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Ferreira MR, Morgado L, Salgueiro CA. Periplasmic electron transfer network in Geobacter sulfurreducens revealed by biomolecular interaction studies. Protein Sci 2024; 33:e5082. [PMID: 38935664 PMCID: PMC11210610 DOI: 10.1002/pro.5082] [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: 01/21/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
Multiheme cytochromes located in different compartments are crucial for extracellular electron transfer in the bacterium Geobacter sulfurreducens to drive important environmental processes and biotechnological applications. Recent studies have unveiled that for particular sets of electron terminal acceptors, discrete respiratory pathways selectively recruit specific cytochromes from both the inner and outer membranes. However, such specificity was not observed for the abundant periplasmic cytochromes, namely the triheme cytochrome family PpcA-E. In this work, the distinctive NMR spectroscopic signatures of these proteins in different redox states were explored to monitor pairwise interactions and electron transfer reactions between each pair of cytochromes. The results showed that the five proteins interact transiently and can exchange electrons between each other revealing intra-promiscuity within the members of this family. This discovery is discussed in the light of the establishment of an effective electron transfer network by this pool of cytochromes. This network is advantageous to the bacteria as it enables the maintenance of the functional working potential redox range within the cells.
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Affiliation(s)
- Marisa R. Ferreira
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
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2
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Portela PC, Shipps CC, Shen C, Srikanth V, Salgueiro CA, Malvankar NS. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nat Commun 2024; 15:2434. [PMID: 38509081 PMCID: PMC10954620 DOI: 10.1038/s41467-024-46192-0] [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: 08/04/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
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Affiliation(s)
- Pilar C Portela
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catharine C Shipps
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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3
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Pimenta AI, Paquete CM, Morgado L, Edwards MJ, Clarke TA, Salgueiro CA, Pereira IAC, Duarte AG. Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation. Protein Sci 2023; 32:e4796. [PMID: 37779214 PMCID: PMC10601379 DOI: 10.1002/pro.4796] [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: 05/24/2023] [Revised: 08/30/2023] [Accepted: 09/16/2023] [Indexed: 10/03/2023]
Abstract
Electroactive bacteria combine the oxidation of carbon substrates with an extracellular electron transfer (EET) process that discharges electrons to an electron acceptor outside the cell. This process involves electron transfer through consecutive redox proteins that efficiently connect the inner membrane to the cell exterior. In this study, we isolated and characterized the quinone-interacting membrane cytochrome c ImcH from Geobacter sulfurreducens, which is involved in the EET process to high redox potential acceptors. Spectroscopic and electrochemical studies show that ImcH hemes have low midpoint redox potentials, ranging from -150 to -358 mV, and connect the oxidation of the quinol-pool to EET, transferring electrons to the highly abundant periplasmic cytochrome PpcA with higher affinity than to its homologues. Despite the larger number of hemes and transmembrane helices, the ImcH structural model has similarities with the NapC/NirT/NrfH superfamily, namely the presence of a quinone-binding site on the P-side of the membrane. In addition, the first heme, likely involved on the quinol oxidation, has apparently an unusual His/Gln coordination. Our work suggests that ImcH is electroneutral and transfers electrons and protons to the same side of the membrane, contributing to the maintenance of a proton motive force and playing a central role in recycling the menaquinone pool.
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Affiliation(s)
- Andreia I. Pimenta
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Catarina M. Paquete
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Leonor Morgado
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | | | - Thomas A. Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and TechnologyUniversidade NOVA de LisboaCaparicaPortugal
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Américo G. Duarte
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
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4
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Portela PC, Morgado L, Silva MA, Denkhaus L, Einsle O, Salgueiro CA. Exploring oxidative stress pathways in Geobacter sulfurreducens: the redox network between MacA peroxidase and triheme periplasmic cytochromes. Front Microbiol 2023; 14:1253114. [PMID: 37860142 PMCID: PMC10582990 DOI: 10.3389/fmicb.2023.1253114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
The recent reclassification of the strict anaerobe Geobacter sulfurreducens bacterium as aerotolerant brought attention for oxidative stress protection pathways. Although the electron transfer pathways for oxygen detoxification are not well established, evidence was obtained for the formation of a redox complex between the periplasmic triheme cytochrome PpcA and the diheme cytochrome peroxidase MacA. In the latter, the reduction of the high-potential heme triggers a conformational change that displaces the axial histidine of the low-potential heme with peroxidase activity. More recently, a possible involvement of the triheme periplasmic cytochrome family (PpcA-E) in the protection from oxidative stress in G. sulfurreducens was suggested. To evaluate this hypothesis, we investigated the electron transfer reaction and the biomolecular interaction between each PpcA-E cytochrome and MacA. Using a newly developed method that relies on the different NMR spectral signatures of the heme proteins, we directly monitored the electron transfer reaction from reduced PpcA-E cytochromes to oxidized MacA. The results obtained showed a complete electron transfer from the cytochromes to the high-potential heme of MacA. This highlights PpcA-E cytochromes' efficient role in providing the necessary reducing power to mitigate oxidative stress situations, hence contributing to a better knowledge of oxidative stress protection pathways in G. sulfurreducens.
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Affiliation(s)
- Pilar C. Portela
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta A. Silva
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Lukas Denkhaus
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
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5
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Fernandes TM, Silva MA, Morgado L, Salgueiro CA. Hemes on a string: insights on the functional mechanisms of PgcA from Geobacter sulfurreducens. J Biol Chem 2023; 299:105167. [PMID: 37595873 PMCID: PMC10570954 DOI: 10.1016/j.jbc.2023.105167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial extracellular reduction of insoluble compounds requires soluble electron shuttles that diffuse in the environment, freely diffusing cytochromes, or direct contact with cellular conductive appendages that release or harvest electrons to assure a continuous balance between cellular requirements and environmental conditions. In this work, we produced and characterized the three cytochrome domains of PgcA, an extracellular triheme cytochrome that contributes to Fe(III) and Mn(IV) oxides reduction in Geobacter sulfurreducens. The three monoheme domains are structurally homologous, but their heme groups show variable axial coordination and reduction potential values. Electron transfer experiments monitored by NMR and visible spectroscopy show the variable extent to which the domains promiscuously exchange electrons while reducing different electron acceptors. The results suggest that PgcA is part of a new class of cytochromes - microbial heme-tethered redox strings - that use low-complexity protein stretches to bind metals and promote intra- and intermolecular electron transfer events through its cytochrome domains.
