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Caviglia B, Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Petrillo C, Peters J, Sterpone F, Paciaroni A. Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability. J Phys Chem Lett 2024; 15:1435-1441. [PMID: 38291814 DOI: 10.1021/acs.jpclett.3c03351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.
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Affiliation(s)
- Beatrice Caviglia
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Daniele Di Bari
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague, Czech Republic
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Judith Peters
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique (CNRS), Univ. Grenoble Alpes, 140 Rue de la Physique, 38402 Saint-Martin-d'Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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2
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Prioretti L, D’Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, Lojou E, Guigliarelli B, Giudici-Orticoni MT, Guiral M. Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes. Life (Basel) 2023; 13:life13030627. [PMID: 36983784 PMCID: PMC10052474 DOI: 10.3390/life13030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.
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Affiliation(s)
- Laura Prioretti
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Giulia D’Ermo
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Pascale Infossi
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Arlette Kpebe
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Elisabeth Lojou
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Bruno Guigliarelli
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | | | - Marianne Guiral
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
- Correspondence:
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3
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Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Seydel T, Beck C, Petrillo C, Derreumaux P, Melchionna S, Sterpone F, Peters J, Paciaroni A. Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death. ACS Cent Sci 2023; 9:93-102. [PMID: 36712493 PMCID: PMC9881203 DOI: 10.1021/acscentsci.2c01078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.
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Affiliation(s)
- Daniele Di Bari
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
| | - Stepan Timr
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- J.
Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23Prague 8, Czechia
| | - Marianne Guiral
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université, 13400Marseille, France
| | | | - Tilo Seydel
- Institut
Laue-Langevin, 38000Grenoble, France
| | | | - Caterina Petrillo
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut Universitaire de France, 75005Paris, France
| | - Simone Melchionna
- ISC-CNR,
Dipartimento di Fisica, Università
Sapienza, 00185Rome, Italy
- Lexma
Technology1337 Massachusetts
Avenue, Arlington, Massachusetts02476, United States
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
| | - Judith Peters
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
- Institut Universitaire de France, 75005Paris, France
| | - Alessandro Paciaroni
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
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4
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Ranava D, Backes C, Karthikeyan G, Ouari O, Soric A, Guiral M, Cárdenas ML, Giudici-Orticoni MT. Metabolic Exchange and Energetic Coupling between Nutritionally Stressed Bacterial Species: Role of Quorum-Sensing Molecules. mBio 2021; 12:e02758-20. [PMID: 33468690 PMCID: PMC7845633 DOI: 10.1128/mbio.02758-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/18/2020] [Indexed: 12/29/2022] Open
Abstract
Formation of multispecies communities allows nearly every niche on earth to be colonized, and the exchange of molecular information among neighboring bacteria in such communities is key for bacterial success. To clarify the principles controlling interspecies interactions, we previously developed a coculture model with two anaerobic bacteria, Clostridium acetobutylicum (Gram positive) and Desulfovibrio vulgaris Hildenborough (Gram negative, sulfate reducing). Under conditions of nutritional stress for D. vulgaris, the existence of tight cell-cell interactions between the two bacteria induced emergent properties. Here, we show that the direct exchange of carbon metabolites produced by C. acetobutylicum allows D vulgaris to duplicate its DNA and to be energetically viable even without its substrates. We identify the molecular basis of the physical interactions and how autoinducer-2 (AI-2) molecules control the interactions and metabolite exchanges between C. acetobutylicum and D. vulgaris (or Escherichia coli and D. vulgaris). With nutrients, D. vulgaris produces a small molecule that inhibits in vitro the AI-2 activity and could act as an antagonist in vivo Sensing of AI-2 by D. vulgaris could induce formation of an intercellular structure that allows directly or indirectly metabolic exchange and energetic coupling between the two bacteria.IMPORTANCE Bacteria have usually been studied in single culture in rich media or under specific starvation conditions. However, in nature they coexist with other microorganisms and build an advanced society. The molecular bases of the interactions controlling this society are poorly understood. Use of a synthetic consortium and reducing complexity allow us to shed light on the bacterial communication at the molecular level. This study presents evidence that quorum-sensing molecule AI-2 allows physical and metabolic interactions in the synthetic consortium and provides new insights into the link between metabolism and bacterial communication.
