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Ullrich SR, Fuchs H, Ashworth-Güth C. Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level. Front Microbiol 2024; 15:1357152. [PMID: 38384274 PMCID: PMC10879576 DOI: 10.3389/fmicb.2024.1357152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
The tendency of the periplasmic redox proteins in acidophiles to have more positive redox potentials (Em) than their homologous counterparts in neutrophiles suggests an adaptation to acidic pH at protein level, since thermodynamics of electron transfer processes are also affected by acidic pH. Since this conclusion is mainly based on the electrochemical characterization of redox proteins from extreme acidophiles of the genus Acidithiobacillus, we aimed to characterize three recombinant redox proteins of the more moderate acidophile Ferrovum sp. PN-J47-F6. We applied protein film voltammetry and linear sweep voltammetry coupled to UV/Vis spectroscopy to characterize the redox behavior of HiPIP-41, CytC-18, and CytC-78, respectively. The Em-values of HiPIP-41 (571 ± 16 mV), CytC-18 (276 ± 8 mV, 416 ± 2 mV), and CytC-78 (308 ± 7 mV, 399 ± 7 mV) were indeed more positive than those of homologous redox proteins in neutrophiles. Moreover, our findings suggest that the adaptation of redox proteins with respect to their Em occurs more gradually in response to the pH, since there are also differences between moderate and more extreme acidophiles. In order to address structure function correlations in these redox proteins with respect to structural features affecting the Em, we conducted a comparative structural analysis of the Ferrovum-derived redox proteins and homologs of Acidithiobacillus spp. and neutrophilic proteobacteria. Hydrophobic contacts in the redox cofactor binding pockets resulting in a low solvent accessibility appear to be the major factor contributing to the more positive Em-values in acidophile-derived redox proteins. While additional cysteines in HiPIPs of acidophiles might increase the effective shielding of the [4Fe-4S]-cofactor, the tight shielding of the heme centers in acidophile-derived cytochromes is achieved by a drastic increase in hydrophobic contacts (A.f. Cyc41), and by a larger fraction of aromatic residues in the binding pockets (CytC-18, CytC-78).
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Affiliation(s)
- Sophie R. Ullrich
- Environmental Microbiology Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Helena Fuchs
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Charlotte Ashworth-Güth
- Salt and Mineral Chemistry Group, Institute for Inorganic Chemistry, TU Bergakademie Freiberg, Freiberg, Germany
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Ullrich SR, Fuchs H, Schlömann M. Shedding light on the electron transfer chain of a moderately acidophilic iron oxidizer: characterization of recombinant HiPIP-41, CytC-18 and CytC-78 derived from Ferrovum sp. PN-J47-F6. Res Microbiol 2024; 175:104088. [PMID: 37348744 DOI: 10.1016/j.resmic.2023.104088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
Efficient electron transfer from the donor to the acceptor couple presents a necessary requirement for acidophilic and neutrophilic iron oxidizers due to the low energy yield of aerobic ferrous iron oxidation. Involved periplasmic electron carriers are very diverse in these bacteria and show adaptations to the respective thermodynamic constraints such as a more positive redox potential reported for extreme acidophilic Acidithiobacillus spp. Respiratory chain candidates of moderately acidophilic members of the genus Ferrovum share similarities with both their neutrophilic iron oxidizing relatives and the more distantly related Acidithiobacillus spp. We examined our previous omics-based conclusions on the potential electron transfer chain in Ferrovum spp. by characterizing the three redox protein candidates CytC-18, CytC-78 and HiPIP-41 of strain PN-J47-F6 which were produced as recombinant proteins in Eschericha coli. UV/Vis-based redox assays suggested that HiPIP-41 has a very positive redox potential while redox potentials of CytC-18 and CytC-78 are more negative than their counterparts in Acidithiobacillus spp. Far Western dot blotting demonstrated interactions between all three recombinant redox proteins while redox assays showed the electron transfer from HiPIP-41 to either of the cytochromes. Altogether, CytC-18, CytC-78 and HiPIP-41 indeed represent very likely candidates of the electron transfer in Ferrovum sp. PN-J4-F6.
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Affiliation(s)
- Sophie R Ullrich
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany.
| | - Helena Fuchs
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany
| | - Michael Schlömann
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany
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Evaluation of Cyc 1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:526-532. [PMID: 35286603 DOI: 10.1007/s12275-022-1645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 10/18/2022]
Abstract
Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1 and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc1 and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.
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Malik L, Hedrich S. Ferric Iron Reduction in Extreme Acidophiles. Front Microbiol 2022; 12:818414. [PMID: 35095822 PMCID: PMC8790237 DOI: 10.3389/fmicb.2021.818414] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.
