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Webb JS, Nikolakakis KC, Willett JLE, Aoki SK, Hayes CS, Low DA. Delivery of CdiA nuclease toxins into target cells during contact-dependent growth inhibition. PLoS One 2013; 8:e57609. [PMID: 23469034 PMCID: PMC3585180 DOI: 10.1371/journal.pone.0057609] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/23/2013] [Indexed: 12/26/2022] Open
Abstract
Bacterial contact-dependent growth inhibition (CDI) is mediated by the CdiB/CdiA family of two-partner secretion proteins. CDI systems deploy a variety of distinct toxins, which are contained within the polymorphic C-terminal region (CdiA-CT) of CdiA proteins. Several CdiA-CTs are nucleases, suggesting that the toxins are transported into the target cell cytoplasm to interact with their substrates. To analyze CdiA transfer to target bacteria, we used the CDI system of uropathogenic Escherichia coli 536 (UPEC536) as a model. Antibodies recognizing the amino- and carboxyl-termini of CdiAUPEC536 were used to visualize transfer of CdiA from CDIUPEC536+ inhibitor cells to target cells using fluorescence microscopy. The results indicate that the entire CdiAUPEC536 protein is deposited onto the surface of target bacteria. CdiAUPEC536 transfer to bamA101 mutants is reduced, consistent with low expression of the CDI receptor BamA on these cells. Notably, our results indicate that the C-terminal CdiA-CT toxin region of CdiAUPEC536 is translocated into target cells, but the N-terminal region remains at the cell surface based on protease sensitivity. These results suggest that the CdiA-CT toxin domain is cleaved from CdiAUPEC536 prior to translocation. Delivery of a heterologous Dickeya dadantii CdiA-CT toxin, which has DNase activity, was also visualized. Following incubation with CDI+ inhibitor cells targets became anucleate, showing that the D.dadantii CdiA-CT was delivered intracellularly. Together, these results demonstrate that diverse CDI toxins are efficiently translocated across target cell envelopes.
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Affiliation(s)
- Julia S. Webb
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Kiel C. Nikolakakis
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Julia L. E. Willett
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Stephanie K. Aoki
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - David A. Low
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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102
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Kulawiak B, Höpker J, Gebert M, Guiard B, Wiedemann N, Gebert N. The mitochondrial protein import machinery has multiple connections to the respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:612-26. [PMID: 23274250 DOI: 10.1016/j.bbabio.2012.12.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/12/2012] [Accepted: 12/17/2012] [Indexed: 01/09/2023]
Abstract
The mitochondrial inner membrane harbors the complexes of the respiratory chain and protein translocases required for the import of mitochondrial precursor proteins. These complexes are functionally interdependent, as the import of respiratory chain precursor proteins across and into the inner membrane requires the membrane potential. Vice versa the membrane potential is generated by the proton pumping complexes of the respiratory chain. Besides this basic codependency four different systems for protein import, processing and assembly show further connections to the respiratory chain. The mitochondrial intermembrane space import and assembly machinery oxidizes cysteine residues within the imported precursor proteins and is able to donate the liberated electrons to the respiratory chain. The presequence translocase of the inner membrane physically interacts with the respiratory chain. The mitochondrial processing peptidase is homologous to respiratory chain subunits and the carrier translocase of the inner membrane even shares a subunit with the respiratory chain. In this review we will summarize the import of mitochondrial precursor proteins and highlight these special links between the mitochondrial protein import machinery and the respiratory chain. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Bogusz Kulawiak
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, Freiburg, Germany
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103
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Webb CT, Heinz E, Lithgow T. Evolution of the β-barrel assembly machinery. Trends Microbiol 2012; 20:612-20. [DOI: 10.1016/j.tim.2012.08.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/10/2012] [Accepted: 08/14/2012] [Indexed: 11/29/2022]
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104
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Misra R. Assembly of the β-Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts. ISRN MOLECULAR BIOLOGY 2012; 2012:708203. [PMID: 27335668 PMCID: PMC4890855 DOI: 10.5402/2012/708203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 10/22/2012] [Indexed: 01/12/2023]
Abstract
In the last decade, there has been an explosion of publications on the assembly of β-barrel outer membrane proteins (OMPs), which carry out diverse cellular functions, including solute transport, protein secretion, and assembly of protein and lipid components of the outer membrane. Of the three outer membrane model systems—Gram-negative bacteria, mitochondria and chloroplasts—research on bacterial and mitochondrial systems has so far led the way in dissecting the β-barrel OMP assembly pathways. Many exciting discoveries have been made, including the identification of β-barrel OMP assembly machineries in bacteria and mitochondria, and potentially the core assembly component in chloroplasts. The atomic structures of all five components of the bacterial β-barrel assembly machinery (BAM) complex, except the β-barrel domain of the core BamA protein, have been solved. Structures reveal that these proteins contain domains/motifs known to facilitate protein-protein interactions, which are at the heart of the assembly pathways. While structural information has been valuable, most of our current understanding of the β-barrel OMP assembly pathways has come from genetic, molecular biology, and biochemical analyses. This paper provides a comparative account of the β-barrel OMP assembly pathways in Gram-negative bacteria, mitochondria, and chloroplasts.
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Affiliation(s)
- Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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105
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Klein A, Israel L, Lackey SWK, Nargang FE, Imhof A, Baumeister W, Neupert W, Thomas DR. Characterization of the insertase for β-barrel proteins of the outer mitochondrial membrane. ACTA ACUST UNITED AC 2012; 199:599-611. [PMID: 23128244 PMCID: PMC3494861 DOI: 10.1083/jcb.201207161] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isolation of the intact TOB complex reveals a 1:1:1 stoichiometry of Tob55, Tob38, and Tob37 with a 140-kD molecular mass, providing new insight into complex structure and function. The TOB–SAM complex is an essential component of the mitochondrial outer membrane that mediates the insertion of β-barrel precursor proteins into the membrane. We report here its isolation and determine its size, composition, and structural organization. The complex from Neurospora crassa was composed of Tob55–Sam50, Tob38–Sam35, and Tob37–Sam37 in a stoichiometry of 1:1:1 and had a molecular mass of 140 kD. A very minor fraction of the purified complex was associated with one Mdm10 protein. Using molecular homology modeling for Tob55 and cryoelectron microscopy reconstructions of the TOB complex, we present a model of the TOB–SAM complex that integrates biochemical and structural data. We discuss our results and the structural model in the context of a possible mechanism of the TOB insertase.
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Affiliation(s)
- Astrid Klein
- Max-Planck Institut für Biochemie, Abteilung für zelluläre Biochemie, D-82152 Martinsried, Germany
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106
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Namdari F, Hurtado-Escobar GA, Abed N, Trotereau J, Fardini Y, Giraud E, Velge P, Virlogeux-Payant I. Deciphering the roles of BamB and its interaction with BamA in outer membrane biogenesis, T3SS expression and virulence in Salmonella. PLoS One 2012; 7:e46050. [PMID: 23144780 PMCID: PMC3489874 DOI: 10.1371/journal.pone.0046050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/27/2012] [Indexed: 11/21/2022] Open
Abstract
The folding and insertion of β-barrel proteins in the outer membrane of Gram-negative bacteria is mediated by the BAM complex, which is composed of the outer membrane protein BamA and four lipoproteins BamB to BamE. In Escherichia coli and/or Salmonella, the BamB lipoprotein is involved in (i) β-barrel protein assembly in the outer membrane, (ii) outer membrane permeability to antibiotics, (iii) the control of the expression of T3SS which are major virulence factors and (iv) the virulence of Salmonella. In E. coli, this protein has been shown to interact directly with BamA. In this study, we investigated the structure-function relationship of BamB in order to assess whether the roles of BamB in these phenotypes were inter-related and whether they require the interaction of BamB with BamA. For this purpose, recombinant plasmids harbouring point mutations in bamB were introduced in a ΔSalmonella bamB mutant. We demonstrated that the residues L173, L175 and R176 are crucial for all the roles of BamB and for the interaction of BamB with BamA. Moreover, the results obtained with a D229A BamB variant, which is unable to immunoprecipitate BamA, suggest that the interaction of BamB with BamA is not absolutely necessary for BamB function in outer-membrane protein assembly, T3SS expression and virulence. Finally, we showed that the virulence defect of the ΔbamB mutant is not related to its increased susceptibility to antimicrobials, as the D227A BamB variant fully restored the virulence of the mutant while having a similar antibiotic susceptibility to the ΔbamB strain. Overall, this study demonstrates that the different roles of BamB are not all inter-related and that L173, L175 and R176 amino-acids are privileged sites for the design of BamB inhibitors that could be used as alternative therapeutics to antibiotics, at least against Salmonella.
