1
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Shevket SH, Gonzalez D, Cartwright JL, Kleanthous C, Ferguson SJ, Redfield C, Mavridou DAI. The CcmC-CcmE interaction during cytochrome c maturation by System I is driven by protein-protein and not protein-heme contacts. J Biol Chem 2018; 293:16778-16790. [PMID: 30206118 PMCID: PMC6204919 DOI: 10.1074/jbc.ra118.005024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/07/2018] [Indexed: 12/30/2022] Open
Abstract
Cytochromes c are ubiquitous proteins, essential for life in most organisms. Their distinctive characteristic is the covalent attachment of heme to their polypeptide chain. This post-translational modification is performed by a dedicated protein system, which in many Gram-negative bacteria and plant mitochondria is a nine-protein apparatus (CcmA-I) called System I. Despite decades of study, mechanistic understanding of the protein-protein interactions in this highly complex maturation machinery is still lacking. Here, we focused on the interaction of CcmC, the protein that sources the heme cofactor, with CcmE, the pivotal component of System I responsible for the transfer of the heme to the apocytochrome. Using in silico analyses, we identified a putative interaction site between these two proteins (residues Asp47, Gln50, and Arg55 on CcmC; Arg73, Asp101, and Glu105 on CcmE), and we validated our findings by in vivo experiments in Escherichia coli Moreover, employing NMR spectroscopy, we examined whether a heme-binding site on CcmE contributes to this interaction and found that CcmC and CcmE associate via protein-protein rather than protein-heme contacts. The combination of in vivo site-directed mutagenesis studies and high-resolution structural techniques enabled us to determine at the residue level the mechanism for the formation of one of the key protein complexes for cytochrome c maturation by System I.
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Affiliation(s)
- Shevket H Shevket
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Diego Gonzalez
- the Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, Switzerland
| | - Jared L Cartwright
- the Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Colin Kleanthous
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Stuart J Ferguson
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom,
| | - Christina Redfield
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom,
| | - Despoina A I Mavridou
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London SW7 2DD, United Kingdom,
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2
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Murphey AC, Mavridou DAI, Hodgkin J, Ferguson SJ. The heme auxotroph Caenorhabditis elegans can cleave the thioether bonds of c-type cytochromes. FEBS Lett 2018; 592:928-938. [PMID: 29430660 DOI: 10.1002/1873-3468.13006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 11/08/2022]
Abstract
Heme is essential and synthesized via highly regulated processes. For this reason, most organisms strive to recycle it or acquire it from their environment. When heme is bound to proteins noncovalently, degradation of the polypeptide is sufficient to release it. However, in some hemoproteins, such as c-type cytochromes, heme is covalently bound to the protein backbone. We use the heme auxotroph Caenorhabditis elegans to investigate if cytochromes c can be a heme source, and we show that this organism must encode a novel system which specifically cleaves the thioether bonds of c-type cytochromes. We also find that at limiting heme concentrations, while somatic tissues develop normally the germline fails to proliferate, suggesting the presence of a heme-sensing checkpoint in C. elegans.
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Affiliation(s)
| | - Despoina A I Mavridou
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, UK
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3
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Singhal RK, Kruse C, Heidler J, Strecker V, Zwicker K, Düsterwald L, Westermann B, Herrmann JM, Wittig I, Rapaport D. Coi1 is a novel assembly factor of the yeast complex III-complex IV supercomplex. Mol Biol Cell 2017; 28:mbc.E17-02-0093. [PMID: 28794267 PMCID: PMC5620370 DOI: 10.1091/mbc.e17-02-0093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 01/30/2023] Open
Abstract
The yeast bc1 complex (complex III) and cytochrome oxidase (complex IV) are mosaics of core subunits encoded by the mitochondrial genome and additional nuclear-encoded proteins imported from the cytosol. Both complexes build in the mitochondrial inner membrane various supramolecular assemblies. The formation of the individual complexes and their supercomplexes depends on the activity of dedicated assembly factors. We identified a so far uncharacterized mitochondrial protein (open reading frame YDR381C-A) as an important assembly factor for complex III, complex IV, and their supercomplexes. Therefore, we named this protein Cox interacting (Coi) 1. Deletion of COI1 results in decreased respiratory growth, reduced membrane potential, and hampered respiration, as well as slow fermentative growth at low temperature. In addition, coi1Δ cells harbour reduced steady-state levels of subunits of complexes III and IV as well as of the assembled complexes and supercomplexes. Interaction of Coi1 with respiratory chain subunits seems transient, as it appears to be a stoichiometric subunit neither of complex III nor of complex IV. Collectively, this work identifies a novel protein that plays a role in the assembly of the mitochondrial respiratory chain.