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Affiliation(s)
- David Ranava
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - Cassandra Backes
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | | | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, ICR, Marseille, France
| | - Audrey Soric
- Aix-Marseille University, CNRS, Centrale Marseille, M2P2, Marseille, France
| | - Marianne Guiral
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - María Luz Cárdenas
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - Marie Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
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Guiral M, Giudici-Orticoni MT. Microbe Profile: Aquifex aeolicus: an extreme heat-loving bacterium that feeds on gases and inorganic chemicals. Microbiology (Reading) 2021; 167. [DOI: 10.1099/mic.0.001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterium ‘
Aquifex aeolicus
’ is the model organism for the deeply rooted phylum
Aquificae
. This ‘water-maker’ is an H2-oxidizing microaerophile that flourishes in extremely hot marine habitats, and it also thrives on the sulphur compounds commonly found in volcanic environments. ‘
A. aeolicus
’ has hyper-stable proteins and a fully sequenced genome, with some of its essential metabolic pathways deciphered (including energy conservation). Many of its proteins have also been characterized (especially structurally), including many of the enzymes involved in replication, transcription, RNA processing and cell envelope biosynthesis. Enzymes that are of promise for biotechnological applications have been widely investigated in this species. ‘
A. aeolicus
’ has also added to our understanding of the origins of life and evolution.
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Affiliation(s)
- Marianne Guiral
- BIP, UMR 7281, CNRS, Aix Marseille Université, Marseille, France
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6
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Baymann F, Schoepp-Cothenet B, Duval S, Guiral M, Brugna M, Baffert C, Russell MJ, Nitschke W. On the Natural History of Flavin-Based Electron Bifurcation. Front Microbiol 2018; 9:1357. [PMID: 30018596 PMCID: PMC6037941 DOI: 10.3389/fmicb.2018.01357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.
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Affiliation(s)
- Frauke Baymann
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | | | - Simon Duval
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Marianne Guiral
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Myriam Brugna
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Carole Baffert
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Michael J. Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Wolfgang Nitschke
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
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Guiral M, Neitzel C, Salvador Castell M, Martinez N, Giudici-Orticoni MT, Peters J. The effect of pH on the dynamics of natural membranes. Eur Phys J E Soft Matter 2018; 41:22. [PMID: 29464436 DOI: 10.1140/epje/i2018-11630-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
Pure phospholipids and membrane fragments from bacterial cells living under various conditions were studied against the influence of the surrounding acidity on the internal dynamics. For that we compared mean square displacements extracted from elastic incoherent neutron scattering data, measured both at low and at neutral pH, of the phospholipids 1,2-dimyristoyl-sn-glycero-3-phosphocholine and of samples from neutralophilic and acidophilic micro-organisms (some being hyperthermophilic and others mesophilic). The lipids showed a slight shift in the phase transition temperature of about 4 degrees under pH variation and became slightly more mobile at lower pH. The membrane fragments not used to extreme acidic conditions were significantly more sensitive to variations in the pH values, whereas the acidophilic and -tolerant samples were much less influenced by this parameter. They presented the higher softness at low pH, which was closer to their native condition. Such findings might be a hint for adaptation mechanisms to different acidity conditions.
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Affiliation(s)
- M Guiral
- Aix Marseille Univ, CNRS, BIP, Marseille, France
| | - C Neitzel
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000, Grenoble, France
- Institut Laue Langevin, Cedex 9, F-38042, Grenoble, France
| | - M Salvador Castell
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000, Grenoble, France
- Institut Laue Langevin, Cedex 9, F-38042, Grenoble, France
| | - N Martinez
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000, Grenoble, France
- Institut Laue Langevin, Cedex 9, F-38042, Grenoble, France
| | | | - J Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000, Grenoble, France.
- Institut Laue Langevin, Cedex 9, F-38042, Grenoble, France.
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Harb F, Giudici-Orticoni MT, Guiral M, Tinland B. Electrophoretic mobility of a monotopic membrane protein inserted into the top of supported lipid bilayers. Eur Phys J E Soft Matter 2016; 39:127. [PMID: 28012146 DOI: 10.1140/epje/i2016-16127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
We have studied the translational migration of a monotopic membrane protein, the bacterial sulfide quinone reductase (SQR) in supported n-bilayers ([Formula: see text]) under the influence of an electric field parallel to the membrane plane. The direction of the migration changes when the charge of the protein changes its sign. Measuring mobilities at different pH enables us to gain experimental physico-chemical data on SQR as its isoelectric point and its estimated oligomeric state (at least trimeric) when inserted in a lipid membrane. Consequently, in addition to the migration study of membrane proteins in a lipid environment, this experimental system, previously used with a transmembrane protein, is thus suitable to define membrane protein properties in conditions approaching the native ones (in the absence of detergent).