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Affiliation(s)
- Luise Malik
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Sabrina Hedrich
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
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Shojapour M, Fatemi F, Farahmand S, Shasaltaneh MD. Investigation of Cyc 1 protein structure stability after H53I mutation using computational approaches to improve redox potential. J Mol Graph Model 2021; 105:107864. [PMID: 33647753 DOI: 10.1016/j.jmgm.2021.107864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium that grows in rigid surroundings and gets its own energy from the oxidation of Fe2+ to Fe3+. These bacteria are involved in the bioleaching process. Cyc1 is a periplasmic protein with a crucial role in electron transportation in the respiratory chain. His53 of the Cyc1 protein, involved in electron transfer to CoxB, was selected for mutation and bioinformatics studies. His53 was substituted by Ile using PyMol software. Molecular dynamics simulations were performed for wild and mutant types of Cyc1 protein. The conformational changes of mutated protein were studied by analyzing RMSD, RMSF, SASA, Rg, H Bond, and DSSP. The results of the RMSF analysis indicated an increase in the flexibility of the ligand in the mutant. Finally, active site instability leads to an increase in the value of E0 at the mutation point and improving electron transfer. On the other, His53 in Cyc1 is interconnected to Glu126 in CoxB through the water molecule (W76) and hydrogen bonding. In the H53I mutation, there was a decrease in the distance between H2O 2030, 2033, and isoleucine 53, and subsequently, the distance to the water molecule 76 between the two proteins was reduced and strengthens the hydrogen bond between Cyc1 and CoxB, finally improves electron transfer and the bioleaching process.
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Affiliation(s)
- Mahnaz Shojapour
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran.
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Somayeh Farahmand
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran
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Wang X, Clément R, Roger M, Bauzan M, Mazurenko I, Poulpiquet AD, Ilbert M, Lojou E. Bacterial Respiratory Chain Diversity Reveals a Cytochrome c Oxidase Reducing O 2 at Low Overpotentials. J Am Chem Soc 2019; 141:11093-11102. [PMID: 31274287 DOI: 10.1021/jacs.9b03268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c oxidases (CcOs) are the terminal enzymes in energy-converting chains of microorganisms, where they reduce oxygen into water. Their affinity for O2 makes them attractive biocatalysts for technological devices in which O2 concentration is limited, but the high overpotentials they display on electrodes severely limit their applicative use. Here, the CcO of the acidophilic bacterium Acidithiobacillus ferrooxidans is studied on various carbon materials by direct protein electrochemistry and mediated one with redox mediators either diffusing or co-immobilized at the electrode surface. The entrapment of the CcO in a network of hydrophobic carbon nanofibers permits a direct electrochemical communication between the enzyme and the electrode. We demonstrate that the CcO displays a μM affinity for O2 and reduces O2 at exceptionally high electrode potentials in the range of +700 to +540 mV vs NHE over a pH range of 4-6. The kinetics of interactions between the enzyme and its physiological partners are fully quantified. Based on these results, an electron transfer pathway allowing O2 reduction in the acidic metabolic chain is proposed.
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Affiliation(s)
- Xie Wang
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
| | - Romain Clément
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
| | - Magali Roger
- School of Natural and Environmental Sciences , Newcastle University , Devonshire Building , NE1 7RX , Newcastle upon Tyne , England
| | - Marielle Bauzan
- Aix-Marseille Univ , CNRS, IMM FR 3479, 31 Chemin Aiguier , 13009 Marseille , France
| | - Ievgen Mazurenko
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
| | - Anne de Poulpiquet
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
| | - Marianne Ilbert
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
| | - Elisabeth Lojou
- Aix-Marseille Univ , CNRS, BIP UMR 7281, 31 Chemin Aiguier , CS 70071, 13402 Marseille Cedex 09 , France
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Wang X, Roger M, Clément R, Lecomte S, Biaso F, Abriata LA, Mansuelle P, Mazurenko I, Giudici-Orticoni MT, Lojou E, Ilbert M. Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin. Chem Sci 2018; 9:4879-4891. [PMID: 29910941 PMCID: PMC5982212 DOI: 10.1039/c8sc01615a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 12/15/2022] Open
Abstract
Acidithiobacillus ferrooxidans, a chemolithoautotrophic Gram-negative bacterium, has a remarkable ability to obtain energy from ferrous iron oxidation at pH 2. Several metalloproteins have been described as being involved in this respiratory chain coupling iron oxidation with oxygen reduction. However, their properties and physiological functions remain largely unknown, preventing a clear understanding of the global mechanism. In this work, we focus on two metalloproteins of this respiratory pathway, a diheme cytochrome c4 (Cyt c4) and a green copper protein (AcoP) of unknown function. We first demonstrate the formation of a complex between these two purified proteins, which allows homogeneous intermolecular electron-transfer in solution. We then mimic the physiological interaction between the two partners by replacing one at a time with electrodes displaying different chemical functionalities. From the electrochemical behavior of individual proteins, we show that, while electron transfer on AcoP requires weak electrostatic interaction, electron transfer on Cyt c4 tolerates different charge and hydrophobicity conditions, suggesting a pivotal role of this protein in the metabolic chain. The electrochemical study of the proteins incubated together demonstrates an intermolecular electron transfer involving the protein complex, in which AcoP is reduced through the high potential heme of Cyt c4. Modelling of the electrochemical signals at different scan rates allows us to estimate the rate constant of this intermolecular electron transfer in the range of a few s-1. Possible routes for electron transfer in the acidophilic bacterium are deduced.