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Affiliation(s)
- Fatémeh Namdari
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Genaro Alejandro Hurtado-Escobar
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Nadia Abed
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Jérôme Trotereau
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Yann Fardini
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Etienne Giraud
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Philippe Velge
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
| | - Isabelle Virlogeux-Payant
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- * E-mail: *
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107
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Dalbey RE, Kuhn A. Protein Traffic in Gram-negative bacteria – how exported and secreted proteins find their way. FEMS Microbiol Rev 2012; 36:1023-45. [DOI: 10.1111/j.1574-6976.2012.00327.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 01/04/2012] [Indexed: 11/27/2022] Open
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108
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Shi LX, Theg SM. The chloroplast protein import system: from algae to trees. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:314-31. [PMID: 23063942 DOI: 10.1016/j.bbamcr.2012.10.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/07/2012] [Accepted: 10/01/2012] [Indexed: 01/15/2023]
Abstract
Chloroplasts are essential organelles in the cells of plants and algae. The functions of these specialized plastids are largely dependent on the ~3000 proteins residing in the organelle. Although chloroplasts are capable of a limited amount of semiautonomous protein synthesis - their genomes encode ~100 proteins - they must import more than 95% of their proteins after synthesis in the cytosol. Imported proteins generally possess an N-terminal extension termed a transit peptide. The importing translocons are made up of two complexes in the outer and inner envelope membranes, the so-called Toc and Tic machineries, respectively. The Toc complex contains two precursor receptors, Toc159 and Toc34, a protein channel, Toc75, and a peripheral component, Toc64/OEP64. The Tic complex consists of as many as eight components, namely Tic22, Tic110, Tic40, Tic20, Tic21 Tic62, Tic55 and Tic32. This general Toc/Tic import pathway, worked out largely in pea chloroplasts, appears to operate in chloroplasts in all green plants, albeit with significant modifications. Sub-complexes of the Toc and Tic machineries are proposed to exist to satisfy different substrate-, tissue-, cell- and developmental requirements. In this review, we summarize our understanding of the functions of Toc and Tic components, comparing these components of the import machinery in green algae through trees. We emphasize recent findings that point to growing complexities of chloroplast protein import process, and use the evolutionary relationships between proteins of different species in an attempt to define the essential core translocon components and those more likely to be responsible for regulation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Lan-Xin Shi
- Department of Plant Biology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
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109
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Abstract
A protein's function is intimately linked to its correct subcellular location, yet the machinery required for protein synthesis is predominately cytosolic. How proteins are trafficked through the confines of the cell and integrated into the appropriate cellular compartments has puzzled and intrigued researchers for decades. Indeed, studies exploring this premise revealed elaborate cellular protein translocation and sorting systems, which ensure that all proteins are shuttled to the appropriate cellular destination, where they fulfill their specific functions. This holds true for mitochondria, where sophisticated molecular machines serve to recognize incoming precursor proteins and integrate them into the functional framework of the organelle. We summarize the recent progress in our understanding of mitochondrial protein sorting and the machineries and mechanisms that mediate and regulate this highly dynamic cellular process essential for survival of virtually all eukaryotic cells.
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110
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Shiota T, Maruyama M, Miura M, Tamura Y, Yamano K, Esaki M, Endo T. The Tom40 assembly process probed using the attachment of different intramitochondrial sorting signals. Mol Biol Cell 2012; 23:3936-47. [PMID: 22933571 PMCID: PMC3469510 DOI: 10.1091/mbc.e12-03-0202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The β-barrel protein Tom40 functions as a protein-conducting channel in the mitochondrial outer membrane. By attaching mitochondrial presequences for various mitochondrial destinations to Tom40, it is possible to follow its sorting process. The results provide insight into the mechanism for the precise delivery of β-barrel proteins to the outer membrane. The TOM40 complex is a protein translocator in the mitochondrial outer membrane and consists of several different subunits. Among them, Tom40 is a central subunit that constitutes a protein-conducting channel by forming a β-barrel structure. To probe the nature of the assembly process of Tom40 in the outer membrane, we attached various mitochondrial presequences to Tom40 that possess sorting information for the intermembrane space (IMS), inner membrane, and matrix and would compete with the inherent Tom40 assembly process. We analyzed the mitochondrial import of those fusion proteins in vitro. Tom40 crossed the outer membrane and/or inner membrane even in the presence of various sorting signals. N-terminal anchorage of the attached presequence to the inner membrane did not prevent Tom40 from associating with the TOB/SAM complex, although it impaired its efficient release from the TOB complex in vitro but not in vivo. The IMS or matrix-targeting presequence attached to Tom40 was effective in substituting for the requirement for small Tim proteins in the IMS for the translocation of Tom40 across the outer membrane. These results provide insight into the mechanism responsible for the precise delivery of β-barrel proteins to the outer mitochondrial membrane.
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Affiliation(s)
- Takuya Shiota
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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111
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Bohnert M, Wenz LS, Zerbes RM, Horvath SE, Stroud DA, von der Malsburg K, Müller JM, Oeljeklaus S, Perschil I, Warscheid B, Chacinska A, Veenhuis M, van der Klei IJ, Daum G, Wiedemann N, Becker T, Pfanner N, van der Laan M. Role of mitochondrial inner membrane organizing system in protein biogenesis of the mitochondrial outer membrane. Mol Biol Cell 2012; 23:3948-56. [PMID: 22918945 PMCID: PMC3469511 DOI: 10.1091/mbc.e12-04-0295] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. We report that MINOS independently interacts with both preprotein translocases of the outer mitochondrial membrane and plays a role in the biogenesis of β-barrel proteins of the outer membrane. Mitochondria contain two membranes, the outer membrane and the inner membrane with folded cristae. The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. MINOS interacts with both preprotein transport machineries of the outer membrane, the translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). It is unknown, however, whether MINOS plays a role in the biogenesis of outer membrane proteins. We have dissected the interaction of MINOS with TOM and SAM and report that MINOS binds to both translocases independently. MINOS binds to the SAM complex via the conserved polypeptide transport–associated domain of Sam50. Mitochondria lacking mitofilin, the large core subunit of MINOS, are impaired in the biogenesis of β-barrel proteins of the outer membrane, whereas mutant mitochondria lacking any of the other five MINOS subunits import β-barrel proteins in a manner similar to wild-type mitochondria. We show that mitofilin is required at an early stage of β-barrel biogenesis that includes the initial translocation through the TOM complex. We conclude that MINOS interacts with TOM and SAM independently and that the core subunit mitofilin is involved in biogenesis of outer membrane β-barrel proteins.
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Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
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112
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Ulrich T, Gross LE, Sommer MS, Schleiff E, Rapaport D. Chloroplast β-barrel proteins are assembled into the mitochondrial outer membrane in a process that depends on the TOM and TOB complexes. J Biol Chem 2012; 287:27467-79. [PMID: 22745120 PMCID: PMC3431683 DOI: 10.1074/jbc.m112.382093] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/27/2012] [Indexed: 11/06/2022] Open
Abstract
Membrane-embedded β-barrel proteins are found in the outer membranes (OM) of Gram-negative bacteria, mitochondria and chloroplasts. In eukaryotic cells, precursors of these proteins are synthesized in the cytosol and have to be sorted to their corresponding organelle. Currently, the signal that ensures their specific targeting to either mitochondria or chloroplasts is ill-defined. To address this issue, we studied targeting of the chloroplast β-barrel proteins Oep37 and Oep24. We found that both proteins can be integrated in vitro into isolated plant mitochondria. Furthermore, upon their expression in yeast cells Oep37 and Oep24 were exclusively located in the mitochondrial OM. Oep37 partially complemented the growth phenotype of yeast cells lacking Porin, the general metabolite transporter of this membrane. Similarly to mitochondrial β-barrel proteins, Oep37 and Oep24 expressed in yeast cells were assembled into the mitochondrial OM in a pathway dependent on the TOM and TOB complexes. Taken together, this study demonstrates that the central mitochondrial components that mediate the import of yeast β-barrel proteins can deal with precursors of chloroplast β-barrel proteins. This implies that the mitochondrial import machinery does not recognize signals that are unique to mitochondrial β-barrel proteins. Our results further suggest that dedicated targeting factors had to evolve in plant cells to prevent mis-sorting of chloroplast β-barrel proteins to mitochondria.