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Affiliation(s)
- Ravi K Singhal
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Christine Kruse
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Valentina Strecker
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Lea Düsterwald
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | | | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence "Macromolecular Complexes", Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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4
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Verissimo AF, Khalfaoui-Hassani B, Hwang J, Steimle S, Selamoglu N, Sanders C, Khatchikian CE, Daldal F. The thioreduction component CcmG confers efficiency and the heme ligation component CcmH ensures stereo-specificity during cytochrome c maturation. J Biol Chem 2017. [PMID: 28634234 DOI: 10.1074/jbc.m117.794586] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In many Gram-negative bacteria, including Rhodobacter capsulatus, cytochrome c maturation (Ccm) is carried out by a membrane-integral machinery composed of nine proteins (CcmA to I). During this process, the periplasmic thiol-disulfide oxidoreductase DsbA is thought to catalyze the formation of a disulfide bond between the Cys residues at the apocytochrome c heme-binding site (CXXCH). Subsequently, a Ccm-specific thioreductive pathway involving CcmG and CcmH reduces this disulfide bond to allow covalent heme ligation. Currently, the sequence of thioredox reactions occurring between these components and apocytochrome c and the identity of their active Cys residues are unknown. In this work, we first investigated protein-protein interactions among the apocytochrome c, CcmG, and the heme-ligation components CcmF, CcmH, and CcmI. We found that they all interact with each other, forming a CcmFGHI-apocytochrome c complex. Using purified wild-type CcmG, CcmH, and apocytochrome c, as well as their respective Cys mutant variants, we determined the rates of thiol-disulfide exchange reactions between selected pairs of Cys residues from these proteins. We established that CcmG can efficiently reduce the disulfide bond of apocytochrome c and also resolve a mixed disulfide bond formed between apocytochrome c and CcmH. We further show that Cys-45 of CcmH and Cys-34 of apocytochrome c are most likely to form this mixed disulfide bond, which is consistent with the stereo-specificity of the heme-apocytochrome c ligation reaction. We conclude that CcmG confers efficiency, and CcmH ensures stereo-specificity during Ccm and present a comprehensive model for thioreduction reactions that lead to heme-apocytochrome c ligation.
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Affiliation(s)
- Andreia F Verissimo
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Bahia Khalfaoui-Hassani
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Josephine Hwang
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Stefan Steimle
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Nur Selamoglu
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Carsten Sanders
- the Department of Physical Sciences, University of Kutztown, Kutztown, Pennsylvania 19530, and
| | - Camilo E Khatchikian
- the Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968
| | - Fevzi Daldal
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019,
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5
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Khalfaoui-Hassani B, Verissimo AF, Shroff NP, Ekici S, Trasnea PI, Utz M, Koch HG, Daldal F. Biogenesis of Cytochrome c Complexes: From Insertion of Redox Cofactors to Assembly of Different Subunits. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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6
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Watkins DW, Armstrong CT, Beesley JL, Marsh JE, Jenkins JMX, Sessions RB, Mann S, Ross Anderson JL. A suite of de novo c-type cytochromes for functional oxidoreductase engineering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:493-502. [PMID: 26556173 DOI: 10.1016/j.bbabio.2015.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 10/22/2022]
Abstract
Central to the design of an efficient de novo enzyme is a robust yet mutable protein scaffold. The maquette approach to protein design offers precisely this, employing simple four-α-helix bundle scaffolds devoid of evolutionary complexity and with proven tolerance towards iterative protein engineering. We recently described the design of C2, a de novo designed c-type cytochrome maquette that undergoes post-translational modification in E. coli to covalently graft heme onto the protein backbone in vivo. This de novo cytochrome is capable of reversible oxygen binding, an obligate step in the catalytic cycle of many oxygen-activating oxidoreductases. Here we demonstrate the flexibility of both the maquette platform and the post-translational machinery of E. coli by creating a suite of functional de novo designed c-type cytochromes. We explore the engineering tolerances of the maquette by selecting alternative binding sites for heme C attachment and creating di-heme maquettes either by appending an additional heme C binding motif to the maquette scaffold or by binding heme B through simple bis-histidine ligation to a second binding site. The new designs retain the essential properties of the parent design but with significant improvements in structural stability. Molecular dynamics simulations aid the rationalization of these functional improvements while providing insight into the rules for engineering heme C binding sites in future iterations. This versatile, functional suite of de novo c-type cytochromes shows significant promise in providing robust platforms for the future engineering of de novo oxygen-activating oxidoreductases. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electron transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Joseph L Beesley
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Jane E Marsh
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Jonathan M X Jenkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen Mann
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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7
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Verissimo AF, Daldal F. Cytochrome c biogenesis System I: an intricate process catalyzed by a maturase supercomplex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:989-98. [PMID: 24631867 DOI: 10.1016/j.bbabio.2014.03.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/16/2022]
Abstract
Cytochromes c are ubiquitous heme proteins that are found in most living organisms and are essential for various energy production pathways as well as other cellular processes. Their biosynthesis relies on a complex post-translational process, called cytochrome c biogenesis, responsible for the formation of stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin IX-Fe) and the thiol groups of apocytochromes c heme-binding site (C1XXC2H) cysteine residues. In some organisms this process involves up to nine (CcmABCDEFGHI) membrane proteins working together to achieve heme ligation, designated the Cytochrome c maturation (Ccm)-System I. Here, we review recent findings related to the Ccm-System I found in bacteria, archaea and plant mitochondria, with an emphasis on protein interactions between the Ccm components and their substrates (apocytochrome c and heme). We discuss the possibility that the Ccm proteins may form a multi subunit supercomplex (dubbed "Ccm machine"), and based on the currently available data, we present an updated version of a mechanistic model for Ccm. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA.
