Core mitochondrial processes such as the electron transport chain, protein translation and the formation of Fe-S clusters (ISC) are of prokaryotic origin and were present in the bacterial ancestor of mitochondria. In animal and fungal models, a family of small Leu-Tyr-Arg motif-containing proteins (LYRMs) uniformly regulates the function of mitochondrial complexes involved in these processes. The action of LYRMs is contingent upon their binding to the acylated form of acyl carrier protein (ACP). This study demonstrates that LYRMs are structurally and evolutionarily related proteins characterized by a core triplet of α-helices. Their widespread distribution across eukaryotes suggests that 12 specialized LYRMs were likely present in the last eukaryotic common ancestor to regulate the assembly and folding of the subunits that are conserved in bacteria but that lack LYRM homologues. The secondary reduction of mitochondria to anoxic environments has rendered the function of LYRMs and their interaction with acylated ACP dispensable. Consequently, these findings strongly suggest that early eukaryotes installed LYRMs in aerobic mitochondria as orchestrated switches, essential for regulating core metabolism and ATP production.

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec 252 50 Czech Republic

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Angerer H. 2015. Eukaryotic LYR proteins interact with mitochondrial protein complexes. Biology (Basel) 4 , 133–150. (10.3390/biology4010133) PubMed DOI PMC

Angerer H, Radermacher M, Mańkowska M, Steger M, Zwicker K, Heide H, Wittig I, Brandt U, Zickermann V. 2014. The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity. Proc. Natl Acad. Sci. USA 111 , 5207–5212. (10.1073/pnas.1322438111) PubMed DOI PMC

Dibley MG, et al. . 2020. The mitochondrial acyl-carrier protein interaction network highlights important roles for LYRM family members in complex I and Mitoribosome Assembly. Mol. Cell. Proteomics 19 , 65–77. (10.1074/mcp.RA119.001784) PubMed DOI PMC

Maio N, Singh A, Uhrigshardt H, Saxena N, Tong WH, Rouault TA. 2014. Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster delivery. Cell Metab. 19 , 445–457. (10.1016/j.cmet.2014.01.015) PubMed DOI PMC

Wiedemann N, et al. . 2006. Essential role of Isd11 in mitochondrial iron-sulfur cluster synthesis on Isu scaffold proteins. EMBO J. 25 , 184–195. (10.1038/sj.emboj.7600906) PubMed DOI PMC

Masud AJ, Kastaniotis AJ, Rahman MT, Autio KJ, Hiltunen JK. 2019. Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function. Biochimica et Biophysica Acta (BBA)—Mol. Cell Res. 1866 , 118540. (10.1016/j.bbamcr.2019.118540) PubMed DOI

Herrera MG, Noguera ME, Sewell KE, Agudelo Suárez WA, Capece L, Klinke S, Santos J. 2019. Structure of the human ACP-ISD11 Heterodimer. Biochemistry 58 , 4596–4609. (10.1021/acs.biochem.9b00539) PubMed DOI

Van Vranken JG, et al. . 2018. ACP acylation is an Acetyl-CoA-dependent modification required for electron transport chain assembly. Mol. Cell 71 , 567–580. (10.1016/j.molcel.2018.06.039) PubMed DOI PMC

Cao XG, et al. . 2010. Overexpression of LYRM1 induces mitochondrial impairment in 3T3-L1 adipocytes. Mol. Genet. Metab. 101 , 395–399. (10.1016/j.ymgme.2010.08.010) PubMed DOI

Haack TB, et al. . 2012. Mutation screening of 75 candidate genes in 152 complex I deficiency cases identifies pathogenic variants in 16 genes including NDUFB9. J. Med. Genet. 49 , 83–89. (10.1136/jmedgenet-2011-100577) PubMed DOI

Invernizzi F, Tigano M, Dallabona C, Donnini C, Ferrero I, Cremonte M, Ghezzi D, Lamperti C, Zeviani M. 2013. A homozygous mutation in LYRM7/MZM1L associated with early onset encephalopathy, lactic acidosis, and severe reduction of mitochondrial complex III activity. Hum. Mutat. 34 , 1619–1622. (10.1002/humu.22441) PubMed DOI PMC