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Affiliation(s)
- Tomás M Fernandes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta A Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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6
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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7
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Teixeira LR, Fernandes TM, Silva MA, Morgado L, Salgueiro CA. Characterization of a Novel Cytochrome Involved in
Geobacter sulfurreducens’
Electron Harvesting Pathways. Chemistry 2022; 28:e202202333. [DOI: 10.1002/chem.202202333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Liliana R. Teixeira
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Tomás M. Fernandes
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Marta A. Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology NOVA University Lisbon 2819-516 Caparica Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Chemistry Department NOVA School of Science and Technology NOVA University Lisbon 2829-516 Caparica Portugal
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Antunes JMA, Silva MA, Salgueiro CA, Morgado L. Electron Flow From the Inner Membrane Towards the Cell Exterior in Geobacter sulfurreducens: Biochemical Characterization of Cytochrome CbcL. Front Microbiol 2022; 13:898015. [PMID: 35620088 PMCID: PMC9129911 DOI: 10.3389/fmicb.2022.898015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Exoelectrogenic microorganisms are in the spotlight due to their unique respiratory mechanisms and potential applications in distinct biotechnological fields, including bioremediation, bioenergy production and microbial electrosynthesis. These applications rely on the capability of these microorganisms to perform extracellular electron transfer, a mechanism that allows the bacteria to transfer electrons to the cell’s exterior by establishing functional interfaces between different multiheme cytochromes at the inner membrane, periplasmic space, and outer membrane. The multiheme cytochrome CbcL from Geobacter sulfurreducens is associated to the inner membrane and plays an essential role in the transfer of electrons to final electron acceptors with a low redox potential, as Fe(III) oxides and electrodes poised at −100 mV. CbcL has a transmembranar di-heme b-type cytochrome domain with six helices, linked to a periplasmic cytochrome domain with nine c-type heme groups. The complementary usage of ultraviolet-visible, circular dichroism and nuclear magnetic resonance permitted the structural and functional characterization of CbcL’s periplasmic domain. The protein was found to have a high percentage of disordered regions and its nine hemes are low-spin and all coordinated by two histidine residues. The apparent midpoint reduction potential of the CbcL periplasmic domain was determined, suggesting a thermodynamically favorable transfer of electrons to the putative redox partner in the periplasm − the triheme cytochrome PpcA. The establishment of a redox complex between the two proteins was confirmed by probing the electron transfer reaction and the molecular interactions between CbcL and PpcA. The results obtained show for the first time how electrons are injected into the periplasm of Geobacter sulfurreducens for subsequent transfer to the cell’s exterior.
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Affiliation(s)
- Jorge M A Antunes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Marta A Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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9
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Morgado L, Salgueiro CA. Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes. Metallomics 2022; 14:6539350. [DOI: 10.1093/mtomcs/mfac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Cytochromes are electron transfer proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electron outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and elucidate the stepwise electron transfer along the respiratory paths. However, investigating direct electron transfer events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. NMR spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor electron transfer within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of electron transfer between c-type cytochromes, using as model a triheme periplasmic cytochrome (PpcA) and a membrane associated monoheme cytochrome (OmcF) from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional electron transfer within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory electron transfer chains.
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Affiliation(s)
- Leonor Morgado
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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10
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From iron to bacterial electroconductive filaments: Exploring cytochrome diversity using Geobacter bacteria. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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11
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Portela PC, Silva MA, Teixeira LR, Salgueiro CA. A unique aromatic residue modulates the redox range of a periplasmic multiheme cytochrome from Geobacter metallireducens. J Biol Chem 2021; 296:100711. [PMID: 33915126 PMCID: PMC8163978 DOI: 10.1016/j.jbc.2021.100711] [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] [Received: 03/12/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/30/2022] Open
Abstract
Geobacter bacteria are able to transfer electrons to the exterior of the cell and reduce extracellular electron acceptors including toxic/radioactive metals and electrode surfaces, with potential applications in bioremediation or electricity harvesting. The triheme c-type cytochrome PpcA from Geobacter metallireducens plays a crucial role in bridging the electron transfer from the inner to the outer membrane, ensuring an effective extracellular electron transfer. This cytochrome shares 80% identity with PpcA from Geobacter sulfurreducens, but their redox properties are markedly different, thus determining the distinctive working redox potential ranges in the two bacteria. PpcA from G. metallireducens possesses two extra aromatic amino acids (Phe-6 and Trp-45) in its hydrophobic heme core, whereas PpcA from G. sulfurreducens has a leucine and a methionine in the equivalent positions. Given the different nature of these residues in the two cytochromes, we have hypothesized that the extra aromatic amino acids could be partially responsible for the observed functional differences. In this work, we have replaced Phe-6 and Trp-45 residues by their nonaromatic counterparts in PpcA from G. sulfurreducens. Using redox titrations followed by UV–visible and NMR spectroscopy we observed that residue Trp-45 shifted the redox potential range 33% toward that of PpcA from G. sulfurreducens, whereas Phe-6 produced a negligible effect. For the first time, it is shown that the inclusion of an aromatic residue at the heme core can modulate the working redox range in abundant periplasmic proteins, paving the way to engineer bacterial strains for optimal microbial bioelectrochemical applications.
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Affiliation(s)
- Pilar C Portela
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica, Portugal
| | - Marta A Silva
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica, Portugal
| | - Liliana R Teixeira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica, Portugal.
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Waghwani HK, Douglas T. Cytochrome C with peroxidase-like activity encapsulated inside the small DPS protein nanocage. J Mater Chem B 2021; 9:3168-3179. [PMID: 33885621 DOI: 10.1039/d1tb00234a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nature utilizes self-assembled protein-based structures as subcellular compartments in prokaryotes to sequester catalysts for specialized biochemical reactions. These protein cage structures provide unique isolated environments for the encapsulated enzymes. Understanding these systems is useful in the bioinspired design of synthetic catalytic organelle-like nanomaterials. The DNA binding protein from starved cells (Dps), isolated from Sulfolobus solfataricus, is a 9 nm dodecameric protein cage making it the smallest known naturally occurring protein cage. It is naturally over-expressed in response to oxidative stress. The small size, natural biodistribution to the kidney, and ability to cross the glomerular filtration barrier in in vivo experiments highlight its potential as a synthetic antioxidant. Cytochrome C (CytC) is a small heme protein with peroxidase-like activity involved in the electron transport chain and also plays a critical role in cellular apoptosis. Here we report the encapsulation of CytC inside the 5 nm interior cavity of Dps and demonstrate the catalytic activity of the resultant Dps nanocage with enhanced antioxidant behavior. The small cavity can accommodate a single CytC and this was achieved through self-assembly of chimeric cages comprising Dps subunits and a Dps subunit to which the CytC was fused. For selective isolation of CytC containing Dps cages, we utilized engineered polyhistidine tag present only on the enzyme fused Dps subunits (6His-Dps-CytC). The catalytic activity of encapsulated CytC was studied using guaiacol and 3,3',5,5'-tetramethylbenzidine (TMB) as two different peroxidase substrates and compared to the free (unencapsulated) CytC activity. The encapsulated CytC showed better pH dependent catalytic activity compared to free enzyme and provides a proof-of-concept model to engineer these small protein cages for their potential as catalytic nanoreactors.
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Affiliation(s)
- Hitesh Kumar Waghwani
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, USA.
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Liang R, Lau MCY, Saitta ET, Garvin ZK, Onstott TC. Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America. ENVIRONMENTAL MICROBIOME 2020; 15:8. [PMID: 33902738 PMCID: PMC8067395 DOI: 10.1186/s40793-020-00355-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. RESULTS Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate. CONCLUSIONS Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.
