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Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Reschke S, Duffus BR, Schrapers P, Mebs S, Teutloff C, Dau H, Haumann M, Leimkühler S. Identification of YdhV as the First Molybdoenzyme Binding a Bis-Mo-MPT Cofactor in Escherichia coli. Biochemistry 2019; 58:2228-2242. [PMID: 30945846 DOI: 10.1021/acs.biochem.9b00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors.
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Affiliation(s)
- Stefan Reschke
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | | | | | - Christian Teutloff
- Institute of Experimental Physics, EPR Spectroscopy of Biological Systems , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | | | | | - Silke Leimkühler
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
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Ma W, Jia J, Huang X, Xie W, Zhang X, Tang J, Lin C, Zhao L, Fang P. Stable isotope labelling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Edwardsiella tarda ATCC 15947 under prolonged cold stress. Microb Pathog 2018; 125:12-19. [PMID: 30201590 DOI: 10.1016/j.micpath.2018.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 01/15/2023]
Abstract
Edwardsiella tarda poses a threat to human health and has resulted in enormous economic losses in aquaculture. Low temperatures are usually applied to contain the growth of this microorganism. In this study, stable isotope labelling by amino acids in cell culture (SILAC) was used to conduct comparative proteomic quantitation of E. tarda ATCC 15947 under cold stress for two weeks. We identified 1391 proteins, of which 898 were quantifiable. Of these, 72 proteins were upregulated and 164 were downregulated in response to cold stress. Even though E. tarda ATCC 15947 is not a psychrophile, several key proteins related to DNA synthesis and transcription were significantly upregulated. Additionally, proteins related to haemolytic activities and gluconeogenesis were upregulated, even though E. tarda ATCC 15497 is considered non-virulent in aquaculture. This study therefore delineated the specific proteomic response of this E. tarda ATCC 15947 to prolonged cold stress.
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Affiliation(s)
- Weixing Ma
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China; Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Juntao Jia
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China.
| | - Xiaohua Huang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Wancui Xie
- Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Xiaoliang Zhang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Jing Tang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Chao Lin
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Liqing Zhao
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Peipei Fang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
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Hartmann S, Frielingsdorf S, Ciaccafava A, Lorent C, Fritsch J, Siebert E, Priebe J, Haumann M, Zebger I, Lenz O. O2-Tolerant H2 Activation by an Isolated Large Subunit of a [NiFe] Hydrogenase. Biochemistry 2018; 57:5339-5349. [DOI: 10.1021/acs.biochem.8b00760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sven Hartmann
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alexandre Ciaccafava
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Johannes Fritsch
- Department of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Elisabeth Siebert
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Jacqueline Priebe
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
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Schrapers P, Ilina J, Gregg CM, Mebs S, Jeoung JH, Dau H, Dobbek H, Haumann M. Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy. PLoS One 2017; 12:e0171039. [PMID: 28178309 PMCID: PMC5298270 DOI: 10.1371/journal.pone.0171039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/13/2017] [Indexed: 11/18/2022] Open
Abstract
Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.
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Affiliation(s)
- Peer Schrapers
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Julia Ilina
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina M. Gregg
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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Birrell JA, Wrede K, Pawlak K, Rodriguez-Maciá P, Rüdiger O, Reijerse EJ, Lubitz W. Artificial Maturation of the Highly Active Heterodimeric [FeFe] Hydrogenase from Desulfovibrio desulfuricans
ATCC 7757. Isr J Chem 2016. [DOI: 10.1002/ijch.201600035] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- James A. Birrell
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Kathrin Wrede
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Krzysztof Pawlak
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Patricia Rodriguez-Maciá
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion; Stiftstraße 34-36 D-45470 Mülheim an der Ruhr Germany
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Khanna N, Lindblad P. Cyanobacterial hydrogenases and hydrogen metabolism revisited: recent progress and future prospects. Int J Mol Sci 2015; 16:10537-61. [PMID: 26006225 PMCID: PMC4463661 DOI: 10.3390/ijms160510537] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 11/25/2022] Open
Abstract
Cyanobacteria have garnered interest as potential cell factories for hydrogen production. In conjunction with photosynthesis, these organisms can utilize inexpensive inorganic substrates and solar energy for simultaneous biosynthesis and hydrogen evolution. However, the hydrogen yield associated with these organisms remains far too low to compete with the existing chemical processes. Our limited understanding of the cellular hydrogen production pathway is a primary setback in the potential scale-up of this process. In this regard, the present review discusses the recent insight around ferredoxin/flavodoxin as the likely electron donor to the bidirectional Hox hydrogenase instead of the generally accepted NAD(P)H. This may have far reaching implications in powering solar driven hydrogen production. However, it is evident that a successful hydrogen-producing candidate would likely integrate enzymatic traits from different species. Engineering the [NiFe] hydrogenases for optimal catalytic efficiency or expression of a high turnover [FeFe] hydrogenase in these photo-autotrophs may facilitate the development of strains to reach target levels of biohydrogen production in cyanobacteria. The fundamental advancements achieved in these fields are also summarized in this review.
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Affiliation(s)
- Namita Khanna
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-75120, Sweden.
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-75120, Sweden.
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Huang GF, Wu XB, Bai LP, Liu K, Jiang LJ, Long MN, Chen QX. Improved O2-tolerance in variants of a H2-evolving [NiFe]-hydrogenase from Klebsiella oxytoca HP1. FEBS Lett 2015; 589:910-8. [PMID: 25747389 DOI: 10.1016/j.febslet.2015.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 02/14/2015] [Accepted: 02/23/2015] [Indexed: 12/29/2022]
Abstract
In this study, we investigated the mechanism of O2 tolerance of Klebsiella oxytoca HP1 H2-evolving hydrogenase 3 (KHyd3) by mutational analysis and three-dimensional structure modeling. Results revealed that certain surface amino acid residues of KHyd3 large subunit, in particular those at the outer entrance of the gas channel, have a visible effect on its oxygen tolerance. Additionally, solution pH, immobilization and O2 partial pressure also affect KHyd3 O2-tolerance to some extent. We propose that the extent of KHyd3 O2-tolerance is determined by a balance between the rate of O2 access to the active center through gas channels and the deoxidation rate of the oxidized active center. Based on our findings, two higher O2-tolerant KHyd3 mutations G300E and G300M were developed.
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Affiliation(s)
- Gang-Feng Huang
- State Key Laboratory of Cellular Stress Biology and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiao-Bing Wu
- State Key Laboratory of Cellular Stress Biology and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Li-Ping Bai
- State Key Laboratory of Cellular Stress Biology and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ke Liu
- State Key Laboratory of Cellular Stress Biology and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Li-Jing Jiang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Min-Nan Long
- School of Energy Research, Xiamen University, Xiamen 361102, China
| | - Qing-Xi Chen
- State Key Laboratory of Cellular Stress Biology and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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