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Affiliation(s)
- Frédéric Harb
- Doctoral school for Science and Technology, platform for research in Nanosciences and Nanotechnology, Lebanese University, Campus Pierre Gemayel, BP 90239, Fanar-Metn, Lebanon
- Aix-Marseille Univ, CINaM-CNRS, UMR7325, 13288, Marseille, France
| | | | - Marianne Guiral
- Aix Marseille Univ, CNRS, BIP UMR 7281, 13402, Marseille, France
| | - Bernard Tinland
- Aix-Marseille Univ, CINaM-CNRS, UMR7325, 13288, Marseille, France.
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Boughanemi S, Lyonnet J, Infossi P, Bauzan M, Kosta A, Lignon S, Giudici-Orticoni MT, Guiral M. Microbial oxidative sulfur metabolism: biochemical evidence of the membrane-bound heterodisulfide reductase-like complex of the bacteriumAquifex aeolicus. FEMS Microbiol Lett 2016; 363:fnw156. [DOI: 10.1093/femsle/fnw156] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
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10
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Harb F, Prunetti L, Giudici-Orticoni MT, Guiral M, Tinland B. Insertion and self-diffusion of a monotopic protein, the Aquifex aeolicus sulfide quinone reductase, in supported lipid bilayers. Eur Phys J E Soft Matter 2015; 38:110. [PMID: 26490251 DOI: 10.1140/epje/i2015-15110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
Monotopic proteins constitute a class of membrane proteins that bind tightly to cell membranes, but do not span them. We present a FRAPP (Fluorescence Recovery After Patterned Photobleaching) study of the dynamics of a bacterial monotopic protein, SQR (sulfide quinone oxidoreductase) from the thermophilic bacteria Aquifex aeolicus, inserted into two different types of lipid bilayers (EggPC: L-α-phosphatidylcholine (Egg, Chicken) and DMPC: 1,2-dimyristoyl-sn-glycero-3-phosphocholine) supported on two different types of support (mica or glass). It sheds light on the behavior of a monotopic protein inside the bilayer. The insertion of SQR is more efficient when the bilayer is in the fluid phase than in the gel phase. We observed diffusion of the protein, with no immobile fraction, and deduced from the diffusion coefficient measurements that the resulting inserted object is the same whatever the incubation conditions, i.e. homogeneous in terms of oligomerization state. As expected, the diffusion coefficient of the SQR is smaller in the gel phase than in the fluid phase. In the supported lipid bilayer, the diffusion coefficient of the SQR is smaller than the diffusion coefficient of phospholipids in both gel and fluid phase. SQR shows a diffusion behavior different from the transmembrane protein α-hemolysin, and consistent with its monotopic character. Preliminary experiments in the presence of the substrate of SQR, DecylUbiquinone, an analogue of quinone, component of transmembrane electrons transport systems of eukaryotic and prokaryotic organisms, have been carried out. Finally, we studied the behavior of SQR, in terms of insertion and diffusion, in bilayers formed with lipids from Aquifex aeolicus. All the conclusions that we have found in the biomimetic systems applied to the biological system.
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Affiliation(s)
- Frédéric Harb
- Department of Biology, Faculty of Sciences - Section II, Lebanese University, Beirut, Lebanon
- CINaM-CNRS, Aix-Marseille Université, UMR7325, 13288, Marseille, France
| | - Laurence Prunetti
- CNRS, BIP UMR 7281, Aix Marseille Université, 13402, Marseille, France
| | | | - Marianne Guiral
- CNRS, BIP UMR 7281, Aix Marseille Université, 13402, Marseille, France
| | - Bernard Tinland
- CINaM-CNRS, Aix-Marseille Université, UMR7325, 13288, Marseille, France.
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Castelle CJ, Roger M, Bauzan M, Brugna M, Lignon S, Nimtz M, Golyshina OV, Giudici-Orticoni MT, Guiral M. The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron. Biochim Biophys Acta 2015; 1847:717-28. [PMID: 25896560 DOI: 10.1016/j.bbabio.2015.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 10/23/2022]
Abstract
The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse ('uphill') electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma.
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Affiliation(s)
- Cindy J Castelle
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Magali Roger
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, Unité de Fermentation, FR 3479, 13402 Marseille, France
| | - Myriam Brugna
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Sabrina Lignon
- CNRS, Aix Marseille Université, Plate-forme Protéomique MaP IBiSA, FR 3479, 13402 Marseille, France
| | - Manfred Nimtz
- Helmholtz Centre for Infection Research, 7 Inhoffen Strasse, 38124 Braunschweig, Germany
| | - Olga V Golyshina
- Helmholtz Centre for Infection Research, 7 Inhoffen Strasse, 38124 Braunschweig, Germany; School of Biological Sciences, Deiniol Road, LL57 2UW, Bangor, UK
| | | | - Marianne Guiral
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France.
