1
|
Xia X. Beyond Trees: Regulons and Regulatory Motif Characterization. Genes (Basel) 2020; 11:genes11090995. [PMID: 32854400 PMCID: PMC7564462 DOI: 10.3390/genes11090995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a set of target genes regulated by a transcription factor by physically binding to regulatory motifs to accomplish a specific biological function, such as the CO-FT regulon for flowering timing and fall growth cessation in trees. Only with a clear characterization of regulatory motifs, can candidate target genes be experimentally validated, but motif characterization represents the weakest feature of regulon research, especially in tree genetics. I review here relevant experimental and bioinformatics approaches in characterizing transcription factors and their binding sites, outline problems in tree regulon research, and demonstrate how transcription factor databases can be effectively used to aid the characterization of tree regulons.
Collapse
Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| |
Collapse
|
2
|
Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
Collapse
|
3
|
Xia X. Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction. SCIENTIFICA 2012; 2012:917540. [PMID: 24278755 PMCID: PMC3820676 DOI: 10.6064/2012/917540] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/11/2012] [Indexed: 05/31/2023]
Abstract
Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods, but also a key component in more advanced computational algorithms (e.g., Gibbs sampler) for characterizing and discovering motifs in nucleotide or amino acid sequences. However, few generally applicable statistical tests are available for evaluating the significance of site patterns, PWM, and PWM scores (PWMS) of putative motifs. Statistical significance tests of the PWM output, that is, site-specific frequencies, PWM itself, and PWMS, are in disparate sources and have never been collected in a single paper, with the consequence that many implementations of PWM do not include any significance test. Here I review PWM-based methods used in motif characterization and prediction (including a detailed illustration of the Gibbs sampler for de novo motif discovery), present statistical and probabilistic rationales behind statistical significance tests relevant to PWM, and illustrate their application with real data. The multiple comparison problem associated with the test of site-specific frequencies is best handled by false discovery rate methods. The test of PWM, due to the use of pseudocounts, is best done by resampling methods. The test of individual PWMS for each sequence segment should be based on the extreme value distribution.
Collapse
Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5
| |
Collapse
|
4
|
Colombini M. VDAC structure, selectivity, and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1457-65. [PMID: 22240010 DOI: 10.1016/j.bbamem.2011.12.026] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 12/02/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
VDAC channels exist in the mitochondrial outer membrane of all eukaryotic organisms. Of the different isoforms present in one organism, it seems that one of these is the canonical VDAC whose properties and 3D structure are highly conserved. The fundamental role of these channels is to control the flux of metabolites between the cytosol and mitochondrial spaces. Based on many functional studies, the fundamental structure of the pore wall consists of one α helix and 13 β strands tilted at a 46° angle. This results in a pore with an estimated internal diameter of 2.5nm. This structure has not yet been resolved. The published 3D structure consists of 19 β strands and is different from the functional structure that forms voltage-gated channels. The selectivity of the channel is exquisite, being able to select for ATP over molecules of the same size and charge. Voltage gating involves two separate gating processes. The mechanism involves the translocation of a positively charged portion of the wall of the channel to the membrane surface resulting in a reduction in pore diameter and volume and an inversion in ion selectivity. This mechanism is consistent with experiments probing changes in selectivity, voltage gating, kinetics and energetics. Other published mechanisms are in conflict with experimental results. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
Collapse
Affiliation(s)
- Marco Colombini
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
5
|
Abstract
The eukaryotic porin or Voltage Dependent Anion-selective Channels (VDAC) is the protein forming the aqueous pore channel in the mitochondrial outer membrane. It can modulate the energy-dependent metabolism of the cell forming a diffusion barrier to ions, adenine-nucleotides and other metabolites and it is probably involved in the regulation of apoptotic-relevant events. For these reasons, VDAC co-responsibility in unphysiological events leading to important pathologies such as onset or sustainment of cancer has been envisaged very early. The knowledge of the VDAC atomic structure is thus a relevant step in the design of modern drugs acting upon the mitochondrial function and its related apoptotic balance. This goal, despite many efforts, has not been gained until now. Several predictive or descriptive techniques have been employed to obtain models or representations of the pore-structure. The results obtained are reported in this review. The emerging picture arising from these many results is coherent and sufficiently informative. From these efforts it appears that VDAC is functionally monomeric but can cluster in tight but regular groups; it is asymmetric with larger exposed domains on the cytosolic side of the outer mitochondrial membrane; the diameter of the pore is between 2.5-3.0 nm and it is apparently free from obstructions (in the open state); the channel wall is mainly formed by typical amphipathic beta-strands; mobile components (the N-terminal ?) can have functional relevance to the pore regulation.
Collapse
|
6
|
The published 3D structure of the VDAC channel: native or not? Trends Biochem Sci 2009; 34:382-9. [PMID: 19647437 DOI: 10.1016/j.tibs.2009.05.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 11/21/2022]
Abstract
The recently published 3D structures of the mitochondrial voltage-dependent anion-selective channel (VDAC) are almost identical to each other. However, they are in conflict with the results of biochemical and functional studies published in the past 18 years. Transmembrane folding patterns based on many biochemical and functional studies differ from the 3D structures in the exclusion of distinct transmembrane strands. These differences might be the consequence of changes observed in vitro that result in the formation of channels with the characteristic functional properties of VDAC. Is it possible to reconcile the discrepancies between the 3D structures and earlier models? As it was refolded from inclusion bodies, the protein used to obtain the 3D structures might not be in the native conformation. Here, I propose structural rearrangements that could occur spontaneously as a possible path to convert the 3D structure to my preferred biochemically determined native structure.
Collapse
|
7
|
Walther DM, Rapaport D. Biogenesis of mitochondrial outer membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:42-51. [PMID: 18501716 DOI: 10.1016/j.bbamcr.2008.04.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/15/2008] [Accepted: 04/25/2008] [Indexed: 11/29/2022]
Abstract
Mitochondria are surrounded by two distinct membranes: the outer and the inner membrane. The mitochondrial outer membrane mediates numerous interactions between the mitochondrial metabolic and genetic systems and the rest of the eukaryotic cell. Proteins of this membrane are nuclear-encoded and synthesized as precursor proteins in the cytosol. They are targeted to the mitochondria and inserted into their target membrane via various pathways. This review summarizes our current knowledge of the sorting signals for this specific targeting and describes the mechanisms by which the mitochondrial import machineries recognize precursor proteins, mediate their membrane integration and facilitate assembly into functional complexes.
Collapse
Affiliation(s)
- Dirk M Walther
- Interfakultäres Institut für Biochemie, Hoppe-Seyler-Str. 4, University of Tübingen, 72076 Tübingen, Germany
| | | |
Collapse
|
8
|
Chapter 5 New Insights into the Mechanism of Precursor Protein Insertion into the Mitochondrial Membranes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 268:147-90. [DOI: 10.1016/s1937-6448(08)00805-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
|
9
|
Hoogenboom BW, Suda K, Engel A, Fotiadis D. The supramolecular assemblies of voltage-dependent anion channels in the native membrane. J Mol Biol 2007; 370:246-55. [PMID: 17524423 DOI: 10.1016/j.jmb.2007.04.073] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 04/27/2007] [Accepted: 04/30/2007] [Indexed: 11/25/2022]
Abstract
Voltage-dependent anion channels (VDACs) are major constituents of the outer mitochondrial membrane (OMM). These primary transporters of nucleotides, ions and metabolites mediate a substantial portion of the OMM molecular traffic. To study the native supramolecular organization of the VDAC, we have isolated, characterized and imaged OMMs from potato tubers. SDS-PAGE and mass spectrometry of OMMs revealed the presence of the VDAC isoforms POM34 and POM36, as well as the translocase of the OMM complex. Tubular two-dimensional crystals of the VDAC spontaneously formed after incubation of OMMs for two to three months at 4 degrees C. Transmission electron microscopy revealed an oblique lattice and unit cells housing six circular depressions arranged in a hexagon. Atomic force microscopy of freshly isolated OMMs demonstrated (i) the existence of monomers to tetramers, hexamers and higher oligomers of the VDAC and (ii) its spatial arrangement within the oligomers in the native membrane. We discuss the importance of the observed oligomerization for modulation of the VDAC function, for the binding of hexokinase and creatine kinase to the OMM and for mitochondria-mediated apoptosis.
