1
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Rubalcava-Gracia D, García-Villegas R, Larsson NG. No role for nuclear transcription regulators in mammalian mitochondria? Mol Cell 2023; 83:832-842. [PMID: 36182692 DOI: 10.1016/j.molcel.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear transcription regulators, as exemplified by MEF2D, MOF, PGC-1α, and hormone receptors, are imported into mammalian mitochondria and directly interact with the mtDNA transcription machinery. However, the supporting experimental evidence for this concept is open to alternate interpretations, and a main issue is the difficulty in distinguishing indirect regulation of mtDNA transcription, caused by altered nuclear gene expression, from direct intramitochondrial effects. We provide a critical discussion and experimental guidelines to stringently assess roles of intramitochondrial factors implicated in direct regulation of mammalian mtDNA transcription.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rodolfo García-Villegas
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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2
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Caspari OD, Garrido C, Law CO, Choquet Y, Wollman FA, Lafontaine I. Converting antimicrobial into targeting peptides reveals key features governing protein import into mitochondria and chloroplasts. PLANT COMMUNICATIONS 2023:100555. [PMID: 36733255 PMCID: PMC10363480 DOI: 10.1016/j.xplc.2023.100555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
We asked what peptide features govern targeting to the mitochondria versus the chloroplast, using antimicrobial peptides as a starting point. This approach was inspired by the endosymbiotic hypothesis that organelle-targeting peptides derive from antimicrobial amphipathic peptides delivered by the host cell, to which organelle progenitors became resistant. To explore the molecular changes required to convert antimicrobial into targeting peptides, we expressed a set of 13 antimicrobial peptides in Chlamydomonas reinhardtii. Peptides were systematically modified to test distinctive features of mitochondrion- and chloroplast-targeting peptides, and we assessed their targeting potential by following the intracellular localization and maturation of a Venus fluorescent reporter used as a cargo protein. Mitochondrial targeting can be achieved by some unmodified antimicrobial peptide sequences. Targeting to both organelles is improved by replacing lysines with arginines. Chloroplast targeting is enabled by the presence of flanking unstructured sequences, additional constraints consistent with chloroplast endosymbiosis having occurred in a cell that already contained mitochondria. If indeed targeting peptides evolved from antimicrobial peptides, then required modifications imply a temporal evolutionary scenario with an early exchange of cationic residues and a late acquisition of chloroplast-specific motifs.
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Affiliation(s)
- Oliver D Caspari
- UMR7141 (CNRS/Sorbonne Université), Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.
| | - Clotilde Garrido
- UMR7141 (CNRS/Sorbonne Université), Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Chris O Law
- Centre for Microscopy and Cellular Imaging, Biology Department Loyola Campus of Concordia University, 7141 Sherbrooke W., Montréal, QC H4B 1R6, Canada
| | - Yves Choquet
- UMR7141 (CNRS/Sorbonne Université), Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Francis-André Wollman
- UMR7141 (CNRS/Sorbonne Université), Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Ingrid Lafontaine
- UMR7141 (CNRS/Sorbonne Université), Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.
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3
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Caspari OD, Lafontaine I. The role of antimicrobial peptides in the evolution of endosymbiotic protein import. PLoS Pathog 2021; 17:e1009466. [PMID: 33857255 PMCID: PMC8049325 DOI: 10.1371/journal.ppat.1009466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Oliver D. Caspari
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), Paris, France
- * E-mail: (ODC); (IL)
| | - Ingrid Lafontaine
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), Paris, France
- * E-mail: (ODC); (IL)
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4
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Gyimesi G, Hediger MA. Sequence Features of Mitochondrial Transporter Protein Families. Biomolecules 2020; 10:E1611. [PMID: 33260588 PMCID: PMC7761412 DOI: 10.3390/biom10121611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical SLC25 (solute carrier family 25) mitochondrial carriers, the past decade has led to the discovery of additional protein families with numerous members that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins, and mitochondrial cation/H+ exchangers. These transport proteins were linked to vital physiological functions and disease. Their structures and transport mechanisms are, however, still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about the sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combine sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanisms and structures of these novel mitochondrial carriers.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, CH-3010 Bern, Switzerland;
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5
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Friedl J, Knopp MR, Groh C, Paz E, Gould SB, Herrmann JM, Boos F. More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites. Mol Biol Cell 2020; 31:2657-2668. [PMID: 32997570 PMCID: PMC8734313 DOI: 10.1091/mbc.e20-08-0524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 11/11/2022] Open
Abstract
Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.
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Affiliation(s)
- Jana Friedl
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael R. Knopp
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Carina Groh
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Eyal Paz
- Departments of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sven B. Gould
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes M. Herrmann
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
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6
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Kreimendahl S, Schwichtenberg J, Günnewig K, Brandherm L, Rassow J. The selectivity filter of the mitochondrial protein import machinery. BMC Biol 2020; 18:156. [PMID: 33121519 PMCID: PMC7596997 DOI: 10.1186/s12915-020-00888-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background The uptake of newly synthesized nuclear-encoded mitochondrial proteins from the cytosol is mediated by a complex of mitochondrial outer membrane proteins comprising a central pore-forming component and associated receptor proteins. Distinct fractions of proteins initially bind to the receptor proteins and are subsequently transferred to the pore-forming component for import. The aim of this study was the identification of the decisive elements of this machinery that determine the specific selection of the proteins that should be imported. Results We identified the essential internal targeting signal of the members of the mitochondrial metabolite carrier proteins, the largest protein family of the mitochondria, and we investigated the specific recognition of this signal by the protein import machinery at the mitochondrial outer surface. We found that the outer membrane import receptors facilitated the uptake of these proteins, and we identified the corresponding binding site, marked by cysteine C141 in the receptor protein Tom70. However, in tests both in vivo and in vitro, the import receptors were neither necessary nor sufficient for specific recognition of the targeting signals. Although these signals are unrelated to the amino-terminal presequences that mediate the targeting of other mitochondrial preproteins, they were found to resemble presequences in their strict dependence on a content of positively charged residues as a prerequisite of interactions with the import pore. Conclusions The general import pore of the mitochondrial outer membrane appears to represent not only the central channel of protein translocation but also to form the decisive general selectivity filter in the uptake of the newly synthesized mitochondrial proteins.
