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Zamarreño Beas J, Videira MAM, Karavaeva V, Lourenço FM, Almeida MR, Sousa F, Saraiva LM. In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase. Front Genet 2023; 14:1199357. [PMID: 37415606 PMCID: PMC10320005 DOI: 10.3389/fgene.2023.1199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
Intracellular heme formation and trafficking are fundamental processes in living organisms. Bacteria and archaea utilize three biogenesis pathways to produce iron protoporphyrin IX (heme b) that diverge after the formation of the common intermediate uroporphyrinogen III (uro'gen III). In this study, we identify and provide a detailed characterization of the enzymes involved in the transformation of uro'gen III into heme in Campylobacter jejuni, demonstrating that this bacterium utilizes the protoporphyrin-dependent (PPD) pathway. In general, limited knowledge exists regarding the mechanisms by which heme b reaches its target proteins after this final step. Specifically, the chaperones necessary for trafficking heme to prevent the cytotoxic effects associated with free heme remain largely unidentified. In C. jejuni, we identified a protein named CgdH2 that binds heme with a dissociation constant of 4.9 ± 1.0 µM, and this binding is impaired upon mutation of residues histidine 45 and 133. We demonstrate that C. jejuni CgdH2 establishes protein-protein interactions with ferrochelatase, suggesting its role in facilitating heme transfer from ferrochelatase to CgdH2. Furthermore, phylogenetic analysis reveals that C. jejuni CgdH2 is evolutionarily distinct from the currently known chaperones. Therefore, CgdH2 is the first protein identified as an acceptor of intracellularly formed heme, expanding our knowledge of the mechanisms underlying heme trafficking within bacterial cells.
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Affiliation(s)
- Jordi Zamarreño Beas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Val Karavaeva
- Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Frederico M. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mafalda R. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipa Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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2
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Yang Q, Zhao J, Zheng Y, Chen T, Wang Z. Microbial Synthesis of Heme b: Biosynthetic Pathways, Current Strategies, Detection, and Future Prospects. Molecules 2023; 28:molecules28083633. [PMID: 37110868 PMCID: PMC10144233 DOI: 10.3390/molecules28083633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Heme b, which is characterized by a ferrous ion and a porphyrin macrocycle, acts as a prosthetic group for many enzymes and contributes to various physiological processes. Consequently, it has wide applications in medicine, food, chemical production, and other burgeoning fields. Due to the shortcomings of chemical syntheses and bio-extraction techniques, alternative biotechnological methods have drawn increasing attention. In this review, we provide the first systematic summary of the progress in the microbial synthesis of heme b. Three different pathways are described in detail, and the metabolic engineering strategies for the biosynthesis of heme b via the protoporphyrin-dependent and coproporphyrin-dependent pathways are highlighted. The UV spectrophotometric detection of heme b is gradually being replaced by newly developed detection methods, such as HPLC and biosensors, and for the first time, this review summarizes the methods used in recent years. Finally, we discuss the future prospects, with an emphasis on the potential strategies for improving the biosynthesis of heme b and understanding the regulatory mechanisms for building efficient microbial cell factories.
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Affiliation(s)
- Qiuyu Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Juntao Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yangyang Zheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
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4
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Transcriptomic Analysis of the Molecular Response Mechanism of Microcystis aeruginosa to Iron Limitation Stress. WATER 2022. [DOI: 10.3390/w14111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Iron is an essential micronutrient for cyanobacteria. It is involved in physiological activities such as photosynthesis, respiration, and the synthesis of pigments. The impact of iron limitation on planktonic algae growth occurs in surface oceans globally, as well as in freshwater ecosystems. However, the molecular and physiological effects and response mechanism of cyanobacteria under iron-limited conditions have not been reported in detail. In this study, the effects of iron limitation on the cell density, chlorophyll content, and photosynthetic activity of Microcystis aeruginosa were determined, and transcriptome sequencing was undertaken. In a severely iron-deficient environment, the cell density and chlorophyll-a content of M. aeruginosa were significantly lower than in the iron-rich group (a 55.42% and 83.51% reduction, respectively). Similarly, the photosynthetic efficiency of M. aeruginosa was also inhibited by iron deficiency, and the maximum photochemical efficiency (Fv/Fm) of the severe iron deficiency group was only 66.72% of the control group. The transcriptome results showed that to cope with the iron-deficient environment, most genes involved in iron absorption and transport in M. aeruginosa were up-regulated. In particular, the fur and perR genes that regulate the iron uptake regulatory protein (Fur) were both up-regulated. Due to the high demand for iron in the photosynthetic electron transport chain of M. aeruginosa, most photosynthesis-related genes were down-regulated, for example, petJ, which regulates iron-containing cytochrome c6. In contrast, most of the genes related to glycolysis and respiration were up-regulated. These changes in gene expression may be a survival strategy for M. aeruginosa to cope with a long-term iron-deficient environment. This study provides insights into the molecular response mechanism of M. aeruginosa under iron limitation stress.
