The Core MICOS Complex Subunit mic60 has Been Substituted by Two Cryptic Mitofilin-containing Proteins in Euglenozoa
Jazyk angličtina Země Spojené státy americké Médium print
Typ dokumentu časopisecké články
Grantová podpora
23-07674S
Czech Science Foundation
CZ.10.03.01/00/22_003/0000003
European Union
Operational Program Just Transition
Czech BioImaging
Czech Ministry of Education
Boehringer Ingelheim Fonds PhD Fellowship
SFB-1638/1-511488495 - P08
Deutsche Forschungsgemeinschaft
FOR-2848-401510699 - P05
Deutsche Forschungsgemeinschaft
67985823
Institute of Physiology
68378050
Institute of Molecular Genetics
Czech Academy of Sciences
Laboratory of Microscopy and Histology
Biology Center, Czech Academy of Sciences
German Research Founda1on
Federal Ministry of Educa1on and Research
Ministry of Science Baden-WürOemberg
Excellence Strategy of the Federal and State Governments of Germany
PubMed
41208531
PubMed Central
PMC12631773
DOI
10.1093/molbev/msaf289
PII: 8317773
Knihovny.cz E-zdroje
- Klíčová slova
- MICOS, cristae, membrane remodeling, mitochondrion,
- MeSH
- Euglenozoa * genetika metabolismus MeSH
- fylogeneze MeSH
- membrány asociované s mitochondriemi MeSH
- mitochondriální proteiny * genetika metabolismus MeSH
- mitochondrie metabolismus MeSH
- molekulární evoluce MeSH
- protozoální proteiny * genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- mitochondriální proteiny * MeSH
- protozoální proteiny * MeSH
Cristae enclose respiratory chain complexes, making them the bioenergetic subcompartments of mitochondria. The Mitochondrial contact site and Cristae Organizing System (MICOS) complex is among the inducers of membrane curvature needed for crista formation. Resembling the respiratory chain complexes, MICOS is organized around a core protein, the mitofilin-domain bearing Mic60, that was inherited from the alphaproteobacterial progenitor of mitochondria. Extant alphaproteobacteria express Mic60 to form their own bioenergetic subcompartments, demonstrating the permeance of Mic60's form and function during prokaryotic and eukaryotic evolution. Yet, unlike virtually all aerobic eukaryotes, Mic60 is not encoded within the genomes of the multifarious protists that comprise the phylum Euglenozoa, including trypanosomes. Here, we show that Mic60 has been replaced in euglenozoans by two cryptic mitofilin domain-containing MICOS subunits, Mic34 and Mic40. Contrasting alphaproteobacterial and mitochondrial Mic60, these are not integral membrane proteins. Mic34 and Mic40 are as diverged from each other as both are to canonical Mic60. Reverse genetics revealed they are intertwined with the oxidative protein folding pathway required for mitochondrial-and crista-biogenesis, veiling a potential membrane remodeling role. Nevertheless, Mic34 binds phospholipid bilayers in vitro. Mic34 and Mic40 heterologous expression remodels gammaproteobacterial cytoplasmic membranes, like Mic60. Unexpectedly, Mic34 overexpression elaborates the simplified tubular mitochondrion of a Trypanosoma brucei life cycle stage with repressed oxidative phosphorylation. Furthermore, this activity was ablated by mutations to Mic34's mitofilin domain that correspond to essential motifs found in yeast Mic60's mitofilin domain. Thus, the mitofilin protein family is more diverse than originally supposed, with two of its structurally most divergent members altering the core of euglenozoan MICOS.
Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
Faculty of Science University of South Bohemia České Budějovice Czech Republic
Heidelberg University Biochemistry Center Heidelberg Germany
Institute of Entomology Biology Center Czech Academy of Sciences České Budějovice Czech Republic
Institute of Parasitology Biology Center Czech Academy of Sciences České Budějovice Czech Republic
Zobrazit více v PubMed
Aaltonen MJ et al. MICOS and phospholipid transfer by Ups2-Mdm35 organize membrane lipid synthesis in mitochondria. J Cell Biol. 2016:213:525–534. 10.1083/jcb.201602007. PubMed DOI PMC
Altschul SF et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997:25:3389–3402. 10.1093/nar/25.17.3389. PubMed DOI PMC
Alvarez-Jarreta J et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Res. 2024:52:D808–D816. 10.1093/nar/gkad1003. PubMed DOI PMC
Barbot M et al. Mic10 oligomerizes to bend mitochondrial inner membranes at cristae junctions. Cell Metab. 2015:21:756–763. 10.1016/j.cmet.2015.04.006. PubMed DOI
Barbot M, Meinecke M. Reconstitutions of mitochondrial inner membrane remodeling. J Struct Biol. 2016:196:20–28. 10.1016/j.jsb.2016.07.014. PubMed DOI
Benning FMC et al. Ancestral sequence reconstruction of Mic60 reveals a residue signature supporting respiration in yeast. Protein Sci. 2025:34:e70207. 10.1002/pro.70207. PubMed DOI PMC
Benz C et al. Kinetoplastid-specific X2-family kinesins interact with a kinesin-like pleckstrin homology domain protein that localizes to the trypanosomal microtubule quartet. Mol Microbiol. 2022:118:155–174. 10.1111/mmi.14958. PubMed DOI
Bílý T et al. Ultrastructural changes of the mitochondrion during the life cycle of PubMed DOI
Bock-Bierbaum T et al. Structural insights into crista junction formation by the Mic60-Mic19 complex. Sci Adv. 2022:8:eabo4946. 10.1126/sciadv.abo4946. PubMed DOI PMC
Burki F, Roger AJ, Brown MW, Simpson AGB. The new tree of eukaryotes. Trends Ecol Evol. 2020:35:43–55. 10.1016/j.tree.2019.08.008. PubMed DOI
Cadena LR et al. Mitochondrial contact site and Cristae organization system and F PubMed DOI PMC
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009:25:1972–1973. 10.1093/bioinformatics/btp348. PubMed DOI PMC
Cavalier-Smith T. Higher classification and phylogeny of euglenozoa. Eur J Protistol. 2016:56:250–276. 10.1016/j.ejop.2016.09.003. PubMed DOI
Chaudhry A, Shi R, Luciani DS. A pipeline for multidimensional confocal analysis of mitochondrial morphology, function, and dynamics in pancreatic β-cells. Am J Physiol Endocrinol Metab. 2020:318:E87–E101. 10.1152/ajpendo.00457.2019. PubMed DOI PMC
Colina-Tenorio L, Horten P, Pfanner N, Rampelt H. Shaping the mitochondrial inner membrane in health and disease. J Intern Med. 2020:287:645–664. 10.1111/joim.13031. PubMed DOI
Daumke O, van der Laan M. Molecular machineries shaping the mitochondrial inner membrane. Nat Rev Mol Cell Biol. 2025:26:706–724. 10.1038/s41580-41025-00854-z. PubMed DOI
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011:7:e1002195. 10.1371/journal.pcbi.1002195. PubMed DOI PMC
Eichenberger C et al. The highly diverged trypanosomal MICOS complex is organized in a nonessential integral membrane and an essential peripheral module. Mol Microbiol. 2019:112:1731–1743. 10.1111/mmi.14389. PubMed DOI
Flaspohler John A, Jensen Bryan C, Saveria T, Kifer Charles T, Parsons M. A novel protein kinase localized to lipid droplets is required for droplet biogenesis in trypanosomes. Eukaryot Cell. 2010:9:1702–1710. 10.1128/EC.00106-10. PubMed DOI PMC
Gleisner M et al. Epsin N-terminal homology domain (ENTH) activity as a function of membrane tension. J Biol Chem. 2016:291:19953–19961. 10.1074/jbc.M116.731612. PubMed DOI PMC
Haindrich AC et al. The intermembrane space protein Erv1 of PubMed DOI