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Affiliation(s)
- X Wang
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - M Roger
- School of Life Sciences , University of Dundee , Dundee , DD1 5EH , Scotland , UK
| | - R Clément
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - S Lecomte
- Institute for Chemistry and Biology of Membrane and Nano-objects , Allée Geoffroy St Hilaire , 33600 Pessac , France
| | - F Biaso
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - L A Abriata
- Laboratory for Biomolecular Modeling , École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics , AAB014, Station 19 , 1015 Lausanne , Switzerland
| | - P Mansuelle
- Aix Marseille Univ , CNRS , Institut de Microbiologie de la Méditerranée , FR 3479, Plate-forme Protéomique, Marseille Protéomique (MaP), B.P. 71 , 13402 Marseille Cedex 20 , France
| | - I Mazurenko
- School of Biomedical Sciences , Leeds , LS2 9JT , UK
| | - M T Giudici-Orticoni
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - E Lojou
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
| | - M Ilbert
- Aix Marseille Univ , CNRS , IMM , BIP , UMR 7281 , 31 Chemin Aiguier , 13009 Marseille , France . ;
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Feifel SC, Stieger KR, Hejazi M, Wang X, Ilbert M, Zouni A, Lojou E, Lisdat F. Dihemic c4-type cytochrome acting as a surrogate electron conduit: Artificially interconnecting a photosystem I supercomplex with electrodes. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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An electrochemical sensing approach for scouting microbial chemolithotrophic metabolisms. Bioelectrochemistry 2018; 123:125-136. [PMID: 29747131 DOI: 10.1016/j.bioelechem.2018.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/25/2018] [Accepted: 04/29/2018] [Indexed: 11/21/2022]
Abstract
The present study was aimed to test an electrochemical sensing approach for the detection of an active chemolithotrophic metabolism (and therefore the presence of chemolithotrophic microorganisms) by using the corrosion of pyrite by Acidithiobacillus ferrooxidans as a model. Different electrochemical techniques were combined with adhesion studies and scanning electron microscopy (SEM). The experiments were performed in presence or absence of A. ferrooxidans and without or with ferrous iron in the culture medium (0 and 0.5 g L-1, respectively). Electrochemical parameters were in agreement with voltammetric studies and SEM showing that it is possible to distinguish between an abiotically-induced corrosion process (AIC) and a microbiologically-induced corrosion process (MIC). The results show that our approach not only allows the detection of chemolithotrophic activity of A. ferrooxidans but also can characterize the corrosion process. This may have different kind of applications, from those related to biomining to life searching missions in other planetary bodies.