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Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia. Int J Mol Sci 2021; 22:ijms22126495. [PMID: 34204357 PMCID: PMC8233740 DOI: 10.3390/ijms22126495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022] Open
Abstract
Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway’s enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.
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Zeb A, Park C, Son M, Baek A, Cho Y, Kim D, Rampogu S, Lee G, Kwak YS, Park SJ, Lee KW. Integration of virtual screening and computational simulation identifies photodynamic therapeutics against human Protoporphyrinogen Oxidase IX (hPPO). ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2018.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Pazderník M, Mareš J, Pilný J, Sobotka R. The antenna-like domain of the cyanobacterial ferrochelatase can bind chlorophyll and carotenoids in an energy-dissipative configuration. J Biol Chem 2019; 294:11131-11143. [PMID: 31167780 DOI: 10.1074/jbc.ra119.008434] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/29/2019] [Indexed: 01/19/2023] Open
Abstract
Ferrochelatase (FeCh) is an essential enzyme catalyzing the synthesis of heme. Interestingly, in cyanobacteria, algae, and plants, FeCh possesses a conserved transmembrane chlorophyll a/b binding (CAB) domain that resembles the first and the third helix of light-harvesting complexes, including a chlorophyll-binding motif. Whether the FeCh CAB domain also binds chlorophyll is unknown. Here, using biochemical and radiolabeled precursor experiments, we found that partially inhibited activity of FeCh in the cyanobacterium Synechocystis PCC 6803 leads to overproduction of chlorophyll molecules that accumulate in the thylakoid membrane and, together with carotenoids, bind to FeCh. We observed that pigments bound to purified FeCh are organized in an energy-dissipative conformation and further show that FeCh can exist in vivo as a monomer or a dimer depending on its own activity. However, pigmented FeCh was purified exclusively as a dimer. Separately expressed and purified FeCH CAB domain contained a pigment composition similar to that of full-length FeCh and retained its quenching properties. Phylogenetic analysis suggested that the CAB domain was acquired by a fusion between FeCh and a single-helix, high light-inducible protein early in the evolution of cyanobacteria. Following this fusion, the FeCh CAB domain with a functional chlorophyll-binding motif was retained in all currently known cyanobacterial genomes except for a single lineage of endosymbiotic cyanobacteria. Our findings indicate that FeCh from Synechocystis exists mostly as a pigment-free monomer in cells but can dimerize, in which case its CAB domain creates a functional pigment-binding segment organized in an energy-dissipating configuration.
