J, Kurisu G, Fujita Y, Reinbothe S. Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction. TRENDS IN PLANT SCIENCE 2010; 15:614-24. [PMID: 20801074 DOI: 10.1016/j.tplants.2010.07.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/14/2010] [Accepted: 07/22/2010] [Indexed: 05/21/2023]
Abstract
Photosynthetic organisms require chlorophyll or bacteriochlorophyll for their light trapping and energy transduction activities. The biosynthetic pathways of chlorophyll and bacteriochlorophyll are similar in most of their early steps, except for the reduction of protochlorophyllide (Pchlide) to chlorophyllide. Whereas angiosperms make use of a light-dependent enzyme, cyanobacteria, algae, bryophytes, pteridophytes and gymnosperms contain an additional, light-independent enzyme dubbed dark-operative Pchlide oxidoreductase (DPOR). Anoxygenic photosynthetic bacteria such as Rhodobacter capsulatus and Rhodobacter sphaeroides rely solely on DPOR. Recent atomic resolution of reductase and catalytic components of DPOR from R. sphaeroides and R. capsulatus, respectively, have revealed their similarity to nitrogenase components. In this review, we discuss the two fundamentally different mechanisms of Pchlide reduction in photosynthetic organisms.
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Affiliation(s)
- Christiane Reinbothe
- Lehrstuhl für Pflanzenphysiologie, Universität Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany.
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18
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Bröcker MJ, Schomburg S, Heinz DW, Jahn D, Schubert WD, Moser J. Crystal structure of the nitrogenase-like dark operative protochlorophyllide oxidoreductase catalytic complex (ChlN/ChlB)2. J Biol Chem 2010; 285:27336-27345. [PMID: 20558746 PMCID: PMC2930732 DOI: 10.1074/jbc.m110.126698] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/15/2010] [Indexed: 11/06/2022] Open
Abstract
During (bacterio)chlorophyll biosynthesis of many photosynthetically active organisms, dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the two-electron reduction of ring D of protochlorophyllide to form chlorophyllide. DPOR is composed of the subunits ChlL, ChlN, and ChlB. Homodimeric ChlL(2) bearing an intersubunit [4Fe-4S] cluster is an ATP-dependent reductase transferring single electrons to the heterotetrameric (ChlN/ChlB)(2) complex. The latter contains two intersubunit [4Fe-4S] clusters and two protochlorophyllide binding sites, respectively. Here we present the crystal structure of the catalytic (ChlN/ChlB)(2) complex of DPOR from the cyanobacterium Thermosynechococcus elongatus at a resolution of 2.4 A. Subunits ChlN and ChlB exhibit a related architecture of three subdomains each built around a central, parallel beta-sheet surrounded by alpha-helices. The (ChlN/ChlB)(2) crystal structure reveals a [4Fe-4S] cluster coordinated by an aspartate oxygen alongside three cysteine ligands. Two equivalent substrate binding sites enriched in aromatic residues for protochlorophyllide substrate binding are located at the interface of each ChlN/ChlB half-tetramer. The complete octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex of DPOR was modeled based on the crystal structure and earlier functional studies. The electron transfer pathway via the various redox centers of DPOR to the substrate is proposed.
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Affiliation(s)
- Markus J Bröcker
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Sebastian Schomburg
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Dirk W Heinz
- Division of Structural Biology, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Wolf-Dieter Schubert
- Division of Structural Biology, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa.
| | - Jürgen Moser
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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Bröcker MJ, Wätzlich D, Saggu M, Lendzian F, Moser J, Jahn D. Biosynthesis of (bacterio)chlorophylls: ATP-dependent transient subunit interaction and electron transfer of dark operative protochlorophyllide oxidoreductase. J Biol Chem 2010; 285:8268-77. [PMID: 20075073 DOI: 10.1074/jbc.m109.087874] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the light-independent two-electron reduction of protochlorophyllide a to form chlorophyllide a, the last common precursor of chlorophyll a and bacteriochlorophyll a biosynthesis. During ATP-dependent DPOR catalysis the homodimeric ChlL(2) subunit carrying a [4Fe-4S] cluster transfers electrons to the corresponding heterotetrameric catalytic subunit (ChlN/ChlB)(2), which also possesses a redox active [4Fe-4S] cluster. To investigate the transient interaction of both subcomplexes and the resulting electron transfer reactions, the ternary DPOR enzyme holocomplex comprising subunits ChlN, ChlB, and ChlL from the cyanobacterium Prochlorococcus marinus was trapped as an octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex after incubation with the nonhydrolyzable ATP analogs adenosine 5'-(gamma-thio)triphosphate, adenosine 5'-(beta,gamma-imido)triphosphate, or MgADP in combination with AlF(4)(-). Additionally, a mutant ChlL(2) protein, with a deleted Leu(153) in the switch II region also allowed for the formation of a stable octameric complex. Furthermore, efficient complex formation required the presence of protochlorophyllide. Electron paramagnetic resonance spectroscopy of ternary DPOR complexes revealed a reduced [4Fe-4S] cluster located on ChlL(2), indicating that complete ATP hydrolysis is a prerequisite for intersubunit electron transfer. Circular dichroism spectroscopic experiments indicated nucleotide-dependent conformational changes for ChlL(2) after ATP binding. A nucleotide-dependent switch mechanism triggering ternary complex formation and electron transfer was concluded. From these results a detailed redox cycle for DPOR catalysis was deduced.