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Norris PR, Laigle L, Slade S. Cytochromes in anaerobic growth of Acidithiobacillus ferrooxidans. Microbiology (Reading) 2018; 164:383-394. [DOI: 10.1099/mic.0.000616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul R. Norris
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Ludovic Laigle
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: The Native Antigen Company, Langford Locks, Kidlington, Oxford, OX5 1LH, UK
| | - Susan Slade
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
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Ai C, Liang Y, Miao B, Chen M, Zeng W, Qiu G. Identification and Analysis of a Novel Gene Cluster Involves in Fe 2+ Oxidation in Acidithiobacillus ferrooxidans ATCC 23270, a Typical Biomining Acidophile. Curr Microbiol 2018; 75:818-826. [PMID: 29464360 DOI: 10.1007/s00284-018-1453-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/12/2018] [Indexed: 11/26/2022]
Abstract
Iron-oxidizing Acidithiobacillus spp. are applied worldwide in biomining industry to extract metals from sulfide minerals. They derive energy for survival through Fe2+ oxidation and generate Fe3+ for the dissolution of sulfide minerals. However, molecular mechanisms of their iron oxidation still remain elusive. A novel two-cytochrome-encoding gene cluster (named tce gene cluster) encoding a high-molecular-weight cytochrome c (AFE_1428) and a c4-type cytochrome c552 (AFE_1429) in A. ferrooxidans ATCC 23270 was first identified in this study. Bioinformatic analysis together with transcriptional study showed that AFE_1428 and AFE_1429 were the corresponding paralog of Cyc2 (AFE_3153) and Cyc1 (AFE_3152) which were encoded by the extensively studied rus operon and had been proven involving in ferrous iron oxidation. Both AFE_1428 and AFE_1429 contained signal peptide and the classic heme-binding motif(s) as their corresponding paralog. The modeled structure of AFE_1429 showed high resemblance to Cyc1. AFE_1428 and AFE_1429 were preferentially transcribed as their corresponding paralogs in the presence of ferrous iron as sole energy source as compared with sulfur. The tce gene cluster is highly conserved in the genomes of four phylogenetic-related A. ferrooxidans strains that were originally isolated from different sites separated with huge geographical distance, which further implies the importance of this gene cluster. Collectively, AFE_1428 and AFE_1429 involve in Fe2+ oxidation like their corresponding paralog by integrating with the metalloproteins encoded by rus operon. This study provides novel insights into the Fe2+ oxidation mechanism in Fe2+-oxidizing A. ferrooxidans ssp.
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Affiliation(s)
- Chenbing Ai
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuting Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Miao Chen
- CSIRO Process Science and Engineering, Clayton, VIC, Australia
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China.
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
- CSIRO Process Science and Engineering, Clayton, VIC, Australia.
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China.
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
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Chiu BK, Kato S, McAllister SM, Field EK, Chan CS. Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone. Front Microbiol 2017; 8:1280. [PMID: 28769885 PMCID: PMC5513912 DOI: 10.3389/fmicb.2017.01280] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/26/2017] [Indexed: 01/11/2023] Open
Abstract
Chemolithotrophic iron-oxidizing bacteria (FeOB) could theoretically inhabit any environment where Fe(II) and O2 (or nitrate) coexist. Until recently, marine Fe-oxidizing Zetaproteobacteria had primarily been observed in benthic and subsurface settings, but not redox-stratified water columns. This may be due to the challenges that a pelagic lifestyle would pose for Zetaproteobacteria, given low Fe(II) concentrations in modern marine waters and the possibility that Fe oxyhydroxide biominerals could cause cells to sink. However, we recently cultivated Zetaproteobacteria from the Chesapeake Bay oxic–anoxic transition zone, suggesting that they can survive and contribute to biogeochemical cycling in a stratified estuary. Here we describe the isolation, characterization, and genomes of two new species, Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8, which are the first Zetaproteobacteria isolates from a pelagic environment. We looked for adaptations enabling strains CP-5 and CP-8 to overcome the challenges of living in a low Fe redoxcline with frequent O2 fluctuations due to tidal mixing. We found that the CP strains produce distinctive dreadlock-like Fe oxyhydroxide structures that are easily shed, which would help cells maintain suspension in the water column. These oxides are by-products of Fe(II) oxidation, likely catalyzed by the putative Fe(II) oxidase encoded by the cyc2 gene, present in both CP-5 and CP-8 genomes; the consistent presence of cyc2 in all microaerophilic FeOB and other FeOB genomes supports its putative role in Fe(II) oxidation. The CP strains also have two gene clusters associated with biofilm formation (Wsp system and the Widespread Colonization Island) that are absent or rare in other Zetaproteobacteria. We propose that biofilm formation enables the CP strains to attach to FeS particles and form flocs, an advantageous strategy for scavenging Fe(II) and developing low [O2] microenvironments within more oxygenated waters. However, the CP strains appear to be adapted to somewhat higher concentrations of O2, as indicated by the presence of genes encoding aa3-type cytochrome c oxidases, but not the cbb3-type found in all other Zetaproteobacteria isolate genomes. Overall, our results reveal adaptations for life in a physically dynamic, low Fe(II) water column, suggesting that niche-specific strategies can enable Zetaproteobacteria to live in any environment with Fe(II).