Collapse
Affiliation(s)
- Bart W Hoogenboom
- M. E. Müller Institute for Microscopy, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | | | | | | |
Collapse
|
10
|
Abstract
BACKGROUND Mitochondrial porins, or voltage-dependent anion-selective channels (VDAC) allow the passage of small molecules across the mitochondrial outer membrane, and are involved in complex interactions regulating organellar and cellular metabolism. Numerous organisms possess multiple porin isoforms, and initial studies indicated an intriguing evolutionary history for these proteins and the genes that encode them. RESULTS In this work, the wealth of recent sequence information was used to perform a comprehensive analysis of the evolutionary history of mitochondrial porins. Fungal porin sequences were well represented, and newly-released sequences from stramenopiles, alveolates, and seed and flowering plants were analyzed. A combination of Neighbour-Joining and Bayesian methods was used to determine phylogenetic relationships among the proteins. The aligned sequences were also used to reassess the validity of previously described eukaryotic porin motifs and to search for signature sequences characteristic of VDACs from plants, animals and fungi. Secondary structure predictions were performed on the aligned VDAC primary sequences and were used to evaluate the sites of intron insertion in a representative set of the corresponding VDAC genes. CONCLUSION Our phylogenetic analysis clearly shows that paralogs have appeared several times during the evolution of VDACs from the plants, metazoans, and even the fungi, suggesting that there are no "ancient" paralogs within the gene family. Sequence motifs characteristic of the members of the crown groups of organisms were identified. Secondary structure predictions suggest a common 16 beta-strand framework for the transmembrane arrangement of all porin isoforms. The GLK (and homologous or analogous motifs) and the eukaryotic porin motifs in the four representative Chordates tend to be in exons that appear to have changed little during the evolution of these metazoans. In fact there is phase correlation among the introns in these genes. Finally, our preliminary data support the notion that introns usually do not interrupt structural protein motifs, namely the predicted beta-strands. These observations concur with the concept of exon shuffling, wherein exons encode structural modules of proteins and the loss and gain of introns and the shuffling of exons via recombination events contribute to the complexity of modern day proteomes.
Collapse
|
11
|
Waldispühl J, Berger B, Clote P, Steyaert JM. Predicting transmembrane beta-barrels and interstrand residue interactions from sequence. Proteins 2006; 65:61-74. [PMID: 16858668 DOI: 10.1002/prot.21046] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. The cellular location and functional diversity of beta-barrel outer membrane proteins (omps) makes them an important protein class. At the present time, very few nonhomologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. A novel method using pairwise interstrand residue statistical potentials derived from globular (nonouter membrane) proteins is introduced to predict the supersecondary structure of transmembrane beta-barrel proteins. The algorithm transFold employs a generalized hidden Markov model (i.e., multitape S-attribute grammar) to describe potential beta-barrel supersecondary structures and then computes by dynamic programming the minimum free energy beta-barrel structure. Hence, the approach can be viewed as a "wrapping" component that may capture folding processes with an initiation stage followed by progressive interaction of the sequence with the already-formed motifs. This approach differs significantly from others, which use traditional machine learning to solve this problem, because it does not require a training phase on known TMB structures and is the first to explicitly capture and predict long-range interactions. TransFold outperforms previous programs for predicting TMBs on smaller (<or=200 residues) proteins and matches their performance for straightforward recognition of longer proteins. An exception is for multimeric porins where the algorithm does perform well when an important functional motif in loops is initially identified. We verify our simulations of the folding process by comparing them with experimental data on the functional folding of TMBs. A Web server running transFold is available and outputs contact predictions and locations for sequences predicted to form TMBs.
Collapse
Affiliation(s)
- J Waldispühl
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | | | | | | |
Collapse
|
12
|
Sherman EL, Taylor RD, Go NE, Nargang FE. Effect of Mutations in Tom40 on Stability of the Translocase of the Outer Mitochondrial Membrane (TOM) Complex, Assembly of Tom40, and Import of Mitochondrial Preproteins. J Biol Chem 2006; 281:22554-65. [PMID: 16757481 DOI: 10.1074/jbc.m601630200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial preproteins synthesized in the cytosol are imported through the mitochondrial outer membrane by the translocase of the outer mitochondrial membrane (TOM) complex. Tom40 is the major component of the complex and is essential for cell viability. We generated 21 different mutations in conserved regions of the Neurospora crassa Tom40 protein. The mutant genes were transformed into a tom40 null nucleus maintained in a sheltered heterokaryon, and 17 of the mutant genes gave rise to viable strains. All mutations reduced the efficiency of the altered Tom40 molecules to assemble into the TOM complex. Mitochondria isolated from seven of the mutant strains had defects for importing mitochondrial preproteins. Only one strain had a general import defect for all preproteins examined. Another mutation resulted in defects in the import of a matrix-destined preprotein and an outer membrane beta-barrel protein, but import of the ADP/ATP carrier to the inner membrane was unaffected. Five strains showed deficiencies in the import of beta-barrel proteins. The latter results suggest that the TOM complex distinguishes beta-barrel proteins from other classes of preprotein during import. This supports the idea that the TOM complex plays an active role in the transfer of preproteins to subsequent translocases for insertion into the correct mitochondrial subcompartment.
Collapse
Affiliation(s)
- E Laura Sherman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | | | | | | |
Collapse
|
13
|
Runke G, Maier E, Summers WAT, Bay DC, Benz R, Court DA. Deletion variants of Neurospora mitochondrial porin: electrophysiological and spectroscopic analysis. Biophys J 2006; 90:3155-64. [PMID: 16500966 PMCID: PMC1432131 DOI: 10.1529/biophysj.105.072520] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial porins are predicted to traverse the outer membrane as a series of beta-strands, but the precise structure of the resulting beta-barrel has remained elusive. Toward determining the positions of the membrane-spanning segments, a series of small deletions was introduced into several of the predicted beta-strands of the Neurospora crassa porin. Overall, three classes of porin variants were identified: i), those producing large, stable pores, indicating deletions likely outside of beta-strands; ii), those with minimal pore-forming ability, indicating disruptions in key beta-strands or beta-turns; and iii), those that formed small unstable pores with a variety of gating and ion-selectivity properties. The latter class presumably results from a subset of proteins that adopt an alternative barrel structure upon the loss of stabilizing residues. Some variants were not sufficiently stable in detergent for structural analysis; circular dichroism spectropolarimetry of those that were did not reveal significant differences in the overall structural composition among the detergent-solubilized porin variants and the wild-type protein. Several of the variants displayed altered tryptophan fluorescence profiles, indicative of differing microenvironments surrounding these residues. Based on these results, modifications to the existing models for porin structure are proposed.
Collapse
Affiliation(s)
- Greg Runke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | | | | | | | | | | |
Collapse
|
14
|
Rapaport D. How does the TOM complex mediate insertion of precursor proteins into the mitochondrial outer membrane? ACTA ACUST UNITED AC 2005; 171:419-23. [PMID: 16260501 PMCID: PMC2171261 DOI: 10.1083/jcb.200507147] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A multisubunit translocase of the outer mitochondrial membrane (TOM complex) mediates both the import of mitochondrial precursor proteins into the internal compartments of the organelle and the insertion of proteins residing in the mitochondrial outer membrane. The proposed β-barrel structure of Tom40, the pore-forming component of the translocase, raises the question of how the apparent uninterrupted β-barrel topology can be compatible with a role of Tom40 in releasing membrane proteins into the lipid core of the bilayer. In this review, I discuss insertion mechanisms of proteins into the outer membrane and present alternative models based on the opening of a multisubunit β-barrel TOM structure or on the interaction of outer membrane precursors with the outer face of the Tom40 β-barrel structure.
Collapse
Affiliation(s)
- Doron Rapaport
- Institute for Physiological Chemistry, Ludwig-Maximilians University, 81377 Munich, Germany.
| |
Collapse
|
15
|
Pavlov E, Grigoriev SM, Dejean LM, Zweihorn CL, Mannella CA, Kinnally KW. The mitochondrial channel VDAC has a cation-selective open state. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1710:96-102. [PMID: 16293222 DOI: 10.1016/j.bbabio.2005.09.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 09/23/2005] [Accepted: 09/30/2005] [Indexed: 11/16/2022]
Abstract
The mitochondrial channel VDAC is known to have two major classes of functional states, a large conductance "open" state that is anion selective, and lower conductance substates that are cation selective. The channel can reversibly switch between open and half-open states, with the latter predominant at increasing membrane voltages of either polarity. We report the presence of a new functional state of VDAC, a cation-selective state with conductance approximately equal to that of the canonical open state. This newly described state of VDAC can be reached from either the half-open cation-selective state or from the open anion-selective state. The latter transition implies that a mechanism exists for selectivity gating in VDAC that is separate from partial closure, which may be relevant to the physiological regulation of this channel and mitochondrial outer membrane permeability.