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Peters J, Giudici-Orticoni MT, Zaccai G, Guiral M. Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria. Eur Phys J E Soft Matter 2013; 36:78. [PMID: 23880731 DOI: 10.1140/epje/i2013-13078-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/01/2013] [Accepted: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Various models on membrane structure and organization of proteins and complexes in natural membranes emerged during the last years. However, the lack of systematic dynamical studies to complement structural investigations hindered the establishment of a more complete picture of these systems. Elastic incoherent neutron scattering gives access to the dynamics on a molecular level and was applied to natural membranes extracted from the hyperthermophile Aquifex aeolicus and the mesophile Wolinella succinogenes bacteria. The results permitted to extract a hierarchy of dynamic flexibility and atomic resilience within the samples, which correlated with the organization of proteins in bioenergetics complexes and the functionality of the membranes.
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Affiliation(s)
- J Peters
- Institut Laue Langevin, 6 rue J. Horowitz, BP 156, F-38042 Grenoble Cedex 9, France.
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Guiral M, Prunetti L, Aussignargues C, Ciaccafava A, Infossi P, Ilbert M, Lojou E, Giudici-Orticoni MT. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv Microb Physiol 2013; 61:125-94. [PMID: 23046953 DOI: 10.1016/b978-0-12-394423-8.00004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.
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Affiliation(s)
- Marianne Guiral
- Unité de Bioénergétique et Ingénierie des Protéines, UMR7281-FR3479, CNRS, Aix-Marseille Université, Marseille, France.
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De Poulpiquet A, Ciaccafava A, Szot K, Pillain B, Infossi P, Guiral M, Opallo M, Giudici-Orticoni MT, Lojou E. Exploring Properties of a Hyperthermophilic Membrane-Bound Hydrogenase at Carbon Nanotube Modified Electrodes for a Powerful H2/O2Biofuel Cell. ELECTROANAL 2013. [DOI: 10.1002/elan.201200405] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Guiral M, Aussignargues C, Prunetti L, Infossi P, Ilbert M, Giudici-Orticoni M. The energy sulfur metabolism of the hyperthermophilic bacterium Aquifex aeolicus. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2012. [DOI: 10.1016/j.bbabio.2012.06.407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Aussignargues C, Giuliani MC, Infossi P, Lojou E, Guiral M, Giudici-Orticoni MT, Ilbert M. Rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism. J Biol Chem 2012; 287:19936-48. [PMID: 22496367 DOI: 10.1074/jbc.m111.324863] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How microorganisms obtain energy is a challenging topic, and there have been numerous studies on the mechanisms involved. Here, we focus on the energy substrate traffic in the hyperthermophilic bacterium Aquifex aeolicus. This bacterium can use insoluble sulfur as an energy substrate and has an intricate sulfur energy metabolism involving several sulfur-reducing and -oxidizing supercomplexes and enzymes. We demonstrate that the cytoplasmic rhodanese SbdP participates in this sulfur energy metabolism. Rhodaneses are a widespread family of proteins known to transfer sulfur atoms. We show that SbdP has also some unusual characteristics compared with other rhodaneses; it can load a long sulfur chain, and it can interact with more than one partner. Its partners (sulfur reductase and sulfur oxygenase reductase) are key enzymes of the sulfur energy metabolism of A. aeolicus and share the capacity to use long sulfur chains as substrate. We demonstrate a positive effect of SbdP, once loaded with sulfur chains, on sulfur reductase activity, most likely by optimizing substrate uptake. Taken together, these results lead us to propose a physiological role for SbdP as a carrier and sulfur chain donor to these key enzymes, therefore enabling channeling of sulfur substrate in the cell as well as greater efficiency of the sulfur energy metabolism of A. aeolicus.