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Affiliation(s)
- Marek Pazderník
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, 379 81, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Jan Mareš
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, 379 81, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic.,Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Jan Pilný
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, 379 81, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, 379 81, Czech Republic .,Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
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9
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Biochemical characterization of protoporphyrinogen dehydrogenase and protoporphyrin ferrochelatase of Vibrio vulnificus and the critical complex formation between these enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2674-2687. [PMID: 30251658 DOI: 10.1016/j.bbagen.2018.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/28/2018] [Accepted: 08/13/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Protoporphyrin IX (PPn), an intermediate in the heme biosynthesis reaction, generates singlet oxygen upon exposure to UV light. It has been proposed that PPn is channeled directly to ferrochelatase within a protoporphyrinogen dehydrogenase (PgdH1)-protoporphyrin ferrochelatase (PpfC) complex as a way to avoid this damaging side reaction. However, the PgdH1-PpfC complex has not been characterized, and the question of how heme affects the activities of PgdH1 has not been addressed. METHODS Protein interactions were explored through pull-down assays and western blotting, and the importance of this complex in vivo was examined using inter-species combinations of the two proteins. The purified PgdH1-PpfC complex was characterized kinetically and used for heme binding studies. RESULTS In Vibrio vulnificus, PgdH1 and PpfC formed an 8:8 heterohexadecameric complex that was important for maintaining PPn at low levels. PpfC catalyzed PPn efficiently whether or not it was part of the complex. Notably, heme was a noncompetitive inhibitor of V. vulnificus PgdH1, but a competitive inhibitor of the human protoporphyrinogen oxidase PgoX. CONCLUSION The PdgH1-PpfC complex is important for protective channeling of PPn and for efficient catalysis of free PPn. The production of PPn by PgdH1 is regulated by feedback inhibition by heme. GENERAL SIGNIFICANCE Both proteobacteria and eukaryotes have evolved mechanisms to prevent the harmful accumulation of the heme biosynthesis intermediate PPn. The data presented here suggest two previously unknown mechanisms: the channeling of PPn through the PgdH1-PpfC complex, and the direct inhibition of PgdH1 activity (PgoX activity as well) by heme.
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10
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Skotnicová P, Sobotka R, Shepherd M, Hájek J, Hrouzek P, Tichý M. The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase. J Biol Chem 2018; 293:12394-12404. [PMID: 29925590 DOI: 10.1074/jbc.ra118.003441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
Protoporphyrinogen IX oxidase (PPO), the last enzyme that is common to both chlorophyll and heme biosynthesis pathways, catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX. PPO has several isoforms, including the oxygen-dependent HemY and an oxygen-independent enzyme, HemG. However, most cyanobacteria encode HemJ, the least characterized PPO form. We have characterized HemJ from the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) as a bona fide PPO; HemJ down-regulation resulted in accumulation of tetrapyrrole precursors and in the depletion of chlorophyll precursors. The expression of FLAG-tagged Synechocystis 6803 HemJ protein (HemJ.f) and affinity isolation of HemJ.f under native conditions revealed that it binds heme b The most stable HemJ.f form was a dimer, and higher oligomeric forms were also observed. Using both oxygen and artificial electron acceptors, we detected no enzymatic activity with the purified HemJ.f, consistent with the hypothesis that the enzymatic mechanism for HemJ is distinct from those of other PPO isoforms. The heme absorption spectra and distant HemJ homology to several membrane oxidases indicated that the heme in HemJ is redox-active and involved in electron transfer. HemJ was conditionally complemented by another PPO, HemG from Escherichia coli. If grown photoautotrophically, the complemented strain accumulated tripropionic tetrapyrrole harderoporphyrin, suggesting a defect in enzymatic conversion of coproporphyrinogen III to protoporphyrinogen IX, catalyzed by coproporphyrinogen III oxidase (CPO). This observation supports the hypothesis that HemJ is functionally coupled with CPO and that this coupling is disrupted after replacement of HemJ by HemG.
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Affiliation(s)
- Petra Skotnicová
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Roman Sobotka
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Mark Shepherd
- the School of Biosciences, RAPID Group, University of Kent, Canterbury CT2 7NZ,United Kingdom
| | - Jan Hájek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Pavel Hrouzek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Martin Tichý
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic, .,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
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Chidgey JW, Jackson PJ, Dickman MJ, Hunter CN. PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase. Mol Microbiol 2017; 106:961-975. [PMID: 29030914 PMCID: PMC5725709 DOI: 10.1111/mmi.13861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
Facultative phototrophs such as Rhodobacter sphaeroides can switch between heterotrophic and photosynthetic growth. This transition is governed by oxygen tension and involves the large-scale production of bacteriochlorophyll, which shares a biosynthetic pathway with haem up to protoporphyrin IX. Here, the pathways diverge with the insertion of Fe2+ or Mg2+ into protoporphyrin by ferrochelatase or magnesium chelatase, respectively. Tight regulation of this branchpoint is essential, but the mechanisms for switching between respiratory and photosynthetic growth are poorly understood. We show that PufQ governs the haem/bacteriochlorophyll switch; pufQ is found within the oxygen-regulated pufQBALMX operon encoding the reaction centre-light-harvesting photosystem complex. A pufQ deletion strain synthesises low levels of bacteriochlorophyll and accumulates the biosynthetic precursor coproporphyrinogen III; a suppressor mutant of this strain harbours a mutation in the hemH gene encoding ferrochelatase, substantially reducing ferrochelatase activity and increasing cellular bacteriochlorophyll levels. FLAG-immunoprecipitation experiments retrieve a ferrochelatase-PufQ-carotenoid complex, proposed to regulate the haem/bacteriochlorophyll branchpoint by directing porphyrin flux toward bacteriochlorophyll production under oxygen-limiting conditions. The co-location of pufQ and the photosystem genes in the same operon ensures that switching of tetrapyrrole metabolism toward bacteriochlorophyll is coordinated with the production of reaction centre and light-harvesting polypeptides.