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Affiliation(s)
- Thomas Ulrich
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen and
| | - Lucia E. Gross
- the Centre of Membrane Proteomics and Cluster of Excellence Frankfurt, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt, Germany
| | - Maik S. Sommer
- the Centre of Membrane Proteomics and Cluster of Excellence Frankfurt, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- the Centre of Membrane Proteomics and Cluster of Excellence Frankfurt, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt, Germany
| | - Doron Rapaport
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen and
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113
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Conserved residues of the putative L6 loop of Escherichia coli BamA play a critical role in the assembly of β-barrel outer membrane proteins, including that of BamA itself. J Bacteriol 2012; 194:4662-8. [PMID: 22753067 DOI: 10.1128/jb.00825-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many members of the Omp85 family of proteins form essential β-barrel outer membrane protein (OMP) biogenesis machinery in Gram-negative bacteria, chloroplasts, and mitochondria. In Escherichia coli, BamA, a member of the Omp85 family, folds into an outer membrane-embedded β-barrel domain and a soluble periplasmic polypeptide-transport-associated (POTRA) domain. Although the high-resolution structures of only the BamA POTRA domain of E. coli are available, the crystal structure of FhaC, an Omp85 family member and a component of the two-partner secretion system in Bordetella pertussis, suggests that the BamA β-barrel likely folds into a 16-stranded β-barrel. The FhaC β-barrel is occluded by an N-terminal α-helix and a large β-barrel loop, L6, which carries residues that are highly conserved among the Omp85 family members. Deletion of L6 in FhaC did not affect its biogenesis but abolished its secretion function. In this study, we tested the hypothesis that the conserved residues of the putative L6 loop, which presumably folds back into the lumen of the BamA β-barrel like the FhaC counterpart, play an important role in OMP and/or BamA biogenesis. The conserved (641)RGF(643) residues of L6 were either deleted or replaced with alanine in various permutations. Phenotypic and biochemical characterization of various BamA L6 mutants revealed that the conserved RGF residues are critical for OMP biogenesis. Moreover, three BamA L6 alterations, ΔRGF, AAA, and AGA, produced a conditional lethal phenotype, concomitant with severely reduced BamA levels and folding defects. Thus, the conserved (641)RGF(643) residues of the BamA L6 loop are important for BamA folding and biogenesis.
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114
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From evolution to pathogenesis: the link between β-barrel assembly machineries in the outer membrane of mitochondria and gram-negative bacteria. Int J Mol Sci 2012; 13:8038-8050. [PMID: 22942688 PMCID: PMC3430219 DOI: 10.3390/ijms13078038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/21/2012] [Accepted: 06/21/2012] [Indexed: 01/29/2023] Open
Abstract
β-barrel proteins are the highly abundant in the outer membranes of Gram-negative bacteria and the mitochondria in eukaryotes. The assembly of β-barrels is mediated by two evolutionary conserved machineries; the β-barrel Assembly Machinery (BAM) in Gram-negative bacteria; and the Sorting and Assembly Machinery (SAM) in mitochondria. Although the BAM and SAM have functionally conserved roles in the membrane integration and folding of β-barrel proteins, apart from the central BamA and Sam50 proteins, the remaining components of each of the complexes have diverged remarkably. For example all of the accessory components of the BAM complex characterized to date are located in the bacterial periplasm, on the same side as the N-terminal domain of BamA. This is the same side of the membrane as the substrates that are delivered to the BAM. On the other hand, all of the accessory components of the SAM complex are located on the cytosolic side of the membrane, the opposite side of the membrane to the N-terminus of Sam50 and the substrate receiving side of the membrane. Despite the accessory subunits being located on opposite sides of the membrane in each system, it is clear that each system is functionally equivalent with bacterial proteins having the ability to use the eukaryotic SAM and vice versa. In this review, we summarize the similarities and differences between the BAM and SAM complexes, highlighting the possible selecting pressures on bacteria and eukaryotes during evolution. It is also now emerging that bacterial pathogens utilize the SAM to target toxins and effector proteins to host mitochondria and this will also be discussed from an evolutionary perspective.
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115
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Dudek J, Rehling P, van der Laan M. Mitochondrial protein import: common principles and physiological networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:274-85. [PMID: 22683763 DOI: 10.1016/j.bbamcr.2012.05.028] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 11/28/2022]
Abstract
Most mitochondrial proteins are encoded in the nucleus. They are synthesized as precursor forms in the cytosol and must be imported into mitochondria with the help of different protein translocases. Distinct import signals within precursors direct each protein to the mitochondrial surface and subsequently onto specific transport routes to its final destination within these organelles. In this review we highlight common principles of mitochondrial protein import and address different mechanisms of protein integration into mitochondrial membranes. Over the last years it has become clear that mitochondrial protein translocases are not independently operating units, but in fact closely cooperate with each other. We discuss recent studies that indicate how the pathways for mitochondrial protein biogenesis are embedded into a functional network of various other physiological processes, such as energy metabolism, signal transduction, and maintenance of mitochondrial morphology. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Jan Dudek
- Abteilung Biochemie II, Universität Göttingen, 37073 Göttingen, Germany
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116
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Dynamic association of BAM complex modules includes surface exposure of the lipoprotein BamC. J Mol Biol 2012; 422:545-55. [PMID: 22683355 DOI: 10.1016/j.jmb.2012.05.035] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/09/2012] [Accepted: 05/30/2012] [Indexed: 11/21/2022]
Abstract
The β-barrel assembly machinery (BAM) complex drives the assembly of β-barrel proteins into the outer membrane of gram-negative bacteria. It is composed of five subunits: BamA, BamB, BamC, BamD, and BamE. We find that the BAM complex isolated from the outer membrane of Escherichia coli consists of a core complex of BamA:B:C:D:E and, in addition, a BamA:B module and a BamC:D module. In the absence of BamC, these modules are destabilized, resulting in increased protease susceptibility of BamD and BamB. While the N-terminus of BamC carries a highly conserved region crucial for stable interaction with BamD, immunofluorescence, immunoprecipitation, and protease-sensitivity assays show that the C-terminal domain of BamC, composed of two helix-grip motifs, is exposed on the surface of E. coli. This unexpected topology of a bacterial lipoprotein is reminiscent of the analogous protein subunits from the mitochondrial β-barrel insertion machinery, the SAM complex. The modular arrangement and topological features provide new insight into the architecture of the BAM complex, towards a better understanding of the mechanism driving β-barrel membrane protein assembly.
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117
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Kenedy MR, Lenhart TR, Akins DR. The role of Borrelia burgdorferi outer surface proteins. ACTA ACUST UNITED AC 2012; 66:1-19. [PMID: 22540535 DOI: 10.1111/j.1574-695x.2012.00980.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/13/2012] [Accepted: 04/25/2012] [Indexed: 12/18/2022]
Abstract
Human pathogenic spirochetes causing Lyme disease belong to the Borrelia burgdorferi sensu lato complex. Borrelia burgdorferi organisms are extracellular pathogens transmitted to humans through the bite of Ixodes spp. ticks. These spirochetes are unique in that they can cause chronic infection and persist in the infected human, even though a robust humoral and cellular immune response is produced by the infected host. How this extracellular pathogen is able to evade the host immune response for such long periods of time is currently unclear. To gain a better understanding of how this organism persists in the infected human, many laboratories have focused on identifying and characterizing outer surface proteins of B. burgdorferi. As the interface between B. burgdorferi and its human host is its outer surface, proteins localized to the outer membrane must play an important role in dissemination, virulence, tissue tropism, and immune evasion. Over the last two decades, numerous outer surface proteins from B. burgdorferi have been identified, and more recent studies have begun to elucidate the functional role(s) of many borrelial outer surface proteins. This review summarizes the outer surface proteins identified in B. burgdorferi to date and provides detailed insight into the functions of many of these proteins as they relate to the unique parasitic strategy of this spirochetal pathogen.