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Affiliation(s)
- Beverly K Chiu
- Department of Geological Sciences, University of Delaware, NewarkDE, United States
| | - Shingo Kato
- Project Team for Development of New-Generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and TechnologyKanagawa, Japan
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, NewarkDE, United States
| | - Erin K Field
- Department of Biology, East Carolina University, GreenvilleNC, United States
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, NewarkDE, United States.,School of Marine Science and Policy, University of Delaware, NewarkDE, United States
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Kucera J, Sedo O, Potesil D, Janiczek O, Zdrahal Z, Mandl M. Comparative proteomic analysis of sulfur-oxidizing Acidithiobacillus ferrooxidans CCM 4253 cultures having lost the ability to couple anaerobic elemental sulfur oxidation with ferric iron reduction. Res Microbiol 2016; 167:587-94. [DOI: 10.1016/j.resmic.2016.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/14/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
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Are there multiple mechanisms of anaerobic sulfur oxidation with ferric iron in Acidithiobacillus ferrooxidans ? Res Microbiol 2016; 167:357-66. [DOI: 10.1016/j.resmic.2016.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/17/2022]
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15
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Roger M, Biaso F, Castelle CJ, Bauzan M, Chaspoul F, Lojou E, Sciara G, Caffarri S, Giudici-Orticoni MT, Ilbert M. Spectroscopic characterization of a green copper site in a single-domain cupredoxin. PLoS One 2014; 9:e98941. [PMID: 24932914 PMCID: PMC4059628 DOI: 10.1371/journal.pone.0098941] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/09/2014] [Indexed: 12/13/2022] Open
Abstract
Cupredoxins are widespread copper-binding proteins, mainly involved in electron transfer pathways. They display a typical rigid greek key motif consisting of an eight stranded β-sandwich. A fascinating feature of cupredoxins is the natural diversity of their copper center geometry. These geometry variations give rise to drastic changes in their color, such as blue, green, red or purple. Based on several spectroscopic and structural analyses, a connection between the geometry of their copper-binding site and their color has been proposed. However, little is known about the relationship between such diversity of copper center geometry in cupredoxins and possible implications for function. This has been difficult to assess, as only a few naturally occurring green and red copper sites have been described so far. We report herein the spectrocopic characterization of a novel kind of single domain cupredoxin of green color, involved in a respiratory pathway of the acidophilic organism Acidithiobacillus ferrooxidans. Biochemical and spectroscopic characterization coupled to bioinformatics analysis reveal the existence of some unusual features for this novel member of the green cupredoxin sub-family. This protein has the highest redox potential reported to date for a green-type cupredoxin. It has a constrained green copper site insensitive to pH or temperature variations. It is a green-type cupredoxin found for the first time in a respiratory pathway. These unique properties might be explained by a region of unknown function never found in other cupredoxins, and by an unusual length of the loop between the second and the fourth copper ligands. These discoveries will impact our knowledge on non-engineered green copper sites, whose involvement in respiratory chains seems more widespread than initially thought.
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Affiliation(s)
- Magali Roger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Frédéric Biaso
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Marielle Bauzan
- Unité de Fermentation, Institut de Microbiologie de la Méditerranée, CNRS-FR 3479, Aix Marseille Université, Marseille, France
| | - Florence Chaspoul
- Unité Chimie Physique, Prévention des Risques et Nuisances Technologiques, Faculté de Pharmacie, CNRS-UMR 7263, Aix-Marseille Université, Marseille, France
| | - Elisabeth Lojou
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Giuliano Sciara
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Stefano Caffarri
- Unité de Biologie Végétale et Microbiologie Environnementales, CNRS-UMR 7265, CEA, Aix Marseille Université, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Marianne Ilbert
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
- * E-mail:
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17
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Reconstitution of supramolecular organization involved in energy metabolism at electrochemical interfaces for biosensing and bioenergy production. Anal Bioanal Chem 2013; 406:1011-27. [DOI: 10.1007/s00216-013-7465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/01/2013] [Accepted: 10/25/2013] [Indexed: 12/26/2022]
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18
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Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics 2013; 14:485. [PMID: 23865623 PMCID: PMC3750248 DOI: 10.1186/1471-2164-14-485] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
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Affiliation(s)
- Alexis P Yelton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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19
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Robin S, Arese M, Forte E, Sarti P, Kolaj-Robin O, Giuffrè A, Soulimane T. Functional dissection of the multi-domain di-heme cytochrome c(550) from Thermus thermophilus. PLoS One 2013; 8:e55129. [PMID: 23383080 PMCID: PMC3561395 DOI: 10.1371/journal.pone.0055129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/18/2012] [Indexed: 11/18/2022] Open
Abstract
In bacteria, oxidation of sulfite to sulfate, the most common strategy for sulfite detoxification, is mainly accomplished by the molybdenum-containing sulfite:acceptor oxidoreductases (SORs). Bacterial SORs are very diverse proteins; they can exist as monomers or homodimers of their core subunit, as well as heterodimers with an additional cytochrome c subunit. We have previously described the homodimeric SOR from Thermus thermophilus HB8 (SOR(TTHB8)), identified its physiological electron acceptor, cytochrome c(550), and demonstrated the key role of the latter in coupling sulfite oxidation to aerobic respiration. Herein, the role of this di-heme cytochrome c was further investigated. The cytochrome was shown to be composed of two conformationally independent domains, each containing one heme moiety. Each domain was separately cloned, expressed in E. coli and purified to homogeneity. Stopped-flow experiments showed that: i) the N-terminal domain is the only one accepting electrons from SOR(TTHB8); ii) the N- and C-terminal domains are in rapid redox equilibrium and iii) both domains are able to transfer electrons further to cytochrome c(552), the physiological substrate of the ba(3) and caa(3) terminal oxidases. These findings show that cytochrome c(550) functions as a electron shuttle, without working as an electron wire with one heme acting as the electron entry and the other as the electron exit site. Although contribution of the cytochrome c(550) C-terminal domain to T. thermophilus sulfur respiration seems to be dispensable, we suggest that di-heme composition of the cytochrome physiologically enables storage of the two electrons generated from sulfite oxidation, thereof ensuring efficient contribution of sulfite detoxification to the respiratory chain-mediated energy generation.