Hess DC, et al. . 2009. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 5 , e1000407. (10.1371/journal.pgen.1000407) PubMed DOI PMC

Richter DJ, Berney C, Strassert JFH, Poh YP, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. 2022. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Commun. J. 2 . (10.24072/pcjournal.173) DOI

The UniProt Consortium . 2013. UniProt: the Universal protein knowledgebase in 2023. Nucleic Acids Res 1 , 13–14. (10.1093/nar/gkaa1100) PubMed DOI PMC

Roger AJ, Muñoz-Gómez SA, Kamikawa R. 2017. The origin and diversification of mitochondria. Curr. Biol. 27 , R1177–R1192. (10.1016/j.cub.2017.09.015) PubMed DOI

Freibert SA, et al. . 2017. Evolutionary conservation and in vitro reconstitution of microsporidian iron-sulfur cluster biosynthesis. Nat. Commun. 8 , 13932. (10.1038/ncomms13932) PubMed DOI PMC

Motyčková A, et al. . 2023. Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis. PLoS Pathog. 19 , e1010773. (10.1371/journal.ppat.1010773) PubMed DOI PMC

Tachezy J, Doležal P. 2007. Iron-sulfur proteins and iron-sulfur cluster assembly in organisms with Hydrogenosomes and Mitosomes. In Origin of mitochondria and Hydrogenosomes (eds Martin WF, Müller M), pp. 105–133. Heidelberg, Germany: Springer. (10.1007/978-3-540-38502-8) DOI

Cory SA, Van Vranken JG, Brignole EJ, Patra S, Winge DR, Drennan CL, Rutter J, Barondeau DP. 2017. Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions. Proc. Natl Acad. Sci. USA 114 , E5325–E5334. (10.1073/pnas.1702849114) PubMed DOI PMC

Evers F, Cabrera-Orefice A, Elurbe DM, Kea-Te Lindert M, Boltryk SD, Voss TS, Huynen MA, Brandt U, Kooij TWA. 2021. Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum. Nat. Commun. 12 , 1–17. (10.1038/s41467-021-23919-x) PubMed DOI PMC

Seidi A, et al. . 2018. Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase. Elife 7 , e38131. (10.7554/eLife.38131) PubMed DOI PMC

Ivanova A, Gill-Hille M, Huang S, Branca RM, Kmiec B, Teixeira PF, Lehtiö J, Whelan J, Murcha MW. 2019. A mitochondrial LYR protein is required for complex I assembly. Plant Physiol. 181 , 1632–1650. (10.1104/pp.19.00822) PubMed DOI PMC

Illergård K, Ardell DH, Elofsson A. 2009. Structure is three to ten times more conserved than sequence—a study of structural response in protein cores. Proteins 77 , 499–508. (10.1002/prot.22458) PubMed DOI

Söding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 , 951–960. (10.1093/bioinformatics/bti125) PubMed DOI

Jumper J, et al. . 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596 , 583–589. (10.1038/s41586-021-03819-2) PubMed DOI PMC

Jiménez-Moreno A, Střelák D, Filipovič J, Carazo JM, Sorzano COS. 2021. DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM. J. Struct. Biol. 213 , 107712. (10.1016/j.jsb.2021.107712) PubMed DOI

van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, Söding J, Steinegger M. 2024. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42 , 243–246. (10.1038/s41587-023-01773-0) PubMed DOI PMC

Braymer JJ, Lill R. 2017. Iron-sulfur cluster biogenesis and trafficking in mitochondria. J. Biol. Chem. 292 , 12754–12763. (10.1074/jbc.R117.787101) PubMed DOI PMC

Richards TA, van der Giezen M. 2006. Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes. Mol. Biol. Evol. 23 , 1341–1344. (10.1093/molbev/msl001) PubMed DOI

