{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:59:47Z","timestamp":1790704787794,"version":"4.1.0"},"reference-count":100,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["221681\/Z\/20\/Z"],"award-info":[{"award-number":["221681\/Z\/20\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204820\/Z\/16\/Z"],"award-info":[{"award-number":["204820\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["UKRI\/MR\/B000325\/1"],"award-info":[{"award-number":["UKRI\/MR\/B000325\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Czech Science Foundation","award":["23-06479X"],"award-info":[{"award-number":["23-06479X"]}],"id":[{"id":"https:\/\/ror.org\/01pv73b02","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["217173\/Z\/19\/Z"],"award-info":[{"award-number":["217173\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["310879\/Z\/24\/Z"],"award-info":[{"award-number":["310879\/Z\/24\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Mitochondrial complexes, such as the mitochondrial electron transport chain (mETC), the F\n                    <jats:sub>1<\/jats:sub>\n                    F\n                    <jats:sub>o<\/jats:sub>\n                    -ATP synthase, the mitochondrial ribosome and the Translocase of the Outer Membrane (TOM) complex are centrally important for mitochondrial function and cell survival. Recently, an unexpected diversity in the composition of these complexes across unicellular eukaryotic lineages, with the apicomplexan parasites featuring prominently, has been revealed. However, whether the observed enlarged and divergent mitochondrial complexes are conserved across the wider lineages has not been investigated. Here, using a complexome profiling proteomic approach, we have characterised the composition of the mitochondrial complexes of the myzozoan parasite of oysters,\n                    <jats:italic>Perkinsus marinus<\/jats:italic>\n                    . We show that it shares new components of ATP synthase and the mETC complexes that in the deadly apicomplexan\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    and\n                    <jats:italic>Toxoplasma<\/jats:italic>\n                    were shown to be important for growth. Moreover, the\n                    <jats:italic>Perkinsus<\/jats:italic>\n                    mitoribosome possesses many of the divergent features recently discovered in apicomplexans, including members of the ApiAP2 family that until recently were all considered to be transcription factors. Our study reveals that the divergent subunit composition of mitochondrial complexes is an ancestral and highly conserved feature of Myzozoa.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1014543","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:21:52Z","timestamp":1790702512000},"page":"e1014543","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Complexome profiling of mitochondria in the myzozoan parasite of oysters, Perkinsus marinus"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9274-9486","authenticated-orcid":true,"given":"Andrew E.","family":"Maclean","sequence":"first","affiliation":[{"name":"University of Edinburgh","place":["Edinburgh, United Kingdom"],"department":["Institute of Immunology and Infection Research"]},{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["Centre for Parasitology"]},{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["School of Infection and Immunity"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orsola","family":"Iorillo","sequence":"additional","affiliation":[{"name":"Czech Academy of Sciences","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Institute of Parasitology, Biology Centre"]},{"name":"University of South Bohemia","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Drahom\u00edra","family":"Faktorov\u00e1","sequence":"additional","affiliation":[{"name":"Czech Academy of Sciences","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Institute of Parasitology, Biology Centre"]},{"name":"University of South Bohemia","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Singh","sequence":"additional","affiliation":[{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["Centre for Parasitology"]},{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["School of Infection and Immunity"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne","family":"McGill","sequence":"additional","affiliation":[{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["College of Medical, Veterinary & Life Sciences Shared Research Facilities"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julius","family":"Luke\u0161","sequence":"additional","affiliation":[{"name":"Czech Academy of Sciences","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Institute of Parasitology, Biology