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Affiliation(s)
- Jack W. Chidgey
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
| | - Philip J. Jackson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - Mark J. Dickman
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - C. Neil Hunter
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
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12
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Borrero-de Acuña JM, Timmis KN, Jahn M, Jahn D. Protein complex formation during denitrification by Pseudomonas aeruginosa. Microb Biotechnol 2017; 10:1523-1534. [PMID: 28857512 PMCID: PMC5658584 DOI: 10.1111/1751-7915.12851] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
The most efficient means of generating cellular energy is through aerobic respiration. Under anaerobic conditions, several prokaryotes can replace oxygen by nitrate as final electron acceptor. During denitrification, nitrate is reduced via nitrite, NO and N2O to molecular nitrogen (N2) by four membrane‐localized reductases with the simultaneous formation of an ion gradient for ATP synthesis. These four multisubunit enzyme complexes are coupled in four electron transport chains to electron donating primary dehydrogenases and intermediate electron transfer proteins. Many components require membrane transport and insertion, complex assembly and cofactor incorporation. All these processes are mediated by fine‐tuned stable and transient protein–protein interactions. Recently, an interactomic approach was used to determine the exact protein–protein interactions involved in the assembly of the denitrification apparatus of Pseudomonas aeruginosa. Both subunits of the NO reductase NorBC, combined with the flavoprotein NosR, serve as a membrane‐localized assembly platform for the attachment of the nitrate reductase NarGHI, the periplasmic nitrite reductase NirS via its maturation factor NirF and the N2O reductase NosZ through NosR. A nitrate transporter (NarK2), the corresponding regulatory system NarXL, various nitrite (NirEJMNQ) and N2O reductase (NosFL) maturation proteins are also part of the complex. Primary dehydrogenases, ATP synthase, most enzymes of the TCA cycle, and the SEC protein export system, as well as a number of other proteins, were found to interact with the denitrification complex. Finally, a protein complex composed of the flagella protein FliC, nitrite reductase NirS and the chaperone DnaK required for flagella formation was found in the periplasm of P. aeruginosa. This work demonstrated that the interactomic approach allows for the identification and characterization of stable and transient protein–protein complexes and interactions involved in the assembly and function of multi‐enzyme complexes.
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Affiliation(s)
| | - Kenneth N Timmis
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, Braunschweig, Germany
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13
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Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev 2017; 81:e00048-16. [PMID: 28123057 PMCID: PMC5312243 DOI: 10.1128/mmbr.00048-16] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
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Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Tamara A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Mark R O'Brian
- Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Martin J Warren
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
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14
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Kobayashi K, Masuda T, Tajima N, Wada H, Sato N. Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX. Genome Biol Evol 2015; 6:2141-55. [PMID: 25108393 PMCID: PMC4231631 DOI: 10.1093/gbe/evu170] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. In the tetrapyrrole biosynthesis pathway, protoporphyrinogen IX oxidase (Protox) catalyzes the formation of protoporphyrin IX, the last common intermediate for the biosynthesis of heme and chlorophyll. Three nonhomologous isofunctional enzymes, HemG, HemJ, and HemY, for Protox have been identified. To reveal the distribution and evolution of the three Protox enzymes, we identified homologs of each along with other heme biosynthetic enzymes by whole-genome clustering across three domains of life. Most organisms possess only one of the three Protox types, with some exceptions. Detailed phylogenetic analysis revealed that HemG is mostly limited to γ-Proteobacteria whereas HemJ may have originated within α-Proteobacteria and transferred to other Proteobacteria and Cyanobacteria. In contrast, HemY is ubiquitous in prokaryotes and is the only Protox in eukaryotes, so this type may be the ancestral Protox. Land plants have a unique HemY homolog that is also shared by Chloroflexus species, in addition to the main HemY homolog originating from Cyanobacteria. Meanwhile, organisms missing any Protox can be classified into two groups; those lacking most heme synthetic genes, which necessarily depend on external heme supply, and those lacking only genes involved in the conversion of uroporphyrinogen III into heme, which would use a precorrin2-dependent alternative pathway. However, hemN encoding coproporphyrinogen IX oxidase was frequently found in organisms lacking Protox enzyme, which suggests a unique role of this gene other than in heme biosynthesis.