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Affiliation(s)
- Sebastian Kreimendahl
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Jan Schwichtenberg
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Kathrin Günnewig
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Lukas Brandherm
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany.
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7
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Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles. Cells 2020; 9:cells9081795. [PMID: 32731621 PMCID: PMC7463930 DOI: 10.3390/cells9081795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signal peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides still display antimicrobial activity. Thus, we provide strong computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides has been instrumental in eukaryogenesis and in the emergence of photosynthetic eukaryotes.
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8
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Lutfullahoğlu-Bal G, Seferoğlu AB, Keskin A, Akdoğan E, Dunn CD. A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells. Sci Rep 2018; 8:16374. [PMID: 30401812 PMCID: PMC6219538 DOI: 10.1038/s41598-018-34646-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/18/2018] [Indexed: 11/18/2022] Open
Abstract
Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.
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Affiliation(s)
- Güleycan Lutfullahoğlu-Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
| | - Ayşe Bengisu Seferoğlu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Abdurrahman Keskin
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Emel Akdoğan
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, United States of America
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland.
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey.
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9
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Río Bártulos C, Rogers MB, Williams TA, Gentekaki E, Brinkmann H, Cerff R, Liaud MF, Hehl AB, Yarlett NR, Gruber A, Kroth PG, van der Giezen M. Mitochondrial Glycolysis in a Major Lineage of Eukaryotes. Genome Biol Evol 2018; 10:2310-2325. [PMID: 30060189 PMCID: PMC6198282 DOI: 10.1093/gbe/evy164] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/21/2022] Open
Abstract
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host’s metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.
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Affiliation(s)
- Carolina Río Bártulos
- Institut für Genetik, Technische Universität Braunschweig.,Fachbereich Biologie, Universität Konstanz, Germany
| | - Matthew B Rogers
- Biosciences, University of Exeter, United Kingdom.,Rangos Research Center, University of Pittsburgh, Children's Hospital, Pittsburgh, PA
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai, Thailand
| | - Henner Brinkmann
- Département de Biochimie, Université de Montréal C.P. 6128, Montréal, Quebec, Canada.,Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Rüdiger Cerff
- Institut für Genetik, Technische Universität Braunschweig
| | | | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Switzerland
| | - Nigel R Yarlett
- Department of Chemistry and Physical Sciences, Pace University
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Germany.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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10
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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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11
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Backes S, Hess S, Boos F, Woellhaf MW, Gödel S, Jung M, Mühlhaus T, Herrmann JM. Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences. J Cell Biol 2018; 217:1369-1382. [PMID: 29382700 PMCID: PMC5881500 DOI: 10.1083/jcb.201708044] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/12/2017] [Accepted: 01/17/2018] [Indexed: 11/22/2022] Open
Abstract
N-terminal matrix-targeting signals (MTSs) are critical for mitochondrial protein import. Backes et al. identified additional internal MTS-like sequences scattered along the sequences of mitochondrial proteins. By binding to Tom70 on the mitochondrial surface, these sequences support the import process. The biogenesis of mitochondria depends on the import of hundreds of preproteins. N-terminal matrix-targeting signals (MTSs) direct preproteins to the surface receptors Tom20, Tom22, and Tom70. In this study, we show that many preproteins contain additional internal MTS-like signals (iMTS-Ls) in their mature region that share the characteristic properties of presequences. These features allow the in silico prediction of iMTS-Ls. Using Atp1 as model substrate, we show that iMTS-Ls mediate the binding to Tom70 and have the potential to target the protein to mitochondria if they are presented at its N terminus. The import of preproteins with high iMTS-L content is significantly impaired in the absence of Tom70, whereas preproteins with low iMTS-L scores are less dependent on Tom70. We propose a stepping stone model according to which the Tom70-mediated interaction with internal binding sites improves the import competence of preproteins and increases the efficiency of their translocation into the mitochondrial matrix.
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Affiliation(s)
- Sandra Backes
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Steffen Hess
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Sabrina Gödel
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Martin Jung
- Medical Biochemistry, Saarland University, Homburg, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern, Germany
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12
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Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora. Curr Biol 2017; 27:2763-2773.e5. [DOI: 10.1016/j.cub.2017.08.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/12/2017] [Accepted: 08/03/2017] [Indexed: 01/03/2023]
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13
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Bock R. Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer. Annu Rev Genet 2017; 51:1-22. [PMID: 28846455 DOI: 10.1146/annurev-genet-120215-035329] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany;
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14
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Lutfullahoğlu-Bal G, Keskin A, Seferoğlu AB, Dunn CD. Bacterial tail anchors can target to the mitochondrial outer membrane. Biol Direct 2017; 12:16. [PMID: 28738827 PMCID: PMC5525287 DOI: 10.1186/s13062-017-0187-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 01/15/2023] Open
Abstract
Background During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol. Results Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM. Conclusions Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins. Reviewers This article was reviewed by Michael Ryan and Thomas Simmen. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0187-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Abdurrahman Keskin
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey.,Present Address: Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Ayşe Bengisu Seferoğlu
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey
| | - Cory D Dunn
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey. .,Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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15
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Wollman FA. An antimicrobial origin of transit peptides accounts for early endosymbiotic events. Traffic 2016; 17:1322-1328. [DOI: 10.1111/tra.12446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 12/11/2022]
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16
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Garg SG, Gould SB. The Role of Charge in Protein Targeting Evolution. Trends Cell Biol 2016; 26:894-905. [PMID: 27524662 DOI: 10.1016/j.tcb.2016.07.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/28/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022]
Abstract
Two eukaryotic compartments are of endosymbiotic origin, the mitochondrion and plastid. These organelles need to import hundreds of proteins from the cytosol. The import machineries of both are of independent origin, but function in a similar fashion and recognize N-terminal targeting sequences that also share similarities. Targeting, however, is generally specific, even though plastid targeting evolved in the presence of established mitochondrial targeting. Here we review current advances on protein import into mitochondria and plastids from diverse eukaryotic lineages and highlight the impact of charged amino acids in targeting. Their presence or absence alone can determine localization, and comparisons across diverse eukaryotes, and their different types of mitochondria and plastids, uncover unexplored avenues of protein import research.