Tsaousis AD. 2019. On the origin of iron/sulfur cluster biosynthesis in eukaryotes. Front. Microbiol. 10 , 2478. (10.3389/fmicb.2019.02478) PubMed DOI PMC

Cui TZ, Smith PM, Fox JL, Khalimonchuk O, Winge DR. 2012. Late-stage maturation of the Rieske Fe/S protein: Mzm1 stabilizes Rip1 but does not facilitate its translocation by the AAA ATPase Bcs1. Mol. Cell. Biol. 32 , 4400–4409. (10.1128/MCB.00441-12) PubMed DOI PMC

Sánchez E, Lobo T, Fox JL, Zeviani M, Winge DR, Fernández-Vizarra E. 2013. LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last steps of mitochondrial complex III assembly in human cells. Biochim. Biophys. Acta 1827 , 285–293. (10.1016/j.bbabio.2012.11.003) PubMed DOI PMC

Maio N, Kim KS, Singh A, Rouault TA. 2017. A single adaptable cochaperone-scaffold complex delivers nascent iron-sulfur clusters to mammalian respiratory chain complexes I-III. Cell Metab. 25 , 945–953. (10.1016/j.cmet.2017.03.010) PubMed DOI

Galemou Yoga E, Parey K, Djurabekova A, Haapanen O, Siegmund K, Zwicker K, Sharma V, Zickermann V, Angerer H. 2020. Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Nat. Commun 11 , 1–8. (10.1038/s41467-020-19778-7) PubMed DOI PMC

Zhu J, Vinothkumar KR, Hirst J. 2016. Structure of mammalian respiratory complex I. Nature 536 , 354–358. (10.1038/nature19095) PubMed DOI PMC

Huang Q, et al. . 2019. LYRM2 directly regulates complex I activity to support tumor growth in colorectal cancer by oxidative phosphorylation. Cancer Lett. 455 , 36–47. (10.1016/j.canlet.2019.04.021) PubMed DOI

Na U, Yu W, Cox J, Bricker DK, Brockmann K, Rutter J, Thummel CS, Winge DR. 2014. The LYR factors SDHAF1 and SDHAF3 mediate maturation of the iron-sulfur subunit of succinate dehydrogenase. Cell Metab. 20 , 253–266. (10.1016/j.cmet.2014.05.014) PubMed DOI PMC

Lefebvre-Legendre L, Vaillier J, Benabdelhak H, Velours J, Slonimski PP, di Rago JP. 2001. Identification of a nuclear gene (FMC1) required for the assembly/stability of yeast mitochondrial F(1)-ATPase in heat stress conditions. J. Biol. Chem. 276 , 6789–6796. (10.1074/jbc.M009557200) PubMed DOI

Li Y, Jourdain AA, Calvo SE, Liu JS, Mootha VK. 2017. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PLoS Comput. Biol. 13 , e1005653. (10.1371/journal.pcbi.1005653) PubMed DOI PMC

Wang ZG, Sheluho D, Gatti DL, Ackerman SH. 2000. The alpha-subunit of the mitochondrial F(1) ATPase interacts directly with the assembly factor Atp12p. EMBO J. 19 , 1486–1493. (10.1093/emboj/19.7.1486) PubMed DOI PMC

Floyd BJ, et al. . 2016. Mitochondrial protein interaction mapping identifies regulators of respiratory chain function. Mol. Cell 63 , 621–632. (10.1016/j.molcel.2016.06.033) PubMed DOI PMC

Henriques BJ, Katrine Jentoft Olsen R, Gomes CM, Bross P. 2021. Electron transfer flavoprotein and its role in mitochondrial energy metabolism in health and disease. Gene 776 , 145407. (10.1016/j.gene.2021.145407) PubMed DOI PMC

Brown A, Rathore S, Kimanius D, Aibara S, Bai X chen, Rorbach J, Amunts A, Ramakrishnan V. 2017. Structures of the human mitochondrial ribosome in native states of assembly. Nat. Struct. Mol. Biol. 24 , 866–869. (10.1038/nsmb.3464) PubMed DOI PMC