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Affiliation(s)
- Koichi Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
| | - Tatsuru Masuda
- Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, Japan
| | - Naoyuki Tajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan CREST, JST, Saitama, Japan
| | - Naoki Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan CREST, JST, Saitama, Japan
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15
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Zheng C, Li Z, Yang N, Ning Z. Quantitative expression of candidate genes affecting eggshell color. Anim Sci J 2014; 85:506-10. [DOI: 10.1111/asj.12182] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 11/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Chuanwei Zheng
- College of Animal Science and Technology; China Agricultural University; Beijing China
| | - Zesheng Li
- College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Ning Yang
- College of Animal Science and Technology; China Agricultural University; Beijing China
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing China
| | - Zhonghua Ning
- College of Animal Science and Technology; China Agricultural University; Beijing China
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing China
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16
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Sobotka R. Making proteins green; biosynthesis of chlorophyll-binding proteins in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2014; 119:223-32. [PMID: 23377990 DOI: 10.1007/s11120-013-9797-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 01/10/2013] [Indexed: 05/20/2023]
Abstract
Chlorophyll (Chl) is an essential component of the photosynthetic apparatus. Embedded into Chl-binding proteins, Chl molecules play a central role in light harvesting and charge separation within the photosystems. It is critical for the photosynthetic cell to not only ensure the synthesis of a sufficient amount of new Chl-binding proteins but also avoids any misbalance between apoprotein synthesis and the formation of potentially phototoxic Chl molecules. According to the available data, Chl-binding proteins are translated on membrane bound ribosomes and their integration into the membrane is provided by the SecYEG/Alb3 translocon machinery. It appears that the insertion of Chl molecules into growing polypeptide is a prerequisite for the correct folding and finishing of Chl-binding protein synthesis. Although the Chl biosynthetic pathway is fairly well-described on the level of enzymatic steps, a link between Chl biosynthesis and the synthesis of apoproteins remains elusive. In this review, I summarize the current knowledge about this issue putting emphasis on protein-protein interactions. I present a model of the Chl biosynthetic pathway organized into a multi-enzymatic complex and physically attached to the SecYEG/Alb3 translocon. Localization of this hypothetical large biosynthetic centre in the cyanobacterial cell is also discussed as well as regulatory mechanisms coordinating the rate of Chl and apoprotein synthesis.
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Affiliation(s)
- Roman Sobotka
- Institute of Microbiology CAS, Opatovický mlyn, Třeboň, Czech Republic,
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17
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Asuru AP, An M, Busenlehner LS. Dissection of Porphyrin-Induced Conformational Dynamics in the Heme Biosynthesis Enzyme Ferrochelatase. Biochemistry 2012; 51:7116-27. [DOI: 10.1021/bi300704c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Awuri P. Asuru
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Mier An
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Laura S. Busenlehner
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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18
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Hunter GA, Al-Karadaghi S, Ferreira GC. FERROCHELATASE: THE CONVERGENCE OF THE PORPHYRIN BIOSYNTHESIS AND IRON TRANSPORT PATHWAYS. J PORPHYR PHTHALOCYA 2012; 15:350-356. [PMID: 21852895 DOI: 10.1142/s108842461100332x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase (also known as PPIX ferrochelatase; Enzyme Commission number 4.9.9.1.1) catalyzes the insertion of ferrous iron into PPIX to form heme. This reaction unites the biochemically synchronized pathways of porphyrin synthesis and iron transport in nearly all living organisms. The ferrochelatases are an evolutionarily diverse family of enzymes with no more than six active site residues known to be perfectly conserved. The availability of over thirty different crystal structures, including many with bound metal ions or porphyrins, has added tremendously to our understanding of ferrochelatase structure and function. It is generally believed that ferrous iron is directly channeled to ferrochelatase in vivo, but the identity of the suspected chaperone remains uncertain despite much recent progress in this area. Identification of a conserved metal ion binding site at the base of the active site cleft may be an important clue as to how ferrochelatases acquire iron, and catalyze desolvation during transport to the catalytic site to complete heme synthesis.