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Affiliation(s)
- Sriram G Garg
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
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17
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Garg S, Stölting J, Zimorski V, Rada P, Tachezy J, Martin WF, Gould SB. Conservation of Transit Peptide-Independent Protein Import into the Mitochondrial and Hydrogenosomal Matrix. Genome Biol Evol 2015; 7:2716-26. [PMID: 26338186 PMCID: PMC4607531 DOI: 10.1093/gbe/evv175] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The origin of protein import was a key step in the endosymbiotic acquisition of mitochondria. Though the main translocon of the mitochondrial outer membrane, TOM40, is ubiquitous among organelles of mitochondrial ancestry, the transit peptides, or N-terminal targeting sequences (NTSs), recognised by the TOM complex, are not. To better understand the nature of evolutionary conservation in mitochondrial protein import, we investigated the targeting behavior of Trichomonas vaginalis hydrogenosomal proteins in Saccharomyces cerevisiae and vice versa. Hydrogenosomes import yeast mitochondrial proteins even in the absence of their native NTSs, but do not import yeast cytosolic proteins. Conversely, yeast mitochondria import hydrogenosomal proteins with and without their short NTSs. Conservation of an NTS-independent mitochondrial import route from excavates to opisthokonts indicates its presence in the eukaryote common ancestor. Mitochondrial protein import is known to entail electrophoresis of positively charged NTSs across the electrochemical gradient of the inner mitochondrial membrane. Our present findings indicate that mitochondrial transit peptides, which readily arise from random sequences, were initially selected as a signal for charge-dependent protein targeting specifically to the mitochondrial matrix. Evolutionary loss of the electron transport chain in hydrogenosomes and mitosomes lifted the selective constraints that maintain positive charge in NTSs, allowing first the NTS charge, and subsequently the NTS itself, to be lost. This resulted in NTS-independent matrix targeting, which is conserved across the evolutionary divide separating trichomonads and yeast, and which we propose is the ancestral state of mitochondrial protein import.
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Affiliation(s)
- Sriram Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Stölting
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Verena Zimorski
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Petr Rada
- Department of Parasitology, Charles University in Prague, Faculty of Science, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Charles University in Prague, Faculty of Science, Czech Republic
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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18
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Rousseau-Gueutin M, Ayliffe MA, Timmis JN. Conservation of plastid sequences in the plant nuclear genome for millions of years facilitates endosymbiotic evolution. PLANT PHYSIOLOGY 2011; 157:2181-93. [PMID: 22034627 PMCID: PMC3327181 DOI: 10.1104/pp.111.185074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/24/2011] [Indexed: 05/03/2023]
Abstract
The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed.
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Affiliation(s)
- Mathieu Rousseau-Gueutin
- School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia.
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19
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Nowack ECM, Vogel H, Groth M, Grossman AR, Melkonian M, Glockner G. Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora. Mol Biol Evol 2010; 28:407-22. [DOI: 10.1093/molbev/msq209] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Affiliation(s)
- Felicity Alcock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne 3800, Australia
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21
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Bodył A, Mackiewicz P, Stiller JW. Early steps in plastid evolution: current ideas and controversies. Bioessays 2009; 31:1219-32. [DOI: 10.1002/bies.200900073] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Liu SL, Zhuang Y, Zhang P, Adams KL. Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus. Mol Biol Evol 2009; 26:875-91. [PMID: 19168566 DOI: 10.1093/molbev/msp011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The transfer of functional mitochondrial genes to the nucleus is an ongoing process during plant evolution that has made a major impact on cytonuclear interactions and mitochondrial genome evolution. Analysis of evolutionarily recent transfers in plants provides insights into the evolutionary dynamics of the process and how transferred genes become functional in the nucleus. Here, we report 42 new transferred genes in various angiosperms, including 9 separate transfers of the succinate dehydrogenase gene sdh3. We performed comparative analyses of gene structures and sequence evolution of 77 genes transferred to the nucleus in various angiosperms, including multiple transfers of 10 genes in different lineages. Many genes contain mitochondrial targeting presequences, and potentially 5' cis-regulatory elements, that were acquired from pre-existing nuclear genes for mitochondrial proteins to create chimeric gene structures. In eight separate cases, the presequence was acquired from either the hsp70 chaperonin gene or the hsp22 chaperonin gene. The most common location of introns is in the presequence, and the least common is in the region transferred from the mitochondrion. Several genes have an intron between the presequence and the core region, or an intron in the 5'UTR (untranslated region) or 3'UTR, suggesting presequence and/or regulatory element acquisition by exon shuffling. Both synonymous and nonsynonymous substitution rates have increased considerably in the transferred genes compared with their mitochondrial counterparts, and the degree of rate acceleration varies by gene, species, and evolutionary timing of transfer. Pairwise and branchwise K(a)/K(s) analysis identified four genes with evidence for positive selection, but positive selection is generally uncommon in transferred genes. This study provides a detailed portrayal of structural and sequence evolution in mitochondrial genes transferred to the nucleus, revealing the frequency of different mechanisms for how presequences and introns are acquired and showing how the sequences of transferred genes evolve after movement between cellular genomes.
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Affiliation(s)
- Shao-Lun Liu
- UBC Botanical Garden and Centre for Plant Research, and Department of Botany, University of British Columbia, Vancouver, BC, Canada
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23
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Baker Brachmann C, Boeke JD. Overview: Fusion proteins: Fundamental and therapeutic applications. Expert Opin Ther Pat 2008. [DOI: 10.1517/13543776.4.9.1037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Complex machinery has evolved to recognise and import nuclear-encoded proteins into mitochondria. Recent work now shows that the plant Tom20 mitochondrial protein import receptor has a similar tertiary structure to animal Tom20, although the proteins are evolutionarily distinct, representing an elegant example of convergent evolution.