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Affiliation(s)
- Sylvain Robin
- Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Marzia Arese
- Department of Biochemical Sciences and Istituto Pasteur – Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Elena Forte
- Department of Biochemical Sciences and Istituto Pasteur – Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Paolo Sarti
- Department of Biochemical Sciences and Istituto Pasteur – Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
- Consiglio Nazionale delle Ricerche Istituto di Biologia e Patologia Molecolari, Rome, Italy
| | - Olga Kolaj-Robin
- Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Alessandro Giuffrè
- Consiglio Nazionale delle Ricerche Istituto di Biologia e Patologia Molecolari, Rome, Italy
- * E-mail: (AG); (TS)
| | - Tewfik Soulimane
- Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
- * E-mail: (AG); (TS)
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20
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Mineral respiration under extreme acidic conditions: from a supramolecular organization to a molecular adaptation in Acidithiobacillus ferrooxidans. Biochem Soc Trans 2012; 40:1324-9. [DOI: 10.1042/bst20120141] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotrophic Gram-negative bacterium that can derive energy from the oxidation of ferrous iron at pH 2 using oxygen as electron acceptor. The study of this bacterium has economic and fundamental biological interest because of its use in the industrial extraction of copper and uranium from ores. For this reason, its respiratory chain has been analysed in detail in recent years. Studies have shown the presence of a functional supercomplex that spans the outer and the inner membranes and allows a direct electron transfer from the extracellular Fe2+ ions to the inner membrane cytochrome c oxidase. Iron induces the expression of two operons encoding proteins implicated in this complex as well as in the regeneration of the reducing power. Most of these are metalloproteins that have been characterized biochemically, structurally and biophysically. For some of them, the molecular basis of their adaptation to the periplasmic acidic environment has been described. Modifications in the metal surroundings have been highlighted for cytochrome c and rusticyanin, whereas, for the cytochrome c oxidase, an additional partner that maintains its stability and activity has been demonstrated recently.
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21
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Ilbert M, Bonnefoy V. Insight into the evolution of the iron oxidation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:161-75. [PMID: 23044392 DOI: 10.1016/j.bbabio.2012.10.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 01/01/2023]
Abstract
Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O(2). This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Marianne Ilbert
- Aix-Marseille Université, CNRS, BIP UMR7281,13009, Marseille, France.
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22
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Schoepp-Cothenet B, van Lis R, Atteia A, Baymann F, Capowiez L, Ducluzeau AL, Duval S, ten Brink F, Russell MJ, Nitschke W. On the universal core of bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:79-93. [PMID: 22982447 DOI: 10.1016/j.bbabio.2012.09.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023]
Abstract
Living cells are able to harvest energy by coupling exergonic electron transfer between reducing and oxidising substrates to the generation of chemiosmotic potential. Whereas a wide variety of redox substrates is exploited by prokaryotes resulting in very diverse layouts of electron transfer chains, the ensemble of molecular architectures of enzymes and redox cofactors employed to construct these systems is stunningly small and uniform. An overview of prominent types of electron transfer chains and of their characteristic electrochemical parameters is presented. We propose that basic thermodynamic considerations are able to rationalise the global molecular make-up and functioning of these chemiosmotic systems. Arguments from palaeogeochemistry and molecular phylogeny are employed to discuss the evolutionary history leading from putative energy metabolisms in early life to the chemiosmotic diversity of extant organisms. Following the Occam's razor principle, we only considered for this purpose origin of life scenarios which are contiguous with extant life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France.
