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Silva MA, Fernandes AP, Turner DL, Salgueiro CA. A Biochemical Deconstruction-Based Strategy to Assist the Characterization of Bacterial Electric Conductive Filaments. Int J Mol Sci 2023; 24:ijms24087032. [PMID: 37108196 PMCID: PMC10138318 DOI: 10.3390/ijms24087032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Periplasmic nanowires and electric conductive filaments made of the polymeric assembly of c-type cytochromes from Geobacter sulfurreducens bacterium are crucial for electron storage and/or extracellular electron transfer. The elucidation of the redox properties of each heme is fundamental to the understanding of the electron transfer mechanisms in these systems, which first requires the specific assignment of the heme NMR signals. The high number of hemes and the molecular weight of the nanowires dramatically decrease the spectral resolution and make this assignment extremely complex or unattainable. The nanowire cytochrome GSU1996 (~42 kDa) is composed of four domains (A to D) each containing three c-type heme groups. In this work, the individual domains (A to D), bi-domains (AB, CD) and full-length nanowire were separately produced at natural abundance. Sufficient protein expression was obtained for domains C (~11 kDa/three hemes) and D (~10 kDa/three hemes), as well as for bi-domain CD (~21 kDa/six hemes). Using 2D-NMR experiments, the assignment of the heme proton NMR signals for domains C and D was obtained and then used to guide the assignment of the corresponding signals in the hexaheme bi-domain CD. This new biochemical deconstruction-based procedure, using nanowire GSU1996 as a model, establishes a new strategy to functionally characterize large multiheme cytochromes.
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Affiliation(s)
- Marta A Silva
- Associate Laboratory, i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Ana P Fernandes
- Associate Laboratory, i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - David L Turner
- Instituto de Tecnologia Química e Biológica António Xavier, NOVA University Lisbon, 2780-157 Oeiras, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory, i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
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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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Structural and functional insights of GSU0105, a unique multiheme cytochrome from G. sulfurreducens. Biophys J 2021; 120:5395-5407. [PMID: 34688593 DOI: 10.1016/j.bpj.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Geobacter sulfurreducens possesses over 100 cytochromes that assure an effective electron transfer to the cell exterior. The most abundant group of cytochromes in this microorganism is the PpcA family, composed of five periplasmic triheme cytochromes with high structural homology and identical heme coordination (His-His). GSU0105 is a periplasmic triheme cytochrome synthetized by G. sulfurreducens in Fe(III)-reducing conditions but is not present in cultures grown on fumarate. This cytochrome has a low sequence identity with the PpcA family cytochromes and a different heme coordination, based on the analysis of its amino acid sequence. In this work, amino acid sequence analysis, site-directed mutagenesis, and complementary biophysical techniques, including ultraviolet-visible, circular dichroism, electron paramagnetic resonance, and nuclear magnetic resonance spectroscopies, were used to characterize GSU0105. The cytochrome has a low percentage of secondary structural elements, with features of α-helices and β-sheets. Nuclear magnetic resonance shows that the protein contains three low-spin hemes (Fe(II), S = 0) in the reduced state. Electron paramagnetic resonance shows that, in the oxidized state, one of the hemes becomes high-spin (Fe(III), S = 5/2), whereas the two others remain low-spin (Fe(III), S = 1/2). The data obtained also indicate that the heme groups have distinct axial coordination. The apparent midpoint reduction potential of GSU0105 (-154 mV) is pH independent in the physiological range. However, the pH modulates the reduction potential of the heme that undergoes the low- to high-spin interconversion. The reduction potential values of cytochrome GSU0105 are more distinct compared to those of the PpcA family members, providing the protein with a larger functional working redox potential range. Overall, the results obtained, together with an amino acid sequence analysis of different multiheme cytochrome families, indicate that GSU0105 is a member of a new group of triheme cytochromes.
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Santos TC, Silva MA, Morgado L, Dantas JM, Salgueiro CA. Diving into the redox properties of Geobacter sulfurreducens cytochromes: a model for extracellular electron transfer. Dalton Trans 2016; 44:9335-44. [PMID: 25906375 DOI: 10.1039/c5dt00556f] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Geobacter bacteria have a remarkable respiratory versatility that includes the dissimilatory reduction of insoluble metal oxides in natural habitats and electron transfer to electrode surfaces from which electricity can be harvested. In both cases, electrons need to be exported from the cell interior to the exterior via a mechanism designated as extracellular electron transfer (EET). Several c-type cytochromes from G. sulfurreducens (Gs) were identified as key players in this process. Biochemical and biophysical data have been obtained for ten Gs cytochromes, including inner-membrane associated (MacA), periplasmic (PpcA, PpcB, PpcC, PpcD, PpcE and GSU1996) and outer membrane-associated (OmcF, OmcS and OmcZ). The redox properties of these cytochromes have been determined, except for PpcC and GSU1996. In this perspective, the reduction potentials of these two cytochromes were determined by potentiometric redox titrations followed by visible spectroscopy. The data obtained are taken together with those available for other key cytochromes to present a thorough overview of the current knowledge of Gs EET mechanisms and provide a possible rationalization for the existence of several multiheme cytochromes involved in the same respiratory pathways.
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Affiliation(s)
- Telma C Santos
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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Unraveling the electron transfer processes of a nanowire protein from Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:7-13. [DOI: 10.1016/j.bbabio.2015.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/04/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022]
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Santos TC, de Oliveira AR, Dantas JM, Salgueiro CA, Cordas CM. Thermodynamic and kinetic characterization of PccH, a key protein in microbial electrosynthesis processes in Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1113-8. [DOI: 10.1016/j.bbabio.2015.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/29/2015] [Accepted: 06/07/2015] [Indexed: 10/23/2022]
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Dantas JM, Tomaz DM, Morgado L, Salgueiro CA. Functional characterization of PccH, a key cytochrome for electron transfer from electrodes to the bacterium Geobacter sulfurreducens. FEBS Lett 2013; 587:2662-8. [PMID: 23851008 DOI: 10.1016/j.febslet.2013.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022]
Abstract
The cytochrome PccH from Geobacter sulfurreducens (Gs) plays a crucial role in current-consuming fumarate-reducing biofilms. Deletion of pccH gene inhibited completely electron transfer from electrodes toward Gs cells. The pccH gene was cloned and the protein heterologously expressed in Escherichia coli. Complementary biophysical techniques including CD, UV-visible and NMR spectroscopy were used to characterize PccH. This cytochrome contains one low-spin c-type heme with His-Met axial coordination and unusual low-reduction potential. This reduction potential is pH-dependent, within the Gs physiological pH range, and is discussed within the context of the electron transfer mechanisms from electrodes to Gs cells.
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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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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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Butler JE, Young ND, Aklujkar M, Lovley DR. Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production. BMC Genomics 2012; 13:471. [PMID: 22967216 PMCID: PMC3495685 DOI: 10.1186/1471-2164-13-471] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/06/2012] [Indexed: 11/22/2022] Open
Abstract
Background A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved. Results Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP) between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb) were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail. Conclusions The improvement in external electron transfer in the KN400 strain does not appear to be due to novel gene acquisition, but rather to changes in the common metabolic network. The increase in electron transfer rate and yield in KN400 may be due to changes in carbon flux towards oxidation pathways and to changes in ATP metabolism, both of which indicate that the overall energy state of the cell may be different. The electrically conductive pili appear to be unchanged, but cytochrome folding, localization, and redox potentials may all be affected, which would alter the electrical connection between the cell and the substrate.
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Affiliation(s)
- Jessica E Butler
- Department of Microbiology, 203 Morrill Science Center IVN, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003, USA.
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Millo D, Harnisch F, Patil SA, Ly HK, Schröder U, Hildebrandt P. Spektroelektrochemische In-situ-Untersuchung von elektrokatalytischen mikrobiellen Biofilmen mit oberflächenverstärkter Resonanz-Raman-Spektroskopie. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Millo D, Harnisch F, Patil SA, Ly HK, Schröder U, Hildebrandt P. In situ spectroelectrochemical investigation of electrocatalytic microbial biofilms by surface-enhanced resonance Raman spectroscopy. Angew Chem Int Ed Engl 2011; 50:2625-7. [PMID: 21370352 DOI: 10.1002/anie.201006046] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 11/29/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Diego Millo
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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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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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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Morgado L, Bruix M, Pessanha M, Londer YY, Salgueiro CA. Thermodynamic characterization of a triheme cytochrome family from Geobacter sulfurreducens reveals mechanistic and functional diversity. Biophys J 2010; 99:293-301. [PMID: 20655858 DOI: 10.1016/j.bpj.2010.04.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/09/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022] Open
Abstract
A family of five periplasmic triheme cytochromes (PpcA-E) was identified in Geobacter sulfurreducens, where they play a crucial role by driving electron transfer from the cytoplasm to the cell exterior and assisting the reduction of extracellular acceptors. The thermodynamic characterization of PpcA using NMR and visible spectroscopies was previously achieved under experimental conditions identical to those used for the triheme cytochrome c(7) from Desulfuromonas acetoxidans. Under such conditions, attempts to obtain NMR data were complicated by the relatively fast intermolecular electron exchange. This work reports the detailed thermodynamic characterization of PpcB, PpcD, and PpcE under optimal experimental conditions. The thermodynamic characterization of PpcA was redone under these new conditions to allow a proper comparison of the redox properties with those of other members of this family. The heme reduction potentials of the four proteins are negative, differ from each other, and cover different functional ranges. These reduction potentials are strongly modulated by heme-heme interactions and by interactions with protonated groups (the redox-Bohr effect) establishing different cooperative networks for each protein, which indicates that they are designed to perform different functions in the cell. PpcA and PpcD appear to be optimized to interact with specific redox partners involving e(-)/H(+) transfer via different mechanisms. Although no evidence of preferential electron transfer pathway or e(-)/H(+) coupling was found for PpcB and PpcE, the difference in their working potential ranges suggests that they may also have different physiological redox partners. This is the first study, to our knowledge, to characterize homologous cytochromes from the same microorganism and provide evidence of their different mechanistic and functional properties. These findings provide an explanation for the coexistence of five periplasmic triheme cytochromes in G. sulfurreducens.
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Affiliation(s)
- Leonor Morgado
- Requimte-Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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