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Affiliation(s)
- Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M310, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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25
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Mackenzie SA. Plant organellar protein targeting: a traffic plan still under construction. Trends Cell Biol 2005; 15:548-54. [PMID: 16143534 DOI: 10.1016/j.tcb.2005.08.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 07/21/2005] [Accepted: 08/22/2005] [Indexed: 11/30/2022]
Abstract
It has long been understood that specific features of a protein and its corresponding import apparatus dictate the behavior of mitochondrial proteins in their intracellular targeting behavior. In plants, the process by which proteins are directed to organelles has been influenced uniquely by the introduction to the cell of plastids. Parallel functions carried out within the mitochondrion and plastid permit the sharing of proteins and emergence of mechanisms to facilitate dual-targeting of the nuclear-encoded products to both compartments. These include transcriptional and translational variations, relaxation of translation initiation controls and conditional cellular influences. Details of the dual targeting system are emerging from recent studies, and evidence of variation in protein targeting behavior across plant families and across organisms implies that the system itself is in flux. This trend towards multi-targeting enhances protein versatility across eukaryotes - one means of cellular response to developmental or environmental influence.
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Affiliation(s)
- Sally A Mackenzie
- Plant Science Initiative, N300 Beadle Center for Genetics Research, University of Nebraska, Lincoln, NE 68588-0660, USA.
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26
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Christensen AC, Lyznik A, Mohammed S, Elowsky CG, Elo A, Yule R, Mackenzie SA. Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons. THE PLANT CELL 2005; 17:2805-16. [PMID: 16169894 PMCID: PMC1242274 DOI: 10.1105/tpc.105.035287] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The processes accompanying endosymbiosis have led to a complex network of interorganellar protein traffic that originates from nuclear genes encoding mitochondrial and plastid proteins. A significant proportion of nucleus-encoded organellar proteins are dual targeted, and the process by which a protein acquires the capacity for both mitochondrial and plastid targeting may involve intergenic DNA exchange coupled with the incorporation of sequences residing upstream of the gene. We evaluated targeting and sequence alignment features of two organellar DNA polymerase genes from Arabidopsis thaliana. Within one of these two loci, protein targeting appeared to be plastidic when the 5' untranslated leader region (UTR) was deleted and translation could only initiate at the annotated ATG start codon but dual targeted when the 5' UTR was included. Introduction of stop codons at various sites within the putative UTR demonstrated that this region is translated and influences protein targeting capacity. However, no ATG start codon was found within this upstream, translated region, suggesting that translation initiates at a non-ATG start. We identified a CTG codon that likely accounts for much of this initiation. Investigation of the 5' region of other nucleus-encoded organellar genes suggests that several genes may incorporate upstream sequences to influence targeting capacity. We postulate that a combination of intergenic recombination and some relaxation of constraints on translation initiation has acted in the evolution of protein targeting specificity for those proteins capable of functioning in both plastids and mitochondria.
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Affiliation(s)
- Alan C Christensen
- School of Biological Sciences, Beadle Center for Genetics Research, University of Nebraska, Lincoln, NE 68588-0660, USA
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27
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Lister R, Hulett JM, Lithgow T, Whelan J. Protein import into mitochondria: origins and functions today (review). Mol Membr Biol 2005; 22:87-100. [PMID: 16092527 DOI: 10.1080/09687860500041247] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mitochondria are organelles derived from alpha-proteobacteria over the course of one to two billion years. Mitochondria from the major eukaryotic lineages display some variation in functions and coding capacity but sequence analysis demonstrates them to be derived from a single common ancestral endosymbiont. The loss of assorted functions, the transfer of genes to the nucleus, and the acquisition of various 'eukaryotic' proteins have resulted in an organelle that contains approximately 1000 different proteins, with most of these proteins imported into the organelle across one or two membranes. A single translocase in the outer membrane and two translocases in the inner membrane mediate protein import. Comparative sequence analysis and functional complementation experiments suggest some components of the import pathways to be directly derived from the eubacterial endosymbiont's own proteins, and some to have arisen 'de novo' at the earliest stages of 'mitochondrification' of the endosymbiont. A third class of components appears lineage-specific, suggesting they were incorporated into the process of protein import long after mitochondria was established as an organelle and after the divergence of the various eukaryotic lineages. Protein sorting pathways inherited from the endosymbiont have been co-opted and play roles in intraorganelle protein sorting after import. The import apparatus of animals and fungi show significant similarity to one another, but vary considerably to the plant apparatus. Increasing complexity in the eukaryotic lineage, i.e., from single celled to multi-cellular life forms, has been accompanied by an expansion in genes encoding each component, resulting in small gene families encoding many components. The functional differences in these gene families remain to be elucidated, but point to a mosaic import apparatus that can be regulated by a variety of signals.
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Affiliation(s)
- Ryan Lister
- Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
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28
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Murcha MW, Rudhe C, Elhafez D, Adams KL, Daley DO, Whelan J. Adaptations required for mitochondrial import following mitochondrial to nucleus gene transfer of ribosomal protein S10. PLANT PHYSIOLOGY 2005; 138:2134-44. [PMID: 16040655 PMCID: PMC1183401 DOI: 10.1104/pp.105.062745] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The minimal requirements to support protein import into mitochondria were investigated in the context of the phenomenon of ongoing gene transfer from the mitochondrion to the nucleus in plants. Ribosomal protein 10 of the small subunit is encoded in the mitochondrion in soybean and many other angiosperms, whereas in several other species it is nuclear encoded and thus must be imported into the mitochondrial matrix to function. When encoded by the nuclear genome, it has adopted different strategies for mitochondrial targeting and import. In lettuce (Lactuca sativa) and carrot (Daucus carota), Rps10 independently gained different N-terminal extensions from other genes, following transfer to the nucleus. (The designation of Rps10 follows the following convention. The gene is indicated in italics. If encoded in the mitochondrion, it is rps10; if encoded in the nucleus, it is Rps10.) Here, we show that the N-terminal extensions of Rps10 in lettuce and carrot are both essential for mitochondrial import. In maize (Zea mays), Rps10 has not acquired an extension upon transfer but can be readily imported into mitochondria. Deletion analysis located the mitochondrial targeting region to the first 20 amino acids. Using site directed mutagenesis, we changed residues in the first 20 amino acids of the mitochondrial encoded soybean (Glycine max) rps10 to the corresponding amino acids in the nuclear encoded maize Rps10 until import was achieved. Changes were required that altered charge, hydrophobicity, predicted ability to form an amphipathic alpha-helix, and generation of a binding motif for the outer mitochondrial membrane receptor, translocase of the outer membrane 20. In addition to defining the changes required to achieve mitochondrial localization, the results demonstrate that even proteins that do not present barriers to import can require substantial changes to acquire a mitochondrial targeting signal.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia
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29
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Vergnolle M, Sawney H, Junne T, Dolfini L, Tokatlidis K. A cryptic matrix targeting signal of the yeast ADP/ATP carrier normally inserted by the TIM22 complex is recognized by the TIM23 machinery. Biochem J 2005; 385:173-80. [PMID: 15320873 PMCID: PMC1134685 DOI: 10.1042/bj20040650] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The yeast ADP/ATP carrier (AAC) is a mitochondrial protein that is targeted to the inner membrane via the TIM10 and TIM22 translocase complexes. AAC is devoid of a typical mitochondrial targeting signal and its targeting and insertion are thought to be guided by internal amino acid sequences. Here we show that AAC contains a cryptic matrix targeting signal that can target up to two thirds of the N-terminal part of the protein to the matrix. This event is coordinated by the TIM23 translocase and displays all the features of the matrix-targeting pathway. However, in the context of the whole protein, this signal is 'masked' and rendered non-functional as the polypeptide is targeted to the inner membrane via the TIM10 and TIM22 translocases. Our data suggest that after crossing the outer membrane the whole polypeptide chain of AAC is necessary to commit the precursor to the TIM22-mediated inner membrane insertion pathway.