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Affiliation(s)
- Renxing Liang
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
- Present address: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Evan T Saitta
- Integrative Research Center, Section of Earth Sciences, Field Museum of Natural History, Chicago, USA
| | - Zachary K Garvin
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
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Ponomarenko NS, Kokhan O, Pokkuluri PR, Mulfort KL, Tiede DM. Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein. PHOTOSYNTHESIS RESEARCH 2020; 143:99-113. [PMID: 31925630 PMCID: PMC6989566 DOI: 10.1007/s11120-019-00697-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/02/2019] [Indexed: 05/18/2023]
Abstract
To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.
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Affiliation(s)
- Nina S Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, Harrisonburg, VA, 22807, USA
| | - Phani R Pokkuluri
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Karen L Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - David M Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
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15
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Dantas JM, Portela PC, Fernandes AP, Londer YY, Yang X, Duke NEC, Schiffer M, Pokkuluri PR, Salgueiro CA. Structural and Functional Relevance of the Conserved Residue V13 in the Triheme Cytochrome PpcA from Geobacter sulfurreducens. J Phys Chem B 2019; 123:3050-3060. [PMID: 30875222 DOI: 10.1021/acs.jpcb.9b01214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant under several growth conditions and is important for extracellular electron transfer. PpcA plays a central role in transferring electrons resulting from the cytoplasmic oxidation of carbon compounds to the cell exterior. This cytochrome is designed to couple electron and proton transfer at physiological pH, a process achieved via the selection of dominant microstates during the redox cycle of the protein, which are ultimately regulated by a well-established order of oxidation of the heme groups. The three hemes are covered only by a polypeptide chain of 71 residues and are located in the small hydrophobic core of the protein. In this work, we used NMR and X-ray crystallography to investigate the structural and functional role of a conserved valine residue (V13) located within van der Waals contact of hemes III and IV. The residue was replaced by alanine (V13A), isoleucine (V13I), serine (V13S), and threonine (V13T) to probe the effects of the side chain volume and polarity. All mutants were found to be as equally thermally stable as the native protein. The V13A and V13T mutants produced crystals and their structures were determined. The side chain of the threonine residue introduced in V13T showed two conformations, but otherwise the two structures did not show significant changes from the native structure. Analysis of the redox behavior of the four mutants showed that for the hydrophobic replacements (V13A and V13I) the redox properties, and hence the order of oxidation of the hemes, were unaffected in spite of the larger side chain, isoleucine, showing two conformations with minor changes of the protein in the heme core. On the other hand, the polar replacements (V13S and V13T) showed the presence of two more distinctive conformations, and the oxidation order of the hemes was altered. Overall, it is striking that a single residue with proper size and polarity, V13, was naturally selected to ensure a unique conformation of the protein and the order of oxidation of the hemes, endowing the cytochrome PpcA with the optimal functional properties necessary to ensure effectiveness in the extracellular electron transfer respiratory pathways of G. sulfurreducens.
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Affiliation(s)
- Joana M Dantas
- UCIBIO-Requimte, Departamento de Química , Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa , Campus Caparica, 2829-516 Caparica , Portugal
| | - Pilar C Portela
- UCIBIO-Requimte, Departamento de Química , Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa , Campus Caparica, 2829-516 Caparica , Portugal
| | - Ana P Fernandes
- UCIBIO-Requimte, Departamento de Química , Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa , Campus Caparica, 2829-516 Caparica , Portugal
| | - Yuri Y Londer
- Biosciences Division , Argonne National Laboratory , 9700 South Cass Avenue , Argonne , Illinois 60439 , United States
| | - Xiaojing Yang
- Biosciences Division , Argonne National Laboratory , 9700 South Cass Avenue , Argonne , Illinois 60439 , United States
| | - Norma E C Duke
- Biosciences Division , Argonne National Laboratory , 9700 South Cass Avenue , Argonne , Illinois 60439 , United States
| | - Marianne Schiffer
- Biosciences Division , Argonne National Laboratory , 9700 South Cass Avenue , Argonne , Illinois 60439 , United States
| | - P Raj Pokkuluri
- Biosciences Division , Argonne National Laboratory , 9700 South Cass Avenue , Argonne , Illinois 60439 , United States
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química , Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa , Campus Caparica, 2829-516 Caparica , Portugal
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Ferreira MR, Salgueiro CA. Biomolecular Interaction Studies Between Cytochrome PpcA From Geobacter sulfurreducens and the Electron Acceptor Ferric Nitrilotriacetate (Fe-NTA). Front Microbiol 2018; 9:2741. [PMID: 30524391 PMCID: PMC6262392 DOI: 10.3389/fmicb.2018.02741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022] Open
Abstract
Geobacter sulfurreducens bacterium exhibits an enormous respiratory versatility, including the utilization of several toxic and radioactive metals as electron acceptors. This versatility is also replicated in the capability of the most abundant cytochrome in G. sulfurreducens, the periplasmic triheme cytochrome PpcA, to reduce uranium, chromium and other metal ions. From all possible electron transfer pathways in G. sulfurreducens, those involved in the iron reduction are the best characterized to date. Previously, we provided structural evidence for the complex interface established between PpcA and the electron acceptor Fe(III)-citrate. However, genetic studies suggested that this acceptor is mainly reduced by outer membrane cytochomes. In the present work, we used UV-visible measurements to demonstrate that PpcA is able to directly reduce the electron acceptor ferric nitrilotriacetate (Fe-NTA), a more outer membrane permeable iron chelated form. In addition, the molecular interactions between PpcA and Fe-NTA were probed by Nuclear Magnetic Resonance (NMR) spectroscopy. The NMR spectra obtained for PpcA samples in the absence and presence of Fe-NTA showed that the interaction is reversible and encompasses a positively charged surface region located in the vicinity of the heme IV. Overall, the study elucidates the formation of an electron transfer complex between PpcA and a readily outer-membrane permeable iron chelated form. The structural and functional relationships obtained explain how a single cytochrome is designed to effectively interact with a wide range of G. sulfurreducens electron acceptors, a feature that can be explored for optimal bioelectrochemical applications.
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Affiliation(s)
- Marisa R Ferreira
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Ponomarenko N, Niklas J, Pokkuluri PR, Poluektov O, Tiede DM. Electron Paramagnetic Resonance Characterization of the Triheme Cytochrome from Geobacter sulfurreducens. Biochemistry 2018; 57:1722-1732. [DOI: 10.1021/acs.biochem.7b00917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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18
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Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens. Biochem J 2017; 474:797-808. [DOI: 10.1042/bcj20161022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens. The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens.
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19
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Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens. Biochem J 2016; 474:231-246. [PMID: 28062839 DOI: 10.1042/bcj20160932] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022]
Abstract
The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e-/H+ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e-/H+ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.
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20
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Dantas JM, Morgado L, Aklujkar M, Bruix M, Londer YY, Schiffer M, Pokkuluri PR, Salgueiro CA. Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies. Front Microbiol 2015; 6:752. [PMID: 26284042 PMCID: PMC4519760 DOI: 10.3389/fmicb.2015.00752] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e−/H+ transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e−/H+ transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential proteins with the aim to develop and improve bioelectrochemical technologies.
