1
|
Fernandes TM, Morgado L, Turner DL, Salgueiro CA. Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria. Antioxidants (Basel) 2021; 10:844. [PMID: 34070486 PMCID: PMC8227773 DOI: 10.3390/antiox10060844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.
Collapse
Affiliation(s)
- Tomás M. Fernandes
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - Leonor Morgado
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal;
| | - Carlos A. Salgueiro
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| |
Collapse
|
2
|
Dai J, Knott GJ, Fu W, Lin TW, Furst AL, Britt RD, Francis MB. Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins. ACS NANO 2021; 15:8110-8119. [PMID: 33285072 DOI: 10.1021/acsnano.0c07165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioenergetic processes in nature have relied on networks of cofactors for harvesting, storing, and transforming the energy from sunlight into chemical bonds. Models mimicking the structural arrangement and functional crosstalk of the cofactor arrays are important tools to understand the basic science of natural systems and to provide guidance for non-natural functional biomaterials. Here, we report an artificial multiheme system based on a circular permutant of the tobacco mosaic virus coat protein (cpTMV). The double disk assembly of cpTMV presents a gap region sandwiched by the two C2-symmetrically related disks. Non-native bis-his coordination sites formed by the mutation of the residues in this gap region were computationally screened and experimentally tested. A cpTMV mutant Q101H was identified to create a circular assembly of 17 protein-embedded hemes. Biophysical characterization using X-ray crystallography, cyclic voltammetry, and electron paramagnetic resonance (EPR) suggested both structural and functional similarity to natural multiheme cytochrome c proteins. This protein framework offers many further engineering opportunities for tuning the redox properties of the cofactors and incorporating non-native components bearing varied porphyrin structures and metal centers. Emulating the electron transfer pathways in nature using a tunable artificial system can contribute to the development of photocatalytic materials and bioelectronics.
Collapse
Affiliation(s)
- Jing Dai
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Wen Fu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Tiffany W Lin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Late Stage Pharmaceutical Development, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Materials Sciences Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Das JK, Pal Choudhury P. Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach. PLoS One 2017; 12:e0175031. [PMID: 28362850 PMCID: PMC5376323 DOI: 10.1371/journal.pone.0175031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 11/19/2022] Open
Abstract
Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study.
Collapse
Affiliation(s)
- Jayanta Kumar Das
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
| |
Collapse
|
5
|
Ferreira MR, Dantas JM, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the electron acceptor Fe(iii) citrate studied by NMR. Dalton Trans 2017; 46:2350-2359. [DOI: 10.1039/c6dt04129a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular interactions betweenGeobacter sulfurreducenstriheme cytochromes and Fe(iii) citrate.
Collapse
Affiliation(s)
- Marisa R. Ferreira
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Joana M. Dantas
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Carlos A. Salgueiro
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Dantas JM, Simões T, Morgado L, Caciones C, Fernandes AP, Silva MA, Bruix M, Pokkuluri PR, Salgueiro CA. Unveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducens. J Phys Chem B 2016; 120:10221-10233. [DOI: 10.1021/acs.jpcb.6b07059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Telma Simões
- UCIBIO-Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- UCIBIO-Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Clara Caciones
- 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
| | - Marta A. Silva
- UCIBIO-Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Marta Bruix
- Departamento
de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - P. Raj Pokkuluri
- Biosciences
Division, Argonne National Laboratory, Lemont, 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
| |
Collapse
|
8
|
Dantas JM, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interaction studies revealed the bifunctional behavior of triheme cytochrome PpcA from Geobacter sulfurreducens toward the redox active analog of humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1129-38. [DOI: 10.1016/j.bbabio.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 11/17/2022]
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Dantas JM, Morgado L, Marques AC, Salgueiro CA. Probing the effect of ionic strength on the functional robustness of the triheme cytochrome PpcA from Geobacter sulfurreducens: a contribution for optimizing biofuel cell's power density. J Phys Chem B 2014; 118:12416-25. [PMID: 25275217 DOI: 10.1021/jp507898x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The increase of conductivity of electrolytes favors the current production in microbial fuel cells (MFCs). Adaptation of cell cultures to higher ionic strength is a promising strategy to increase electricity production. The bacterium Geobacter sulfurreducens is considered a leading candidate for MFCs. Therefore, it is important to evaluate the impact of the ionic strength on the functional properties of key periplasmic proteins that warrants electron transfer to cell exterior. The effect of the ionic strength on the functional properties of triheme cytochrome PpcA, the most abundant periplasmic cytochrome in G. sulfurreducens, was investigated by NMR and potentiometric methods. The redox properties of heme IV are the most affected ones. Chemical shift perturbation measurements on the backbone NMR signals, at increasing ionic strength, also showed that the region close to heme IV is the most affected due to the large number of positively charged residues, which confer a highly positive electrostatic surface around this heme. The shielding of these positive charges at high ionic strength explain the observed decrease in the reduction potential of heme IV and shows that PpcA was designed to maintain its functional mechanistic features even at high ionic strength.
Collapse
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
| | | | | | | |
Collapse
|