Centre"]},{"name":"University of South Bohemia","place":["\u010cesk\u00e9 Bud\u011bjovice, Czech Republic"],"department":["Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilach","family":"Sheiner","sequence":"additional","affiliation":[{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["Centre for Parasitology"]},{"name":"University of Glasgow","place":["Glasgow, United Kingdom"],"department":["School of Infection and Immunity"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"ppat.1014543.ref001","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2017.09.015","article-title":"The Origin and Diversification of Mitochondria","volume":"27","author":"AJ Roger","year":"2017","journal-title":"Curr Biol"},{"key":"ppat.1014543.ref002","doi-asserted-by":"crossref","first-page":"111204","DOI":"10.1016\/j.molbiopara.2019.111204","article-title":"Same same, but different: Uncovering unique features of the mitochondrial respiratory chain of apicomplexans","volume":"232","author":"JA Hayward","year":"2019","journal-title":"Mol Biochem Parasitol"},{"issue":"12","key":"ppat.1014543.ref003","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1016\/j.pt.2022.09.008","article-title":"The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain","volume":"38","author":"AE Maclean","year":"2022","journal-title":"Trends Parasitol"},{"issue":"4","key":"ppat.1014543.ref004","doi-asserted-by":"crossref","DOI":"10.1128\/mmbr.00197-22","article-title":"Adaptations and metabolic evolution of myzozoan protists across diverse lifestyles and environments","volume":"88","author":"RF Waller","year":"2024","journal-title":"Microbiol Mol Biol Rev"},{"issue":"5","key":"ppat.1014543.ref005","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/molbev\/msv021","article-title":"Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites","volume":"32","author":"P Flegontov","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"4","key":"ppat.1014543.ref006","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1051\/alr:2004050","article-title":"Perkinsosis in molluscs: A review","volume":"17","author":"A Villalba","year":"2004","journal-title":"Aquat Living Resour"},{"issue":"13","key":"ppat.1014543.ref007","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2021.04.028","article-title":"Parallel functional reduction in the mitochondria of apicomplexan parasites","volume":"31","author":"V Mathur","year":"2021","journal-title":"Curr Biol"},{"issue":"1","key":"ppat.1014543.ref008","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s12915-021-01007-2","article-title":"Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans","volume":"19","author":"ED Salomaki","year":"2021","journal-title":"BMC Biol"},{"issue":"8","key":"ppat.1014543.ref009","doi-asserted-by":"crossref","first-page":"1424","DOI":"10.1038\/s41594-025-01531-7","article-title":"Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex","volume":"32","author":"AE MacLean","year":"2025","journal-title":"Nat Struct Mol Biol"},{"issue":"3","key":"ppat.1014543.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009301","article-title":"Complexome profile of Toxoplasma gondii mitochondria identifies divergent subunits of respiratory chain complexes including new subunits of cytochrome bc1 complex","volume":"17","author":"AE Maclean","year":"2021","journal-title":"PLoS Pathog"},{"issue":"1","key":"ppat.1014543.ref011","doi-asserted-by":"crossref","first-page":"3820","DOI":"10.1038\/s41467-021-23919-x","article-title":"Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum","volume":"12","author":"F Evers","year":"2021","journal-title":"Nat Commun"},{"issue":"6","key":"ppat.1014543.ref012","doi-asserted-by":"crossref","first-page":"230463","DOI":"10.1098\/rsob.230463","article-title":"A myzozoan-specific protein is an essential membrane-anchoring component of the succinate dehydrogenase complex in Toxoplasma parasites","volume":"14","author":"SM Zwahlen","year":"2024","journal-title":"Open Biol"},{"issue":"12","key":"ppat.1014543.ref013","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011867","article-title":"Functional and biochemical characterization of the Toxoplasma gondii succinate dehydrogenase complex","volume":"19","author":"MF Silva","year":"2023","journal-title":"PLoS Pathog"},{"issue":"2","key":"ppat.1014543.ref014","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009211","article-title":"Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites","volume":"17","author":"JA Hayward","year":"2021","journal-title":"PLoS Pathog"},{"key":"ppat.1014543.ref015","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.38131","article-title":"Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase","volume":"7","author":"A