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Affiliation(s)
- Gregory A Hunter
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida, 33620
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19
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Sobotka R, Tichy M, Wilde A, Hunter CN. Functional assignments for the carboxyl-terminal domains of the ferrochelatase from Synechocystis PCC 6803: the CAB domain plays a regulatory role, and region II is essential for catalysis. PLANT PHYSIOLOGY 2011; 155:1735-47. [PMID: 21081693 PMCID: PMC3091120 DOI: 10.1104/pp.110.167528] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 11/09/2010] [Indexed: 05/20/2023]
Abstract
Ferrochelatase (FeCH) catalyzes the insertion of Fe(2+) into protoporphyrin, forming protoheme. In photosynthetic organisms, FeCH and magnesium chelatase lie at a biosynthetic branch point where partitioning down the heme and chlorophyll (Chl) pathways occurs. Unlike their mammalian, yeast, and other bacterial counterparts, cyanobacterial and algal FeCHs as well as FeCH2 isoform from plants possess a carboxyl-terminal Chl a/b-binding (CAB) domain with a conserved Chl-binding motif. The CAB domain is connected to the FeCH catalytic core by a proline-rich linker sequence (region II). In order to dissect the regulatory, catalytic, and structural roles of the region II and CAB domains, we analyzed a FeCH ΔH347 mutant that retains region II but lacks the CAB domain and compared it with the ΔH324-FeCH mutant that lacks both these domains. We found that the CAB domain is not required for catalytic activity but is essential for dimerization of FeCH; its absence causes aberrant accumulation of Chl-protein complexes under high light accompanied by high levels of the Chl precursor chlorophyllide. Thus, the CAB domain appears to serve mainly a regulatory function, possibly in balancing Chl biosynthesis with the synthesis of cognate apoproteins. Region II is essential for the catalytic function of the plastid-type FeCH enzyme, although the low residual activity of the ΔH324-FeCH is more than sufficient to furnish the cellular demand for heme. We propose that the apparent surplus of FeCH activity in the wild type is critical for cell viability under high light due to a regulatory role of FeCH in the distribution of Chl into apoproteins.
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Affiliation(s)
- Roman Sobotka
- Institute of Microbiology, Department of Autotrophic Microorganisms, 379 81 Trebon, Czech Republic.
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20
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Kořený L, Oborník M. Sequence evidence for the presence of two tetrapyrrole pathways in Euglena gracilis. Genome Biol Evol 2011; 3:359-64. [PMID: 21444293 PMCID: PMC5654406 DOI: 10.1093/gbe/evr029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2011] [Indexed: 11/16/2022] Open
Abstract
Genes encoding enzymes of the tetrapyrrole biosynthetic pathway were searched within Euglena gracilis EST databases and 454 genome reads and their 5' end regions were sequenced when not available. Phylogenetic analyses and protein localization predictions support the hypothesis concerning the presence of two separated tetrapyrrole pathways in E. gracilis. One of these pathways resembles the heme synthesis in primarily heterotrophic eukaryotes and was presumably present in the host cell prior to secondary endosymbiosis with a green alga. The second pathway is similar to the plastid-localized tetrapyrrole syntheses in plants and photosynthetic algae. It appears to be localized to the secondary plastid, presumably derived from an algal endosymbiont and probably serves only for the production of plastidial heme and chlorophyll. Thus, E. gracilis represents an evolutionary intermediate in a metabolic transformation of a primary heterotroph to a photoautotroph through secondary endosymbiosis. We propose here that the tetrapyrrole pathway serves as a highly informative marker for the evolution of plastids and plays a crucial role in the loss of plastids.