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Affiliation(s)
- Maïlys A. S. Vergnolle
- *School of Biological Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Helen Sawney
- *School of Biological Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Tina Junne
- †Biozentrum, Univeristy of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Luisita Dolfini
- †Biozentrum, Univeristy of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Kostas Tokatlidis
- *School of Biological Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
- ‡Institute of Molecular Biology and Biotechnology IMBB-FORTH, P.O. Box 1527, GR-711 10 Heraklion, Greece
- §Department of Chemistry, University of Crete, P.O. Box 1470, GR-71409 Heraklion, Greece
- To whom correspondence should be addressed (email )
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30
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Abstract
Mitochondria and plastids (including chloroplasts) have a small but vital genetic coding capacity, but what are the properties of some genes that dictate that they must remain encoded in organelles? Mitochondria and plastids (including chloroplasts) have a small but vital genetic coding capacity, but what are the properties of some genes that dictate that they must remain encoded in organelles?
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Affiliation(s)
- Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, S106 91, Sweden
| | - James Whelan
- Plant Molecular Biology Group, School of Biomedical and Chemical Science, University of Western Australia, Nedlands 6009, Western Australia, Australia
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31
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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.
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Affiliation(s)
- Rebecca Lucattini
- Russell Grimwade School of Biochemistry and Molecular Biology, University of Melbourne, Australia
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33
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He XY, Yang YZ, Peehl DM, Lauderdale A, Schulz H, Yang SY. Oxidative 3alpha-hydroxysteroid dehydrogenase activity of human type 10 17beta-hydroxysteroid dehydrogenase. J Steroid Biochem Mol Biol 2003; 87:191-8. [PMID: 14672739 DOI: 10.1016/j.jsbmb.2003.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In vitro enzyme assays have demonstrated that human type 10 17beta-hydroxysteroid dehydrogenase (17beta-HSD10) catalyzes the oxidation of 5alpha-androstane-3alpha,17beta-diol (adiol), an almost inactive androgen, to dihydrotestosterone (DHT) rather than androsterone or androstanedione. To further investigate the role of this steroid-metabolizing enzyme in intact cells, we produced stable transfectants expressing 17beta-HSD10 or its catalytically inactive Y168F mutant in human embryonic kidney (HEK) 293 cells. It was found that DHT levels in HEK 293 cells expressing 17beta-HSD10, but not its catalytically inactive mutant, will dramatically increase if adiol is added to culture media. Moreover, certain malignant prostatic epithelial cells have more 17beta-HSD10 than normal controls, and can generate DHT, the most potent androgen, from adiol. This event might promote prostate cancer growth. Analysis of the 17beta-HSD10 sequence shows that this enzyme does not have any ER retention signal or transmembrane segments and has not originated by divergence from a retinol dehydrogenase. The data suggest that the unique mitochondrial location of this HSD [Eur. J. Biochem. 268 (2001) 4899] does not prevent it from oxidizing the 3alpha-hydroxyl group of a C19 sterol in living cells. The experimental results lead to the conclusion that mitochondrial 17beta-HSD10 plays a significant part in a non-classical androgen synthesis pathway along with microsomal retinol dehydrogenases.
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Affiliation(s)
- Xue-Ying He
- Department of Pharmacology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
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34
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Abstract
During the evolution of mitochondria from free-living alpha-proteobacteria, many bacterial genes were transferred into the nuclear genome of eukaryotic cells. This required the development of both targeting signals on the respective polypeptides and protein translocation machineries (translocases) in the mitochondrial membranes. Most components of these translocases have no obvious homologies to bacterial proteins or proteins found in other organelles. Membrane integration of many inner membrane proteins, however, apparently occurs via a conserved sorting pathway whose components and characteristics resemble protein translocation in bacteria. Consistent with this, the topogenic signals of these mitochondrial inner membrane proteins mimic those of bacterial proteins. The requirement for post-translational transport to their final destination has placed considerable constraints on the evolution of mitochondrial protein sequences.
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Affiliation(s)
- Johannes M Herrmann
- Institut für Physiologische Chemie, Universität München, Butenandtstrasse 5, 81377 Münich, Germany.
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35
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Doolittle WF, Boucher Y, Nesbø CL, Douady CJ, Andersson JO, Roger AJ. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 2003; 358:39-57; discussion 57-8. [PMID: 12594917 PMCID: PMC1693099 DOI: 10.1098/rstb.2002.1185] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.
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Affiliation(s)
- W F Doolittle
- Genome Atlantic, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada.