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Affiliation(s)
- Markus J Bröcker
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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Yamamoto H, Kurumiya S, Ohashi R, Fujita Y. Oxygen sensitivity of a nitrogenase-like protochlorophyllide reductase from the cyanobacterium Leptolyngbya boryana. PLANT & CELL PHYSIOLOGY 2009; 50:1663-1673. [PMID: 19643808 DOI: 10.1093/pcp/pcp111] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dark-operative protochlorophyllide (Pchlide) oxido-reductase (DPOR) is a nitrogenase-like enzyme that catalyzes Pchlide reduction, the penultimate step of chlorophyll a biosynthesis. DPOR is distributed widely among oxygenic phototrophs such as cyanobacteria, green algae and gymnosperms. To determine how DPOR operates in oxygenic photosynthetic cells, we constructed two shuttle vectors for overexpression of Strep-tagged L-protein (ChlL) and Strep-tagged NB-protein (ChlN-ChlB) in Leptolyngbya boryana (formerly Plectonema boryanum) and introduced them into mutants lacking chlL and chlB. Both transformants restored the ability to produce chlorophyll in the dark. The DPOR activity was reconstituted by L-protein and NB-protein purified from the transformants under anaerobic conditions. L-protein activity disappeared within 5 min of exposure to air while NB-protein activity persisted for >30 min in an aerobic condition, indicating that the L-protein of DPOR components is the primary target of oxygen in cyanobacterial cells. These results suggested that the DPOR from an oxygenic photosynthetic organism did not acquire oxygen tolerance during evolution; but that the cyanobacterial cell developed a mechanism to protect DPOR from oxygen.
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Affiliation(s)
- Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
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Wätzlich D, Bröcker MJ, Uliczka F, Ribbe M, Virus S, Jahn D, Moser J. Chimeric nitrogenase-like enzymes of (bacterio)chlorophyll biosynthesis. J Biol Chem 2009; 284:15530-40. [PMID: 19336405 DOI: 10.1074/jbc.m901331200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrogenase-like light-independent protochlorophyllide oxidoreductase (DPOR) is involved in chlorophyll biosynthesis. Bacteriochlorophyll formation additionally requires the structurally related chlorophyllide oxidoreductase (COR). During catalysis, homodimeric subunit BchL(2) or ChlL(2) of DPOR transfers electrons to the corresponding heterotetrameric catalytic subunit, (BchNB)(2) or (ChlNB)(2). Analogously, subunit BchX(2) of the COR enzymes delivers electrons to subunit (BchYZ)(2). Various chimeric DPOR enzymes formed between recombinant subunits (BchNB)(2) and BchL(2) from Chlorobaculum tepidum or (ChlNB)(2) and ChlL(2) from Prochlorococcus marinus and Thermosynechococcus elongatus were found to be enzymatically active, indicating a conserved docking surface for the interaction of both DPOR protein subunits. Biotin label transfer experiments revealed the interaction of P. marinus ChlL(2) with both subunits, ChlN and ChlB, of the (ChlNB)(2) tetramer. Based on these findings and on structural information from the homologous nitrogenase system, a site-directed mutagenesis approach yielded 10 DPOR mutants for the characterization of amino acid residues involved in protein-protein interaction. Surface-exposed residues Tyr(127) of subunit ChlL, Leu(70) and Val(107) of subunit ChlN, and Gly(66) of subunit ChlB were found essential for P. marinus DPOR activity. Next, the BchL(2) or ChlL(2) part of DPOR was exchanged with electron-transferring BchX(2) subunits of COR and NifH(2) of nitrogenase. Active chimeric DPOR was generated via a combination of BchX(2) from C. tepidum or Roseobacter denitrificans with (BchNB)(2) from C. tepidum. No DPOR activity was observed for the chimeric enzyme consisting of NifH(2) from Azotobacter vinelandii in combination with (BchNB)(2) from C. tepidum or (ChlNB)(2) from P. marinus and T. elongatus, respectively.
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Affiliation(s)
- Denise Wätzlich
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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