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Affiliation(s)
- Joana M Dantas
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
| | - Leonor Morgado
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
| | - Muktak Aklujkar
- Department of Biological Sciences, Towson University Towson, MD, USA
| | - Marta Bruix
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Yuri Y Londer
- Biosciences Division, Argonne National Laboratory Lemont, IL, USA
| | | | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory Lemont, IL, USA
| | - Carlos A Salgueiro
- Research Unit on Applied Molecular Biosciences (UCIBIO), Rede de Química e Tecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Caparica, Portugal
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21
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Heterologous expression and purification of a multiheme cytochrome from a Gram-positive bacterium capable of performing extracellular respiration. Protein Expr Purif 2015; 111:48-52. [DOI: 10.1016/j.pep.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/12/2015] [Accepted: 03/15/2015] [Indexed: 01/16/2023]
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22
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Dantas JM, Salgueiro CA, Bruix M. Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcD from Geobacter sulfurreducens. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:211-214. [PMID: 25209145 DOI: 10.1007/s12104-014-9576-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/03/2014] [Indexed: 06/03/2023]
Abstract
Gene knock-out studies on Geobacter sulfurreducens (Gs) cells showed that the periplasmic triheme cytochrome PpcD is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. More recently, it was also shown that the gene encoding for PpcD has higher transcript abundance when Gs cells utilize graphite electrodes as sole electron donors to reduce fumarate. This sets PpcD as the first multiheme cytochrome to be involved in Gs respiratory pathways that bridge the electron transfer between the cytoplasm and cell exterior in both directions. Nowadays, extracellular electron transfer (EET) processes are explored for several biotechnological applications, which include bioremediation, bioenergy and biofuel production. Therefore, the structural characterization of PpcD is a fundamental step to understand the mechanisms underlying EET. However, compared to non-heme proteins, the presence of numerous proton-containing groups in the redox centers presents additional challenges for protein signal assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the reduced form of PpcD.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516, Caparica, Portugal
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23
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Kokhan O, Ponomarenko NS, Pokkuluri PR, Schiffer M, Mulfort KL, Tiede DM. Bidirectional Photoinduced Electron Transfer in Ruthenium(II)-Tris-bipyridyl-Modified PpcA, a Multi-heme c-Type Cytochrome from Geobacter sulfurreducens. J Phys Chem B 2015; 119:7612-24. [PMID: 25731703 DOI: 10.1021/jp511558f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PpcA, a tri-heme cytochrome c7 from Geobacter sulfurreducens, was investigated as a model for photosensitizer-initiated electron transfer within a multi-heme "molecular wire" protein architecture. Escherichia coli expression of PpcA was found to be tolerant of cysteine site-directed mutagenesis, demonstrated by the successful expression of natively folded proteins bearing cysteine mutations at a series of sites selected to vary characteristically with respect to the three -CXXCH- heme binding domains. The introduced cysteines readily reacted with Ru(II)-(2,2'-bpy)2(4-bromomethyl-4'-methyl-2,2'-bipyridine) to form covalently linked constructs that support both photo-oxidative and photo-reductive quenching of the photosensitizer excited state, depending upon the initial heme redox state. Excited-state electron-transfer times were found to vary from 6 × 10(-12) to 4 × 10(-8) s, correlated with the distance and pathways for electron transfer. The fastest rate is more than 10(3)-fold faster than previously reported for photosensitizer-redox protein constructs using amino acid residue linking. Clear evidence for inter-heme electron transfer within the multi-heme protein is not detected within the lifetimes of the charge-separated states. These results demonstrate an opportunity to develop multi-heme c-cytochromes for investigation of electron transfer in protein "molecular wires" and to serve as frameworks for metalloprotein designs that support multiple-electron-transfer redox chemistry.
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Affiliation(s)
- Oleksandr Kokhan
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Nina S Ponomarenko
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - P Raj Pokkuluri
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Marianne Schiffer
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Karen L Mulfort
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - David M Tiede
- †Chemical Sciences and Engineering Division and ‡Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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24
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Morgado L, Lourenço S, Londer YY, Schiffer M, Pokkuluri PR, Salgueiro CA. Dissecting the functional role of key residues in triheme cytochrome PpcA: a path to rational design of G. sulfurreducens strains with enhanced electron transfer capabilities. PLoS One 2014; 9:e105566. [PMID: 25153891 PMCID: PMC4143306 DOI: 10.1371/journal.pone.0105566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/21/2014] [Indexed: 11/24/2022] Open
Abstract
PpcA is the most abundant member of a family of five triheme cytochromes c7 in the bacterium Geobacter sulfurreducens (Gs) and is the most likely carrier of electrons destined for outer surface during respiration on solid metal oxides, a process that requires extracellular electron transfer. This cytochrome has the highest content of lysine residues (24%) among the family, and it was suggested to be involved in e−/H+ energy transduction processes. In the present work, we investigated the functional role of lysine residues strategically located in the vicinity of each heme group. Each lysine was replaced by glutamine or glutamic acid to evaluate the effects of a neutral or negatively charged residue in each position. The results showed that replacing Lys9 (located near heme IV), Lys18 (near heme I) or Lys22 (between hemes I and III) has essentially no effect on the redox properties of the heme groups and are probably involved in redox partner recognition. On the other hand, Lys43 (near heme IV), Lys52 (between hemes III and IV) and Lys60 (near heme III) are crucial in the regulation of the functional mechanism of PpcA, namely in the selection of microstates that allow the protein to establish preferential e−/H+ transfer pathways. The results showed that the preferred e−/H+ transfer pathways are only established when heme III is the last heme to oxidize, a feature reinforced by a higher difference between its reduction potential and that of its predecessor in the order of oxidation. We also showed that K43 and K52 mutants keep the mechanistic features of PpcA by establishing preferential e−/H+ transfer pathways at lower reduction potential values than the wild-type protein, a property that can enable rational design of Gs strains with optimized extracellular electron transfer capabilities.
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Affiliation(s)
- Leonor Morgado
- Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (FCT/UNL), Caparica, Portugal
| | - Sílvia Lourenço
- Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (FCT/UNL), Caparica, Portugal
| | - Yuri Y. Londer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Marianne Schiffer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - P. Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Carlos A. Salgueiro
- Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (FCT/UNL), Caparica, Portugal
- * E-mail:
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Kokhan O, Ponomarenko N, Pokkuluri PR, Schiffer M, Tiede DM. Multimerization of solution-state proteins by tetrakis(4-sulfonatophenyl)porphyrin. Biochemistry 2014; 53:5070-9. [PMID: 25028772 DOI: 10.1021/bi500278g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Surface binding and interactions of anionic porphyins bound to cationic proteins have been studied for nearly three decades and are relevant as models for protein surface molecular recognition and photoinitiated electron transfer. However, interpretation of data in nearly all reports explicitly or implicitly assumed interaction of porphyrin with monodisperse proteins in solutions. In this report, using small-angle X-ray scattering with solution phase samples, we demonstrate that horse heart cytochrome (cyt) c, triheme cytochrome c7 PpcA from Geobacter sulfurreducens, and hen egg lysozyme multimerize in the presence of zinc tetrakis(4-sulfonatophenyl)porphyrin (ZnTPPS). Multimerization of cyt c showed a pH dependence with a stronger apparent binding affinity under alkaline conditions and was weakened in the presence of a high salt concentration. Ferric-cyt c formed complexes larger than those formed by ferro-cyt c. Free base TPPS and FeTPPS facilitated formation of complexes larger than those of ZnTPPS. No increase in protein aggregation state for cationic proteins was observed in the presence of cationic porphyrins. All-atom molecular dynamics simulations of cyt c and PpcA with free base TPPS corroborated X-ray scattering results and revealed a mechanism by which the tetrasubstituted charged porphyrins serve as bridging ligands nucleating multimerization of the complementarily charged protein. The final aggregation products suggest that multimerization involves a combination of electrostatic and hydrophobic interactions. The results demonstrate an overlooked complexity in the design of multifunctional ligands for protein surface recognition.