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36
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Apt KE, Zaslavkaia L, Lippmeier JC, Lang M, Kilian O, Wetherbee R, Grossman AR, Kroth PG. In vivo characterization of diatom multipartite plastid targeting signals. J Cell Sci 2002; 115:4061-9. [PMID: 12356911 DOI: 10.1242/jcs.00092] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plastids of diatoms and related algae are delineated by four membranes: the outermost membrane (CER) is continuous with the endoplasmic reticulum while the inner two membranes are homologous to plastid envelope membranes of vascular plants and green algae. Proteins are transported into these plastids by pre-sequences that have two recognizable domains. To characterize targeting of polypeptides within diatom cells, we generated constructs encoding green fluorecent protein (GFP) fused to leader sequences. A fusion of GFP to the pre-sequence of BiP [an endoplasmic reticulum (ER)-localized chaperone] resulted in accumulation of GFP within the ER; a construct encoding the pre-sequence of a plastid protein fused to GFP was directed into the plastids. Additional constructs demonstrated that the N-terminal region of the bipartite plastid targeting pre-sequence was necessary for transport of polypeptides to the lumen of the ER, while the C-terminal region was shown to enable the proteins to traverse the plastid double envelope membrane. Our data strongly support the hypothesis of a multi-step plastid targeting process in chromophytic algae and raises questions about the continuity of the ER and CER and the function of the latter in polypeptide trafficking.
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Affiliation(s)
- Kirk E Apt
- Martek Biosciences Corp, 6480 Dobbin Rd., Columbia, MD 21045, USA.
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Daley DO, Adams KL, Clifton R, Qualmann S, Millar AH, Palmer JD, Pratje E, Whelan J. Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 30:11-21. [PMID: 11967089 DOI: 10.1046/j.1365-313x.2002.01263.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The evolutionarily recent transfer of the gene for cytochrome c oxidase subunit 2 (cox2) from the mitochondrion to the nucleus in legumes is shown to have involved novel gene-activation steps. The acquired mitochondrial targeting presequence is bordered by two introns. Characterization of the import of soybean Cox2 indicates that the presequence is cleaved in a three-step process which is independent of assembly. The final processing step takes place only in the mitochondria of legume species, and not in several non-legume plants. The unusually long presequence of 136 amino acids consists of three regions: the first 20 amino acids are required for mitochondrial targeting and can be replaced by another presequence; the central portion of the presequence is required for efficient import of the Cox2 protein into mitochondria; and the last 12 amino acids, derived from the mitochondrially encoded protein, are required for correct maturation of the imported protein. The acquisition of a unique presequence, and the capacity for legume mitochondria to remove this presequence post-import, are considered to be essential adaptations for targeting of Cox2 to the mitochondrion and therefore activation of the transferred gene in the nucleus.
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Affiliation(s)
- Daniel O Daley
- Department of Biochemistry, University of Western Australia, Nedlands 6907, Australia
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38
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Wedel N, Klein R, Ljungberg U, Andersson B, Herrmann RG. The single-copy genepsbScodes for a phylogenetically intriguing 22 kDa polypeptide of photosystem II. FEBS Lett 2001; 314:61-6. [PMID: 1360412 DOI: 10.1016/0014-5793(92)81462-u] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recombinant phages that encode the complete precursor polypeptide for the 22 kDa polypeptide associated with photosystem II have been serologically selected from two lambda gt11 expression libraries made from polyadenylated RNA of spinach seedlings. The cDNAs hybridize to a 1.3 kb RNA species. The precursor protein is comprised of 274 amino acid residues and carries an N-terminal transit peptide of probably 69 amino acid residues. The mature protein exhibits four predicted transmembrane segments and is shown to be an integral component of photosystem II originating in a single-copy gene. The unique characteristics of this protein are: (i) it is the result of a gene-internal duplication of an ancestor with two membrane spans, (ii) a striking resemblance to LHC I/II, CP24/CP29 apoproteins, and ELIPs, although it does not bind chlorophyll and is present in cyanobacteria, and, as these proteins, (iii) it integrates into the membrane with uncleaved routing signals that display remarkable resemblance to patterns found in bipartite transit peptides.
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Affiliation(s)
- N Wedel
- Botanisches Institut, Ludwig-Maximilians-Universität, München, Germany
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39
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Abstract
Most mitochondrial proteins are nuclear-encoded and synthesised as preproteins on polysomes in the cytosol. They must be targeted to and translocated into mitochondria. Newly synthesised preproteins interact with cytosolic factors until their recognition by receptors on the surface of mitochondria. Import into or across the outer membrane is mediated by a dynamic protein complex coined the translocase of the outer membrane (TOM). Preproteins that are imported into the matrix or inner membrane of mitochondria require the action of one of two translocation complexes of the inner membrane (TIMs). The import pathway of preproteins is predetermined by their intrinsic targeting and sorting signals. Energy input in the form of ATP and the electrical gradient across the inner membrane is required for protein translocation into mitochondria. Newly imported proteins may require molecular chaperones for their correct folding.
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Affiliation(s)
- K N Truscott
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann-Herder-Strasse 7, D-79104 Freiburg, Germany
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40
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Adams KL, Rosenblueth M, Qiu YL, Palmer JD. Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution. Genetics 2001; 158:1289-300. [PMID: 11454775 PMCID: PMC1461739 DOI: 10.1093/genetics/158.3.1289] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unlike in animals, the functional transfer of mitochondrial genes to the nucleus is an ongoing process in plants. All but one of the previously reported transfers in angiosperms involve ribosomal protein genes. Here we report frequent transfer of two respiratory genes, sdh3 and sdh4 (encoding subunits 3 and 4 of succinate dehydrogenase), and we also show that these genes are present and expressed in the mitochondria of diverse angiosperms. Southern hybridization surveys reveal that sdh3 and sdh4 have been lost from the mitochondrion about 40 and 19 times, respectively, among the 280 angiosperm genera examined. Transferred, functional copies of sdh3 and sdh4 were characterized from the nucleus in four and three angiosperm families, respectively. The mitochondrial targeting presequences of two sdh3 genes are derived from preexisting genes for anciently transferred mitochondrial proteins. On the basis of the unique presequences of the nuclear genes and the recent mitochondrial gene losses, we infer that each of the seven nuclear sdh3 and sdh4 genes was derived from a separate transfer to the nucleus. These results strengthen the hypothesis that angiosperms are experiencing a recent evolutionary surge of mitochondrial gene transfer to the nucleus and reveal that this surge includes certain respiratory genes in addition to ribosomal protein genes.