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23
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Chang HY, Ahn Y, Pace LA, Lin MT, Lin YH, Gennis RB. The diheme cytochrome c(4) from Vibrio cholerae is a natural electron donor to the respiratory cbb(3) oxygen reductase. Biochemistry 2010; 49:7494-503. [PMID: 20715760 DOI: 10.1021/bi1004574] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The respiratory chain of Vibrio cholerae contains three bd-type quinol oxygen reductases as well as one cbb(3) oxygen reductase. The cbb(3) oxygen reductase has been previously isolated and characterized; however, the natural mobile electron donor(s) that shuttles electrons between the bc(1) complex and the cbb(3) oxygen reductase is not known. The most likely candidates are the diheme cytochrome c(4) and monoheme cytochrome c(5), which have been previously shown to be present in the periplasm of aerobically grown cultures of V. cholerae. Both cytochromes c(4) and c(5) from V. cholerae have been cloned and expressed heterologously in Escherichia coli. It is shown that reduced cytochrome c(4) is a substrate for the purified cbb(3) oxygen reductase and can support steady state oxygen reductase activity of at least 300 e(-1)/s. In contrast, reduced cytochrome c(5) is not a good substrate for the cbb(3) oxygen reductase. Surprisingly, the dependence of the oxygen reductase activity on the concentration of cytochrome c(4) does not exhibit saturation. Global spectroscopic analysis of the time course of the oxidation of cytochrome c(4) indicates that the apparent lack of saturation is due to the strong dependence of K(M) and V(max) on the concentration of oxidized cytochrome c(4). Whether this is an artifact of the in vitro assay or has physiological significance remains unknown. Cyclic voltammetry was used to determine that the midpoint potentials of the two hemes in cytochrome c(4) are 240 and 340 mV (vs standard hydrogen electrode), similar to the electrochemical properties of other c(4)-type cytochromes. Genomic analysis shows a strong correlation between the presence of a c(4)-type cytochrome and a cbb(3) oxygen reductase within the beta- and gamma-proteobacterial clades, suggesting that cytochrome c(4) is the likely natural electron donor to the cbb(3) oxygen reductases within these organisms. These would include the beta-proteobacteria Neisseria meningitidis and Neisseria gonnorhoeae, in which the cbb(3) oxygen reductases are the only terminal oxidases in their respiratory chains, and the gamma-proteobacterium Pseudomonas stutzeri.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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24
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Overexpression of Rusticyanin in Acidithiobacillus ferrooxidans ATCC19859 Increased Fe(II) Oxidation Activity. Curr Microbiol 2010; 62:320-4. [DOI: 10.1007/s00284-010-9708-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
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25
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Castelle C, Ilbert M, Infossi P, Leroy G, Giudici-Orticoni MT. An unconventional copper protein required for cytochrome c oxidase respiratory function under extreme acidic conditions. J Biol Chem 2010; 285:21519-25. [PMID: 20442397 PMCID: PMC2898452 DOI: 10.1074/jbc.m110.131359] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 04/30/2010] [Indexed: 11/06/2022] Open
Abstract
Very little is known about the processes used by acidophile organisms to preserve stability and function of respiratory pathways. Here, we reveal a potential strategy of these organisms for protecting and keeping functional key enzymes under extreme conditions. Using Acidithiobacillus ferrooxidans, we have identified a protein belonging to a new cupredoxin subfamily, AcoP, for "acidophile CcO partner," which is required for the cytochrome c oxidase (CcO) function. We show that it is a multifunctional copper protein with at least two roles as follows: (i) as a chaperone-like protein involved in the protection of the Cu(A) center of the CcO complex and (ii) as a linker between the periplasmic cytochrome c and the inner membrane cytochrome c oxidase. It could represent an interesting model for investigating the multifunctionality of proteins known to be crucial in pathways of energy metabolism.