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8
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Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
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Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
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9
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Anderson JLR, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL. Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci 2013; 5:507-514. [PMID: 24634717 DOI: 10.1039/c3sc52019f] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The successful use of man-made proteins to advance synthetic biology requires both the fabrication of functional artificial proteins in a living environment, and the ability of these proteins to interact productively with other proteins and substrates in that environment. Proteins made by the maquette method integrate sophisticated oxidoreductase function into evolutionarily naive, non-computationally designed protein constructs with sequences that are entirely unrelated to any natural protein. Nevertheless, we show here that we can efficiently interface with the natural cellular machinery that covalently incorporates heme into natural cytochromes c to produce in vivo an artificial c-type cytochrome maquette. Furthermore, this c-type cytochrome maquette is designed with a displaceable histidine heme ligand that opens to allow functional oxygen binding, the primary event in more sophisticated functions ranging from oxygen storage and transport to catalytic hydroxylation. To exploit the range of functions that comes from the freedom to bind a variety of redox cofactors within a single maquette framework, this c-type cytochrome maquette is designed with a second, non-heme C, tetrapyrrole binding site, enabling the construction of an elementary electron transport chain, and when the heme C iron is replaced with zinc to create a Zn porphyrin, a light-activatable artificial redox protein. The work we describe here represents a major advance in de novo protein design, offering a robust platform for new c-type heme based oxidoreductase designs and an equally important proof-of-principle that cofactor-equipped man-made proteins can be expressed in living cells, paving the way for constructing functionally useful man-made proteins in vivo.
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Affiliation(s)
- J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.,The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Goutham Kodali
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Bruce R Lichtenstein
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Joshua A Mancini
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Aimee L Boyle
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Tammer A Farid
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Christopher C Moser
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - P Leslie Dutton
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
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10
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Mavridou DAI, Clark MN, Choulat C, Ferguson SJ, Stevens JM. Probing heme delivery processes in cytochrome c biogenesis System I. Biochemistry 2013; 52:7262-70. [PMID: 24044352 PMCID: PMC3806149 DOI: 10.1021/bi400398t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Cytochromes c comprise
a diverse and widespread
family of proteins containing covalently bound heme that are central
to the life of most organisms. In many bacteria and in certain mitochondria,
the synthesis of cytochromes c is performed by a
complex post-translational modification apparatus called System I
(or cytochrome c maturation, Ccm, system). In Escherichia coli, there are eight maturation proteins,
several of which are involved in heme handling, but the mechanism
of heme transfer from one protein to the next is not known. Attachment
of the heme to the apocytochrome occurs via a novel covalent bond
to a histidine residue of the heme chaperone CcmE. The discovery of
a variant maturation system (System I*) has provided a new tool for
studying cytochrome c assembly because the variant
CcmE functions via a cysteine residue in the place of the histidine
of System I. In this work, we use site-directed mutagenesis on both
maturation systems to probe the function of the individual component
proteins as well as their concerted action in transferring heme to
the cytochrome c substrate. The roles of CcmA, CcmC,
CcmE, and CcmF in the heme delivery process are compared between Systems
I and I*. We show that a previously proposed quinone-binding site
on CcmF is not essential for either system. Significant differences
in the heme chemistry involved in the formation of cytochromes c in the variant system add new pieces to the cytochrome c biogenesis puzzle.
