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Kiss É, Talbot J, Adams NBP, Opekar S, Moos M, Pilný J, Kvasov T, Schneider E, Koník P, Šimek P, Sobotka R. Chlorophyll biosynthesis under the control of arginine metabolism. Cell Rep 2023; 42:113265. [PMID: 37864789 PMCID: PMC10783636 DOI: 10.1016/j.celrep.2023.113265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/11/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
In natural environments, photosynthetic organisms adjust their metabolism to cope with the fluctuating availability of combined nitrogen sources, a growth-limiting factor. For acclimation, the dynamic degradation/synthesis of tetrapyrrolic pigments, as well as of the amino acid arginine, is pivotal; however, there has been no evidence that these processes could be functionally coupled. Using co-immunopurification and spectral shift assays, we found that in the cyanobacterium Synechocystis sp. PCC 6803, the arginine metabolism-related ArgD and CphB enzymes form protein complexes with Gun4, an essential protein for chlorophyll biosynthesis. Gun4 binds ArgD with high affinity, and the Gun4-ArgD complex accumulates in cells supplemented with ornithine, a key intermediate of the arginine pathway. Elevated ornithine levels restricted de novo synthesis of tetrapyrroles, which arrested the recovery from nitrogen deficiency. Our data reveal a direct crosstalk between tetrapyrrole biosynthesis and arginine metabolism that highlights the importance of balancing photosynthetic pigment synthesis with nitrogen homeostasis.
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Affiliation(s)
- Éva Kiss
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Jana Talbot
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Nathan B P Adams
- NanoTemper Technologies, Floessegasse 4, 81369 Munich, Germany; Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Stanislav Opekar
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Martin Moos
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Jan Pilný
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Tatjana Kvasov
- NanoTemper Technologies, Floessegasse 4, 81369 Munich, Germany
| | | | - Peter Koník
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Petr Šimek
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Roman Sobotka
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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Shvarev D, Scholz AI, Moeller A. Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis. mBio 2023; 14:e0189323. [PMID: 37737632 PMCID: PMC10653834 DOI: 10.1128/mbio.01893-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
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Affiliation(s)
- Dmitry Shvarev
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Alischa Ira Scholz
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Arne Moeller
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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Adams NBP, Bisson C, Brindley AA, Farmer DA, Davison PA, Reid JD, Hunter CN. The active site of magnesium chelatase. NATURE PLANTS 2020; 6:1491-1502. [PMID: 33257858 DOI: 10.1038/s41477-020-00806-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
The insertion of magnesium into protoporphyrin initiates the biosynthesis of chlorophyll, the pigment that underpins photosynthesis. This reaction, catalysed by the magnesium chelatase complex, couples ATP hydrolysis by a ChlID motor complex to chelation within the ChlH subunit. We probed the structure and catalytic function of ChlH using a combination of X-ray crystallography, computational modelling, mutagenesis and enzymology. Two linked domains of ChlH in an initially open conformation of ChlH bind protoporphyrin IX, and the rearrangement of several loops envelops this substrate, forming an active site cavity. This induced fit brings an essential glutamate (E660), proposed to be the key catalytic residue for magnesium insertion, into proximity with the porphyrin. A buried solvent channel adjacent to E660 connects the exterior bulk solvent to the active site, forming a possible conduit for the delivery of magnesium or abstraction of protons.
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Affiliation(s)
- Nathan B P Adams
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
| | - Claudine Bisson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
- Centre for Ultrastructural Imaging, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - David A Farmer
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - James D Reid
- Department of Chemistry, The University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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Mahdi R, Stuart D, Hansson M, Youssef HM. Heterologous Expression of the Barley (Hordeum vulgare L.) Xantha-f, -g and -h Genes that Encode Magnesium Chelatase Subunits. Protein J 2020; 39:554-562. [PMID: 32737834 PMCID: PMC7704502 DOI: 10.1007/s10930-020-09913-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosynthesis of chlorophyll involves several enzymatic reactions of which many are shared with the heme biosynthesis pathway. Magnesium chelatase is the first specific enzyme in the chlorophyll pathway. It catalyzes the formation of Mg-protoporphyrin IX from the insertion of Mg2+ into protoporphyrin IX. The enzyme consists of three subunits encoded by three genes. The three genes are named Xantha-h, Xantha-g and Xantha-f in barley (Hordeum vulgare L.). The products of the genes have a molecular weight of 38, 78 and 148 kDa, respectively, as mature proteins in the chloroplast. Most studies on magnesium chelatase enzymes have been performed using recombinant proteins of Rhodobacter capsulatus, Synechocystis sp. PCC6803 and Thermosynechococcus elongatus, which are photosynthetic bacteria. In the present study we established a recombinant expression system for barley magnesium chelatase with the long-term goal to obtain structural information of this enigmatic enzyme complex from a higher plant. The genes Xantha-h, -g and -f were cloned in plasmid pET15b, which allowed the production of the three subunits as His-tagged proteins in Escherichia coli BL21(DE3)pLysS. The purified subunits stimulated magnesium chelatase activity of barley plastid extracts and produced activity in assays with only recombinant proteins. In preparation for future structural analyses of the barley magnesium chelatase, stability tests were performed on the subunits and activity assays were screened to find an optimal buffer system and pH.