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Affiliation(s)
- K L Adams
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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41
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He XY, Merz G, Yang YZ, Pullakart R, Mehta P, Schulz H, Yang SY. Function of human brain short chain L-3-hydroxyacyl coenzyme A dehydrogenase in androgen metabolism. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1484:267-77. [PMID: 10760475 DOI: 10.1016/s1388-1981(00)00014-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Human brain short chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) has been demonstrated to be a unique 3alpha-hydroxysteroid dehydrogenase (HSD) that can convert 5alpha-androstane-3alpha, 17beta-diol (3alpha-adiol) to dihydrotestosterone (DHT), whose affinity to the androgen receptor is 10(5)-fold higher than that of 3alpha-adiol. The catalytic efficiency of human SCHAD for this oxidative 3alpha-HSD reaction was estimated to be 164 min(-1) mM(-1), about 10-fold higher than that measured for the backward reaction. Thus, human brain SCHAD may function in androgen metabolism as a new kind of 3alpha-HSD by counteracting all other known 3alpha-HSDs, which would unidirectionally catalyze the reduction of DHT to the almost inactive 3alpha-adiol. Human SCHAD is identical to an amyloid-beta binding protein (ERAB) involved in Alzheimer's disease, which was previously reported to be associated with the endoplasmic reticulum. This protein is, in fact, localized in mitochondria, not endoplasmic reticulum, as evidenced by immunocytochemical studies and its noncleavable mitochondrial targeting sequence and lack of endoplasmic reticulum targeting signals or transmembrane segments. These results prompt the suggestion that the mitochondrion plays not only an essential role in the initial step of steroidogenesis, but also important roles in the intracellular homeostasis of sex steroid hormones. Northern blot analysis revealed that the human SCHAD gene is expressed in both gonadal and peripheral tissues including the prostate whose growth notably requires DHT, the most potent androgen. This study represents the first report of a 3alpha-HSD that could act to generate DHT from 3alpha-adiol and thereby maintain intracellular DHT levels. We propose that inhibitors of the 3alpha-HSD activity of human brain SCHAD could be useful for the treatment of benign prostatic hyperplasia and other disorders involving DHT metabolism, in combination with known inhibitors of steroid 5alpha-reductases.
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Affiliation(s)
- X Y He
- Department of Pharmacology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
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42
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Abe Y, Shodai T, Muto T, Mihara K, Torii H, Nishikawa S, Endo T, Kohda D. Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell 2000; 100:551-60. [PMID: 10721992 DOI: 10.1016/s0092-8674(00)80691-1] [Citation(s) in RCA: 399] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Most mitochondrial proteins are synthesized in the cytosol as precursor proteins with a cleavable N-terminal presequence and are imported into mitochondria. We report here the NMR structure of a general import receptor, rat Tom20, in a complex with a presequence peptide derived from rat aldehyde dehydrogenase. The cytosolic domain of Tom20 forms an all alpha-helical structure with a groove to accommodate the presequence peptide. The bound presequence forms an amphiphilic helical structure with hydrophobic leucines aligned on one side to interact with a hydrophobic patch in the Tom20 groove. Although the positive charges of the presequence are essential for import ability, presequence binding to Tom20 is mediated mainly by hydrophobic rather than ionic interactions.
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Affiliation(s)
- Y Abe
- Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka, Japan
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43
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Kubo N, Harada K, Hirai A, Kadowaki K. A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: common use of the same mitochondrial targeting signal for different proteins. Proc Natl Acad Sci U S A 1999; 96:9207-11. [PMID: 10430921 PMCID: PMC17758 DOI: 10.1073/pnas.96.16.9207] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rice mitochondrial genome has a sequence homologous to the gene for ribosomal protein S14 (rps14), but the coding sequence is interrupted by internal stop codons. A functional rps14 gene was isolated from the rice nuclear genome, suggesting a gene-transfer event from the mitochondrion to the nucleus. The nuclear rps14 gene encodes a long N-terminal extension showing significant similarity to a part of mitochondrial succinate dehydrogenase subunit B (SDHB) protein from human and a malarial parasite (Plasmodium falciparum). Isolation of a functional rice sdhB cDNA and subsequent sequence comparison to the nuclear rps14 indicate that the 5' portions of the two cDNAs are identical. The sdhB genomic sequence shows that the SDHB-coding region is divided into two exons. Surprisingly, the RPS14-coding region is located between the two exons. DNA gel blot analysis indicates that both sdhB and rps14 are present at a single locus in the rice nucleus. These findings strongly suggest that the two gene transcripts result from a single mRNA precursor by alternative splicing. Protein blot analysis shows that the size of the mature RPS14 is 16.5 kDa, suggesting removal of the N-terminal 22.6-kDa peptide region. Considering that the rice mitochondrial genome lacks the sdhB gene but contains the rps14-related sequence, transfer of the sdhB gene seems to have occurred before the transfer of the rps14 gene. The migration of the mitochondrial rps14 sequence into the already existing sdhB gene could bestow the capacity for nuclear expression and mitochondrial targeting.
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Affiliation(s)
- N Kubo
- Faculty of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-0092, Japan
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44
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Martin W, Herrmann RG. Gene transfer from organelles to the nucleus: how much, what happens, and Why? PLANT PHYSIOLOGY 1998; 118:9-17. [PMID: 9733521 PMCID: PMC1539188 DOI: 10.1104/pp.118.1.9] [Citation(s) in RCA: 443] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- W Martin
- Institut fur Genetik, Technische Universitat Braunschweig, Spielmannstrasse 7, D-38023 Braunschweig, Germany (W.M.)
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45
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Doolittle WF. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 1998; 14:307-11. [PMID: 9724962 DOI: 10.1016/s0168-9525(98)01494-2] [Citation(s) in RCA: 364] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent phylogenetic analyses reveal that many eukaryotic nuclear genes whose prokaryotic ancestry can be pinned down are of bacterial origin. Among them are genes whose products function exclusively in cytosolic metabolism. The results are surprising: we had come to believe that the eukaryotic nuclear genome shares a most recent common ancestor with archaeal genomes, thus most of its gene should be 'archaeal' (loosely speaking). Some genes of bacterial origin were expected as the result of transfer from mitochondria, of course, but these were thought to be relatively few, and limited to producing proteins reimported into mitochondria. Here, I suggest that the presence of many bacterial genes with many kinds of functions should not be a surprise. The operation of a gene transfer ratchet would inevitably result in the replacement of nuclear genes of early eukaryotes by genes from the bacteria taken by them as food.