Hammond MJ et al. A uniquely Complex mitochondrial proteome from euglena gracilis. Mol Biol Evol. 2020:37:2173–2191. 10.1093/molbev/msaa061. PubMed DOI PMC
Hashimi H. A parasite's take on the evolutionary cell biology of MICOS. PLoS Pathog. 2019:15:e1008166. 10.1371/journal.ppat.1008166. PubMed DOI PMC
Hessenberger M et al. Regulated membrane remodeling by Mic60 controls formation of mitochondrial crista junctions. Nat Commun. 2017:8:15258. 10.1038/ncomms15258. PubMed DOI PMC
Hirumi H, Hirumi K. Continuous cultivation of trypanosoma brucei blood stream forms in a medium containing a low concentration of serum protein without feeder cell layers. J Parasitol. 1989:75:985–989. 10.2307/3282883. PubMed DOI
Horvath SE, Daum G. Lipids of mitochondria. Prog Lipid Res. 2013:52:590–614. 10.1016/j.plipres.2013.07.002. PubMed DOI
Huerta-Cepas J, Serra F, Bork P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 2016:33:1635–1638. 10.1093/molbev/msw046. PubMed DOI PMC
Hughes L, Borrett S, Towers K, Starborg T, Vaughan S. Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy. J Cell Sci. 2017:130:637–647. 10.1242/jcs.198887. PubMed DOI
Huynen MA, Muhlmeister M, Gotthardt K, Guerrero-Castillo S, Brandt U. Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex. Biochim Biophys Acta. 2016:1863:91–101. 10.1016/j.bbamcr.2015.10.009. PubMed DOI
Jakob M et al. Mitochondrial growth during the cell cycle of PubMed DOI PMC
Johnston HE et al. Solvent precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads. Anal Chem. 2022:94:10320–10328. 10.1021/acs.analchem.1c04200. PubMed DOI PMC
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019:20:1160–1166. 10.1093/bib/bbx108. PubMed DOI PMC
Kaurov I et al. The essential cysteines in the CIPC motif of the thioredoxin-like trypanosoma brucei MICOS subunit TbMic20 do not form an intramolecular disulfide bridge in vivo. Mol Biochem Parasitol. 2022:248:111463. 10.1016/j.molbiopara.2022.111463. PubMed DOI
Kaurov I et al. The diverged trypanosome MICOS complex as a hub for mitochondrial cristae shaping and protein import. Curr Biol. 2018:28:3393–3407.e5. 10.1016/j.cub.2018.09.008. PubMed DOI
Kostygov AY et al. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol. 2021:11:200407. 10.1098/rsob.200407. PubMed DOI PMC
Kroppen B et al. Cooperativity of membrane-protein and protein–protein interactions control membrane remodeling by epsin 1 and affects clathrin-mediated endocytosis. Cell Mol Life Sci. 2021:78:2355–2370. 10.1007/s00018-020-03647-z. PubMed DOI PMC
Kühlbrandt W. Structure and mechanisms of F-type ATP synthases. Annu Rev Biochem. 2019:88:515–549. 10.1146/annurev-biochem-013118-110903. PubMed DOI
Lax G et al. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogen Evol. 2021:159:107088. 10.1016/j.ympev.2021.107088. PubMed DOI
Letunic I, Bork P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024:52:W78–W82. 10.1093/nar/gkae268. PubMed DOI PMC
Mastronarde DN, Held SR. Automated tilt series alignment and tomographic reconstruction in IMOD. J Struct Biol. 2017:197:102–113. 10.1016/j.jsb.2016.07.011. PubMed DOI PMC
Meng EC et al. UCSF chimeraX: tools for structure building and analysis. Protein Sci. 2023:32:e4792. 10.1002/pro.4792. PubMed DOI PMC
Michaud M et al. Atmic60 is involved in plant mitochondria lipid trafficking and is part of a large complex. Curr Biol. 2016:26:627–639. 10.1016/j.cub.2016.01.011. PubMed DOI PMC
Miroux B, Walker JE. Over-production of proteins in PubMed DOI
Mordas A, Tokatlidis K. The MIA pathway: a key regulator of mitochondrial oxidative protein folding and biogenesis. Acc Chem Res. 2015:48:2191–2199. 10.1021/acs.accounts.5b00150. PubMed DOI PMC
Muñoz-Gómez SA et al. Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr Biol. 2023:33:1099–1111.e6. 10.1016/j.cub.2023.02.059. PubMed DOI