Pei J, Zhang J, Cong Q. 2022. Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. Bioinformatics 38 , 4301–4311. (10.1093/bioinformatics/btac527) PubMed DOI

Soleimanpour-Lichaei HR, et al. . 2007. mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG. Mol. Cell 27 , 745–757. (10.1016/j.molcel.2007.06.031) PubMed DOI PMC

Koumandou VL, Wickstead B, Ginger ML, van der Giezen M, Dacks JB, Field MC. 2013. Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48 , 373–396. (10.3109/10409238.2013.821444) PubMed DOI PMC

Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJG. 2018. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557 , 101–105. (10.1038/s41586-018-0059-5) PubMed DOI

Muñoz-Gómez SA, Susko E, Williamson K, Eme L, Slamovits CH, Moreira D, López-García P, Roger AJ. 2022. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. 6 , 253–262. (10.1038/s41559-021-01638-2) PubMed DOI

Spang A, Stairs CW, Dombrowski N, Eme L, Lombard J, Caceres EF, Greening C, Baker BJ, Ettema TJG. 2019. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4 , 1138–1148. (10.1038/s41564-019-0406-9) PubMed DOI

Zaremba-Niedzwiedzka K, et al. . 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541 , 353–358. (10.1038/nature21031) PubMed DOI

Enright AJ, Ouzounis CA. 2001. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2 , 1–7. (10.1186/gb-2001-2-9-research0034) PubMed DOI PMC

Boniecki MT, Freibert SA, Mühlenhoff U, Lill R, Cygler M. 2017. Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat. Commun. 8 , 1287. (10.1038/s41467-017-01497-1) PubMed DOI PMC

Szklarczyk D, et al. . 2021. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49 , 605–612. (10.1093/nar/gkaa1074) PubMed DOI PMC

Agrawal RK, Sharma MR, Yassin A, Lahiri I, Spremulli inda L. 2011. Structure and function of Organellar Ribosomes as revealed by Cryo-EM BT–Ribosomes: structure, function, and dynamics, pp. 83–96. Vienna, Austria: Springer.

Parey K, Wirth C, Vonck J, Zickermann V. 2020. Respiratory complex I—structure, mechanism and evolution. Curr. Opin. Struct. Biol. 63 , 1–9. (10.1016/j.sbi.2020.01.004) PubMed DOI

Yan R, Friemel M, Aloisi C, Huynen M, Taylor IA, Leimkühler S, Pastore A. 2016. The eukaryotic-specific ISD11 Is a complex-orphan protein with ability to bind the prokaryotic IscS. PLoS One 11 , e0157895. (10.1371/journal.pone.0157895) PubMed DOI PMC

Angerer H. 2013. The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins. Biochem. Soc. Trans. 41 , 1335–1341. (10.1042/BST20130116) PubMed DOI

Falekun S, Sepulveda J, Jami-Alahmadi Y, Park H, Wohlschlegel JA, Sigala PA. 2021. Divergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasites. Elife 10 , e71636. (10.7554/eLife.71636) PubMed DOI PMC

Cronan JE, Fearnley IM, Walker JE. 2005. Mammalian mitochondria contain a soluble acyl carrier protein. FEBS Lett. 579 , 4892–4896. (10.1016/j.febslet.2005.07.077) PubMed DOI

Burger G, Gray MW, Forget L, Lang BF. 2013. Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol. Evol. 5 , 418–438. (10.1093/gbe/evt008) PubMed DOI PMC

Gray MW, et al. . 2020. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol. 18 , 22. (10.1186/s12915-020-0741-6) PubMed DOI PMC

Horváthová L, et al. . 2021. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat. Commun. 12 , 2947. (10.1038/s41467-021-23046-7) PubMed DOI PMC

Petrů M, Wideman J, Moore K, Alcock F, Palmer T, Doležal P. 2018. Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria. BMC Biol. 16 , 141. (10.1186/s12915-018-0607-3) PubMed DOI PMC