Collapse
Affiliation(s)
- Evgeny Pavlov
- Department of Basic Sciences, New York University, College of Dentistry, 345 East 24th Street, New York, NY 10010, USA
| | | | | | | | | | | |
Collapse
|
16
|
Becker L, Bannwarth M, Meisinger C, Hill K, Model K, Krimmer T, Casadio R, Truscott KN, Schulz GE, Pfanner N, Wagner R. Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J Mol Biol 2005; 353:1011-20. [PMID: 16213519 DOI: 10.1016/j.jmb.2005.09.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Revised: 09/06/2005] [Accepted: 09/07/2005] [Indexed: 11/23/2022]
Abstract
Tom40 is the central pore-forming component of the translocase of the outer mitochondrial membrane (TOM complex). Different views exist about the secondary structure and electrophysiological characteristics of Tom40 from Saccharomyces cerevisiae and Neurospora crassa. We have directly compared expressed and renatured Tom40 from both species and find a high content of beta-structure in circular dichroism measurements in agreement with refined secondary structure predictions. The electrophysiological characterization of renatured Tom40 reveals the same characteristics as the purified TOM complex or mitochondrial outer membrane vesicles, with two exceptions. The total conductance of the TOM complex and outer membrane vesicles is twofold higher than the total conductance of renatured Tom40, consistent with the presence of two TOM pores. TOM complex and outer membrane vesicles possess a strongly enhanced sensitivity to a mitochondrial presequence compared to Tom40 alone, in agreement with the presence of several presequence binding sites in the TOM complex, suggesting a role of the non-channel Tom proteins in regulating channel activity.
Collapse
Affiliation(s)
- Lars Becker
- Biophysik, Universität Osnabrück, FB Biologie/Chemie, D-49034 Osnabrück, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Waizenegger T, Schmitt S, Zivkovic J, Neupert W, Rapaport D. Mim1, a protein required for the assembly of the TOM complex of mitochondria. EMBO Rep 2005; 6:57-62. [PMID: 15608614 PMCID: PMC1299228 DOI: 10.1038/sj.embor.7400318] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/29/2004] [Accepted: 11/19/2004] [Indexed: 11/09/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM complex) is the general entry site for newly synthesized proteins into mitochondria. This complex is essential for the formation and maintenance of mitochondria. Here, we report on the role of the integral outer membrane protein, Mim1 (mitochondrial import), in the biogenesis of mitochondria. Depletion of Mim1 abrogates assembly of the TOM complex and results in accumulation of Tom40, the principal constituent of the TOM complex, as a low-molecular-mass species. Like all mitochondrial beta-barrel proteins, the precursor of Tom40 is inserted into the outer membrane by the TOB complex. Mim1 is likely to be required for a step after this TOB-complex-mediated insertion. Mim1 is a constituent of neither the TOM complex nor the TOB complex; rather, it seems to be a subunit of another, as yet unidentified, complex. We conclude that Mim1 has a vital and specific function in the assembly of the TOM complex.
Collapse
Affiliation(s)
- Thomas Waizenegger
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, 81377 Munich, Germany
| | - Simone Schmitt
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, 81377 Munich, Germany
| | - Jelena Zivkovic
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, 81377 Munich, Germany
| | - Walter Neupert
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, 81377 Munich, Germany
| | - Doron Rapaport
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, 81377 Munich, Germany
- Tel: +49 89 2180 77128; Fax: +49 89 2180 77093; E-mail:
| |
Collapse
|
18
|
Al Jamal JA. Involvement of porin N,N-dicyclohexylcarbodiimide-reactive domain in hexokinase binding to the outer mitochondrial membrane. Protein J 2005; 24:1-8. [PMID: 15756812 DOI: 10.1007/s10930-004-0600-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The proportion of hexokinase that is bound to the outer mitochondrial membrane is tissue specific and metabolically regulated. This study examined the role of the N,N-dicyclohexylcarbodiimide-binding domain of mitochondrial porin in binding to hexokinase 1. Selective proteolytic cleavage of porin protein was performed and peptides were assayed for their, effect on hexokinase I binding to isolated mitochondria. Specificity of DCCD-reactive domain binding to hexokinase I was demonstrated by competition of the peptides for porin binding sites on hexokinase as well as by blockage hexokinase binding by N,N-dicyclohexylcarbodiimide. One of the peptides, designated as 5 kDa (the smallest of the porin peptides, which contains a DCCD-reactive site), totally blocked binding of the enzyme to the mitochondrial membrane, and significantly enhanced the release of the mitochondrially bound enzyme. These experiments demonstrate that there exists a direct and specific interaction between the DCCD-reactive domain of VDAC and hexokinase I. The peptides were further characterized with respect to their effects on certain functional properties of hexokinase I. None had any detectable effect on catalytic properties, including inhibition by glucose 6-phosphate. To evaluate further the outer mitochondrial membrane's role in the hexokinase binding, insertion of VDAC was examined using isolated rat mitochondria. Preincubation of mitochondria with purified porin strongly increases hexokinase I binding to rat liver mitochondria. Collectively, the results imply that the high hexokinase-binding capability of porin-enriched mitochondria was due to a quantitative difference in binding sites.
Collapse
|
19
|
Abstract
Research on VDAC has accelerated as evidence grows of its importance in mitochondrial function and in apoptosis. New investigators entering the field are often confounded by the VDAC literature and its many apparent conflicts and contradictions. This review is an effort to shed light on the situation and identify reliable information from more questionable claims. Our views on the most important controversial issues are as follows: VDAC is only present in the mitochondrial outer membrane. VDAC functions as a monomer. VDAC functions normally with or without Ca(2+). It does not form channels that mediate the flux of proteins through membranes (peptides and unfolded proteins are excluded from this statement). Closure of VDAC, not VDAC opening, leads to mitochondria outer membrane permeabilization and apoptosis.
Collapse
Affiliation(s)
- Tatiana K Rostovtseva
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
20
|
Taylor RD, Pfanner N. The protein import and assembly machinery of the mitochondrial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1658:37-43. [PMID: 15282172 DOI: 10.1016/j.bbabio.2004.04.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 04/19/2004] [Indexed: 12/21/2022]
Abstract
The process of mitochondrial protein import has been studied for many years. Despite this attention, many processes associated with mitochondrial biogenesis are poorly understood. Insight into one of these processes, assembly of beta-barrel proteins into the mitochondrial outer membrane, will be discussed. This review focuses on recent data that suggest that assembly of beta-barrel proteins into the outer mitochondrial membrane is dependent on a newly identified protein complex termed the sorting and assembly machinery (SAM complex). Members of the SAM complex have been identified in both eukaryotic and prokaryotic organisms, suggesting that the process of beta-barrel assembly into membranes has been conserved through evolution.
Collapse
Affiliation(s)
- Rebecca D Taylor
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann-Herder-Strasse 7, D-79104 Freiburg, Germany
| | | |
Collapse
|
21
|
Suzuki H, Kadowaki T, Maeda M, Sasaki H, Nabekura J, Sakaguchi M, Mihara K. Membrane-embedded C-terminal Segment of Rat Mitochondrial TOM40 Constitutes Protein-conducting Pore with Enriched β-Structure. J Biol Chem 2004; 279:50619-29. [PMID: 15347672 DOI: 10.1074/jbc.m408604200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TOM40 is the central component of the preprotein translocase of the mitochondrial outer membrane (TOM complex). We purified recombinant rat TOM40 (rTOM40), which was refolded in Brij35 after solubilization from inclusion bodies by guanidine HCl. rTOM40 (i) consisted of a 63% beta-sheet structure and (ii) bound a matrix-targeted preprotein with high affinity and partially translocated it into the rTOM40 pore. This partial translocation was inhibited by stabilization of the mature domain of the precursor. (iii) rTOM40 bound preprotein initially through ionic interactions, followed by salt-resistant non-ionic interactions, and (iv) exhibited presequence-sensitive, cation-specific channel activity in reconstituted liposomes. Based on the domain structure of rTOM40 deduced by protease treatment, we purified the elastase-resistant and membrane-embedded C-terminal segment (rTOM40(DeltaN165)) as a recombinant protein with 62% beta-structure that exhibited properties comparable with those of full-size rTOM40. We concluded that the membrane-embedded C-terminal half of rTOM40 constitutes the preprotein recognition domain with an enriched beta-structure, which forms the preprotein conducting pore containing a salt-sensitive cis-binding site and a salt-resistant trans-binding site.