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Affiliation(s)
- Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, USA
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118
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Kim KH, Aulakh S, Paetzel M. The bacterial outer membrane β-barrel assembly machinery. Protein Sci 2012; 21:751-68. [PMID: 22549918 DOI: 10.1002/pro.2069] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 03/20/2012] [Indexed: 12/31/2022]
Abstract
β-Barrel proteins found in the outer membrane of Gram-negative bacteria serve a variety of cellular functions. Proper folding and assembly of these proteins are essential for the viability of bacteria and can also play an important role in virulence. The β-barrel assembly machinery (BAM) complex, which is responsible for the proper assembly of β-barrels into the outer membrane of Gram-negative bacteria, has been the focus of many recent studies. This review summarizes the significant progress that has been made toward understanding the structure and function of the bacterial BAM complex.
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Affiliation(s)
- Kelly H Kim
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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119
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Genetic, biochemical, and molecular characterization of the polypeptide transport-associated domain of Escherichia coli BamA. J Bacteriol 2012; 194:3512-21. [PMID: 22544271 DOI: 10.1128/jb.06740-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The BamA protein of Escherichia coli plays a central role in the assembly of β-barrel outer membrane proteins (OMPs). The C-terminal domain of BamA folds into an integral outer membrane β-barrel, and the N terminus forms a periplasmic polypeptide transport-associated (POTRA) domain for OMP reception and assembly. We show here that BamA misfolding, caused by the deletion of the R44 residue from the α2 helix of the POTRA 1 domain (ΔR44), can be overcome by the insertion of alanine 2 residues upstream or downstream from the ΔR44 site. This highlights the importance of the side chain orientation of the α2 helix residues for normal POTRA 1 activity. The ΔR44-mediated POTRA folding defect and its correction by the insertion of alanine were further demonstrated by using a construct expressing just the soluble POTRA domain. Besides misfolding, the expression of BamA(ΔR44) from a low-copy-number plasmid confers a severe drug hypersensitivity phenotype. A spontaneous drug-resistant revertant of BamA(ΔR44) was found to carry an A18S substitution in the α1 helix of POTRA 1. In the BamA(ΔR44, A18S) background, OMP biogenesis improved dramatically, and this correlated with improved BamA folding, BamA-SurA interactions, and LptD (lipopolysaccharide transporter) biogenesis. The presence of the A18S substitution in the wild-type BamA protein did not affect the activity of BamA. The discovery of the A18S substitution in the α1 helix of the POTRA 1 domain as a suppressor of the folding defect caused by ΔR44 underscores the importance of the helix 1 and 2 regions in BamA folding.
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120
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Anwari K, Webb CT, Poggio S, Perry AJ, Belousoff M, Celik N, Ramm G, Lovering A, Sockett RE, Smit J, Jacobs-Wagner C, Lithgow T. The evolution of new lipoprotein subunits of the bacterial outer membrane BAM complex. Mol Microbiol 2012; 84:832-44. [PMID: 22524202 PMCID: PMC3359395 DOI: 10.1111/j.1365-2958.2012.08059.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The β-barrel assembly machine (BAM) complex is an essential feature of all bacteria with an outer membrane. The core subunit of the BAM complex is BamA and, in Escherichia coli, four lipoprotein subunits: BamB, BamC, BamD and BamE, also function in the BAM complex. Hidden Markov model analysis was used to comprehensively assess the distribution of subunits of the BAM lipoproteins across all subclasses of proteobacteria. A patchwork distribution was detected which is readily reconciled with the evolution of the α-, β-, γ-, δ- and ε-proteobacteria. Our findings lead to a proposal that the ancestral BAM complex was composed of two subunits: BamA and BamD, and that BamB, BamC and BamE evolved later in a distinct sequence of events. Furthermore, in some lineages novel lipoproteins have evolved instead of the lipoproteins found in E. coli. As an example of this concept, we show that no known species of α-proteobacteria has a homologue of BamC. However, purification of the BAM complex from the model α-proteobacterium Caulobacter crescentus identified a novel subunit we refer to as BamF, which has a conserved sequence motif related to sequences found in BamC. BamF and BamD can be eluted from the BAM complex under similar conditions, mirroring the BamC:D module seen in the BAM complex of γ-proteobacteria such as E. coli.
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Affiliation(s)
- Khatira Anwari
- Department of Biochemistry & Molecular Biology, Monash University, Melbourne 3800, Australia
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121
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Lenhart TR, Kenedy MR, Yang X, Pal U, Akins DR. BB0324 and BB0028 are constituents of the Borrelia burgdorferi β-barrel assembly machine (BAM) complex. BMC Microbiol 2012; 12:60. [PMID: 22519960 PMCID: PMC3356241 DOI: 10.1186/1471-2180-12-60] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/20/2012] [Indexed: 11/24/2022] Open
Abstract
Background Similar to Gram-negative bacteria, the outer membrane (OM) of the pathogenic spirochete, Borrelia burgdorferi, contains integral OM-spanning proteins (OMPs), as well as membrane-anchored lipoproteins. Although the mechanism of OMP biogenesis is still not well-understood, recent studies have indicated that a heterooligomeric OM protein complex, known as BAM (β-barrel assembly machine) is required for proper assembly of OMPs into the bacterial OM. We previously identified and characterized the essential β-barrel OMP component of this complex in B. burgdorferi, which we determined to be a functional BamA ortholog. Results In the current study, we report on the identification of two additional protein components of the B. burgdorferi BAM complex, which were identified as putative lipoproteins encoded by ORFs BB0324 and BB0028. Biochemical assays with a BamA-depleted B. burgdorferi strain indicate that BB0324 and BB0028 do not readily interact with the BAM complex without the presence of BamA, suggesting that the individual B. burgdorferi BAM components may associate only when forming a functional BAM complex. Cellular localization assays indicate that BB0324 and BB0028 are OM-associated subsurface lipoproteins, and in silico analyses indicate that BB0324 is a putative BamD ortholog. Conclusions The combined data suggest that the BAM complex of B. burgdorferi contains unique protein constituents which differ from those found in other proteobacterial BAM complexes. The novel findings now allow for the B. burgdorferi BAM complex to be further studied as a model system to better our understanding of spirochetal OM biogenesis in general.
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Affiliation(s)
- Tiffany R Lenhart
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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122
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Jiang JH, Tong J, Gabriel K. Hijacking Mitochondria: Bacterial Toxins that Modulate Mitochondrial Function. IUBMB Life 2012; 64:397-401. [DOI: 10.1002/iub.1021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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123
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Lin L, Pan G, Li T, Dang X, Deng Y, Ma C, Chen J, Luo J, Zhou Z. The protein import pore Tom40 in the microsporidian Nosema bombycis. J Eukaryot Microbiol 2012; 59:251-7. [PMID: 22486892 DOI: 10.1111/j.1550-7408.2012.00618.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 12/11/2012] [Accepted: 12/09/2012] [Indexed: 11/28/2022]
Abstract
Microsporidia, an unusual group of unicellular parasites related to fungi, possess a highly reduced mitochondrion known as the mitosome. Since mitosomes lack an organellar genome, their proteins must be translated in the cytosol before being imported into the mitosome via translocases. We have identified a Tom40 gene (NbTom40), the main component of the translocase of the outer mitochondrial membrane, in the genome of the microsporidian Nosema bombycis. NbTom40 is reduced in size, but it is predicted to form a β-barrel structure composed of 19 β-strands. Phylogenetic analysis confirms that NbTom40 forms a clade with Tom40 sequences from other species, distinct from a related clade of voltage-dependent anion channels (VDACs). The NbTom40 contains a β-signal motif that the polar residue is substituted by glycine. Furthermore, we show that expression of NbTom40, as a GFP fusion protein within yeast cells, directs GFP to mitochondria of yeast. These findings suggest that NbTom40 may serve as an import channel of the microsporidian mitosome and facilitate protein translocation into this organelle.