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Affiliation(s)
- Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Lemont, Illinois 60439, United States
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Fuciños P, Atanes E, López-López O, Solaroli M, Cerdán ME, González-Siso MI, Pastrana L, Rúa ML. Cloning, expression, purification and characterization of an oligomeric His-tagged thermophilic esterase from Thermus thermophilus HB27. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Dantas JM, Morgado L, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:750-60. [PMID: 24530867 DOI: 10.1016/j.bbabio.2014.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 11/25/2022]
Abstract
The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Carlos A Salgueiro
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:484-92. [DOI: 10.1016/j.bbabio.2012.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/11/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
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Pokkuluri PR, Yang X, Londer YY, Schiffer M. Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2012; 13:227-32. [PMID: 23099666 PMCID: PMC4109977 DOI: 10.1007/s10969-012-9147-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022]
Abstract
PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examination of the crystal packing has revealed the origin of this unexpected structural change. The site of mutation is within Van der Waals distance from another protein molecule related by a crystallographic twofold axis within the crystal. The structural changes occurred at or near the mutation site have led to a slight adjustment of the surface residues in contact. The observed deviations between the native and the mutant molecular structures are derived from the new crystal packing even though the two crystals are essentially isomorphous. Without careful consideration of the crystal lattice a non-expert looking at only the coordinates deposited in the Protein Data Bank could draw erroneous conclusion that mutation in one part of the molecule affected the structure of the protein in a distant part of the molecule.
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Affiliation(s)
- P. R. Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - X. Yang
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Y. Y. Londer
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - M. Schiffer
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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Role of Met(58) in the regulation of electron/proton transfer in trihaem cytochrome PpcA from Geobacter sulfurreducens. Biosci Rep 2012; 33:11-22. [PMID: 23030844 PMCID: PMC3522473 DOI: 10.1042/bsr20120086] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The bacterium Gs (Geobacter sulfurreducens) is capable of oxidizing a large variety of compounds relaying electrons out of the cytoplasm and across the membranes in a process designated as extracellular electron transfer. The trihaem cytochrome PpcA is highly abundant in Gs and is most probably the reservoir of electrons destined for the outer surface. In addition to its role in electron transfer pathways, we have previously shown that this protein could perform e(-)/H(+) energy transduction. This mechanism is achieved by selecting the specific redox states that the protein can access during the redox cycle and might be related to the formation of proton electrochemical potential gradient across the periplasmic membrane. The regulatory role of haem III in the functional mechanism of PpcA was probed by replacing Met(58), a residue that controls the solvent accessibility of haem III, with serine, aspartic acid, asparagine or lysine. The data obtained from the mutants showed that the preferred e(-)/H(+) transfer pathway observed for PpcA is strongly dependent on the reduction potential of haem III. It is striking to note that one residue can fine tune the redox states that can be accessed by the trihaem cytochrome enough to alter the functional pathways.
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On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens: functional and structural characterization of multihaem cytochromes. Biochem Soc Trans 2012; 40:1295-301. [DOI: 10.1042/bst20120099] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Extracellular electron transfer is one of the physiological hallmarks of Geobacter sulfurreducens, allowing these bacteria to reduce toxic and/or radioactive metals and grow on electrode surfaces. Aiming to functionally optimize the respiratory electron-transfer chains, such properties can be explored through genetically engineered strains. Geobacter species comprise a large number of different multihaem c-type cytochromes involved in the extracellular electron-transfer pathways. The functional characterization of multihaem proteins is particularly complex because of the coexistence of several microstates in solution, connecting the fully reduced and oxidized states. NMR spectroscopy has been used to monitor the stepwise oxidation of each individual haem and thus to obtain information on each microstate. For the structural study of these proteins, a cost-effective isotopic labelling of the protein polypeptide chains was combined with the comparative analysis of 1H-13C HSQC (heteronuclear single-quantum correlation) NMR spectra obtained for labelled and unlabelled samples. These new methodological approaches allowed us to study G. sulfurreducens haem proteins functionally and structurally, revealing functional mechanisms and key residues involved in their electron-transfer capabilities. Such advances can now be applied to the design of engineered haem proteins to improve the bioremediation and electricity-harvesting skills of G. sulfurreducens.
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Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA. Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system. J Biol Inorg Chem 2012; 17:647-62. [PMID: 22382353 PMCID: PMC3412176 DOI: 10.1007/s00775-012-0885-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein "small tetraheme c" replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 °C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-Å-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Evan T. Judd
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Bilal Sayyed
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Tyler Goelzer
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Sean J. Elliott
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Marius Schmidt
- Department of Physics, 1900 E. Kenwood Blvd, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
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Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens. Biochem J 2012; 441:179-87. [PMID: 21861844 DOI: 10.1042/bj20111103] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25 Å (1 Å=0.1 nm) for the backbone atoms and 0.99 Å for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions.
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Dantas JM, Morgado L, Londer YY, Fernandes AP, Louro RO, Pokkuluri PR, Schiffer M, Salgueiro CA. Pivotal role of the strictly conserved aromatic residue F15 in the cytochrome c7 family. J Biol Inorg Chem 2011; 17:11-24. [PMID: 21805398 DOI: 10.1007/s00775-011-0821-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 07/09/2011] [Indexed: 10/17/2022]
Abstract
Cytochromes c(7) are periplasmic triheme proteins that have been reported exclusively in δ-proteobacteria. The structures of five triheme cytochromes identified in Geobacter sulfurreducens and one in Desulfuromonas acetoxidans have been determined. In addition to the hemes and axial histidines, a single aromatic residue is conserved in all these proteins-phenylalanine 15 (F15). PpcA is a member of the G. sulfurreducens cytochrome c(7) family that performs electron/proton energy transduction in addition to electron transfer that leads to the reduction of extracellular electron acceptors. For the first time we probed the role of the F15 residue in the PpcA functional mechanism, by replacing this residue with the aliphatic leucine by site-directed mutagenesis. The analysis of NMR spectra of both oxidized and reduced forms showed that the heme core and the overall fold of the mutated protein were not affected. However, the analysis of (1)H-(15)N heteronuclear single quantum coherence NMR spectra evidenced local rearrangements in the α-helix placed between hemes I and III that lead to structural readjustments in the orientation of heme axial ligands. The detailed thermodynamic characterization of F15L mutant revealed that the reduction potentials are more negative and the redox-Bohr effect is decreased. The redox potential of heme III is most affected. It is of interest that the mutation in F15, located between hemes I and III in PpcA, changes the characteristics of the two hemes differently. Altogether, these modifications disrupt the balance of the global network of cooperativities, preventing the F15L mutant protein from performing a concerted electron/proton transfer.