Collapse
Affiliation(s)
- Hiroyuki Suzuki
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | | | | | | | | | | | | |
Collapse
|
22
|
Bodył A. Evolutionary origin of a preprotein translocase in the periplastid membrane of complex plastids: a hypothesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2004; 6:513-518. [PMID: 15375721 DOI: 10.1055/s-2004-821092] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plastids with four envelope membranes have evolved from red and green algae engulfed by phagotrophic protozoans. It is assumed that the Sec translocon resides in their outermost membrane, while in the two innermost membranes the Toc-Tic supercomplex is embedded. However, such a single Sec/single Toc-Tic model cannot explain the passage of proteins across the second (or periplastid) membrane which represents the endosymbiont plasmalemma. One of the most recent models postulates that this membrane contains the Toc75 channel which was relocated here from the endosymbiont plastid. Unfortunately, the precursor of this protein carries a bipartite presequence, which means that its insertion into the new membrane would require relocation and/or modification of two different processing peptidases. I suggest that these obstacles can be easily bypassed by the assumption that the mitochondrial Tim23 channel was inserted into the endosymbiont plasmalemma. In contrast to Toc75, this protein has an internal, uncleavable targeting signal and its insertion into the new membrane would require neither relocation nor modification of additional proteins. Besides, such a relocated Tim23 channel could import not only plastid, but also mitochondrial proteins. I hypothesize that from the latter proteins, initially directed to the endosymbiont mitochondrion, periplastid proteins have evolved which are now targeted to the former cytosol and/or nucleus of the eukaryotic algal endosymbiont.
Collapse
Affiliation(s)
- A Bodył
- Department of Biodiversity and Evolutionary Taxonomy, Zoological Institute, University of Wrocław, ul. Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
| |
Collapse
|
23
|
Rapaport D. Finding the right organelle. Targeting signals in mitochondrial outer-membrane proteins. EMBO Rep 2004; 4:948-52. [PMID: 14528265 PMCID: PMC1326395 DOI: 10.1038/sj.embor.embor937] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 07/16/2003] [Indexed: 12/19/2022] Open
Abstract
The mitochondrial outer membrane contains a diverse set of proteins that includes enzymes, components of the preprotein translocation machinery, pore-forming proteins, regulators of programmed cell death, and those that control the morphology of the organelle. All these proteins, like the vast majority of mitochondrial proteins, are encoded in the nucleus, so they are synthesized in the cytosol and contain signals that are essential for their subsequent import into mitochondria. This review summarizes our current knowledge of the signals that target mitochondrial outer-membrane proteins to their correct intracellular location. In addition, the mechanisms by which these signals are decoded by the mitochondria are discussed.
Collapse
Affiliation(s)
- Doron Rapaport
- Institut für Physiologische Chemie der Universität München, Butenandtstrasse 5, D-81377 Munich, Germany.
| |
Collapse
|
24
|
Nakamura Y, Suzuki H, Sakaguchi M, Mihara K. Targeting and Assembly of Rat Mitochondrial Translocase of Outer Membrane 22 (TOM22) into the TOM Complex. J Biol Chem 2004; 279:21223-32. [PMID: 14985332 DOI: 10.1074/jbc.m314156200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tom22 is a preprotein receptor and organizer of the mitochondrial outer membrane translocase complex (TOM complex). Rat Tom22 (rTOM22) is a 142-residue protein, embedded in the outer membrane through the internal transmembrane domain (TMD) with 82 N-terminal residues in the cytosol and 41 C-terminal residues in the intermembrane space. We analyzed the signals that target rTOM22 to the mitochondrial outer membrane and assembly into the TOM complex in cultured mammalian cells. Deletions or mutations were systematically introduced into the molecule, and the intracellular localization of the mutant constructs in HeLa cells was examined by confocal microscopy and cell fractionation. Their assembly into the TOM complex was also examined using blue native gel electrophoresis. These experiments revealed three separate structural elements: a cytoplasmic 10-residue segment with an acidic alpha-helical structure located 30 residues upstream of the TMD (the import sequence), TMD with an appropriate hydrophobicity, and a 20-residue C-terminal segment located 22 residues downstream of the TMD (C-tail signal). The import sequence and TMD were both essential for targeting and integration into the TOM complex, whereas the C-tail signal affected the import efficiency. The import sequence combined with foreign TMD functioned as a mitochondrial targeting and anchor signal but failed to integrate the construct into the TOM complex. Thus, the mitochondrial-targeting and TOM integration signal could be discriminated. A yeast two-hybrid assay revealed that the import sequence interacted with two intramolecular elements, the TMD and C-tail signal, and that it also interacted with the import receptor Tom20.
Collapse
Affiliation(s)
- Yasuhiko Nakamura
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-0054, Japan
| | | | | | | |
Collapse
|
25
|
Milenkovic D, Kozjak V, Wiedemann N, Lohaus C, Meyer HE, Guiard B, Pfanner N, Meisinger C. Sam35 of the Mitochondrial Protein Sorting and Assembly Machinery Is a Peripheral Outer Membrane Protein Essential for Cell Viability. J Biol Chem 2004; 279:22781-5. [PMID: 15067005 DOI: 10.1074/jbc.c400120200] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial outer membrane contains two integral proteins essential for cell viability, Tom40 of the translocase of the outer membrane (TOM complex) and Sam50 of the sorting and assembly machinery (SAM complex). Here we report the identification of Sam35, the first peripheral mitochondrial outer membrane protein that is essential for cell viability. Sam35 (encoded by the Saccharomyces cerevisiae ORF YHR083w) is a novel subunit of the SAM complex and is crucial for the assembly pathway of outer membrane beta-barrel proteins, such as the precursors of Tom40 and porin. Sam35 is not required for the import of inner membrane or matrix targeted proteins. The presence of two essential proteins in the SAM complex, Sam35 and Sam50, indicates that it plays a central role in mitochondrial biogenesis.
Collapse
Affiliation(s)
- Dusanka Milenkovic
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Wiedemann N, Truscott KN, Pfannschmidt S, Guiard B, Meisinger C, Pfanner N. Biogenesis of the protein import channel Tom40 of the mitochondrial outer membrane: intermembrane space components are involved in an early stage of the assembly pathway. J Biol Chem 2004; 279:18188-94. [PMID: 14978039 DOI: 10.1074/jbc.m400050200] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tom40 forms the central channel of the preprotein translocase of the mitochondrial outer membrane (TOM complex). The precursor of Tom40 is encoded in the nucleus, synthesized in the cytosol, and imported into mitochondria via a multi-step assembly pathway that involves the mature TOM complex and the sorting and assembly machinery of the outer membrane (SAM complex). We report that opening of the mitochondrial intermembrane space by swelling blocks the assembly pathway of the beta-barrel protein Tom40. Mitochondria with defects in small Tim proteins of the intermembrane space are impaired in the Tom40 assembly pathway. Swelling as well as defects in the small Tim proteins inhibit an early stage of the Tom40 import pathway that is needed for formation of a Tom40-SAM intermediate. We propose that the biogenesis pathway of beta-barrel proteins of the outer mitochondrial membrane not only requires TOM and SAM components, but also involves components of the intermembrane space.
Collapse
Affiliation(s)
- Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany
| | | | | | | | | | | |
Collapse
|
27
|
Marques EJ, Carneiro CM, Silva AS, Krasilnikov OV. Does VDAC insert into membranes in random orientation? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1661:68-77. [PMID: 14967476 DOI: 10.1016/j.bbamem.2003.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 11/20/2003] [Accepted: 11/25/2003] [Indexed: 11/29/2022]
Abstract
It is widely accepted that voltage-dependent anion-selective channel (VDAC) inserts into planar lipid bilayers in a random orientation. This is in contrast to the well-documented oriented insertion of various channel-forming proteins. Because of the potential importance of this issue, we have examined the orientation of VDAC inserted in membranes. The time constants of the VDAC-current relaxation in response to applied positive and negative voltage pulses were used to characterize the channel orientation. We have found that VDAC channels can be separated into two groups according to differences in the time constant ratio. The difference in time constant ratio between the two main groups of VDAC channels was quantitative, and not qualitative as would be expected for opposite topologies. This finding allows us to hypothesize that both groups of VDAC channels possess a qualitatively similar asymmetry with respect to the localization of voltage-gated domains and, consequently, with respect to its entire molecular structure. The probability of having each type of VDAC channel conformation is predetermined by the protein structure in aqueous solution. A striking resemblance between asymmetry in voltage sensitivity at the single-channel and multi-channel levels was also demonstrated. The first inserted channel seems to direct subsequent insertions of channels with a similar conformation.