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Affiliation(s)
- Lipeng Lin
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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124
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Discovery of an archetypal protein transport system in bacterial outer membranes. Nat Struct Mol Biol 2012; 19:506-10, S1. [DOI: 10.1038/nsmb.2261] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 02/09/2012] [Indexed: 01/10/2023]
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125
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Rao S, Schmidt O, Harbauer AB, Schönfisch B, Guiard B, Pfanner N, Meisinger C. Biogenesis of the preprotein translocase of the outer mitochondrial membrane: protein kinase A phosphorylates the precursor of Tom40 and impairs its import. Mol Biol Cell 2012; 23:1618-27. [PMID: 22419819 PMCID: PMC3338429 DOI: 10.1091/mbc.e11-11-0933] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM) is essential for the import of proteins into mitochondria. Cytosolic protein kinase A phosphorylates the precursor of the channel-forming protein Tom40 and inhibits its import into mitochondria, thus regulating the biogenesis of the protein entry gate of mitochondria. The preprotein translocase of the outer mitochondrial membrane (TOM) functions as the main entry gate for the import of nuclear-encoded proteins into mitochondria. The major subunits of the TOM complex are the three receptors Tom20, Tom22, and Tom70 and the central channel-forming protein Tom40. Cytosolic kinases have been shown to regulate the biogenesis and activity of the Tom receptors. Casein kinase 2 stimulates the biogenesis of Tom22 and Tom20, whereas protein kinase A (PKA) impairs the receptor function of Tom70. Here we report that PKA exerts an inhibitory effect on the biogenesis of the β-barrel protein Tom40. Tom40 is synthesized as precursor on cytosolic ribosomes and subsequently imported into mitochondria. We show that PKA phosphorylates the precursor of Tom40. The phosphorylated Tom40 precursor is impaired in import into mitochondria, whereas the nonphosphorylated precursor is efficiently imported. We conclude that PKA plays a dual role in the regulation of the TOM complex. Phosphorylation by PKA not only impairs the receptor activity of Tom70, but it also inhibits the biogenesis of the channel protein Tom40.
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Affiliation(s)
- Sanjana Rao
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, 79104 Freiburg, Germany
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126
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Becker T, Böttinger L, Pfanner N. Mitochondrial protein import: from transport pathways to an integrated network. Trends Biochem Sci 2012; 37:85-91. [PMID: 22178138 DOI: 10.1016/j.tibs.2011.11.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 01/24/2023]
Abstract
Mitochondria, the powerhouses of the cell, import most of their proteins from the cytosol. It was originally assumed that mitochondria imported precursor proteins via a general pathway but recent studies have revealed a remarkable variety of import pathways and mechanisms. Currently, five different protein import pathways can be distinguished. However, the import machineries cooperate with each other and are connected to other systems that function in the respiratory chain, mitochondrial membrane organization, protein quality control and endoplasmic reticulum-mitochondria junctions. In this Opinion, we propose that mitochondrial protein import should not be seen as an independent task of the organelle and that a network of cooperating machineries is responsible for major mitochondrial functions.
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Affiliation(s)
- Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
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127
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Heinz E, Lithgow T. Back to basics: a revealing secondary reduction of the mitochondrial protein import pathway in diverse intracellular parasites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:295-303. [PMID: 22366436 DOI: 10.1016/j.bbamcr.2012.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/09/2012] [Accepted: 02/09/2012] [Indexed: 12/31/2022]
Abstract
Mitochondria are present in all eukaryotes, but remodeling of their metabolic contribution has in some cases left them almost unrecognizable and they are referred to as mitochondria-like organelles, hydrogenosomes or, in the case where evolution has led to a great deal of simplification, as mitosomes. Mitochondria rely on the import of proteins encoded in the nucleus and the protein import machinery has been investigated in detail in yeast: several sophisticated molecular machines act in concert to import substrate proteins across the outer mitochondrial membrane and deliver them to a precise sub-mitochondrial compartment. Because these machines are so sophisticated, it has been a major challenge to conceptualize the first phase of their evolution. Here we review recent studies on the protein import pathway in parasitic species that have mitosomes: in the course of their evolution for highly specialized niches these parasites, particularly Cryptosporidia and Microsporidia, have secondarily lost numerous protein functions, in accordance with the evolution of their genomes towards a minimal size. Microsporidia are related to fungi, Cryptosporidia are apicomplexans and kin to the malaria parasite Plasmodium; and this great phylogenetic distance makes it remarkable that Microsporidia and Cryptosporidia have independently evolved skeletal protein import pathways that are almost identical. We suggest that the skeletal pathway reflects the protein import machinery of the first eukaryotes, and defines the essential roles of the core elements of the mitochondrial protein import machinery. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Eva Heinz
- Department of Biochemistry & Molecular Biology, Monash University, Clayton Campus, Melbourne 3800, Australia.
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128
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Activation of the Escherichia coli β-barrel assembly machine (Bam) is required for essential components to interact properly with substrate. Proc Natl Acad Sci U S A 2012; 109:3487-91. [PMID: 22331884 DOI: 10.1073/pnas.1201362109] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer membrane (OM) of gram-negative bacteria such as Escherichia coli contains lipoproteins and integral β-barrel proteins (outer-membrane proteins, OMPs) assembled into an asymmetrical lipid bilayer. Insertion of β-barrel proteins into the OM is mediated by a protein complex that contains the OMP BamA and four associated lipoproteins (BamBCDE). The mechanism by which the Bam complex catalyzes the assembly of OMPs is not known. We report here the isolation and characterization of a temperature-sensitive lethal mutation, bamAE373K, which alters the fifth polypeptide transport-associated domain and disrupts the interaction between the BamAB and BamCDE subcomplexes. Suppressor mutations that map to codon 197 in bamD restore Bam complex function to wild-type levels. However, these suppressors do not restore the interaction between BamA and BamD; rather, they bypass the requirement for stable holocomplex formation by activating BamD. These results imply that BamA and BamD interact directly with OMP substrates.
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129
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Töpel M, Ling Q, Jarvis P. Neofunctionalization within the Omp85 protein superfamily during chloroplast evolution. PLANT SIGNALING & BEHAVIOR 2012; 7:161-4. [PMID: 22307047 PMCID: PMC3405695 DOI: 10.4161/psb.18677] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Toc75 and OEP80 proteins reside in the chloroplast outer envelope membrane. Both are members of the Omp85 superfamily of β-barrel proteins, and both are essential in Arabidopsis plants with important roles throughout development. Toc75 forms the translocation channel of the TOC complex, which is responsible for importing nucleus-encoded proteins into chloroplasts, while the function of OEP80 remains uncertain. Deficiency of Toc75 in plants that have artificially reduced OEP80 levels suggests that the latter may be involved in the biogenesis of β-barrel proteins, in similar fashion to Omp85-related proteins in other systems. To elucidate the evolutionary relationship between the two proteins, we conducted a phylogenetic analysis using 48 sequences from diverse species. This indicated that Toc75 and OEP80 belong to sister groups in the Omp85 superfamily, and originate from a gene duplication in an ancient eukaryotic organism > 1.2 billion years ago. Our analysis also supports the notion that the Toc75 family has undergone a phase of neofunctionalization to accommodate the organelle's newly acquired need to import proteins.
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Affiliation(s)
- Mats Töpel
- Department of Plant and Environmental Sciences; Göteborg University; Göteborg, Sweden
| | - Qihua Ling
- Department of Biology; University of Leicester; Leicester, UK
| | - Paul Jarvis
- Department of Biology; University of Leicester; Leicester, UK
- Correspondence to: Paul Jarvis,
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130
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Mitochondrial sorting and assembly machinery subunit Sam37 in Candida albicans: insight into the roles of mitochondria in fitness, cell wall integrity, and virulence. EUKARYOTIC CELL 2012; 11:532-44. [PMID: 22286093 DOI: 10.1128/ec.05292-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent studies indicate that mitochondrial functions impinge on cell wall integrity, drug tolerance, and virulence of human fungal pathogens. However, the mechanistic aspects of these processes are poorly understood. We focused on the mitochondrial outer membrane SAM (Sorting and Assembly Machinery) complex subunit Sam37 in Candida albicans. Inactivation of SAM37 in C. albicans leads to a large reduction in fitness, a phenotype not conserved with the model yeast Saccharomyces cerevisiae. Our data indicate that slow growth of the sam37ΔΔ mutant results from mitochondrial DNA loss, a new function for Sam37 in C. albicans, and from reduced activity of the essential SAM complex subunit Sam35. The sam37ΔΔ mutant was hypersensitive to drugs that target the cell wall and displayed altered cell wall structure, supporting a role for Sam37 in cell wall integrity in C. albicans. The sensitivity of the mutant to membrane-targeting antifungals was not significantly altered. The sam37ΔΔ mutant was avirulent in the mouse model, and bioinformatics showed that the fungal Sam37 proteins are distant from their animal counterparts and could thus represent potential drug targets. Our study provides the first direct evidence for a link between mitochondrial function and cell wall integrity in C. albicans and is further relevant for understanding mitochondrial function in fitness, antifungal drug tolerance, and virulence of this major pathogen. Beyond the relevance to fungal pathogenesis, this work also provides new insight into the mitochondrial and cellular roles of the SAM complex in fungi.