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Affiliation(s)
- Joana M Dantas
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
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Morgado L, Paixão VB, Salgueiro CA, Bruix M. Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcA from Geobacter sulfurreducens. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:113-116. [PMID: 21069484 DOI: 10.1007/s12104-010-9280-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 10/21/2010] [Indexed: 05/30/2023]
Abstract
Gene knock-out studies on Geobacter sulfurreducens cells showed that the periplasmic triheme cytochrome PpcA is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. The crucial role of this protein in bridging the electron transfer between the cytoplasm and cell exterior was further supported by proteomics studies. In comparison with non-heme proteins, the presence of numerous proton-containing groups in the heme groups causes additional challenges to the full protein assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with the (1)H and (15)N backbone and side chain assignments of the reduced form of PpcA.
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Affiliation(s)
- Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, Portugal
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Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
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Abstract
Answering questions about proteins' structures and functions in the new era of systems biology and genomics requires the development of new methods for heterologous production of numerous proteins from newly sequenced genomes. Cytochromes c - electron transfer proteins carrying one or more hemes covalently bound to the polypeptide chain - are one of the most recalcitrant classes of proteins with respect to heterologous expression because post-translational incorporation of hemes is required for proper folding and stability. However, significant advances in expression of recombinant cytochromes c have been made during the last decade. It has been shown that a single gene cluster, ccmA-H, is responsible for cytochrome c maturation in Escherichia coli under anaerobic conditions and that constitutive co-expression of this cluster under aerobic conditions is sufficient to provide heme incorporation in many different types of cytochromes c, regardless of their origin, as long as the nascent polypeptide is translocated to the periplasm. Using conditions that result in sub-maximal protein induction can dramatically increase the yield of mature protein. The intrinsic peroxidase activity of hemes can be used as a highly selective and sensitive detection method of mature cytochromes in samples resolved by gel electrophoresis.
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38
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Yip ES, Burnside DM, Cianciotto NP. Cytochrome c4 is required for siderophore expression by Legionella pneumophila, whereas cytochromes c1 and c5 promote intracellular infection. MICROBIOLOGY-SGM 2010; 157:868-878. [PMID: 21178169 PMCID: PMC3081086 DOI: 10.1099/mic.0.046490-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A panel of cytochrome c maturation (ccm) mutants of Legionella pneumophila displayed a loss of siderophore (legiobactin) expression, as measured by both the chrome azurol S assay and a Legionella-specific bioassay. These data, coupled with the finding that ccm transcripts are expressed by wild-type bacteria grown in deferrated medium, indicate that the Ccm system promotes siderophore expression by L. pneumophila. To determine the basis of this newfound role for Ccm, we constructed and tested a set of mutants specifically lacking individual c-type cytochromes. Whereas ubiquinol-cytochrome c reductase (petC) mutants specifically lacking cytochrome c1 and cycB mutants lacking cytochrome c5 had normal siderophore expression, cyc4 mutants defective for cytochrome c4 completely lacked legiobactin. These data, along with the expression pattern of cyc4 mRNA, indicate that cytochrome c4 in particular promotes siderophore expression. In intracellular infection assays, petC mutants and cycB mutants, but not cyc4 mutants, had a reduced ability to infect both amoebae and macrophage hosts. Like ccm mutants, the cycB mutants were completely unable to grow in amoebae, highlighting a major role for cytochrome c5 in intracellular infection. To our knowledge, these data represent both the first direct documentation of the importance of a c-type cytochrome in expression of a biologically active siderophore and the first insight into the relative importance of c-type cytochromes in intracellular infection events.
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Affiliation(s)
- Emily S Yip
- Department of Microbiology and Immunology, Northwestern University Medical School, 320 East Superior St, Chicago, IL 60611, USA
| | - Denise M Burnside
- Department of Microbiology and Immunology, Northwestern University Medical School, 320 East Superior St, Chicago, IL 60611, USA
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Medical School, 320 East Superior St, Chicago, IL 60611, USA
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Pokkuluri PR, Londer YY, Duke NEC, Pessanha M, Yang X, Orshonsky V, Orshonsky L, Erickson J, Zagyanskiy Y, Salgueiro CA, Schiffer M. Structure of a novel dodecaheme cytochrome c from Geobacter sulfurreducens reveals an extended 12 nm protein with interacting hemes. J Struct Biol 2010; 174:223-33. [PMID: 21130881 DOI: 10.1016/j.jsb.2010.11.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/18/2010] [Accepted: 11/29/2010] [Indexed: 10/18/2022]
Abstract
Multiheme cytochromes c are important in electron transfer pathways in reduction of both soluble and insoluble Fe(III) by Geobacter sulfurreducens. We determined the crystal structure at 3.2Å resolution of the first dodecaheme cytochrome c (GSU1996) along with its N-terminal and C-terminal hexaheme fragments at 2.6 and 2.15Å resolution, respectively. The macroscopic reduction potentials of the full-length protein and its fragments were measured. The sequence of GSU1996 can be divided into four c(7)-type domains (A, B, C and D) with homology to triheme cytochromes c(7). In cytochromes c(7) all three hemes are bis-His coordinated, whereas in c(7)-type domains the last heme is His-Met coordinated. The full-length GSU1996 has a 12nm long crescent shaped structure with the 12 hemes arranged along a polypeptide to form a "nanowire" of hemes; it has a modular structure. Surprisingly, while the C-terminal half of the protein consists of two separate c(7)-type domains (C and D) connected by a small linker, the N-terminal half of the protein has two c(7)-type domains (A and B) that form one structural unit. This is also observed in the AB fragment. There is an unexpected interaction between the hemes at the interface of domains A and B, which form a heme-pair with nearly parallel stacking of their porphyrin rings. The hemes adjacent to each other throughout the protein are within van der Waals distance which enables efficient electron exchange between them. For the first time, the structural details of c(7)-type domains from one multiheme protein were compared.
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Affiliation(s)
- P R Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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40
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One simple step in the identification of the cofactors signals, one giant leap for the solution structure determination of multiheme proteins. Biochem Biophys Res Commun 2010; 393:466-70. [PMID: 20152799 DOI: 10.1016/j.bbrc.2010.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 02/05/2010] [Indexed: 11/24/2022]
Abstract
Multiheme proteins play major roles in various biological systems. Structural information on these systems in solution is crucial to understand their functional mechanisms. However, the presence of numerous proton-containing groups in the heme cofactors and the magnetic properties of the heme iron, in particular in the oxidised state, complicates significantly the assignment of the NMR signals. Consequently, the multiheme proteins superfamily is extremely under-represented in structural databases, which constitutes a severe bottleneck in the elucidation of their structural-functional relationships. In this work, we present a strategy that simplifies the assignment of the NMR signals in multiheme proteins and, concomitantly, their solution structure determination, using the triheme cytochrome PpcA from the bacterium Geobacter sulfurreducens as a model. Cost-effective isotopic labeling was used to double label (13C/15N) the protein in its polypeptide chain, with the correct folding and heme post-translational modifications. The combined analysis of 1H-13C HSQC NMR spectra obtained for labeled and unlabeled samples of PpcA allowed a straight discrimination between the heme cofactors and the polypeptide chain signals and their confident assignment. The results presented here will be the foundations to assist solution structure determination of multiheme proteins, which are still very scarce in the literature.