Collapse
Affiliation(s)
- Edson J Marques
- Laboratory of Membrane Biophysics, Department of Biophysics and Radiobiology, Federal University of Pernambuco, 50670-901, Recife, PE, Brazil.
| | | | | | | |
Collapse
|
28
|
Lucattini R, Likic VA, Lithgow T. Bacterial proteins predisposed for targeting to mitochondria. Mol Biol Evol 2004; 21:652-8. [PMID: 14739247 DOI: 10.1093/molbev/msh058] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondria evolved from an endosymbiotic proteobacterium in a process that required the transfer of genes from the bacterium to the host cell nucleus, and the translocation of proteins thereby made in the host cell cytosol into the internal compartments of the organelle. According to current models for this evolution, two highly improbable events are required to occur simultaneously: creation of a protein translocation machinery to import proteins back into the endosymbiont and creation of targeting sequences on the protein substrates themselves. Using a combination of two independent prediction methods, validated through tests on simulated genomes, we show that at least 5% of proteins encoded by an extant proteobacterium are predisposed for targeting to mitochondria, and propose we that mitochondrial targeting information was preexisting for many proteins of the endosymbiont. We analyzed a family of proteins whose members exist both in bacteria and in mitochondria of eukaryotes and show that the amino-terminal extensions occasionally found in bacterial family members can function as a crude import sequence when the protein is presented to isolated mitochondria. This activity leaves the development of a primitive translocation channel in the outer membrane of the endosymbiont as a single hurdle to initiating the evolution of mitochondria.
Collapse
Affiliation(s)
- Rebecca Lucattini
- Russell Grimwade School of Biochemistry and Molecular Biology, University of Melbourne, Australia
| | | | | |
Collapse
|
29
|
Kozjak V, Wiedemann N, Milenkovic D, Lohaus C, Meyer HE, Guiard B, Meisinger C, Pfanner N. An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer membrane. J Biol Chem 2003; 278:48520-3. [PMID: 14570913 DOI: 10.1074/jbc.c300442200] [Citation(s) in RCA: 260] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The preprotein translocase of the outer mitochondrial membrane (TOM complex) contains one essential subunit, the channel Tom40. The assembly pathway of the precursor of Tom40 involves the TOM complex and the sorting and assembly machinery (SAM complex) with the non-essential subunit Mas37. We have identified Sam50, the second essential protein of the mitochondrial outer membrane. Sam50 contains a beta-barrel domain conserved from bacteria to man and is a subunit of the SAM complex. Yeast mutants of Sam50 are defective in the assembly pathways of Tom40 and the abundant outer membrane protein porin, while the import of matrix proteins is not affected. Thus the protein sorting and assembly machinery of the mitochondrial outer membrane involves an essential, conserved protein.
Collapse
Affiliation(s)
- Vera Kozjak
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Carneiro CMM, Merzlyak PG, Yuldasheva LN, Silva LG, Thinnes FP, Krasilnikov OV. Probing the volume changes during voltage gating of Porin 31BM channel with nonelectrolyte polymers. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1612:144-53. [PMID: 12787932 DOI: 10.1016/s0005-2736(03)00113-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To probe the volume changes of the voltage-dependent anion-selective channel (VDAC), the nonelectrolyte exclusion technique was taken because it is one of the few existing methods that may define quite accurately the rough geometry of lumen of ion channels (in membranes) for which there is no structural data.Here, we corroborate the data from our previous study [FEBS Lett. 416 (1997) 187] that the gross structural features of VDAC in its highest conductance state are asymmetric with respect to the plane of the membrane, and state that this asymmetry is not dependent on sign of voltage applied. Hence, the plasticity of VDAC does not play a role in the determination of lumen geometry at this state and the asymmetry is an internal property of the channel. We also show that the apparent diameter of the cis segment of the pore decreases slightly from 2 to 1.8 nm when the channel's conductance decreases from its high to low state. However, the trans funnel segment undergoes a more marked change in polymer accessible volume. Specifically, its larger diameter decreases from approximately 4 to 2.4 nm. Supposing the channel's total length is 4.6 nm, the apparent change in channel volume during this transition is estimated to be about 10 nm(3), i.e. about 40% of the channel's volume in the high conductance state.
Collapse
Affiliation(s)
- Carlos M M Carneiro
- Laboratory of Membrane Biophysics, Department of Biophysics and Radiobiology, Federal University of Pernambuco, 50670-901, Recife, PE, Brazil
| | | | | | | | | | | |
Collapse
|
31
|
Bay DC, Court DA. Origami in the outer membrane: the transmembrane arrangement of mitochondrial porins. Biochem Cell Biol 2003; 80:551-62. [PMID: 12440696 DOI: 10.1139/o02-149] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Voltage-dependent anion-selective channels (VDAC), also known as mitochondrial porins, are key regulators of metabolite flow across the mitochondrial outer membrane. Porins from a wide variety of organisms share remarkably similar electrophysiological properties, in spite of considerable sequence dissimilarity, indicating that they share a common structure. Based on primary sequence considerations, analogy with bacterial porins, and circular dichroism analysis, it is agreed that VDAC spans the outer membrane as a beta-barrel. However, the residues that form the antiparallel beta-strands comprising this barrel remain unknown. Various predictive methods, largely based on the known structures of bacterial beta-barrels, have been applied to the primary sequences of VDAC. Refinement and confirmation of these predictions have developed through numerous investigations of wild-type and variant porins, both in mitochondria and in artificial membranes. These experiments have involved VDAC from several sources, precluding the generation of a unified model. Herein, using the Neurospora VDAC sequence as a template, the published structural information and predictions have been reassessed to delineate a model that satisfies most of the available data.
Collapse
Affiliation(s)
- Denice C Bay
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | | |
Collapse
|
32
|
Taylor RD, McHale BJ, Nargang FE. Characterization of Neurospora crassa Tom40-deficient mutants and effect of specific mutations on Tom40 assembly. J Biol Chem 2003; 278:765-75. [PMID: 12399467 DOI: 10.1074/jbc.m208083200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The TOM complex (Translocase of the Outer mitochondrial Membrane) is responsible for the recognition of mitochondrial preproteins synthesized in the cytosol and for their translocation across or into the outer mitochondrial membrane. Tom40 is the major component of the TOM complex and forms the translocation pore. We have created a tom40 mutant of Neurospora crassa and have demonstrated that the gene is essential for the viability of the organism. Mitochondria with reduced levels of Tom40 were deficient for import of mitochondrial preproteins and contained reduced levels of the TOM complex components Tom22 and Tom6, suggesting that the import and/or stability of these proteins is dependent on the presence of Tom40. Mutant Tom40 preproteins were analyzed for their ability to be assembled into the TOM complex. In vitro import assays revealed that conserved regions near the N terminus (residues 51-60) and the C terminus (residues 321-323) of the 349-amino acid protein were required for assembly beyond a 250-kDa intermediate form. Mutant strains expressing Tom40 with residues 51-60 deleted were viable but exhibited growth defects. Slow growing mutants expressing Tom40, where residues 321-323 were changed to Ala residues, were isolated but showed TOM complex defects, whereas strains in which residues 321-323 were deleted could not be isolated. Analysis of the assembly of mutant Tom40 precursors in vitro supported a previous model in which Tom40 precursors progress from the 250-kDa intermediate to a 100-kDa form and then assemble into the 400-kDa TOM complex. Surprisingly, when wild type mitochondria containing Tom40 precursors arrested at the 250-kDa intermediate were treated with sodium carbonate, further assembly of intermediates into the TOM complex occurred, suggesting that disruption of protein-protein interactions may facilitate assembly. Import of wild type Tom40 precursor into mitochondria containing a mutant Tom40 lacking residues 40-48 revealed an alternate assembly pathway and demonstrated that the N-terminal region of pre-existing Tom40 molecules in the TOM complex plays a role in the assembly of incoming Tom40 molecules.