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Affiliation(s)
- Cindy Castelle
- From the Laboratoire de Bioénergétique et Ingénierie des Protéines, IMM-CNRS, 13402 Marseille Cedex 20, France
| | - Marianne Ilbert
- From the Laboratoire de Bioénergétique et Ingénierie des Protéines, IMM-CNRS, 13402 Marseille Cedex 20, France
| | - Pascale Infossi
- From the Laboratoire de Bioénergétique et Ingénierie des Protéines, IMM-CNRS, 13402 Marseille Cedex 20, France
| | - Gisèle Leroy
- From the Laboratoire de Bioénergétique et Ingénierie des Protéines, IMM-CNRS, 13402 Marseille Cedex 20, France
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26
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Zheng Z, Gunner MR. Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV. Proteins 2009; 75:719-34. [PMID: 19003997 DOI: 10.1002/prot.22282] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. It is a challenge to determine how proteins manage to achieve this enormous range of E(m)s with a single type of redox cofactor. Proteins containing 141 unique hemes of a-, b-, and c-type, with bis-His, His-Met, and aquo-His ligation were calculated using Multi-Conformation Continuum Electrostatics (MCCE). The experimental E(m)s range over 800 mV from -350 mV in cytochrome c(3) to 450 mV in cytochrome c peroxidase (vs. SHE). The quantitative analysis of the factors that modulate heme electrochemistry includes the interactions of the heme with its ligands, the solvent, the protein backbone, and sidechains. MCCE calculated E(m)s are in good agreement with measured values. Using no free parameters the slope of the line comparing calculated and experimental E(m)s is 0.73 (R(2) = 0.90), showing the method accounts for 73% of the observed E(m) range. Adding a +160 mV correction to the His-Met c-type hemes yields a slope of 0.97 (R(2) = 0.93). With the correction 65% of the hemes have an absolute error smaller than 60 mV and 92% are within 120 mV. The overview of heme proteins with known structures and E(m)s shows both the lowest and highest potential hemes are c-type, whereas the b-type hemes are found in the middle E(m) range. In solution, bis-His ligation lowers the E(m) by approximately 205 mV relative to hemes with His-Met ligands. The bis-His, aquo-His, and His-Met ligated b-type hemes all cluster about E(m)s which are approximately 200 mV more positive in protein than in water. In contrast, the low potential bis-His c-type hemes are shifted little from in solution, whereas the high potential His-Met c-type hemes are raised by approximately 300 mV from solution. The analysis shows that no single type of interaction can be identified as the most important in setting heme electrochemistry in proteins. For example, the loss of solvation (reaction field) energy, which raises the E(m), has been suggested to be a major factor in tuning in situ E(m)s. However, the calculated solvation energy vs. experimental E(m) shows a slope of 0.2 and R(2) of 0.5 thus correlates weakly with E(m)s. All other individual interactions show even less correlation with E(m). However the sum of these terms does reproduce the range of observed E(m)s. Therefore, different proteins use different aspects of their structures to modulate the in situ heme electrochemistry. This study also shows that the calculated E(m)s are relatively insensitive to different heme partial charges and to the protein dielectric constant used in the simulation.
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Affiliation(s)
- Zhong Zheng
- Department of Physics, The City College of New York, New York, NY, USA
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27
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Physicochemical properties of diheme cytochrome c4 of unknown function from Vibrio parahaemolyticus strain RIMD2210633. Biosci Biotechnol Biochem 2008; 72:2791-4. [PMID: 18838782 DOI: 10.1271/bbb.80380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To characterize a diheme cytochrome c4 of unknown functional of the Vibrio genus for the first time, the Vibrio parahaemolyticus cytochrome c4 was overexpressed in Escherichia coli periplasm using the endogenous signal sequence. The physicochemical properties of the purified recombinant protein, viz., molecular mass, UV/Vis, and CD spectra, and the redox potentials of the N- and C-terminal domain hemes were determined.
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28
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Castelle C, Guiral M, Malarte G, Ledgham F, Leroy G, Brugna M, Giudici-Orticoni MT. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J Biol Chem 2008; 283:25803-11. [PMID: 18632666 PMCID: PMC3258861 DOI: 10.1074/jbc.m802496200] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/16/2008] [Indexed: 01/23/2023] Open
Abstract
The iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans involves various metalloenzymes. Here we demonstrate that the oxygen reduction pathway from ferrous iron (named downhill pathway) is organized as a supercomplex constituted of proteins located in the outer and inner membranes as well as in the periplasm. For the first time, the outer membrane-bound cytochrome c Cyc2 was purified, and we showed that it is responsible for iron oxidation and determined that its redox potential is the highest measured to date for a cytochrome c. The organization of metalloproteins inside the supramolecular structure was specified by protein-protein interaction experiments. The isolated complex spanning the two membranes had iron oxidase as well as oxygen reductase activities, indicating functional electron transfer between the first iron electron acceptor, Cyc2, and the Cu(A) center of cytochrome c oxidase aa(3). This is the first characterization of a respirasome from an acidophilic bacterium. In Acidithiobacillus ferrooxidans,O(2) reduction from ferrous iron must be coupled to the energy-consuming reduction of NAD(+)(P) from ferrous iron (uphill pathway) required for CO(2) fixation and other anabolic processes. Besides the proteins involved in the O(2) reduction, there were additional proteins in the supercomplex, involved in uphill pathway (bc complex and cytochrome Cyc(42)), suggesting a possible physical link between these two pathways.
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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