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41
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Matsuno T, Mie Y, Yoshimune K, Yumoto I. Physiological role and redox properties of a small cytochrome c5, cytochrome c-552, from alkaliphile, Pseudomonas alcaliphila AL15-21T. J Biosci Bioeng 2009; 108:465-70. [DOI: 10.1016/j.jbiosc.2009.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 05/14/2009] [Accepted: 06/10/2009] [Indexed: 10/20/2022]
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42
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Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:222-32. [PMID: 19857457 DOI: 10.1016/j.bbabio.2009.10.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/16/2009] [Accepted: 10/20/2009] [Indexed: 11/23/2022]
Abstract
Periplasmic cytochromes c(7) are important in electron transfer pathway(s) in Fe(III) respiration by Geobacter sulfurreducens. The genome of G. sulfurreducens encodes a family of five 10-kDa, three-heme cytochromes c(7). The sequence identity between the five proteins (designated PpcA, PpcB, PpcC, PpcD, and PpcE) varies between 45% and 77%. Here, we report the high-resolution structures of PpcC, PpcD, and PpcE determined by X-ray diffraction. This new information made it possible to compare the sequences and structures of the entire family. The triheme cores are largely conserved but are not identical. We observed changes, due to different crystal packing, in the relative positions of the hemes between two molecules in the crystal. The overall protein fold of the cytochromes is similar. The structure of PpcD differs most from that of the other homologs, which is not obvious from the sequence comparisons of the family. Interestingly, PpcD is the only cytochrome c(7) within the family that has higher abundance when G. sulfurreducens is grown on insoluble Fe(III) oxide compared to ferric citrate. The structures have the highest degree of conservation around "heme IV"; the protein surface around this heme is positively charged in all of the proteins, and therefore all cytochromes c(7) could interact with similar molecules involving this region. The structures and surface characteristics of the proteins near the other two hemes, "heme I" and "heme III", differ within the family. The above observations suggest that each of the five cytochromes c(7) could interact with its own redox partner via an interface involving the regions of heme I and/or heme III; this provides a possible rationalization for the existence of five similar proteins in G. sulfurreducens.
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43
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Londer YY, Giuliani SE, Peppler T, Collart FR. Addressing Shewanella oneidensis “cytochromome”: The first step towards high-throughput expression of cytochromes c. Protein Expr Purif 2008; 62:128-37. [DOI: 10.1016/j.pep.2008.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 06/23/2008] [Indexed: 01/20/2023]
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44
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Mamoto R, Hu X, Chiue H, Fujioka Y, Kawai F. Cloning and expression of soluble cytochrome c and its role in polyvinyl alcohol degradation by polyvinyl alcohol-utilizing Sphingopyxis sp. strain 113P3. J Biosci Bioeng 2008; 105:147-51. [PMID: 18343342 DOI: 10.1263/jbb.105.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 11/19/2007] [Indexed: 11/17/2022]
Abstract
The gene encoding cytocrome c in the pva operon of Sphingopyxis sp. strain 113P3 was cloned, on the basis of the sequence of the gene for cytochrome c (GenBank accession no. AB190288). The deduced amino acid sequence of the gene showed homologies (37% and 47% identities) with two cytochromes c of different origins. The recombinant cytochrome c tagged with hexahistidines was expressed in the periplasm of Escherichia coli BL21(DE3) harboring pT-GroE, which was in accordance with the localization of cytochrome c in strain 113P3; the protein was purified to homogeneity. The purified recombinant cytochrome c was a monomeric protein with a molecular weight of 16.5 kDa. The oxidized and reduced forms of the protein showed absorption maxima at 409 nm and at 414, 520 and 550 nm, respectively. The recombinant cytochrome c was fully reduced by polyvinyl alcohol (PVA), coupled with a catalytic amount (1/10 molar concentration) of the recombinant PVA dehydrogenase (PVADH) of the same origin, suggesting that the cytochrome c involved in the pva operon is a physiological primary electron acceptor for PVADH and that PVA dehydrogenation is linked with the respiratory chain in Sphingopyxis sp. strain 113P3.
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Affiliation(s)
- Rie Mamoto
- Faculty of Nutrition, Kobe Gakuin University, Kobe, Hyogo 651-2180, Japan
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45
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Morgado L, Bruix M, Orshonsky V, Londer YY, Duke NEC, Yang X, Pokkuluri PR, Schiffer M, Salgueiro CA. Structural insights into the modulation of the redox properties of two Geobacter sulfurreducens homologous triheme cytochromes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1157-65. [PMID: 18534185 DOI: 10.1016/j.bbabio.2008.04.043] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 04/07/2008] [Accepted: 04/28/2008] [Indexed: 11/17/2022]
Abstract
The redox properties of a periplasmic triheme cytochrome, PpcB from Geobacter sulfurreducens, were studied by NMR and visible spectroscopy. The structure of PpcB was determined by X-ray diffraction. PpcB is homologous to PpcA (77% sequence identity), which mediates cytoplasmic electron transfer to extracellular acceptors and is crucial in the bioenergetic metabolism of Geobacter spp. The heme core structure of PpcB in solution, probed by 2D-NMR, was compared to that of PpcA. The results showed that the heme core structures of PpcB and PpcA in solution are similar, in contrast to their crystal structures where the heme cores of the two proteins differ from each other. NMR redox titrations were carried out for both proteins and the order of oxidation of the heme groups was determined. The microscopic properties of PpcB and PpcA redox centers showed important differences: (i) the order in which hemes become oxidized is III-I-IV for PpcB, as opposed to I-IV-III for PpcA; (ii) the redox-Bohr effect is also different in the two proteins. The different redox features observed between PpcB and PpcA suggest that each protein uniquely modulates the properties of their co-factors to assure effectiveness in their respective metabolic pathways. The origins of the observed differences are discussed.
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Affiliation(s)
- Leonor Morgado
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
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46
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Fernandes AP, Couto I, Morgado L, Londer YY, Salgueiro CA. Isotopic labeling of c-type multiheme cytochromes overexpressed in E. coli. Protein Expr Purif 2008; 59:182-8. [PMID: 18343156 DOI: 10.1016/j.pep.2008.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 02/06/2008] [Accepted: 02/07/2008] [Indexed: 11/30/2022]
Abstract
Progresses made in bacterial genome sequencing show a remarkable profusion of multiheme c-type cytochromes in many bacteria, highlighting the importance of these proteins in different cellular events. However, the characterization of multiheme cytochromes has been significantly retarded by the numerous experimental challenges encountered by researchers who attempt to overexpress these proteins, especially if isotopic labeling is required. Here we describe a methodology for isotopic labeling of multiheme cytochromes c overexpressed in Escherichia coli, using the triheme cytochrome PpcA from Geobacter sulfurreducens as a model protein. By combining different strategies previously described and using E. coli cells containing the gene coding for PpcA and the cytochrome c maturation gene cluster, an experimental labeling methodology was developed that is based on two major aspects: (i) use of a two-step culture growth procedure, where cell growth in rich media was followed by transfer to minimal media containing (15)N-labeled ammonium chloride, and (ii) incorporation of the heme precursor delta-aminolevulinic acid in minimal culture media. The yields of labeled protein obtained were comparable to those obtained for expression of PpcA in rich media. Proper protein folding and labeling were confirmed by UV-visible and NMR spectroscopy. To our knowledge, this is the first report of a recombinant multiheme cytochrome labeling and it represents a major breakthrough for functional and structural studies of multiheme cytochromes.