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Affiliation(s)
- Clément Aussignargues
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée-CNRS, Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Ciaccafava A, Infossi P, Ilbert M, Guiral M, Lecomte S, Giudici-Orticoni MT, Lojou E. Electrochemistry, AFM, and PM-IRRA Spectroscopy of Immobilized Hydrogenase: Role of a Hydrophobic Helix in Enzyme Orientation for Efficient H2 Oxidation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201107053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ciaccafava A, Infossi P, Ilbert M, Guiral M, Lecomte S, Giudici-Orticoni MT, Lojou E. Electrochemistry, AFM, and PM-IRRA spectroscopy of immobilized hydrogenase: role of a hydrophobic helix in enzyme orientation for efficient H2 oxidation. Angew Chem Int Ed Engl 2011; 51:953-6. [PMID: 22173906 DOI: 10.1002/anie.201107053] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Alexandre Ciaccafava
- Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée-CNRS, 31 Chemin Aiguier, 13009 Marseille, France
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Prunetti L, Brugna M, Lebrun R, Giudici-Orticoni MT, Guiral M. The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus. PLoS One 2011; 6:e21616. [PMID: 21738733 PMCID: PMC3128077 DOI: 10.1371/journal.pone.0021616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba3-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper oxidases, enzymes that are far less studied than the ones from family A. Here, we describe the presence in this enzyme of an additional transmembrane helix “subunit IIa”, which is composed of 41 amino acid residues with a measured molecular mass of 5105 Da. Moreover, we show that subunit II, as expected, is in fact longer than the originally annotated protein (from the genome) and contains a transmembrane domain. Using Aquifex aeolicus genomic sequence analyses, N-terminal sequencing, peptide mass fingerprinting and mass spectrometry analysis on entire subunits, we conclude that the B-type enzyme from this bacterium is a three-subunit complex. It is composed of subunit I (encoded by coxA2) of 59000 Da, subunit II (encoded by coxB2) of 16700 Da and subunit IIa which contain 12, 1 and 1 transmembrane helices respectively. A structural model indicates that the structural organization of the complex strongly resembles that of the ba3 cytochrome c oxidase from the bacterium Thermus thermophilus, the IIa helical subunit being structurally the lacking N-terminal transmembrane helix of subunit II present in the A-type oxidases. Analysis of the genomic context of genes encoding oxidases indicates that this third subunit is present in many of the bacterial oxidases from B-family, enzymes that have been described as two-subunit complexes.
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Affiliation(s)
- Laurence Prunetti
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, Institut de Microbiologie de la Méditerranée (IFR88)-Centre National de la Recherche Scientifique, Marseille, France
| | - Myriam Brugna
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, Institut de Microbiologie de la Méditerranée (IFR88)-Centre National de la Recherche Scientifique, Marseille, France
- Université de Provence, Marseille, France
| | - Régine Lebrun
- Plate-forme Protéomique de l'IFR88-Centre National de la Recherche Scientifique, Marseille Protéomique, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, Institut de Microbiologie de la Méditerranée (IFR88)-Centre National de la Recherche Scientifique, Marseille, France
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, Institut de Microbiologie de la Méditerranée (IFR88)-Centre National de la Recherche Scientifique, Marseille, France
- * E-mail:
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Prunetti L, Infossi P, Brugna M, Ebel C, Giudici-Orticoni MT, Guiral M. New functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium Aquifex aeolicus. J Biol Chem 2010; 285:41815-26. [PMID: 20971847 DOI: 10.1074/jbc.m110.167841] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. It was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (H(2)S) to molecular oxygen. H(2)S is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. We have purified and characterized a novel membrane-bound multienzyme supercomplex that brings together all the molecular components involved in this bioenergetic chain. Our results indicate that this purified structure consists of one dimeric bc(1) complex (complex III), one cytochrome c oxidase (complex IV), and one or two sulfide quinone reductases as well as traces of the monoheme cytochrome c(555) and quinone molecules. In addition, this work strongly suggests that the cytochrome c oxidase in the supercomplex is a ba(3)-type enzyme. The supercomplex has a molecular mass of about 350 kDa and is enzymatically functional, reducing O(2) in the presence of the electron donor, H(2)S. This is the first demonstration of the existence of such a respirasome carrying a sulfide oxidase-oxygen reductase activity. Moreover, the kinetic properties of the sulfide quinone reductase change slightly when integrated in the supercomplex, compared with the free enzyme. We previously purified a complete respirasome involved in hydrogen oxidation and sulfur reduction from Aquifex aeolicus. Thus, two different bioenergetic pathways (sulfur reduction and sulfur oxidation) are organized in this bacterium as supramolecular structures in the membrane. A model for the energetic sulfur metabolism of Aquifex aeolicus is proposed.