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131
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Dolezal P, Aili M, Tong J, Jiang JH, Marobbio CM, Lee SF, Schuelein R, Belluzzo S, Binova E, Mousnier A, Frankel G, Giannuzzi G, Palmieri F, Gabriel K, Naderer T, Hartland EL, Lithgow T. Legionella pneumophila secretes a mitochondrial carrier protein during infection. PLoS Pathog 2012; 8:e1002459. [PMID: 22241989 PMCID: PMC3252375 DOI: 10.1371/journal.ppat.1002459] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 11/09/2011] [Indexed: 12/25/2022] Open
Abstract
The Mitochondrial Carrier Family (MCF) is a signature group of integral membrane proteins that transport metabolites across the mitochondrial inner membrane in eukaryotes. MCF proteins are characterized by six transmembrane segments that assemble to form a highly-selective channel for metabolite transport. We discovered a novel MCF member, termed Legionellanucleotide carrier Protein (LncP), encoded in the genome of Legionella pneumophila, the causative agent of Legionnaire's disease. LncP was secreted via the bacterial Dot/Icm type IV secretion system into macrophages and assembled in the mitochondrial inner membrane. In a yeast cellular system, LncP induced a dominant-negative phenotype that was rescued by deleting an endogenous ATP carrier. Substrate transport studies on purified LncP reconstituted in liposomes revealed that it catalyzes unidirectional transport and exchange of ATP transport across membranes, thereby supporting a role for LncP as an ATP transporter. A hidden Markov model revealed further MCF proteins in the intracellular pathogens, Legionella longbeachae and Neorickettsia sennetsu, thereby challenging the notion that MCF proteins exist exclusively in eukaryotic organisms. Mitochondrial carrier proteins evolved during endosymbiosis to transport substrates across the mitochondrial inner membrane. As such the proteins are associated exclusively with eukaryotic organisms. Despite this, we identified putative mitochondrial carrier proteins in the genomes of different intracellular bacterial pathogens, including Legionella pneumophila, the causative agent of Legionnaire's disease. We named the mitochondrial carrier protein from L. pneumophila LncP and determined that the protein is translocated into host cells during infection by the bacterial Dot/Icm type IV secretion system. From there, LncP accesses the classical mitochondrial import pathway and is incorporated into the mitochondrial inner membrane as an integral membrane protein. Remarkably, LncP crosses five biological membranes to reach its final location. Biochemically, LncP is a unidirectional nucleotide transporter similar to Aac1 in yeast. Although not essential for intracellular replication, the high carriage rate of lncP among isolates of L. pneumophila suggests that the ability of the pathogen to manipulate mitochondrial ATP transport assists survival of the bacteria in an intracellular environment.
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Affiliation(s)
- Pavel Dolezal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - Margareta Aili
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Janette Tong
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Jhih-Hang Jiang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Carlo M. Marobbio
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
| | - Sau fung Lee
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Ralf Schuelein
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Simon Belluzzo
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Eva Binova
- Department of Tropical Medicine, 1st Faculty of Medicine, Charles University in Prague and Faculty Hospital Bulovka, Prague, Czech Republic
| | - Aurelie Mousnier
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Giulia Giannuzzi
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
| | - Ferdinando Palmieri
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
| | - Kipros Gabriel
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Thomas Naderer
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Elizabeth L. Hartland
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
- * E-mail: (ELH); (TL)
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- * E-mail: (ELH); (TL)
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Abstract
Depending on the organism, mitochondria consist approximately of 500-1,400 different proteins. By far most of these proteins are encoded by nuclear genes and synthesized on cytosolic ribosomes. Targeting signals direct these proteins into mitochondria and there to their respective subcompartment: the outer membrane, the intermembrane space (IMS), the inner membrane, and the matrix. Membrane-embedded translocation complexes allow the translocation of proteins across and, in the case of membrane proteins, the insertion into mitochondrial membranes. A small number of proteins are encoded by the mitochondrial genome: Most mitochondrial translation products represent hydrophobic proteins of the inner membrane which-together with many nuclear-encoded proteins-form the respiratory chain complexes. This chapter gives an overview on the mitochondrial protein translocases and the mechanisms by which they drive the transport and assembly of mitochondrial proteins.
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133
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Wojtkowska M, Jąkalski M, Pieńkowska JR, Stobienia O, Karachitos A, Przytycka TM, Weiner J, Kmita H, Makałowski W. Phylogenetic analysis of mitochondrial outer membrane β-barrel channels. Genome Biol Evol 2011; 4:110-25. [PMID: 22155732 PMCID: PMC3273162 DOI: 10.1093/gbe/evr130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have β-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial β-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane β-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta.
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Affiliation(s)
- Małgorzata Wojtkowska
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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134
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Fan E, Fiedler S, Jacob-Dubuisson F, Müller M. Two-partner secretion of gram-negative bacteria: a single β-barrel protein enables transport across the outer membrane. J Biol Chem 2011; 287:2591-9. [PMID: 22134917 DOI: 10.1074/jbc.m111.293068] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanisms of protein secretion by pathogenic bacteria remain poorly understood. In gram-negative bacteria, the two-partner secretion pathway exports large, mostly virulence-related "TpsA" proteins across the outer membrane via their dedicated "TpsB" transporters. TpsB transporters belong to the ubiquitous Omp85 superfamily, whose members are involved in protein translocation across, or integration into, cellular membranes. The filamentous hemagglutinin/FhaC pair of Bordetella pertussis is a model two-partner secretion system. We have reconstituted the TpsB transporter FhaC into proteoliposomes and demonstrate that FhaC is the sole outer membrane protein required for translocation of its cognate TpsA protein. This is the first in vitro system for analyzing protein secretion across the outer membrane of gram-negative bacteria. Our data also provide clear evidence for the protein translocation function of Omp85 transporters.
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Affiliation(s)
- Enguo Fan
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Zellforschung, University of Freiburg, 79104 Freiburg, Germany
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135
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Substitutions in the BamA β-barrel domain overcome the conditional lethal phenotype of a ΔbamB ΔbamE strain of Escherichia coli. J Bacteriol 2011; 194:317-24. [PMID: 22037403 DOI: 10.1128/jb.06192-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BamA interacts with the BamBCDE lipoproteins, and together they constitute the essential β-barrel assembly machine (BAM) of Escherichia coli. The simultaneous absence of BamB and BamE confers a conditional lethal phenotype and a severe β-barrel outer membrane protein (OMP) biogenesis defect. Without BamB and BamE, wild-type BamA levels are significantly reduced, and the folding of the BamA β-barrel, as assessed by the heat-modifiability assay, is drastically compromised. Single-amino-acid substitutions in the β-barrel domain of BamA improve both bacterial growth and OMP biogenesis in a bamB bamE mutant and restore BamA levels close to the BamB(+) BamE(+) level. The substitutions alter BamA β-barrel folding, and folding in the mutants becomes independent of BamB and BamE. Remarkably, BamA β-barrel alterations also improve OMP biogenesis in cells lacking the major periplasmic chaperone, SurA, which, together with BamB, is thought to facilitate the transfer of partially folded OMPs to the soluble POTRA (polypeptide-transport-associated) domain of BamA. Unlike the bamB bamE mutant background, the absence of BamB or SurA does not affect BamA β-barrel folding. Thus, substitutions in the outer membrane-embedded BamA β-barrel domain overcome OMP biogenesis defects that occur at the POTRA domain of BamA in the periplasm. Based on the structure of FhaC, the altered BamA residues are predicted to lie on a highly conserved loop that folds inside the β-barrel and in regions pointing outside the β-barrel, suggesting that they influence BamA function by both direct and indirect mechanisms.