Angerer H, et al. . 2017. Acyl modification and binding of mitochondrial ACP to multiprotein complexes. Biochim. Biophys. Acta Mol. Cell Res. 1864 , 1913–1920. (10.1016/j.bbamcr.2017.08.006) PubMed DOI

Kursu VAS, et al. . 2013. Defects in mitochondrial fatty acid synthesis result in failure of multiple aspects of mitochondrial biogenesis in Saccharomyces cerevisiae. Mol. Microbiol. 90 , 824–840. (10.1111/mmi.12402) PubMed DOI PMC

Nowinski SM, Van Vranken JG, Dove KK, Rutter J. 2018. Impact of mitochondrial fatty acid synthesis on mitochondrial biogenesis. Curr. Biol. 28 , 1212–1219. (10.1016/j.cub.2018.08.022) PubMed DOI PMC

Okuno D, Iino R, Noji H. 2011. Rotation and structure of FoF1-ATP synthase. J. Biochem. 149 , 655–664. (10.1093/jb/mvr049) PubMed DOI

Shears MJ, Botté CY, McFadden GI. 2015. Fatty acid metabolism in the plasmodium apicoplast: drugs, doubts and knockouts. Mol. Biochem. Parasitol. 199 , 34–50. (10.1016/j.molbiopara.2015.03.004) PubMed DOI

Martincová E, Voleman L, Pyrih J, Žárský V, Vondráčková P, Kolísko M, Tachezy J, Doležal P. 2015. Probing the biology of Giardia intestinalis mitosomes using in vivo enzymatic tagging. Mol. Cell. Biol. 35 , 2864–2874. (10.1128/MCB.00448-15) PubMed DOI PMC

Tovar J, León-Avila G, Sánchez LB, Sutak R, Tachezy J, van der Giezen M, Hernández M, Müller M, Lucocq JM. 2003. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 426 , 172–176. (10.1038/nature01945) PubMed DOI

Itoh Y, Singh V, Khawaja A, Naschberger A, Nguyen MD, Rorbach J, Amunts A. 2022. Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. Elife 11 , e77460. (10.7554/eLife.77460) PubMed DOI PMC

UniProt Consortium . 2021. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49 , D480–D489. (10.1093/nar/gkaa1100) PubMed DOI PMC

Richter DJ, Berney C, Strassert JFH, Poh YP, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community Journal 2 . (10.24072/pcjournal.173) DOI

Mistry J, et al. . 2021. Pfam: The protein families database in 2021. Nucleic Acids Res. 49 , D412–D419. (10.1093/nar/gkaa913) PubMed DOI PMC

Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39 , W29–37. (10.1093/nar/gkr367) PubMed DOI PMC

Katoh K, Misawa K, Kuma K ichi, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 , 3059–3066. (10.1093/nar/gkf436) PubMed DOI PMC

Likic VA, Dolezal P, Celik N, Dagley M, Lithgow T. 2010. Using hidden Markov models to discover new protein transport machines. Methods Mol. Biol. 619 , 271–284. (10.1007/978-1-60327-412-8_16) PubMed DOI

Blum M, et al. . 2021. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49 , D344–D354. (10.1093/nar/gkaa977) PubMed DOI PMC

Zimmermann L, et al. . 2018. A completely reimplemented MPI bioinformatics toolkit with A new HHpred server at its core. J. Mol. Biol. 430 , 2237–2243. (10.1016/j.jmb.2017.12.007) PubMed DOI

Krivák R, Hoksza D. 2018. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J. Cheminform. 10 , 39. (10.1186/s13321-018-0285-8) PubMed DOI PMC

Eberhardt J, Santos-Martins D, Tillack AF, Forli S. 2021. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model. 61 , 3891–3898. (10.1021/acs.jcim.1c00203) PubMed DOI PMC

Trott O, Olson AJ. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 , 455–461. (10.1002/jcc.21334) PubMed DOI PMC

Dohnálek V, Dolezal P. 2024. Supplementary material from: Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion. Figshare. (10.6084/m9.figshare.c.7214460) PubMed DOI PMC

Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion