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Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
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2
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Long-term survive of Aliarcobacter butzleri in two models symbiotic interaction with Acanthamoeba castellanii. Arch Microbiol 2022; 204:610. [DOI: 10.1007/s00203-022-03223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/02/2022]
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3
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Araiso Y, Imai K, Endo T. Role of the TOM Complex in Protein Import into Mitochondria: Structural Views. Annu Rev Biochem 2022; 91:679-703. [PMID: 35287471 DOI: 10.1146/annurev-biochem-032620-104527] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are central to energy production, metabolism and signaling, and apoptosis. To make new mitochondria from preexisting mitochondria, the cell needs to import mitochondrial proteins from the cytosol into the mitochondria with the aid of translocators in the mitochondrial membranes. The translocase of the outer membrane (TOM) complex, an outer membrane translocator, functions as an entry gate for most mitochondrial proteins. Although high-resolution structures of the receptor subunits of the TOM complex were deposited in the early 2000s, those of entire TOM complexes became available only in 2019. The structural details of these TOM complexes, consisting of the dimer of the β-barrel import channel Tom40 and four α-helical membrane proteins, revealed the presence of several distinct paths and exits for the translocation of over 1,000 different mitochondrial precursor proteins. High-resolution structures of TOM complexes now open up a new era of studies on the structures, functions, and dynamics of the mitochondrial import system. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yuhei Araiso
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan; .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
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4
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The Diversity of the Mitochondrial Outer Membrane Protein Import Channels: Emerging Targets for Modulation. Molecules 2021; 26:molecules26134087. [PMID: 34279427 PMCID: PMC8272145 DOI: 10.3390/molecules26134087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022] Open
Abstract
The functioning of mitochondria and their biogenesis are largely based on the proper function of the mitochondrial outer membrane channels, which selectively recognise and import proteins but also transport a wide range of other molecules, including metabolites, inorganic ions and nucleic acids. To date, nine channels have been identified in the mitochondrial outer membrane of which at least half represent the mitochondrial protein import apparatus. When compared to the mitochondrial inner membrane, the presented channels are mostly constitutively open and consequently may participate in transport of different molecules and contribute to relevant changes in the outer membrane permeability based on the channel conductance. In this review, we focus on the channel structure, properties and transported molecules as well as aspects important to their modulation. This information could be used for future studies of the cellular processes mediated by these channels, mitochondrial functioning and therapies for mitochondria-linked diseases.
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Rodriguez-Anaya LZ, Félix-Sastré ÁJ, Lares-Villa F, Lares-Jiménez LF, Gonzalez-Galaviz JR. Application of the omics sciences to the study of Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris: current status and future projections. Parasite 2021; 28:36. [PMID: 33843581 PMCID: PMC8040595 DOI: 10.1051/parasite/2021033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
In this review, we focus on the sequenced genomes of the pathogens Naegleria fowleri, Acanthamoeba spp. and Balamuthia mandrillaris, and the remarkable discoveries regarding the pathogenicity and genetic information of these organisms, using techniques related to the various omics branches like genomics, transcriptomics, and proteomics. Currently, novel data produced through comparative genomics analyses and both differential gene and protein expression in these free-living amoebas have allowed for breakthroughs to identify genes unique to N. fowleri, genes with active transcriptional activity, and their differential expression in conditions of modified virulence. Furthermore, orthologous genes of the various nuclear genomes within the Naegleria and Acanthamoeba genera have been clustered. The proteome of B. mandrillaris has been reconstructed through transcriptome data, and its mitochondrial genome structure has been thoroughly described with a unique characteristic that has come to light: a type I intron with the capacity of interrupting genes through its self-splicing ribozymes activity. With the integration of data derived from the diverse omic sciences, there is a potential approximation that reflects the molecular complexity required for the identification of virulence factors, as well as crucial information regarding the comprehension of the molecular mechanisms with which these interact. Altogether, these breakthroughs could contribute to radical advances in both the fields of therapy design and medical diagnosis in the foreseeable future.
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Affiliation(s)
| | - Ángel Josué Félix-Sastré
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora Ciudad Obregón 85000 Sonora México
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora Ciudad Obregón 85000 Sonora México
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora Ciudad Obregón 85000 Sonora México
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6
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Kreimendahl S, Rassow J. The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity. Int J Mol Sci 2020; 21:E7262. [PMID: 33019591 PMCID: PMC7583919 DOI: 10.3390/ijms21197262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023] Open
Abstract
Tom70 is a versatile adaptor protein of 70 kDa anchored in the outer membrane of mitochondria in metazoa, fungi and amoeba. The tertiary structure was resolved for the Tom70 of yeast, showing 26 α-helices, most of them participating in the formation of 11 tetratricopeptide repeat (TPR) motifs. Tom70 serves as a docking site for cytosolic chaperone proteins and co-chaperones and is thereby involved in the uptake of newly synthesized chaperone-bound proteins in mitochondrial biogenesis. In yeast, Tom70 additionally mediates ER-mitochondria contacts via binding to sterol transporter Lam6/Ltc1. In mammalian cells, TOM70 promotes endoplasmic reticulum (ER) to mitochondria Ca2+ transfer by association with the inositol-1,4,5-triphosphate receptor type 3 (IP3R3). TOM70 is specifically targeted by the Bcl-2-related protein MCL-1 that acts as an anti-apoptotic protein in macrophages infected by intracellular pathogens, but also in many cancer cells. By participating in the recruitment of PINK1 and the E3 ubiquitin ligase Parkin, TOM70 can be implicated in the development of Parkinson's disease. TOM70 acts as receptor of the mitochondrial antiviral-signaling protein (MAVS) and thereby participates in the corresponding system of innate immunity against viral infections. The protein encoded by Orf9b in the genome of SARS-CoV-2 binds to TOM70, probably compromising the synthesis of type I interferons.
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Affiliation(s)
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44801 Bochum, Germany;
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Medina G, Leyán P, da Silva CV, Flores-Martin S, Manosalva C, Fernández H. Intra-amoebic localization of Arcobacter butzleri as an endocytobiont of Acanthamoeba castellanii. Arch Microbiol 2019; 201:1447-1452. [PMID: 31302710 DOI: 10.1007/s00203-019-01699-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/19/2019] [Accepted: 07/01/2019] [Indexed: 11/29/2022]
Abstract
Acanthamoeba castellanii is a free-living amoeba found mainly in humid environments and Arcobacter butzleri is an emerging zoonotic pathogen, both can establish in vitro endosymbiotic relationships in the absence of bacterial replication. We analyzed the localization of A. butzleri within A. castellanii establishing their association with endoplasmic reticulum vesicles and mitochondria. Through confocal microscopy, we observed that during the early stages of endosymbiosis, there is not colocalization between amoebic vacuoles containing A. butzleri and mitochondria or ER vesicles of A. castellanii. Considering that energy production of this bacterium occurs via metabolism of amino acids or the tricarboxylic acid cycle, these results contribute to explain the absence of bacterial replication, since A. butzleri would not have access to the nutrients found in endoplasmic reticulum vesicles and mitochondria. In addition, we observe that A. butzleri induces significantly the actin polymerization of A. castellanii during the early stages of endosymbiosis.
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Affiliation(s)
- G Medina
- Faculty of Health Sciences, Department of Diagnostic Processes and Evaluation, Universidad Católica de Temuco, PO. BOX 15-D, Temuco, Chile.
| | - P Leyán
- Faculty of Health Sciences, Department of Diagnostic Processes and Evaluation, Universidad Católica de Temuco, PO. BOX 15-D, Temuco, Chile
| | - C Viera da Silva
- Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 6T, Campus Umuarama, CEP, Uberlândia, MG, 38400-902, Brazil
| | - S Flores-Martin
- Institute of Clinical Microbiology,Faculty of Medicine, Universidad Austral de Chile, PO. BOX 567, Valdivia, Chile
| | - C Manosalva
- Institute of Pharmacy, Faculty of Science, Universidad Austral de Chile, Valdivia, Chile
| | - H Fernández
- Institute of Clinical Microbiology,Faculty of Medicine, Universidad Austral de Chile, PO. BOX 567, Valdivia, Chile
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8
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Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS Microbiol Rev 2019; 43:415-434. [DOI: 10.1093/femsre/fuz011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
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Affiliation(s)
- Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Marie-Hélène Rodier
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Estelle Cateau
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
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9
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Makki A, Rada P, Žárský V, Kereïche S, Kováčik L, Novotný M, Jores T, Rapaport D, Tachezy J. Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biol 2019; 17:e3000098. [PMID: 30608924 PMCID: PMC6334971 DOI: 10.1371/journal.pbio.3000098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 12/11/2018] [Indexed: 11/30/2022] Open
Abstract
Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, an unexpected diversity of subunits between eukaryotic lineages has been predicted. However, experimental knowledge is limited to a few organisms, and so far, it remains unsettled whether the triplet-pore or the twin-pore structure is the generic form of TOM complex. Here, we analysed the TOM complex in hydrogenosomes, a metabolically specialised anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. We demonstrate that the highly divergent β-barrel T. vaginalis TOM (TvTom)40-2 forms a translocation channel to conduct hydrogenosomal protein import. TvTom40-2 is present in high molecular weight complexes, and their analysis revealed the presence of four tail-anchored (TA) proteins. Two of them, Tom36 and Tom46, with heat shock protein (Hsp)20 and tetratricopeptide repeat (TPR) domains, can bind hydrogenosomal preproteins and most likely function as receptors. A third subunit, Tom22-like protein, has a short cis domain and a conserved Tom22 transmembrane segment but lacks a trans domain. The fourth protein, hydrogenosomal outer membrane protein 19 (Homp19) has no known homology. Furthermore, our data indicate that TvTOM is associated with sorting and assembly machinery (Sam)50 that is involved in β-barrel assembly. Visualisation of TvTOM by electron microscopy revealed that it forms three pores and has an unconventional skull-like shape. Although TvTOM seems to lack Tom7, our phylogenetic profiling predicted Tom7 in free-living excavates. Collectively, our results suggest that the triplet-pore TOM complex, composed of three conserved subunits, was present in the last common eukaryotic ancestor (LECA), while receptors responsible for substrate binding evolved independently in different eukaryotic lineages. The highly divergent outer membrane translocase (TOM) from the Trichomonas hydrogenosome (an organelle related to mitochondria) is composed of conserved core and lineage-specific subunits, and has an unconventional skull-like triplet-pore structure. Mitochondria carry out many vital functions in the eukaryotic cells, from energy metabolism to programmed cell death. These organelles descended from bacterial endosymbionts, and during their evolution, the cell established a mechanism to transport nuclear-encoded proteins into mitochondria. Embedded in the mitochondrial outer membrane is a molecular machine, known as the translocase of the outer membrane (TOM) complex, that plays a key role in protein import and biogenesis of the organelle. Here, we provide evidence that the TOM complex of hydrogenosomes, a metabolically specialised anaerobic form of mitochondria in Trichomonas vaginalis, is composed of highly divergent core subunits and lineage-specific peripheral subunits. Despite the evolutionary distance, the T. vaginalis TOM (TvTOM) complex has a conserved triplet-pore structure but with a unique skull-like shape suggesting that the TOM in the early mitochondrion could have formed three pores. Our results contribute to a better understanding of the evolution and adaptation of protein import machinery in anaerobic forms of mitochondria.
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Affiliation(s)
- Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Sami Kereïche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lubomír Kováčik
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- * E-mail:
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Fukasawa Y, Oda T, Tomii K, Imai K. Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages. Mol Biol Evol 2017; 34:1574-1586. [PMID: 28369657 PMCID: PMC5455965 DOI: 10.1093/molbev/msx096] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases’ evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex.
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Affiliation(s)
- Yoshinori Fukasawa
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Toshiyuki Oda
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
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11
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Abstract
Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
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Affiliation(s)
- Michelle M Leger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura A Hug
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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12
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Mani J, Meisinger C, Schneider A. Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes. Mol Biol Evol 2015; 33:337-51. [PMID: 26474847 DOI: 10.1093/molbev/msv219] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are essential for eukaryotic life and more than 95% of their proteins are imported as precursors from the cytosol. The targeting signals for this posttranslational import are conserved in all eukaryotes. However, this conservation does not hold true for the protein translocase of the mitochondrial outer membrane that serves as entry gate for essentially all precursor proteins. Only two of its subunits, Tom40 and Tom22, are conserved and thus likely were present in the last eukaryotic common ancestor. Tom7 is found in representatives of all supergroups except the Excavates. This suggests that it was added to the core of the translocase after the Excavates segregated from all other eukaryotes. A comparative analysis of the biochemically and functionally characterized outer membrane translocases of yeast, plants, and trypanosomes, which represent three eukaryotic supergroups, shows that the receptors that recognize the conserved import signals differ strongly between the different systems. They present a remarkable example of convergent evolution at the molecular level. The structural diversity of the functionally conserved import receptors therefore provides insight into the early evolutionary history of mitochondria.
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Affiliation(s)
- Jan Mani
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Chris Meisinger
- Institut für Biochemie und Molekularbiologie, ZBMZ and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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