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136
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Jiang JH, Davies JK, Lithgow T, Strugnell RA, Gabriel K. Targeting of Neisserial PorB to the mitochondrial outer membrane: an insight on the evolution of β-barrel protein assembly machines. Mol Microbiol 2011; 82:976-87. [DOI: 10.1111/j.1365-2958.2011.07880.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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137
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Kim KH, Aulakh S, Tan W, Paetzel M. Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1350-8. [PMID: 22102230 DOI: 10.1107/s174430911103363x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 08/18/2011] [Indexed: 11/10/2022]
Abstract
In Gram-negative bacteria, the BAM complex catalyzes the essential process of assembling outer membrane proteins. The BAM complex in Escherichia coli consists of five proteins: one β-barrel membrane protein, BamA, and four lipoproteins, BamB, BamC, BamD and BamE. Here, the crystal structure of the C-terminal domain of E. coli BamC (BamC(C): Ala224-Ser343) refined to 1.5 Å resolution in space group H3 is reported. BamC(C) consists of a six-stranded antiparallel β-sheet, three α-helices and one 3(10)-helix. Sequence and surface analysis reveals that most of the conserved residues within BamC(C) are localized to form a continuous negatively charged groove that is involved in a major crystalline lattice contact in which a helix from a neighbouring BamC(C) binds against this surface. This interaction is topologically and architecturally similar to those seen in the substrate-binding grooves of other proteins with BamC-like folds. Taken together, these results suggest that an identified surface on the C-terminal domain of BamC may serve as an important protein-binding surface for interaction with other BAM-complex components or substrates.
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Affiliation(s)
- Kelly H Kim
- Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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138
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Liu Z, Li X, Zhao P, Gui J, Zheng W, Zhang Y. Tracing the evolution of the mitochondrial protein import machinery. Comput Biol Chem 2011; 35:336-40. [PMID: 22099629 DOI: 10.1016/j.compbiolchem.2011.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/01/2011] [Indexed: 10/16/2022]
Abstract
Mitochondria are eukaryotic organelles originated from a single bacterial endosymbiosis about 2 billion years ago. One of the earliest events in the evolution of mitochondria was the acquisition of a mechanism that facilitated the import of proteins from cytosol. The mitochondrial protein import machinery consists of dozens of subunits, and they are of modular design. However, to date, it is not clear when certain component was added to the machinery. Using extensive homology searches, the evolutionary history of the mitochondrial protein import machinery was reconstructed. The results indicated that 6 of the 35 subunits have homologs in prokaryote, suggesting that they were prokaryotic origin; the major subunit gains were occurred in the earliest stage of eukaryotic evolution; subsequent to the gain of these conserved set of subunits, the mitochondrial protein import machinery components diversified along the eukaryotic lineages and a number of lineage-specific subunits can be observed. Furthermore, protein import systems of mitochondria-like organelles (hydrogenosomes and mitosomes) have dramatically reduced their subunit contents, however, they share most of the prokaryotic origin components with mitochondrion.
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Affiliation(s)
- Zhen Liu
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064 Chengdu, People's Republic of China.
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139
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Alcock F, Webb CT, Dolezal P, Hewitt V, Shingu-Vasquez M, Likić VA, Traven A, Lithgow T. A small Tim homohexamer in the relict mitochondrion of Cryptosporidium. Mol Biol Evol 2011; 29:113-22. [PMID: 21984067 DOI: 10.1093/molbev/msr165] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The apicomplexan parasite Cryptosporidium parvum possesses a mitosome, a relict mitochondrion with a greatly reduced metabolic capability. This mitosome houses a mitochondrial-type protein import apparatus, but elements of the protein import pathway have been reduced, and even lost, through evolution. The small Tim protein family is a case in point. The genomes of C. parvum and related species of Cryptosporidium each encode just one small Tim protein, CpTimS. This observation challenged the tenet that small Tim proteins are always found in pairs as α3β3 hexamers. We show that the atypical CpTimS exists as a relatively unstable homohexamer, shedding light both on the early evolution of the small Tim protein family and on small Tim hexamer formation in contemporary eukaryotes.
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Affiliation(s)
- Felicity Alcock
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
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140
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Papic D, Krumpe K, Dukanovic J, Dimmer KS, Rapaport D. Multispan mitochondrial outer membrane protein Ugo1 follows a unique Mim1-dependent import pathway. ACTA ACUST UNITED AC 2011; 194:397-405. [PMID: 21825074 PMCID: PMC3153653 DOI: 10.1083/jcb.201102041] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The mitochondrial outer membrane (MOM) harbors several multispan proteins that execute various functions. Despite their importance, the mechanisms by which these proteins are recognized and inserted into the outer membrane remain largely unclear. In this paper, we address this issue using yeast mitochondria and the multispan protein Ugo1. Using a specific insertion assay and analysis by native gel electrophoresis, we show that the import receptor Tom70, but not its partner Tom20, is involved in the initial recognition of the Ugo1 precursor. Surprisingly, the import pore formed by the translocase of the outer membrane complex appears not to be required for the insertion process. Conversely, the multifunctional outer membrane protein mitochondrial import 1 (Mim1) plays a central role in mediating the insertion of Ugo1. Collectively, these results suggest that Ugo1 is inserted into the MOM by a novel pathway in which Tom70 and Mim1 contribute to the efficiency and selectivity of the process.
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Affiliation(s)
- Drazen Papic
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
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141
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Lackey SWK, Wideman JG, Kennedy EK, Go NE, Nargang FE. The Neurospora crassa TOB complex: analysis of the topology and function of Tob38 and Tob37. PLoS One 2011; 6:e25650. [PMID: 21980517 PMCID: PMC3182244 DOI: 10.1371/journal.pone.0025650] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022] Open
Abstract
The TOB or SAM complex is responsible for assembling several proteins into the mitochondrial outer membrane, including all β-barrel proteins. We have identified several forms of the complex in Neurospora crassa. One form contains Tob55, Tob38, and Tob37; another contains these three subunits plus the Mdm10 protein; while additional complexes contain only Tob55. As previously shown for Tob55, both Tob37 and Tob38 are essential for viability of the organism. Mitochondria deficient in Tob37 or Tob38 have reduced ability to assemble β-barrel proteins. The function of two hydrophobic domains in the C-terminal region of the Tob37 protein was investigated. Mutant Tob37 proteins lacking either or both of these regions are able to restore viability to cells lacking the protein. One of the domains was found to anchor the protein to the outer mitochondrial membrane but was not necessary for targeting or association of the protein with mitochondria. Examination of the import properties of mitochondria containing Tob37 with deletions of the hydrophobic domains reveals that the topology of Tob37 may be important for interactions between specific classes of β-barrel precursors and the TOB complex.
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Affiliation(s)
| | - Jeremy G. Wideman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Erin K. Kennedy
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nancy E. Go
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Frank E. Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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142
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Dimmer KS, Rapaport D. Unresolved mysteries in the biogenesis of mitochondrial membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1085-90. [PMID: 21889926 DOI: 10.1016/j.bbamem.2011.08.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/10/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
Abstract
Mitochondria are essential eukaryotic organelles that are surrounded by two membranes. Both membranes contain a variety of different integral membrane proteins. After three decades of research on mitochondrial biogenesis five major import complexes with more than 40 subunits altogether were identified and characterized. In the current contribution we want to draw attention to some unexplored issues regarding the integration of mitochondrial membrane proteins and to formulate crucial questions that remain unanswered. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.
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143
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Ricci DP, Silhavy TJ. The Bam machine: a molecular cooper. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1067-84. [PMID: 21893027 DOI: 10.1016/j.bbamem.2011.08.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/08/2011] [Accepted: 08/15/2011] [Indexed: 11/24/2022]
Abstract
The bacterial outer membrane (OM) is an exceptional biological structure with a unique composition that contributes significantly to the resiliency of Gram-negative bacteria. Since all OM components are synthesized in the cytosol, the cell must efficiently transport OM-specific lipids and proteins across the cell envelope and stably integrate them into a growing membrane. In this review, we discuss the challenges associated with these processes and detail the elegant solutions that cells have evolved to address the topological problem of OM biogenesis. Special attention will be paid to the Bam machine, a highly conserved multiprotein complex that facilitates OM β-barrel folding. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Dante P Ricci
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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144
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Abstract
The majority of outer membrane proteins (OMPs) from gram-negative bacteria and many of mitochondria and chloroplasts are β-barrels. Insertion and assembly of these proteins are catalyzed by the Omp85 protein family in a seemingly conserved process. All members of this family exhibit a characteristic N-terminal polypeptide-transport-associated (POTRA) and a C-terminal 16-stranded β-barrel domain. In plants, two phylogenetically distinct and essential Omp85's exist in the chloroplast outer membrane, namely Toc75-III and Toc75-V. Whereas Toc75-V, similar to the mitochondrial Sam50, is thought to possess the original bacterial function, its homolog, Toc75-III, evolved to the pore-forming unit of the TOC translocon for preprotein import. In all current models of OMP biogenesis and preprotein translocation, a topology of Omp85 with the POTRA domain in the periplasm or intermembrane space is assumed. Using self-assembly GFP-based in vivo experiments and in situ topology studies by electron cryotomography, we show that the POTRA domains of both Toc75-III and Toc75-V are exposed to the cytoplasm. This unexpected finding explains many experimental observations and requires a reevaluation of current models of OMP biogenesis and TOC complex function.