Collapse
Affiliation(s)
- Rebecca D Taylor
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | | |
Collapse
|
33
|
Pfanner N, Chacinska A. The mitochondrial import machinery: preprotein-conducting channels with binding sites for presequences. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1592:15-24. [PMID: 12191764 DOI: 10.1016/s0167-4889(02)00260-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mitochondrial preproteins with amino-terminal presequences must cross two membranes to reach the matrix of the organelle. Both outer and inner membranes contain hydrophilic high-conductance channels that are responsible for selective translocation of preproteins. The channels are embedded in dynamic protein complexes, the TOM complex of the outer membrane and the TIM23 complex of the inner membrane. Both channel-forming proteins, Tom40 and Tim23, carry specific binding sites for presequences, but differ in their pore size and response to a membrane potential. Studies with the TOM machinery show that other subunits of the translocase complex also provide specific binding sites for preproteins, modulate the channel activity and are critical for assembly of the channel.
Collapse
Affiliation(s)
- Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann-Herder-Strasse 7, D-79104, Freiburg Germany.
| | | |
Collapse
|
34
|
Zhai Y, Saier MH. The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci 2002; 11:2196-207. [PMID: 12192075 PMCID: PMC2373602 DOI: 10.1110/ps.0209002] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Many outer membrane proteins (OMPs) in Gram-negative bacteria possess known beta-barrel three-dimensional (3D) structures. These proteins, including channel-forming transmembrane porins, are diverse in sequence but exhibit common structural features. We here report computational analyses of six outer membrane proteins of known 3D structures with respect to (1) secondary structure, (2) hydropathy, and (3) amphipathicity. Using these characteristics, as well as the presence of an N-terminal targeting sequence, a program was developed allowing prediction of integral membrane beta-barrel proteins encoded within any completely sequenced prokaryotic genome. This program, termed the beta-barrel finder (BBF) program, was used to analyze the proteins encoded within the Escherichia coli genome. Out of 4290 sequences examined, 118 (2.8%) were retrieved. Of these, almost all known outer membrane proteins with established beta-barrel structures as well as many probable outer membrane proteins were identified. This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes.
Collapse
Affiliation(s)
- Yufeng Zhai
- Department of Biology, University of California at San Diego, La Jolla, California 92093-0116, USA
| | | |
Collapse
|
35
|
Hinnah SC, Wagner R, Sveshnikova N, Harrer R, Soll J. The chloroplast protein import channel Toc75: pore properties and interaction with transit peptides. Biophys J 2002; 83:899-911. [PMID: 12124272 PMCID: PMC1302194 DOI: 10.1016/s0006-3495(02)75216-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The channel properties of Toc75 (the protein import pore of the outer chloroplastic membrane) were further characterized by electrophysiological measurements in planar lipid bilayers. After improvement of the Toc75 reconstitution procedure the voltage dependence of the channel open probability resembled those observed for other beta-barrel pores. Studies concerning the pore size of the reconstituted Toc75 indicate the presence of a narrow restriction zone corresponding to the selectivity filter and a wider pore vestibule with diameters of approximately 14 A and 26 A, respectively. Interactions between Toc75 and different peptides (a genuine chloroplastic transit peptide, a synthetic peptide resembling a transit peptide, and a mitochondrial presequence) show that Toc75 itself is able to differentiate between these peptides and the recognition is based on both conformational and electrostatic interactions.
Collapse
Affiliation(s)
- Silke C Hinnah
- Fachbereich Biologie/Chemie, Universität Osnabrück, D-49034 Osnabrück, Germany
| | | | | | | | | |
Collapse
|
36
|
Abstract
Eukaryotic porins are a group of membrane proteins whose best known role is to form an aqueous pore channel in the mitochondrial outer membrane. As opposed to the bacterial porins (a large family of protein whose 3D structure has been determined by X-ray diffraction), the structure of eukaryotic porins (also termed VDACs, voltage-dependent anion-selective channels) is still a matter of debate. We analysed the secondary structure of VDAC from the yeast Saccharomyces cerevisiae, the fungus Neurospora crassa and the mouse with different types of neural network-based predictors. The predictors were able to discriminate membrane beta-strands, globular alpha-helices and membrane alpha-helices and localised, in all three VDAC sequences, 16 beta-strands along the chain. For all three sequences the N-terminal region showed a high propensity to form a globular alpha-helix. The 16 beta-strand VDAC motif was thus aligned to a bacterial porin-derived template containing a similar 16 beta-strand motif. The alignment of the VDAC sequence with the bacterial porin sequence was used to compute a set of 3D coordinates, which constitutes the first 3D prediction of a eukaryotic porin. All the predicted structures assume a beta-barrel structure composed of 16 beta-strands with the N-terminus outside the membrane. Loops are shorter in this side of the membrane than in the other, where two long loops are protruding. The shape of the pore varies between almost circular for Neurospora and mouse and slightly oval for yeast. Average values between 3 and 2.5 nm at the C-carbon backbone are found for the diameter of the channels. In this model VDAC shows large portions of the structure exposed on both sides of the membrane. The architecture we determine allows speculation about the mechanism of possible interactions between VDAC and other proteins on both sides of the mitochondrial outer membrane. The computed 3D model is consistent with most of the experimental results so far reported.
Collapse
Affiliation(s)
- Rita Casadio
- Laboratory of Biocomputing, Centro Interdipartimentale per le Ricerche Biotecnologiche, Bologna, Italy
| | | | | | | |
Collapse
|
37
|
Horie C, Suzuki H, Sakaguchi M, Mihara K. Characterization of signal that directs C-tail-anchored proteins to mammalian mitochondrial outer membrane. Mol Biol Cell 2002; 13:1615-25. [PMID: 12006657 PMCID: PMC111131 DOI: 10.1091/mbc.01-12-0570] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We analyzed the signal that directs the outer membrane protein with the C-terminal transmembrane segment (TMS) to mammalian mitochondria by using yeast Tom5 as a model and green fluorescent protein as a reporter. Deletions or mutations were systematically introduced into the TMS or the flanking regions and their intracellular localization in COS-7 cells was examined using confocal microscopy and cell fractionation. 1) Three basic amino acid residues within the C-terminal five-residue segment (C-segment) contained the information required for mitochondrial-targeting. Reduction of the net positive charge in this segment decreased mitochondrial specificity, and the mutants were distributed throughout the intracellular membranes. 2) Elongation of the TMS interfered with the function of the C-segment and the mutants were delivered to the intracellular membranes. 3) Separation of the TMS and C-segment by linker insertion severely impaired mitochondrial targeting function, leading to mislocalization to the cytoplasm. 4) Mutations or small deletions in the region of the TMS flanking the C-segment also impaired the mitochondrial targeting. Therefore, the moderate length of the TMS, the positive charges in the C-segment, and the distance between or context of the TMS and C-segment are critical for the targeting signal. The structural characteristics of the signal thus defined were also confirmed with mammalian C-tail-anchored protein OMP25.
Collapse
Affiliation(s)
- Chika Horie
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | | | | | | |
Collapse
|
38
|
Abstract
The translocase at the outer membrane of mitochondria (TOM complex) mediates the initial steps of the import of preproteins into the organelle, which are essential for mitochondrial biogenesis and, therefore, for eukaryotic cell viability. The TOM complex is a multisubunit molecular machine with a dynamic structure. The biogenesis of TOM is of special interest because the complex is required for its own biogenesis. This article describes the mechanisms by which Tom components are targeted to the mitochondria and inserted into the outer membrane. The assembly of newly synthesized subunits into the functional TOM complex might occur via assembly intermediates that are in equilibrium with the mature complex.
Collapse
Affiliation(s)
- Doron Rapaport
- Institut für Physiologische Chemie der Universität München Butenandtstr. 5, Haus B D-81377, München, Germany.
| |
Collapse
|
39
|
Rapaport D, Taylor RD, Käser M, Langer T, Neupert W, Nargang FE. Structural requirements of Tom40 for assembly into preexisting TOM complexes of mitochondria. Mol Biol Cell 2001; 12:1189-98. [PMID: 11359915 PMCID: PMC34577 DOI: 10.1091/mbc.12.5.1189] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Tom40 is the major subunit of the translocase of the outer mitochondrial membrane (the TOM complex). To study the assembly pathway of Tom40, we have followed the integration of the protein into the TOM complex in vitro and in vivo using wild-type and altered versions of the Neurospora crassa Tom40 protein. Upon import into isolated mitochondria, Tom40 precursor proteins lacking the first 20 or the first 40 amino acid residues were assembled as the wild-type protein. In contrast, a Tom40 precursor lacking residues 41 to 60, which contains a highly conserved region of the protein, was arrested at an intermediate stage of assembly. We constructed mutant versions of Tom40 affecting this region and transformed the genes into a sheltered heterokaryon containing a tom40 null nucleus. Homokaryotic strains expressing the mutant Tom40 proteins had growth rate defects and were deficient in their ability to form conidia. Analysis of the TOM complex in these strains by blue native gel electrophoresis revealed alterations in electrophoretic mobility and a tendency to lose Tom40 subunits from the complex. Thus, both in vitro and in vivo studies implicate residues 41 to 60 as containing a sequence required for proper assembly/stability of Tom40 into the TOM complex. Finally, we found that TOM complexes in the mitochondrial outer membrane were capable of exchanging subunits in vitro. A model is proposed for the integration of Tom40 subunits into the TOM complex.