Muñoz-Gómez SA et al. Ancient homology of the mitochondrial contact site and cristae organizing system points to an endosymbiotic origin of mitochondrial cristae. Curr Biol. 2015:25:1489–1495. 10.1016/j.cub.2015.04.006. PubMed DOI
Muñoz-Gomez SA, Wideman JG, Roger AJ, Slamovits CH. The origin of mitochondrial cristae from alphaproteobacteria. Mol Biol Evol. 2017:34:943–956. 10.1093/molbev/msw298. PubMed DOI
Niemann M et al. Mitochondrial outer membrane proteome of trypanosoma brucei reveals novel factors required to maintain mitochondrial morphology. Mol Cell Proteom. 2013:12:515–528. 10.1074/mcp.M112.023093. PubMed DOI PMC
Pánek T, Eliáš M, Vancová M, Lukeš J, Hashimi H. Returning to the fold for lessons in mitochondrial Crista diversity and evolution. Curr Biol. 2020:30:R575–R588. 10.1016/j.cub.2020.02.053. PubMed DOI
Peikert CD et al. Charting organellar importomes by quantitative mass spectrometry. Nat Commun. 2017:8:15272. 10.1038/ncomms15272. PubMed DOI PMC
Poon SK, Peacock L, Gibson W, Gull K, Kelly S. A modular and optimized single marker system for generating PubMed DOI PMC
Prokopchuk G et al. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc. 2023:98:1910–1927. 10.1111/brv.12988. PubMed DOI PMC
Rabl R et al. Formation of cristae and crista junctions in mitochondria depends on antagonism between Fcj1 and su PubMed DOI PMC
Rampelt H et al. Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth. Cell Rep. 2022:38:110290. 10.1016/j.celrep.2021.110290. PubMed DOI PMC
Richter DJ et al. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. 10.24072/pcjournal.173. DOI
Roger AJ, Munoz-Gomez SA, Kamikawa R. The origin and diversification of mitochondria. Curr Biol. 2017:27:R1177–R1192. 10.1016/j.cub.2017.09.015. PubMed DOI
Schindelin J et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012:9:676–682. 10.1038/nmeth.2019. PubMed DOI PMC
Smith JT, Singha UK, Misra S, Chaudhuri M. Divergent small tim homologues are associated with TbTim17 and critical for the biogenesis of TbTim17 protein complexes in PubMed DOI PMC
Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005:33:W244–W248. 10.1093/nar/gki408. PubMed DOI PMC
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014:30:1312–1313. 10.1093/bioinformatics/btu033. PubMed DOI PMC
Stephan T et al. MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO J. 2020:39:e104105. 10.15252/embj.2019104105. PubMed DOI PMC
Tarasenko D et al. The MICOS component Mic60 displays a conserved membrane-bending activity that is necessary for normal cristae morphology. J Cell Biol. 2017:216:889–899. 10.1083/jcb.201609046. PubMed DOI PMC
Turra GL et al. PubMed DOI PMC
Van Laar VS, Berman SB, Hastings TG. Mic60/mitofilin overexpression alters mitochondrial dynamics and attenuates vulnerability of dopaminergic cells to dopamine and rotenone. Neurobiol Dis. 2016:91:247–261. 10.1016/j.nbd.2016.03.015. PubMed DOI PMC
Varabyova A et al. Mia40 and MINOS act in parallel with Ccs1 in the biogenesis of mitochondrial Sod1. FEBS J. 2013:280:4943–4959. 10.1111/febs.12409. PubMed DOI
von der Malsburg K et al. Dual role of mitofilin in mitochondrial membrane organization and protein biogenesis. Dev Cell. 2011:21:694–707. 10.1016/j.devcel.2011.08.026. PubMed DOI
Wenger C, Oeljeklaus S, Warscheid B, Schneider A, Harsman A. A trypanosomal orthologue of an intermembrane space chaperone has a non-canonical function in biogenesis of the single mitochondrial inner membrane protein translocase. PLoS Pathog. 2017:13:e1006550. 10.1371/journal.ppat.1006550. PubMed DOI PMC
Wheeler RJ. A resource for improved predictions of trypanosoma and leishmania protein three-dimensional structure. PLoS One. 2021:16:e0259871. 10.1371/journal.pone.0259871. PubMed DOI PMC
Zíková A. Mitochondrial adaptations throughout the PubMed DOI