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Affiliation(s)
- Laurence Prunetti
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, IMM, IFR88-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Guiral M, Prunetti L, Lignon S, Lebrun R, Moinier D, Giudici-Orticoni MT. New Insights into the Respiratory Chains of the Chemolithoautotrophic and Hyperthermophilic Bacterium Aquifex aeolicus. J Proteome Res 2009; 8:1717-30. [DOI: 10.1021/pr8007946] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Laurence Prunetti
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Sabrina Lignon
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Régine Lebrun
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Danielle Moinier
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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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: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Baraquet C, Théraulaz L, Guiral M, Lafitte D, Méjean V, Jourlin-Castelli C. TorT, a Member of a New Periplasmic Binding Protein Family, Triggers Induction of the Tor Respiratory System upon Trimethylamine N-Oxide Electron-acceptor Binding in Escherichia coli. J Biol Chem 2006; 281:38189-99. [PMID: 17040909 DOI: 10.1074/jbc.m604321200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In anaerobiosis, Escherichia coli can use trimethylamine N-oxide (TMAO) as a terminal electron acceptor. Reduction of TMAO in trimethylamine (TMA) is mainly performed by the respiratory TMAO reductase. This system is encoded by the torCAD operon, which is induced in the presence of TMAO. This regulation involves a two-component system comprising TorS, an unorthodox histidine kinase, and TorR, a response regulator. A third protein, TorT, sharing homologies with periplasmic binding proteins, plays a key role in this regulation because disruption of the torT gene abolishes tor expression. In this study we showed that TMAO protects TorT against degradation by the GluC endoproteinase and modifies its temperature-induced CD spectrum. We also isolated a TorT negative mutant that is no longer protected by TMAO from degradation by GluC. Isothermal titration calorimetry confirmed that TorT binds TMAO with a binding constant of 150 mum. Therefore, we conclude that TorT binds TMAO and that this binding promotes a conformational change of TorT. We also showed that TorT interacts with the periplasmic domain of TorS in both the presence and absence of TMAO but the TorT-TMAO complex induces a higher GluC protection of TorS than TorT alone. These results support the idea that TMAO binding to TorT induces a cascade of conformational changes from TorT to TorS, leading to TorS activation. We identified several homologues of the TorT protein that define a new family of periplasmic binding proteins. We thus propose that the members of this family bind TMAO or related compounds and that they are involved in signal transduction or even substrate transport.
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Affiliation(s)
- Claudine Baraquet
- Laboratoire de Chimie Bactérienne, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Guiral M, Tron P, Aubert C, Gloter A, Iobbi-Nivol C, Giudici-Orticoni MT. A Membrane-bound Multienzyme, Hydrogen-oxidizing, and Sulfur-reducing Complex from the Hyperthermophilic Bacterium Aquifex aeolicus. J Biol Chem 2005; 280:42004-15. [PMID: 16236714 DOI: 10.1074/jbc.m508034200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aquifex aeolicus is a hyperthermophilic, chemolithoautotrophic, hydrogen-oxidizing, and microaerophilic bacterium growing at 85 degrees C. We have shown that it can grow on an H2/S degrees medium and produce H2S from sulfur in the later exponential phase. The complex carrying the sulfur reducing activity (electron transport from H2 to S degrees ) has been purified and characterized. It is a membrane-bound multiprotein complex containing a [NiFe] hydrogenase and a sulfur reductase connected via quinones. The sulfur reductase is encoded by an operon annotated dms (dimethyl sulfoxide reductase) that we have renamed sre and is composed of three subunits. Sequence analysis showed that it belongs to the Me2SO reductase molybdoenzyme family and is similar to the sulfur/polysulfide/thiosulfate/tetrathionate reductases. The study of catalytic properties clearly demonstrated that it can reduce tetrathionate, sulfur, and polysulfide, but cannot reduce Me2SO and thiosulfate, and that NADPH increases the sulfur reducing activity. To date, this is the first characterization of a supercomplex from a bacterium that couples hydrogen oxidation and sulfur reduction. The distinctive feature in A. aeolicus is the cytoplasmic localization of the sulfur reduction, which is in accordance with the presence of sulfur globules in the cytoplasm. Association of this sulfur-reducing complex with a hydrogen-oxygen pathway complex (hydrogenase I, bc1 complex) in the membrane suggests that subcomplexes involved in respiratory chains in this bacterium are part of supramolecular organization.
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Affiliation(s)
- Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 13402 Marseille, France
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Abstract
Aquifex aeolicus is a microaerophilic, hydrogen-oxidizing, hyperthermophilic bacterium containing three [NiFe] hydrogenases. Two of these three enzymes (one membrane-bound and one soluble) have been purified and characterized. The Aquifex hydrogenases are thermostable and tolerant to oxygen. A cellular function for the three hydrogenases has been proposed. The two membrane-bound periplasmic hydrogenases may function in energy conservation, whereas the soluble cytoplasmic hydrogenase is probably involved in the CO(2) fixation pathway.