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Affiliation(s)
- Despoina A I Mavridou
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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11
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Goldbeck CP, Jensen HM, TerAvest MA, Beedle N, Appling Y, Hepler M, Cambray G, Mutalik V, Angenent LT, Ajo-Franklin CM. Tuning promoter strengths for improved synthesis and function of electron conduits in Escherichia coli. ACS Synth Biol 2013; 2:150-9. [PMID: 23656438 DOI: 10.1021/sb300119v] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Introduction of the electron transfer complex MtrCAB from Shewanella oneidensis MR-1 into a heterologous host provides a modular and molecularly defined route for electrons to be transferred to an extracellular inorganic solid. However, an Escherichia coli strain expressing this pathway displayed limited control of MtrCAB expression and impaired cell growth. To overcome these limitations and to improve heterologous extracellular electron transfer, we used an E. coli host with a more tunable induction system and a panel of constitutive promoters to generate a library of strains that separately transcribe the mtr and cytochrome c maturation (ccm) operons over 3 orders of magnitude. From this library, we identified strains that show 2.2 times higher levels of MtrC and MtrA and that have improved cell growth. We find that a ~300-fold decrease in the efficiency of MtrC and MtrA synthesis with increasing mtr promoter activity critically limits the maximum expression level of MtrC and MtrA. We also tested the extracellular electron transfer capabilities of a subset of the strains using a three-electrode microbial electrochemical system. Interestingly, the strain with improved cell growth and fewer morphological changes generated the largest maximal current per cfu, rather than the strain with more MtrC and MtrA. This strain also showed ~30-fold greater maximal current per cfu than its ccm-only control strain. Thus, the conditions for optimal MtrCAB expression and anode reduction are distinct, and minimal perturbations to cell morphology are correlated with improved extracellular electron transfer in E. coli.
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Affiliation(s)
| | - Heather M. Jensen
- Department
of Chemistry, University of California,
Berkeley, California 94720,
United States
| | - Michaela A. TerAvest
- Department
of Biological and
Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | | | - Matt Hepler
- Department
of Chemistry, University of California,
Berkeley, California 94720,
United States
| | - Guillaume Cambray
- BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), Emeryville,
California 94608, United States
- California Institute for Quantitative
Biosciences, University of California,
Berkeley, California, 94720, United States
| | - Vivek Mutalik
- BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), Emeryville,
California 94608, United States
| | - Largus T. Angenent
- Department
of Biological and
Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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12
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Mavridou DAI, Ferguson SJ, Stevens JM. Cytochrome c assembly. IUBMB Life 2013; 65:209-16. [PMID: 23341334 DOI: 10.1002/iub.1123] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/29/2012] [Indexed: 11/08/2022]
Abstract
Cytochromes c are central proteins in energy transduction processes by virtue of their functions in electron transfer in respiration and photosynthesis. They have heme covalently attached to a characteristic CXXCH motif via protein-catalyzed post-translational modification reactions. Several systems with diverse constituent proteins have been identified in different organisms and are required to perform the heme attachment and associated functions. The necessary steps are translocation of the apocytochrome polypeptide to the site of heme attachment, transport and provision of heme to the appropriate compartment, reduction and chaperoning of the apocytochrome, and finally, formation of the thioether bonds between heme and two cysteines in the cytochrome. Here we summarize the established classical models for these processes and present recent progress in our understanding of the individual steps within the different cytochrome c biogenesis systems.
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13
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Verissimo AF, Mohtar MA, Daldal F. The heme chaperone ApoCcmE forms a ternary complex with CcmI and apocytochrome c. J Biol Chem 2013; 288:6272-83. [PMID: 23319598 DOI: 10.1074/jbc.m112.440024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c maturation (Ccm) is a post-translational process that occurs after translocation of apocytochromes c to the positive (p) side of energy-transducing membranes. Ccm is responsible for the formation of covalent bonds between the thiol groups of two cysteines residues at the heme-binding sites of the apocytochromes and the vinyl groups of heme b (protoporphyrin IX-Fe). Among the proteins (CcmABCDEFGHI and CcdA) required for this process, CcmABCD are involved in loading heme b to apoCcmE. The holoCcmE thus formed provides heme b to the apocytochromes. Catalysis of the thioether bonds between the apocytochromes c and heme b is mediated by the heme ligation core complex, which in Rhodobacter capsulatus contains at least the CcmF, CcmH, and CcmI components. In this work we show that the heme chaperone apoCcmE binds to the apocytochrome c and the apocytochrome c chaperone CcmI to yield stable binary and ternary complexes in the absence of heme in vitro. We found that during these protein-protein interactions, apoCcmE favors the presence of a disulfide bond at the apocytochrome c heme-binding site. We also establish using detergent-dispersed membranes that apoCcmE interacts directly with CcmI and CcmH of the heme ligation core complex CcmFHI. Implications of these findings are discussed with respect to heme transfer from CcmE to the apocytochromes c during heme ligation assisted by the core complex CcmFHI.