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145
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Affiliation(s)
- Christine L. Hagan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; ,
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146
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Zhang W, Shao J, Liu G, Tang F, Lu Y, Zhai Z, Wang Y, Wu Z, Yao H, Lu C. Immunoproteomic analysis of bacterial proteins of Actinobacillus pleuropneumoniae serotype 1. Proteome Sci 2011; 9:32. [PMID: 21703014 PMCID: PMC3148531 DOI: 10.1186/1477-5956-9-32] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 06/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background Actinobacillus pleuropneumoniae (APP) is one of the most important swine pathogens worldwide. Identification and characterization of novel antigenic APP vaccine candidates are underway. In the present study, we use an immunoproteomic approach to identify APP protein antigens that may elicit an immune response in serotype 1 naturally infected swine and serotype 1 virulent strain S259-immunized rabbits. Results Proteins from total cell lysates of serotype 1 APP were separated by two-dimensional electrophoresis (2DE). Western blot analysis revealed 21 immunoreactive protein spots separated in the pH 4-7 range and 4 spots in the pH 7-11 range with the convalescent sera from swine; we found 5 immunoreactive protein spots that separated in the pH 4-7 range and 2 in the pH 7-11 range with hyperimmune sera from S259-immunized rabbits. The proteins included the known antigens ApxIIA, protective surface antigen D15, outer membrane proteins P5, subunit NqrA. The remaining antigens are being reported as immunoreactive proteins in APP for the first time, to our knowledge. Conclusions We identified a total of 42 immunoreactive proteins of the APP serotype 1 virulent strain S259 which represented 32 different proteins, including some novel immunoreactive factors which could be researched as vaccine candidates.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Shao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangjin Liu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang Tang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhipeng Zhai
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Wang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongfu Wu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huochun Yao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengping Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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147
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Stroud DA, Becker T, Qiu J, Stojanovski D, Pfannschmidt S, Wirth C, Hunte C, Guiard B, Meisinger C, Pfanner N, Wiedemann N. Biogenesis of mitochondrial β-barrel proteins: the POTRA domain is involved in precursor release from the SAM complex. Mol Biol Cell 2011; 22:2823-33. [PMID: 21680715 PMCID: PMC3154879 DOI: 10.1091/mbc.e11-02-0148] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The mitochondrial outer membrane contains proteinaceous machineries for the translocation of precursor proteins. The sorting and assembly machinery (SAM) is required for the insertion of β-barrel proteins into the outer membrane. Sam50 is the channel-forming core subunit of the SAM complex and belongs to the BamA/Sam50/Toc75 family of proteins that have been conserved from Gram-negative bacteria to mitochondria and chloroplasts. These proteins contain one or more N-terminal polypeptide transport-associated (POTRA) domains. POTRA domains can bind precursor proteins, however, different views exist on the role of POTRA domains in the biogenesis of β-barrel proteins. It has been suggested that the single POTRA domain of mitochondrial Sam50 plays a receptor-like function at the SAM complex. We established a system to monitor the interaction of chemical amounts of β-barrel precursor proteins with the SAM complex of wild-type and mutant yeast in organello. We report that the SAM complex lacking the POTRA domain of Sam50 efficiently binds β-barrel precursors, but is impaired in the release of the precursors. These results indicate the POTRA domain of Sam50 is not essential for recognition of β-barrel precursors but functions in a subsequent step to promote the release of precursor proteins from the SAM complex.
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Affiliation(s)
- David A Stroud
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
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148
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Delattre A, Saint N, Clantin B, Willery E, Lippens G, Locht C, Villeret V, Jacob‐Dubuisson F. Substrate recognition by the POTRA domains of TpsB transporter FhaC. Mol Microbiol 2011; 81:99-112. [DOI: 10.1111/j.1365-2958.2011.07680.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anne‐Sophie Delattre
- Inserm U1019, Center for Infection and Immunity of Lille, F‐59019 Lille, France
- Institut Pasteur de Lille, F‐59019 Lille, France
- Univ Lille Nord de France, F‐59000 Lille, France
- CNRS UMR8204, F‐59021 Lille, France
| | - Nathalie Saint
- INSERM U1046, Université de Montpellier 1 et 2, F‐34090 Montpellier cedex, France
| | - Bernard Clantin
- CNRS USR3078, Institut de Recherche Interdisciplinaire – Université de Lille 1 – Université de Lille 2, F‐59658 Villeneuve d'Ascq, France
| | - Eve Willery
- Inserm U1019, Center for Infection and Immunity of Lille, F‐59019 Lille, France
- Institut Pasteur de Lille, F‐59019 Lille, France
- Univ Lille Nord de France, F‐59000 Lille, France
- CNRS UMR8204, F‐59021 Lille, France
| | - Guy Lippens
- CNRS UMR 8576 – Université de Lille I, F‐59655 Villeneuve d'Ascq – France
| | - Camille Locht
- Inserm U1019, Center for Infection and Immunity of Lille, F‐59019 Lille, France
- Institut Pasteur de Lille, F‐59019 Lille, France
- Univ Lille Nord de France, F‐59000 Lille, France
- CNRS UMR8204, F‐59021 Lille, France
| | - Vincent Villeret
- CNRS USR3078, Institut de Recherche Interdisciplinaire – Université de Lille 1 – Université de Lille 2, F‐59658 Villeneuve d'Ascq, France
| | - Françoise Jacob‐Dubuisson
- Inserm U1019, Center for Infection and Immunity of Lille, F‐59019 Lille, France
- Institut Pasteur de Lille, F‐59019 Lille, France
- Univ Lille Nord de France, F‐59000 Lille, France
- CNRS UMR8204, F‐59021 Lille, France
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149
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Kozjak-Pavlovic V, Ott C, Götz M, Rudel T. Neisserial Omp85 protein is selectively recognized and assembled into functional complexes in the outer membrane of human mitochondria. J Biol Chem 2011; 286:27019-26. [PMID: 21652692 DOI: 10.1074/jbc.m111.232249] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As a consequence of their bacterial origin, mitochondria contain β-barrel proteins in their outer membrane (OMM). These proteins require the translocase of the outer membrane (TOM) complex and the conserved sorting and assembly machinery (SAM) complex for transport and integration into the OMM. The SAM complex and the β-barrel assembly machinery (BAM) required for biogenesis of β-barrel proteins in bacteria are evolutionarily related. Despite this homology, we show that bacterial β-barrel proteins are not universally recognized and integrated into the OMM of human mitochondria. Selectivity exists both at the level of the TOM and the SAM complex. Of all of the proteins we tested, human mitochondria imported only β-barrel proteins originating from Neisseria sp., and only Omp85, the central component of the neisserial BAM complex, integrated into the OMM. PorB proteins from different Neisseria, although imported by the TOM, were not recognized by the SAM complex and formed membrane complexes only when functional Omp85 was present at the same time in mitochondria. Omp85 alone was capable of integrating other bacterial β-barrel proteins in human mitochondria, but could not substitute for the function of its mitochondrial homolog Sam50. Thus, signals and machineries for transport and assembly of β-barrel proteins in bacteria and human mitochondria differ enough to allow only a certain type of β-barrel proteins to be targeted and integrated in mitochondrial membranes in human cells.
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Affiliation(s)
- Vera Kozjak-Pavlovic
- Biozentrum, Department of Microbiology, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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150
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Delage L, Leblanc C, Nyvall Collén P, Gschloessl B, Oudot MP, Sterck L, Poulain J, Aury JM, Cock JM. In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus. PLoS One 2011; 6:e19540. [PMID: 21611166 PMCID: PMC3097184 DOI: 10.1371/journal.pone.0019540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/31/2011] [Indexed: 01/24/2023] Open
Abstract
The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes.
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Affiliation(s)
- Ludovic Delage
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Catherine Leblanc
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Pi Nyvall Collén
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Bernhard Gschloessl
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Pierre Oudot
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lieven Sterck
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Julie Poulain
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - J. Mark Cock
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
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