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Affiliation(s)
- M Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Guiral M, Leroy G, Bianco P, Gallice P, Guigliarelli B, Bruschi M, Nitschke W, Giudici-Orticoni MT. Interaction and electron transfer between the high molecular weight cytochrome and cytochrome c3 from Desulfovibrio vulgaris Hildenborough: Kinetic, microcalorimetric, EPR and electrochemical studies. Biochim Biophys Acta Gen Subj 2005; 1723:45-54. [PMID: 15780995 DOI: 10.1016/j.bbagen.2005.01.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Revised: 01/27/2005] [Accepted: 01/28/2005] [Indexed: 11/26/2022]
Abstract
The complex formation between the tetraheme cytochrome c3 and hexadecaheme high molecular weight cytochrome c (Hmc), the structure of which has recently been resolved, has been characterized by cross-linking experiments, EPR, electrochemistry and kinetic analysis, and some key parameters of the interaction were determined. The analysis of electron transfer between [Fe] hydrogenase, cytochrome c3 and Hmc demonstrates a redox-shuttling role of cytochrome c3 in the pathway from hydrogenase to Hmc, and shows an effect of redox state on the interaction between the two cytochromes. The role of polyheme cytochromes in electron transfer from periplasmic hydrogenase to membrane redox proteins is assessed. A model with cytochrome c3 as an intermediate between hydrogenase and various polyheme cytochromes is proposed and its physiological consequences are discussed.
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Affiliation(s)
- Marianne Guiral
- Bioénergétique et Ingénierie des Protéines, CNRS, IBSM, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Pasternak SH, Guiral M, Callahan JW, Mahuran DJ. P4-255 Characterizing the lysosomal gamma-secretase. Neurobiol Aging 2004. [DOI: 10.1016/s0197-4580(04)81813-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Tropak MB, Reid SP, Guiral M, Withers SG, Mahuran D. Pharmacological enhancement of beta-hexosaminidase activity in fibroblasts from adult Tay-Sachs and Sandhoff Patients. J Biol Chem 2004; 279:13478-87. [PMID: 14724290 PMCID: PMC2904802 DOI: 10.1074/jbc.m308523200] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tay-Sachs and Sandhoff diseases are lysosomal storage disorders that result from an inherited deficiency of beta-hexosaminidase A (alphabeta). Whereas the acute forms are associated with a total absence of hexosaminidase A and early death, the chronic adult forms exist with activity and protein levels of approximately 5%, and unaffected individuals have been found with only 10% of normal levels. Surprisingly, almost all disease-associated missense mutations do not affect the active site of the enzyme but, rather, inhibit its ability to obtain and/or retain its native fold in the endoplasmic reticulum, resulting in its retention and accelerated degradation. By growing adult Tay-Sachs fibroblasts in culture medium containing known inhibitors of hexosaminidase we have raised the residual protein and activity levels of intralysosomal hexosaminidase A well above the critical 10% of normal levels. A similar effect was observed in fibroblasts from an adult Sandhoff patient. We propose that these hexosaminidase inhibitors function as pharmacological chaperones, enhancing the stability of the native conformation of the enzyme, increasing the amount of hexosaminidase A capable of exiting the endoplasmic reticulum for transport to the lysosome. Therefore, pharmacological chaperones could provide a novel approach to the treatment of adult Tay-Sachs and possibly Sandhoff diseases.
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Affiliation(s)
- Michael B. Tropak
- Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8
| | - Stephen P. Reid
- Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1
| | - Marianne Guiral
- Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8
| | - Stephen G. Withers
- Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1
| | - Don Mahuran
- Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8
- Department of Laboratory Medicine and Pathology, University of Toronto, Banting Institute, Toronto, Ontario M5G 1L5, Canada
- To whom correspondence should be addressed: Research Institute, Rm. 9146A, Elm Wing, Hospital for Sick Children, 555 University Ave., Toronto M5G 1X8, Ontario. Tel.: 416-813-6161; Fax: 416-813-8700;
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Pasternak SH, Bagshaw RD, Guiral M, Zhang S, Ackerley CA, Pak BJ, Callahan JW, Mahuran DJ. Presenilin-1, nicastrin, amyloid precursor protein, and gamma-secretase activity are co-localized in the lysosomal membrane. J Biol Chem 2003; 278:26687-94. [PMID: 12736250 DOI: 10.1074/jbc.m304009200] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Alzheimer's disease (AD) is caused by the cerebral deposition of beta-amyloid (Abeta), a 38-43-amino acid peptide derived by proteolytic cleavage of the amyloid precursor protein (APP). Initial studies indicated that final cleavage of APP by the gamma-secretase (a complex containing presenilin and nicastrin) to produce Abeta occurred in the endosomal/lysosomal system. However, other studies showing a predominant endoplasmic reticulum localization of the gamma-secretase proteins and a neutral pH optimum of in vitro gamma-secretase assays have challenged this conclusion. We have recently identified nicastrin as a major lysosomal membrane protein. In the present work, we use Western blotting and immunogold electron microscopy to demonstrate that significant amounts of mature nicastrin, presenilin-1, and APP are co-localized with lysosomal associated membrane protein-1 (cAMP-1) in the outer membranes of lysosomes. Furthermore, we demonstrate that these membranes contain an acidic gamma-secretase activity, which is immunoprecipitable with an antibody to nicastrin. These experiments establish APP, nicastrin, and presenilin-1 as resident lysosomal membrane proteins and indicate that gamma-secretase is a lysosomal protease. These data reassert the importance of the lysosomal/endosomal system in the generation of Abeta and suggest a role for lysosomes in the pathophysiology of AD.