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Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19014-6019, USA
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Prokaryotic assembly factors for the attachment of flavin to complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:637-47. [PMID: 22985599 DOI: 10.1016/j.bbabio.2012.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
Complex II (also known as Succinate dehydrogenase or Succinate-ubiquinone oxidoreductase) is an important respiratory enzyme that participates in both the tricarboxylic acid cycle and electron transport chain. Complex II consists of four subunits including a catalytic flavoprotein (SdhA), an iron-sulphur subunit (SdhB) and two hydrophobic membrane anchors (SdhC and SdhD). Complex II also contains a number of redox cofactors including haem, Fe-S clusters and FAD, which mediate electron transfer from succinate oxidation to the reduction of the mobile electron carrier ubiquinone. The flavin cofactor FAD is an important redox cofactor found in many proteins that participate in oxidation/reduction reactions. FAD is predominantly bound non-covalently to flavoproteins, with only a small percentage of flavoproteins, such as complex II, binding FAD covalently. Aside from a few examples, the mechanisms of flavin attachment have been a relatively unexplored area. This review will discuss the FAD cofactor and the mechanisms used by flavoproteins to covalently bind FAD. Particular focus is placed on the attachment of FAD to complex II with an emphasis on SdhE (a DUF339/SDH5 protein previously termed YgfY), the first protein identified as an assembly factor for FAD attachment to flavoproteins in prokaryotes. The molecular details of SdhE-dependent flavinylation of complex II are discussed and comparisons are made to known cofactor chaperones. Furthermore, an evolutionary hypothesis is proposed to explain the distribution of SdhE homologues in bacterial and eukaryotic species. Mechanisms for regulating SdhE function and how this may be linked to complex II function in different bacterial species are also discussed. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Malvankar NS, Lovley DR. Microbial nanowires: a new paradigm for biological electron transfer and bioelectronics. CHEMSUSCHEM 2012; 5:1039-1046. [PMID: 22614997 DOI: 10.1002/cssc.201100733] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/06/2012] [Indexed: 06/01/2023]
Abstract
The discovery that Geobacter sulfurreducens can produce protein filaments with metallic-like conductivity, known as microbial nanowires, that facilitate long-range electron transport is a paradigm shift in biological electron transfer and has important implications for biogeochemistry, microbial ecology, and the emerging field of bioelectronics. Although filaments in a wide diversity of microorganisms have been called microbial nanowires, the type IV pili of G. sulfurreducens and G. metallireducens are the only filaments that have been shown to be required for extracellular electron transport to extracellular electron acceptors or for conduction of electrons through biofilms. Studies of G. sulfurreducens pili preparations and intact biofilms under physiologically relevant conditions have provided multiple lines of evidence for metallic-like conduction along the length of pili and for the possibility of pili networks to confer high conductivity within biofilms. This mechanism of electron conduction contrasts with the previously known mechanism for biological electron transfer via electron tunneling or hopping between closely associated molecules, a strategy unlikely to be well adapted for long-range electron transport outside the cell. In addition to promoting electron exchange with abiotic electron acceptors, microbial nanowires have recently been shown to be involved in direct interspecies electron transfer between syntrophic partners. An improved understanding of the mechanisms for metallic-like conductivity in microbial nanowires, as well as engineering microorganisms with desirable catalytic abilities with nanowires, could lead to new applications in microbial electrosynthesis and bioelectronics.
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Affiliation(s)
- Nikhil S Malvankar
- Department of Microbiology, University of Massachusetts, Amherst, 203, Morrill Science Center IVN, 639 North Pleasant Street, Amherst, MA 01003, USA
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Ferguson SJ. New perspectives on assembling c-type cytochromes, particularly from sulphate reducing bacteria and mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1754-8. [PMID: 22609324 DOI: 10.1016/j.bbabio.2012.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 12/18/2022]
Abstract
Some recent new developments emerging from studies of the Systems I and III for c-type cytochrome biogenesis are discussed, particularly in regard to developments in studying System I in sulphate reducing bacteria. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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