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Affiliation(s)
- Rabab Mahdi
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Helmy M Youssef
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden. .,Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
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Abstract
Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.
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Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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Gao YS, Wang YL, Wang X, Liu L. Hexameric structure of the ATPase motor subunit of magnesium chelatase in chlorophyll biosynthesis. Protein Sci 2020; 29:1040-1046. [PMID: 31891428 DOI: 10.1002/pro.3816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 11/06/2022]
Abstract
Magnesium chelatase (MgCh) is a heterotrimeric enzyme complex, composed of two AAA+ family subunits that can assembly into a double ring structure and a large catalytic subunit. The small AAA+ subunit has ATPase activity and can self-oligomerize into a ring structure, while the other AAA+ subunit lacks independent ATPase activity. Previous structural studies of the ATPase motor subunit of MgCh from a bacteriochlorophyll-synthesizing bacterium have identified a unique ATPase clade, but the model of oligomeric assembly is unclear. Here we present the hexameric structure of the MgCh ATPase motor subunit from the chlorophyll-synthesizing cyanobacterium Synechocystis sp. PCC 6803. This structure reveals details of how the hexameric ring is assembled, and thus provides a basis for further studying the heterotrimeric complex.
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Affiliation(s)
- Yong-Shan Gao
- School of Life Sciences and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui, China
| | - Yan-Li Wang
- School of Life Sciences and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui, China
| | - Xiao Wang
- School of Life Sciences and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui, China
| | - Lin Liu
- School of Life Sciences and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui, China
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Kiss É, Knoppová J, Aznar GP, Pilný J, Yu J, Halada P, Nixon PJ, Sobotka R, Komenda J. A Photosynthesis-Specific Rubredoxin-Like Protein Is Required for Efficient Association of the D1 and D2 Proteins during the Initial Steps of Photosystem II Assembly. THE PLANT CELL 2019; 31:2241-2258. [PMID: 31320483 PMCID: PMC6751121 DOI: 10.1105/tpc.19.00155] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/04/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Oxygenic photosynthesis relies on accessory factors to promote the assembly and maintenance of the photosynthetic apparatus in the thylakoid membranes. The highly conserved membrane-bound rubredoxin-like protein RubA has previously been implicated in the accumulation of both PSI and PSII, but its mode of action remains unclear. Here, we show that RubA in the cyanobacterium Synechocystis sp PCC 6803 is required for photoautotrophic growth in fluctuating light and acts early in PSII biogenesis by promoting the formation of the heterodimeric D1/D2 reaction center complex, the site of primary photochemistry. We find that RubA, like the accessory factor Ycf48, is a component of the initial D1 assembly module as well as larger PSII assembly intermediates and that the redox-responsive rubredoxin-like domain is located on the cytoplasmic surface of PSII complexes. Fusion of RubA to Ycf48 still permits normal PSII assembly, suggesting a spatiotemporal proximity of both proteins during their action. RubA is also important for the accumulation of PSI, but this is an indirect effect stemming from the downregulation of light-dependent chlorophyll biosynthesis induced by PSII deficiency. Overall, our data support the involvement of RubA in the redox control of PSII biogenesis.
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Affiliation(s)
- Éva Kiss
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
| | - Jana Knoppová
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
| | - Guillem Pascual Aznar
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Jan Pilný
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
| | - Jianfeng Yu
- Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Petr Halada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, 14220 Praha 4-Krc, Czech Republic
| | - Peter J Nixon
- Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Roman Sobotka
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Josef Komenda
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
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The ChlD subunit links the motor and porphyrin binding subunits of magnesium chelatase. Biochem J 2019; 476:1875-1887. [PMID: 31164400 PMCID: PMC6604950 DOI: 10.1042/bcj20190095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/22/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
Magnesium chelatase initiates chlorophyll biosynthesis, catalysing the MgATP2−-dependent insertion of a Mg2+ ion into protoporphyrin IX. The catalytic core of this large enzyme complex consists of three subunits: Bch/ChlI, Bch/ChlD and Bch/ChlH (in bacteriochlorophyll and chlorophyll producing species, respectively). The D and I subunits are members of the AAA+ (ATPases associated with various cellular activities) superfamily of enzymes, and they form a complex that binds to H, the site of metal ion insertion. In order to investigate the physical coupling between ChlID and ChlH in vivo and in vitro, ChlD was FLAG-tagged in the cyanobacterium Synechocystis sp. PCC 6803 and co-immunoprecipitation experiments showed interactions with both ChlI and ChlH. Co-production of recombinant ChlD and ChlH in Escherichia coli yielded a ChlDH complex. Quantitative analysis using microscale thermophoresis showed magnesium-dependent binding (Kd 331 ± 58 nM) between ChlD and H. The physical basis for a ChlD–H interaction was investigated using chemical cross-linking coupled with mass spectrometry (XL–MS), together with modifications that either truncate ChlD or modify single residues. We found that the C-terminal integrin I domain of ChlD governs association with ChlH, the Mg2+ dependence of which also mediates the cooperative response of the Synechocystis chelatase to magnesium. The interaction site between the AAA+ motor and the chelatase domain of magnesium chelatase will be essential for understanding how free energy from the hydrolysis of ATP on the AAA+ ChlI subunit is transmitted via the bridging subunit ChlD to the active site on ChlH.
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