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Affiliation(s)
- Stephen H Pasternak
- Research Institute, The Hospital for Sick Children, University of Toronto, Toronto M5G 1X8, Canada
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Abstract
PRH (proline-rich homeodomain protein) is strongly expressed in the hematopoietic compartment. Here we show that PRH is a repressor of transcription in hematopoietic cells. A fragment of PRH that includes the homeodomain can bind to TATA box sequences in vitro and can also bind to the TATA box-binding protein. PRH represses transcription from TATA box-containing promoters in intact cells but does not repress transcription from a promoter lacking a TATA box. A mutation in the PRH homeodomain that blocks binding to DNA but that has little or no effect on binding to the TATA box-binding protein significantly reduces the ability of the protein to repress transcription and provides the first clear demonstration that a homeodomain can bring about transcriptional repression in vivo by binding to a TATA box. However, we also show that mutation of the PRH homeodomain does not block the ability of PRH to repress transcription when this protein is tethered upstream of the TATA box via a heterologous DNA-binding domain. PRH also contains an N-terminal proline-rich repression domain that is separate from the homeodomain. Deletion mapping suggests that this repression domain contains at least two regions that both independently contribute to transcriptional repression.
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Affiliation(s)
- M Guiral
- Department of Biochemistry, University of Bristol, University Walk, Bristol, United Kingdom
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Wijker JE, Jensen PR, Snoep JL, Vaz Gomes A, Guiral M, Jongsma AP, de Waal A, Hoving S, van Dooren S, van der Weijden CC. Energy, control and DNA structure in the living cell. Biophys Chem 1995; 55:153-65. [PMID: 7632875 DOI: 10.1016/0301-4622(94)00148-d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Maintenance (let alone growth) of the highly ordered living cell is only possible through the continuous input of free energy. Coupling of energetically downhill processes (such as catabolic reactions) to uphill processes is essential to provide this free energy and is catalyzed by enzymes either directly or via "storage" in an intermediate high energy form, i.e., high ATP/ADP ratio or H+ ion gradient. Although maintenance of a sufficiently high ATP/ADP ratio is essential to overcome the thermodynamic burden of uphill processes, it is not clear to what degree enzymes that control this ratio also control cell physiology. Indeed, in the living cell homeostatic control mechanisms might exist for the free-energy transduction pathways so as to prevent perturbation of cellular function when the Gibbs energy supply is compromised. This presentation addresses the extent to which the intracellular ATP level is involved in the control of cell physiology, how the elaborate control of cell function may be analyzed theoretically and quantitatively, and if this can be utilized selectively to affect certain cell types.
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Affiliation(s)
- J E Wijker
- Department of Microbiology, Technical University of Denmark, Lyngby
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Abstract
Most of the multidrug resistant human tumor cell lines overexpress the MDR1 gene product P-glycoprotein (P-gp) which is believed to function as an energy-dependent drug efflux pump. Here we describe a novel method that allows the kinetic characterization of P-gp-mediated active drug transport. This method is based on the fluorescence quenching of anthracyclines transported into DNA-loaded plasma membrane vesicles. The uptake of daunorubicin (DNR) into the plasma membrane vesicles was saturable in terms of the extravesicular DNR concentration with a Km of 1.5 +/- 0.1 microM. This transport occurred by a cooperative process with a Hill coefficient close to 2 for DNR. A model is discussed in which P-gp pumps two molecules of drug per turnover.
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Affiliation(s)
- M Guiral
- Free University Hospital, Department of Medical Oncology, Amsterdam, The Netherlands
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