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Affiliation(s)
- Ana P Fernandes
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL), Campus Caparica, 2829-516 Caparica, Portugal
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47
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Morgado L, Bruix M, Londer YY, Pokkuluri PR, Schiffer M, Salgueiro CA. Redox-linked conformational changes of a multiheme cytochrome from Geobacter sulfurreducens. Biochem Biophys Res Commun 2007; 360:194-8. [PMID: 17583674 DOI: 10.1016/j.bbrc.2007.06.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 06/05/2007] [Indexed: 11/29/2022]
Abstract
Multiheme c-type cytochromes from members of the Desulfovibrionacea and Geobactereacea families play crucial roles in the bioenergetics of these microorganisms. Thermodynamic studies using NMR and visible spectroscopic techniques on tetraheme cytochromes c(3) isolated from Desulfovibrio spp. and more recently on a triheme cytochrome from Geobacter sulfurreducens showed that the properties of each redox centre are modulated by the neighbouring redox centres enabling these proteins to perform energy transduction and thus contributing to cellular energy conservation. Electron/proton transfer coupling relies on redox-linked conformational changes that were addressed for some multiheme cytochromes from the comparison of protein structure of fully reduced and fully oxidised forms. In this work, we identify for the first time in a multiheme cytochrome the simultaneous presence of two different conformations in solution. This was achieved by probing the different oxidation stages of a triheme cytochrome isolated from G. sulfurreducens using 2D-NMR techniques. The results presented here will be the foundations to evaluate the modulation of the redox centres properties by conformational changes that occur during the reoxidation of a multiheme protein.
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Affiliation(s)
- Leonor Morgado
- Requimte - CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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48
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Londer YY, Dementieva IS, D'Ausilio CA, Pokkuluri PR, Schiffer M. Characterization of a c-type heme-containing PAS sensor domain from Geobacter sulfurreducens representing a novel family of periplasmic sensors in Geobacteraceae and other bacteria. FEMS Microbiol Lett 2006; 258:173-81. [PMID: 16640569 DOI: 10.1111/j.1574-6968.2006.00220.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Geobacter sulfurreducens encodes one of the largest numbers of proteins annotated as parts of the two-component signal transduction and/or chemotaxis pathways. Ten of these signal transducers have homologous periplasmic sensor domains that contain the sequence signature for c-type hemes. One such sensor domain encoded by gene GSU0303 was isolated and characterized. The protein was expressed in Escherichia coli and was isolated as two colored species (green and red). The green species is a monomer of the sensor domain with a five-coordinated high-spin heme and the red species is probably a noncovalent dimer of the sensor domain which might have an uncharacterized ligand bound to the dimer. The UV-VIS spectrum of the green species indicates that it has a c'-type heme, but its structure is predicted to be homologous to CitA, a periplasmic PAS domain that does not contain heme. The GSU0303 sensor domain represents a previously unreported family of PAS-type periplasmic sensor domains that contain c-type hemes; these proteins could be part of an important mechanism for sensing redox potential or small ligands in the periplasm. Homologs to the sensor domains we identified in G. sulfurreducens are observed in various bacteria although they occur in larger numbers in the Geobacteraceae.
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Affiliation(s)
- Yuri Y Londer
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
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49
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Londer YY, Pokkuluri PR, Orshonsky V, Orshonsky L, Schiffer M. Heterologous expression of dodecaheme “nanowire” cytochromes c from Geobacter sulfurreducens. Protein Expr Purif 2006; 47:241-8. [PMID: 16403647 DOI: 10.1016/j.pep.2005.11.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 11/11/2005] [Accepted: 11/18/2005] [Indexed: 11/30/2022]
Abstract
Multiheme cytochromes c are difficult to produce in heterologous systems. The genome of delta-proteobacterium Geobacter sulfurreducens contains more than a hundred genes coding for c-type cytochromes. Among those are two dodecaheme cytochromes c representing a new class of multiheme cytochromes, whose putative structure is a one-dimensional array of small highly homologous domains that contain three hemes and are covalently bound by short linkers. They are likely to form "nanowires" that are part of the electron transfer chain. We cloned the genes coding for the two cytochromes into a vector we developed for ligation-independent cloning of proteins targeted to the Escherichia coli periplasmic space. We expressed the proteins in E. coli co-transformed with a plasmid harboring the cytochrome c maturation genes. Expression levels were optimized by varying IPTG concentrations used for induction. Although both proteins appeared insoluble or strongly associated with cell membranes, they were solubilized using 0.5 M sodium chloride which was more selective than conventional solubilizing agents, such as HEGA-10 or beta-octylglucoside. The solubilized proteins were dialyzed and purified by cation exchange chromatography followed by gel filtration. Mass-spectrometry analysis confirmed that both purified proteins contained the complete set of covalently attached hemes, 12 per molecule. Their visible spectra were typical of c-type cytochromes. Both proteins were successfully crystallized.
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Affiliation(s)
- Yuri Y Londer
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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50
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Londer YY, Pokkuluri PR, Erickson J, Orshonsky V, Schiffer M. Heterologous expression of hexaheme fragments of a multidomain cytochrome from Geobacter sulfurreducens representing a novel class of cytochromes c. Protein Expr Purif 2005; 39:254-60. [PMID: 15642477 DOI: 10.1016/j.pep.2004.10.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Revised: 10/14/2004] [Indexed: 11/26/2022]
Abstract
Multiheme cytochromes c are of great interest for researchers for a variety of reasons but difficult to obtain in quantities sufficient for the majority of studies. The genome of delta-proteobacterium Geobacter sulfurreducens contains more than a hundred genes coding for c-type cytochromes. Three of them represent a new class of multiheme cytochromes characterized by a mixed type of heme coordination and multidomain organization. We cloned and expressed in Escherichia coli three hexaheme fragments corresponding to two-domain fragments of one such protein containing 12 heme binding motifs and believed to consist of four triheme domains. Despite high sequence similarity among the fragments, expression levels varied significantly. Expression was optimized either by host strain variation or by reducing the rate of apoprotein synthesis. All three fragments were purified by cation exchange followed by gel filtration and were shown to contain six covalently attached hemes as confirmed by mass spectrometry. Their visible spectra are typical of c-type cytochromes. One of the fragments was crystallized and its preliminary X-ray structure shows two separate domains.
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Affiliation(s)
- Yuri Y Londer
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.
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