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Affiliation(s)
- Luděk Kořený
- Department of Molecular Biology of Protists, Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Department of Molecular Biology of Protists, Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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21
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Layer G, Reichelt J, Jahn D, Heinz DW. Structure and function of enzymes in heme biosynthesis. Protein Sci 2010; 19:1137-61. [PMID: 20506125 DOI: 10.1002/pro.405] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. Heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors. Heme is synthesized in most organisms via a highly conserved biosynthetic route. In humans, defects in heme biosynthesis lead to severe metabolic disorders called porphyrias. The elucidation of the 3D structures for all heme biosynthetic enzymes over the last decade provided new insights into their function and elucidated the structural basis of many known diseases. In terms of structure and function several rather unique proteins were revealed such as the V-shaped glutamyl-tRNA reductase, the dipyrromethane cofactor containing porphobilinogen deaminase, or the "Radical SAM enzyme" coproporphyrinogen III dehydrogenase. This review summarizes the current understanding of the structure-function relationship for all heme biosynthetic enzymes and their potential interactions in the cell.
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Affiliation(s)
- Gunhild Layer
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig D-38106, Germany
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22
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Schultz IJ, Chen C, Paw BH, Hamza I. Iron and porphyrin trafficking in heme biogenesis. J Biol Chem 2010; 285:26753-26759. [PMID: 20522548 DOI: 10.1074/jbc.r110.119503] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Iron is an essential element for diverse biological functions. In mammals, the majority of iron is enclosed within a single prosthetic group: heme. In metazoans, heme is synthesized via a highly conserved and coordinated pathway within the mitochondria. However, iron is acquired from the environment and subsequently assimilated into various cellular pathways, including heme synthesis. Both iron and heme are toxic but essential cofactors. How is iron transported from the extracellular milieu to the mitochondria? How are heme and heme intermediates coordinated with iron transport? Although recent studies have answered some questions, several pieces of this intriguing puzzle remain unsolved.
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Affiliation(s)
- Iman J Schultz
- Department of Medicine, Hematology Division, Brigham and Women's Hospital, and the Hematology-Oncology Division, Department of Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115
| | - Caiyong Chen
- Department of Animal and Avian Sciences and Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Barry H Paw
- Department of Medicine, Hematology Division, Brigham and Women's Hospital, and the Hematology-Oncology Division, Department of Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115.
| | - Iqbal Hamza
- Department of Animal and Avian Sciences and Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742.
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23
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Zappa S, Li K, Bauer CE. The tetrapyrrole biosynthetic pathway and its regulation in Rhodobacter capsulatus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 675:229-50. [PMID: 20532744 PMCID: PMC2883787 DOI: 10.1007/978-1-4419-1528-3_13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The purple anoxygenic photosynthetic bacterium Rhodobacter capsulatus is capable of growing in aerobic or anaerobic conditions, in the dark or using light, etc. Achieving versatile metabolic adaptations from respiration to photosynthesis requires the use of tetrapyrroles such as heme and bacteriochlorophyll, in order to carry oxygen, to transfer electrons, and to harvest light energy. A third tetrapyrrole, cobalamin (vitamin B(12)), is synthesized and used as a cofactor for many enzymes. Heme, bacteriochlorophyll, and vitamin B(12) constitute three major end products of the tetrapyrrole biosynthetic pathway in purple bacteria. Their respective synthesis involves a plethora of enzymes, several that have been characterized and several that are uncharacterized, as described in this review. To respond to changes in metabolic requirements, the pathway undergoes complex regulation to direct the flow of tetrapyrrole intermediates into a specific branch(s) at the expense of other branches of the pathway. Transcriptional regulation of the tetrapyrrole synthesizing enzymes by redox conditions and pathway intermediates is reviewed. In addition, we discuss the involvement of several transcription factors (RegA, CrtJ, FnrL, AerR, HbrL, Irr) as well as the role of riboswitches. Finally, the interdependence of the tetrapyrrole branches on each other synthesis is discussed.
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Affiliation(s)
- Sébastien Zappa
- Biology Department, Indiana University, Bloomington, IN 47405, USA.
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24
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Affiliation(s)
- Scott Severance
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Iqbal Hamza
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
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