Collapse
Affiliation(s)
- D Rapaport
- Department of Biochemistry, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | | | | | | | | | | |
Collapse
|
40
|
Ahting U, Thieffry M, Engelhardt H, Hegerl R, Neupert W, Nussberger S. Tom40, the pore-forming component of the protein-conducting TOM channel in the outer membrane of mitochondria. J Cell Biol 2001; 153:1151-60. [PMID: 11402060 PMCID: PMC2192023 DOI: 10.1083/jcb.153.6.1151] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Tom40 is the main component of the preprotein translocase of the outer membrane of mitochondria (TOM complex). We have isolated Tom40 of Neurospora crassa by removing the receptor Tom22 and the small Tom components Tom6 and Tom7 from the purified TOM core complex. Tom40 is organized in a high molecular mass complex of approximately 350 kD. It forms a high conductance channel. Mitochondrial presequence peptides interact specifically with Tom40 reconstituted into planar lipid membranes and decrease the ion flow through the pores in a voltage-dependent manner. The secondary structure of Tom40 comprises approximately 31% beta-sheet, 22% alpha-helix, and 47% remaining structure as determined by circular dichroism measurements and Fourier transform infrared spectroscopy. Electron microscopy of purified Tom40 revealed particles primarily with one center of stain accumulation. They presumably represent an open pore with a diameter of approximately 2.5 nm, similar to the pores found in the TOM complex. Thus, Tom40 is the core element of the TOM translocase; it forms the protein-conducting channel in an oligomeric assembly.
Collapse
Affiliation(s)
- Uwe Ahting
- Institut für Physiologische Chemie, Universität München, D-81377 München, Germany
| | - Michel Thieffry
- Laboratoire de Neurobiologie, Cellulaire et Moléculaire, Centre National de Recherche Scientifique, F-91198 Gif-sur-Yvette, France
| | - Harald Engelhardt
- Laboratoire de Neurobiologie, Cellulaire et Moléculaire, Centre National de Recherche Scientifique, F-91198 Gif-sur-Yvette, France
| | - Reiner Hegerl
- Abteilung für Molekulare Strukturbiologie, Max-Planck Institut für Biochemie, D-82152 Martinsried, Germany
| | - Walter Neupert
- Institut für Physiologische Chemie, Universität München, D-81377 München, Germany
| | - Stephan Nussberger
- Institut für Physiologische Chemie, Universität München, D-81377 München, Germany
| |
Collapse
|
41
|
Gordon DM, Wang J, Amutha B, Pain D. Self-association and precursor protein binding of Saccharomyces cerevisiae Tom40p, the core component of the protein translocation channel of the mitochondrial outer membrane. Biochem J 2001; 356:207-15. [PMID: 11336653 PMCID: PMC1221829 DOI: 10.1042/0264-6021:3560207] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The precursor protein translocase of the mitochondrial outer membrane (Tom) is a multi-subunit complex containing receptors and a general import channel, of which the core component is Tom40p. Nuclear-encoded mitochondrial precursor proteins are first recognized by surface receptors and then pass through the import channel. The Tom complex has been purified; however, the protein-protein interactions that drive its assembly and maintain its stability have been difficult to study. Here we show that Saccharomyces cerevisiae Tom40p expressed in bacteria and purified to homogeneity associates efficiently with itself. The self-association is very strong and can withstand up to 4 M urea or 1 M salt. The tight self-association does not require the N-terminal segment of Tom40p. Furthermore, purified Tom40p preferentially recognizes the targeting sequence of mitochondrial precursor proteins. Although the binding of the targeting sequence to Tom40p is inhibited by urea concentrations in excess of 1 M, it is moderately resistant to 1 M salt. Simultaneous self-assembly and precursor protein binding suggest that Tom40p contains at least two different domains mediating these processes. The experimental approach described here should be useful for analysing protein-protein interactions involving individual or groups of components of the mitochondrial import machinery.
Collapse
Affiliation(s)
- D M Gordon
- Department of Physiology, University of Pennsylvania School of Medicine, 3700 Hamilton Walk, D403 Richards Building, Philadelphia, PA 19104-6085, USA
| | | | | | | |
Collapse
|
42
|
Krimmer T, Rapaport D, Ryan MT, Meisinger C, Kassenbrock CK, Blachly-Dyson E, Forte M, Douglas MG, Neupert W, Nargang FE, Pfanner N. Biogenesis of porin of the outer mitochondrial membrane involves an import pathway via receptors and the general import pore of the TOM complex. J Cell Biol 2001; 152:289-300. [PMID: 11266446 PMCID: PMC2199606 DOI: 10.1083/jcb.152.2.289] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Porin, also termed the voltage-dependent anion channel, is the most abundant protein of the mitochondrial outer membrane. The process of import and assembly of the protein is known to be dependent on the surface receptor Tom20, but the requirement for other mitochondrial proteins remains controversial. We have used mitochondria from Neurospora crassa and Saccharomyces cerevisiae to analyze the import pathway of porin. Import of porin into isolated mitochondria in which the outer membrane has been opened is inhibited despite similar levels of Tom20 as in intact mitochondria. A matrix-destined precursor and the porin precursor compete for the same translocation sites in both normal mitochondria and mitochondria whose surface receptors have been removed, suggesting that both precursors utilize the general import pore. Using an assay established to monitor the assembly of in vitro-imported porin into preexisting porin complexes we have shown that besides Tom20, the biogenesis of porin depends on the central receptor Tom22, as well as Tom5 and Tom7 of the general import pore complex (translocase of the outer mitochondrial membrane [TOM] core complex). The characterization of two new mutant alleles of the essential pore protein Tom40 demonstrates that the import of porin also requires a functional Tom40. Moreover, the porin precursor can be cross-linked to Tom20, Tom22, and Tom40 on its import pathway. We conclude that import of porin does not proceed through the action of Tom20 alone, but requires an intact outer membrane and involves at least four more subunits of the TOM machinery, including the general import pore.
Collapse
Affiliation(s)
- Thomas Krimmer
- Institute for Biochemistry and Molecular Biology, University of Freiburg, D-79104 Freiburg, Germany
- Faculty for Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Doron Rapaport
- Institute for Physiological Chemistry, Munich University, D-80336 Munich, Germany
| | - Michael T. Ryan
- Institute for Biochemistry and Molecular Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Chris Meisinger
- Institute for Biochemistry and Molecular Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - C. Kenneth Kassenbrock
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Michael Forte
- Oregon Health Sciences University, Portland, Oregon 97201
| | - Michael G. Douglas
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Walter Neupert
- Institute for Physiological Chemistry, Munich University, D-80336 Munich, Germany
| | - Frank E. Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Nikolaus Pfanner
- Institute for Biochemistry and Molecular Biology, University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
43
|
Gabriel K, Buchanan SK, Lithgow T. The alpha and the beta: protein translocation across mitochondrial and plastid outer membranes. Trends Biochem Sci 2001; 26:36-40. [PMID: 11165515 DOI: 10.1016/s0968-0004(00)01684-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In the evolution of mitochondria and plastids from endosymbiotic bacteria, most of the proteins that make up these organelles have become encoded by nuclear genes and must therefore be transported across the organellar membranes, following synthesis in the cytosol. The core component of the protein translocation machines in both the mitochondrial and plastid outer membranes appears to be a beta-barrel protein, perhaps a relic from their bacterial ancestry, distinguishing these translocases from the alpha-helical-based protein translocation pores found in all other eukaryotic membranes.