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Affiliation(s)
- W F Doolittle
- Department of Biochemistry, Dalhousie University, Nova Scotia, Canada.
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46
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Boukaftane Y, Mitchell GA. Cloning and characterization of the human mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase gene. Gene 1997; 195:121-6. [PMID: 9305755 DOI: 10.1016/s0378-1119(97)00067-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report the characterization of lambda and P1 phage clones containing the entire human mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase (mHS) gene. The human mHS locus (HMGCS2) on chromosome 1p12-13 spans 25 kb and contains 10 exons. Exon 1 contains most of the mitochondrial leader, consistent with a recent hypothesis of the evolution of the ketogenic pathway. By primer extension and cDNA amplification (RACE-PCR) we localized the transcription start point (tsp) to 60 bp upstream of the initiation codon. Nine blocks of conserved sequence were identified by comparing the 5' flanking regions of the mHS genes of human and rat. The 5' flanking region contains potential binding sites for TATA-binding protein, Sp1, nuclear factor 1 (NF1), CAAT-box binding protein (C/EBP), hepatocyte nuclear factors 1 and 5 (HNF1, HNF5) and activator proteins 1 and 2 (AP1, AP2).
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Affiliation(s)
- Y Boukaftane
- Service de génétique médicale, Hôpital Ste-Justine, Université de Montréal, Québec, Canada
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47
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Kaplan CP, Tugal HB, Baker A. Isolation of a cDNA encoding an Arabidopsis galactokinase by functional expression in yeast. PLANT MOLECULAR BIOLOGY 1997; 34:497-506. [PMID: 9225860 DOI: 10.1023/a:1005816104743] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA clone encoding Arabidopsis thaliana galactokinase was fortuitously isolated during the course of a screen for plant homologues of a Saccharomyces cerevisiae peroxisome assembly gene, PAS9. Clones were sought which restored the ability of pas9 cells to grow on oleate as a sole carbon source, as oleate metabolism requires peroxisomal beta-oxidation and therefore functional peroxisomes. Subsequent experiments showed that high level expression of the galactokinase cDNA did not complement the peroxisomal assembly defect, but instead permitted the cells to grow on agar plates in the absence of an external carbon source. Agar plates were shown to contain a small amount of galactose released from the agar as a result of autoclaving. The galactokinase clone was shown to be functional, as it could complement a S. cerevisiae galactokinase mutant. Galactokinase is a single copy gene in Arabidopsis, which has been designated AGK1, and is expressed in all the major organs of the plant.
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Affiliation(s)
- C P Kaplan
- Centre for Plant Biochemistry and Biotechnology, University of Leeds, UK
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48
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Roise D. Recognition and binding of mitochondrial presequences during the import of proteins into mitochondria. J Bioenerg Biomembr 1997; 29:19-27. [PMID: 9067798 DOI: 10.1023/a:1022403604273] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nuclear-encoded mitochondrial proteins are imported into mitochondria due to the presence of a targeting sequence, the presequence, on their amino termini. Presequences, which are typically proteolyzed after a protein has been imported into a mitochondrion, lack any strictly conserved primary structure but are positively charged and are predicted to form amphiphilic alpha-helices. Studies with synthetic peptides corresponding to various presequences argue that presequences can partition nonspecifically into the mitochondrial outer membrane and that the specificity of translocation of precursors into mitochondria may depend on interactions of the presequence with the electrical potential of the inner membrane. Although proteins of the outer membrane that are necessary for the translocation of precursor proteins have been proposed to function as receptors for presequences, the binding of presequences to these proteins has not been demonstrated directly. Proteins of the mitochondrial outer membrane may not be responsible for the specificity of translocation of precursors but may instead function, together with cytosolic molecular chaperones, to maintain precursor proteins in conformations that are competent for translocation as the precursors associate with the mitochondrial surface.
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Affiliation(s)
- D Roise
- Palo Alto Institute of Molecular Medicine, Mountain View, California 94043, USA
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49
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Abstract
Mitochondria import many hundreds of different proteins that are encoded by nuclear genes. These proteins are targeted to the mitochondria, translocated through the mitochondrial membranes, and sorted to the different mitochondrial subcompartments. Separate translocases in the mitochondrial outer membrane (TOM complex) and in the inner membrane (TIM complex) facilitate recognition of preproteins and transport across the two membranes. Factors in the cytosol assist in targeting of preproteins. Protein components in the matrix partake in energetically driving translocation in a reaction that depends on the membrane potential and matrix-ATP. Molecular chaperones in the matrix exert multiple functions in translocation, sorting, folding, and assembly of newly imported proteins.
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Affiliation(s)
- W Neupert
- Institut für Physiologische Chemie der Universität München, Germany
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50
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Kadowaki K, Kubo N, Ozawa K, Hirai A. Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals. EMBO J 1996; 15:6652-61. [PMID: 8978691 PMCID: PMC452489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have cloned a gene for mitochondrial ribosomal protein S11 (RPS11), which is encoded in lower plants by the mitochondrial genome, in higher plants by the nuclear genome, demonstrating genetic information transfer from the mitochondrial genome to the nucleus during flowering plant evolution. The sequence s11-1 encodes an N-terminal extension as well as an organelle-derived RPS11 region. Surprisingly, the N-terminal region has high amino acid sequence similarity with the presequence of the beta-subunit of ATP synthase from plant mitochondria, suggesting a common lineage of the presequences. The deduced N-terminal region of s11-2, a second nuclear-encoded homolog of rps11, shows high sequence similarity with the putative presequence of cytochrome oxidase subunit Vb. The sharing of the N-terminal region together with its 5' flanking untranslated nucleotide sequence in different proteins strongly suggests an involvement of duplication/recombination for targeting signal acquisition after gene migration. A remnant of ancestral rps11 sequence, transcribed and subjected to RNA editing, is found in the mitochondrial genome, indicating that inactivation of mitochondrial rps11 gene expression was initiated at the translational level prior to termination of transcription.
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Affiliation(s)
- K Kadowaki
- National Institute of Agrobiological Resources, Department of Molecular Biology, Tsukuba, Ibaraki, Japan
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