Collapse
Affiliation(s)
- K Gabriel
- Russell Grimwade School of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, Australia
| | | | | |
Collapse
|
44
|
Abrecht H, Goormaghtigh E, Ruysschaert JM, Homble F. Structure and orientation of two voltage-dependent anion-selective channel isoforms. An attenuated total reflection fourier-transform infrared spectroscopy study. J Biol Chem 2000; 275:40992-9. [PMID: 11018035 DOI: 10.1074/jbc.m006437200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two VDAC (voltage-dependent anion-selective channel) isoforms were purified from seed cotyledons of Phaseolus vulgaris by chromatofocusing chromatography. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was used to study the structural properties of the two isoforms reconstituted in a mixture of asolectin and 5% stigmasterol. The IR spectra of the two VDAC isoforms were highly similar indicating 50 to 53% anti-parallel beta-sheet. The orientation of the beta-strands relative to the barrel axis was calculated from the experimentally obtained dichroic ratios of the amide I beta-sheet component and the amide II band. Comparing the IR spectra of the reconstituted VDAC isoforms with the IR spectra of the bacterial porin OmpF, for which a high resolution structure is available, provided evidence for a general structural organization of the VDAC isoforms similar to that of bacterial porins. Hydrogen-deuterium exchange measurements indicated that the exchange of the amide protons occurs to a higher extent in the two VDAC isoforms than in the OmpF porin.
Collapse
Affiliation(s)
- H Abrecht
- Laboratoire de Physiologie Végétale, CP 206/2, Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, B-1050 Brussels, Belgium
| | | | | | | |
Collapse
|
45
|
Kanaji S, Iwahashi J, Kida Y, Sakaguchi M, Mihara K. Characterization of the signal that directs Tom20 to the mitochondrial outer membrane. J Cell Biol 2000; 151:277-88. [PMID: 11038175 PMCID: PMC2192658 DOI: 10.1083/jcb.151.2.277] [Citation(s) in RCA: 165] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Tom20 is a major receptor of the mitochondrial preprotein translocation system and is bound to the outer membrane through the NH(2)-terminal transmembrane domain (TMD) in an Nin-Ccyt orientation. We analyzed the mitochondria-targeting signal of rat Tom20 (rTom20) in COS-7 cells, using green fluorescent protein (GFP) as the reporter by systematically introducing deletions or mutations into the TMD or the flanking regions. Moderate TMD hydrophobicity and a net positive charge within five residues of the COOH-terminal flanking region were both critical for mitochondria targeting. Constructs without net positive charges within the flanking region, as well as those with high TMD hydrophobicity, were targeted to the ER-Golgi compartments. Intracellular localization of rTom20-GFP fusions, determined by fluorescence microscopy, was further verified by cell fractionation. The signal recognition particle (SRP)-induced translation arrest and photo-cross-linking demonstrated that SRP recognized the TMD of rTom20-GFP, but with reduced affinity, while the positive charge at the COOH-terminal flanking segment inhibited the translation arrest. The mitochondria-targeting signal identified in vivo also functioned in the in vitro system. We conclude that NH(2)-terminal TMD with a moderate hydrophobicity and a net positive charge in the COOH-terminal flanking region function as the mitochondria-targeting signal of the outer membrane proteins, evading SRP-dependent ER targeting.
Collapse
Affiliation(s)
- S Kanaji
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | | | | | | | | |
Collapse
|
46
|
Donzeau M, Káldi K, Adam A, Paschen S, Wanner G, Guiard B, Bauer MF, Neupert W, Brunner M. Tim23 links the inner and outer mitochondrial membranes. Cell 2000; 101:401-12. [PMID: 10830167 DOI: 10.1016/s0092-8674(00)80850-8] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tim23, a key component of the mitochondrial preprotein translocase, is anchored in the inner membrane by its C-terminal domain and exposes an intermediate domain in the intermembrane space that functions as a presequence receptor. We show that the N-terminal domain of Tim23 is exposed on the surface of the outer membrane. The two-membrane-spanning topology of Tim23 is a novel characteristic in membrane biology. By the simultaneous integration into two membranes, Tim23 forms contacts between the outer and inner mitochondrial membranes. Tethering the inner membrane translocase to the outer membrane facilitates the transfer of precursor proteins from the TOM complex to the TIM23 complex and increases the efficiency of protein import.
Collapse
Affiliation(s)
- M Donzeau
- Institut für Physiologische Chemie der Universität München, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Steinkamp T, Hill K, Hinnah SC, Wagner R, Röhl T, Pohlmeyer K, Soll J. Identification of the pore-forming region of the outer chloroplast envelope protein OEP16. J Biol Chem 2000; 275:11758-64. [PMID: 10766798 DOI: 10.1074/jbc.275.16.11758] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The chloroplast outer envelope protein OEP16 forms a cation-selective high conductance channel with permeability to amines and amino acids. The region of OEP16 directly involved in channel formation has been identified by electrophysiological analysis of a selection of reconstituted OEP16 mutants. Because analysis of these mutants depended on the use of recombinant protein, we evaluated the electrophysiological properties of OEP16 isolated directly from pea chloroplasts and of the recombinant protein produced in Escherichia coli. The results show that the basic properties like conductance, selectivity, and open probability of the channel formed by native pea OEP16 are comparable with the channel activity formed by the recombinant source of the protein. Following electrophysiological analysis of OEP16 mutants we found that point mutations and insertion of additional amino acid residues in the region of the putative helix 1 (Glu(73) to Val(91)) did not change the properties of the OEP16 channel. The only exception was a Cys(71)-->Ser mutation, which led to a loss of the CuCl(2) sensitivity of the channel. Analysis of N- and C-terminal deletion mutants of OEP16 and mutants containing defined shuffled domains indicated that the minimal continuous region of OEP16, which is able to form a channel in liposomes, lies in the first half of the protein between amino acid residues 21 and 93.
Collapse
Affiliation(s)
- T Steinkamp
- Fachbereich Biologie/Chemie, Universität Osnabrück, D-49034 Osnabrück, Germany
| | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
Mitochondria are made up of two membrane systems that subdivide this organelle into two aqueous subcompartments: the matrix, which is enclosed by the inner membrane, and the intermembrane space, which is located between the inner and the outer membrane. Protein import into mitochondria is a complex reaction, as every protein has to be routed to its specific destination within the organelle. In the past few years, studies with mitochondria of Neurospora crassa and Saccharomyces cerevisiae have led to the identification of four distinct translocation machineries that are conserved among eukaryotes. These translocases, in a concerted fashion, mediate import and sorting of proteins into the mitochondrial subcompartments.
Collapse
Affiliation(s)
- J M Herrmann
- Adolf-Butenandt-Institut für Physiologische Chemie, München, 80336, Germany
| | | |
Collapse
|
49
|
Abstract
Most mitochondrial proteins are synthesized in the cytosol as preproteins with a cleavable presequence and are delivered to the import receptors on the mitochondria by cytoplasmic import factors. The proteins are then imported to the intramitochondrial compartments by the import systems of the outer and inner membranes, TOM and TIM. Mitochondrial outer membrane proteins are synthesized without a cleavable presequence and most of them contain hydrophobic transmembrane domains, which, in conjunction with the flanking segments, function as the mitochondria import signals. Some of the proteins are inserted into the outer membrane by the TOM machinery; the import signal probably arrests further translocation and is released from the translocation channel to the lipid bilayer. The other proteins are inserted into the membrane by a novel pathway independent of the TOM machinery. This article reviews recent developments in the biogenesis of mitochondrial outer membrane proteins.
Collapse
Affiliation(s)
- K Mihara
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan.
| |
Collapse
|
50
|
Rivera IL, Shore GC, Schleiff E. Cloning and characterization of a 35-kDa mouse mitochondrial outer membrane protein MOM35 with high homology to Tom40. J Bioenerg Biomembr 2000; 32:111-21. [PMID: 11768756 DOI: 10.1023/a:1005524815130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have cloned a 35-kDa protein from a mouse cDNA library with a 25% overall amino acid identity to yTom40 and 27% identity to nTom40. This homolog toTom40 was named MOM35. It contains two possible start codons 36 amino acids apart from each other. Both the long and the short version of MOM35 can be imported in vitro into mouse mitochondria. The identified protein is imported into the outer mitochondrial membrane and comprises a trypsin-resistance pattern similar to that of nTom40. Tom40 of N. crassa, S. cerevisiae, and the protein identified herein contains a highly conserved region with possible physiological importance. Subsequent investigation has revealed that this region interacts specifically in vitro with preproteins proposed to be imported by a Tom40-dependent pathway.
Collapse
Affiliation(s)
- I L Rivera
- Department of Biochemistry, McGill University, Montreal Quebec, Canada
| | | | | |
Collapse
|