Seidi","year":"2018","journal-title":"Elife"},{"issue":"1","key":"ppat.1014543.ref016","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3390\/genes10010029","article-title":"Novel Characteristics of Mitochondrial Electron Transport Chain from Eimeria tenella","volume":"10","author":"M Matsubayashi","year":"2019","journal-title":"Genes (Basel)"},{"issue":"1","key":"ppat.1014543.ref017","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41467-020-20381-z","article-title":"ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria","volume":"12","author":"A M\u00fchleip","year":"2021","journal-title":"Nat Commun"},{"key":"ppat.1014543.ref018","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.38097","article-title":"Identification of cryptic subunits from an apicomplexan ATP synthase","volume":"7","author":"D Huet","year":"2018","journal-title":"Elife"},{"issue":"7","key":"ppat.1014543.ref019","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2006128","article-title":"Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii","volume":"16","author":"R Salunke","year":"2018","journal-title":"PLoS Biol"},{"key":"ppat.1014543.ref020","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev-micro-091014-104449","article-title":"The Organellar Genomes of Chromera and Vitrella, the Phototrophic Relatives of Apicomplexan Parasites","volume":"69","author":"M Oborn\u00edk","year":"2015","journal-title":"Annu Rev Microbiol"},{"issue":"5","key":"ppat.1014543.ref021","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1101\/gr.266403.120","article-title":"A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia","volume":"31","author":"S Namasivayam","year":"2021","journal-title":"Genome Res"},{"key":"ppat.1014543.ref022","doi-asserted-by":"crossref","first-page":"751775","DOI":"10.3389\/fmicb.2021.751775","article-title":"The elusive mitochondrial genomes of apicomplexa: where are we now?","volume":"12","author":"L Bern\u00e1","year":"2021","journal-title":"Front Microbiol"},{"issue":"1","key":"ppat.1014543.ref023","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1038\/s41467-025-56057-9","article-title":"Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements","volume":"16","author":"S Shikha","year":"2025","journal-title":"Nat Commun"},{"issue":"1","key":"ppat.1014543.ref024","doi-asserted-by":"crossref","first-page":"10689","DOI":"10.1038\/s41467-024-55033-z","article-title":"Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine","volume":"15","author":"C Wang","year":"2024","journal-title":"Nat Commun"},{"issue":"10","key":"ppat.1014543.ref025","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac191","article-title":"Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes","volume":"39","author":"SG Gornik","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"4","key":"ppat.1014543.ref026","doi-asserted-by":"crossref","first-page":"125830","DOI":"10.1016\/j.protis.2021.125830","article-title":"Development of the Myzozoan Aquatic Parasite Perkinsus marinus as A Versatile Experimental Genetic Model Organism","volume":"172","author":"E Einarsson","year":"2021","journal-title":"Protist"},{"issue":"4","key":"ppat.1014543.ref027","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1016\/j.cmet.2012.08.009","article-title":"Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly complex","volume":"16","author":"H Heide","year":"2012","journal-title":"Cell Metab"},{"key":"ppat.1014543.ref028","doi-asserted-by":"crossref","first-page":"796128","DOI":"10.3389\/fcell.2021.796128","article-title":"Complexome profiling - exploring mitochondrial protein complexes in health and disease","volume":"9","author":"A Cabrera-Orefice","year":"2021","journal-title":"Front Cell Dev Biol"},{"issue":"15","key":"ppat.1014543.ref029","doi-asserted-by":"crossref","first-page":"7809","DOI":"10.3390\/ijms22157809","article-title":"Complexome Profiling: Assembly and Remodeling of Protein Complexes","volume":"22","author":"I Wittig","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"48","key":"ppat.1014543.ref030","doi-asserted-by":"crossref","first-page":"41312","DOI":"10.1074\/jbc.M111.290973","article-title":"ATP synthase complex of Plasmodium falciparum: dimeric assembly in mitochondrial membranes and resistance to genetic disruption","volume":"286","author":"PB Nina","year":"2011","journal-title":"J Biol Chem"},{"issue":"1","key":"ppat.1014543.ref031","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.molbiopara.2007.09.007","article-title":"Transfection of the protozoan parasite Perkinsus marinus","volume":"157","author":"JA Fern\u00e1ndez-Robledo","year":"2008","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1014543.ref032","article-title":"Structure of the II2-III2-IV2 mitochondrial supercomplex from the parasite Perkinsus marinus","author":"F W\u00fa","year":"2024"},{"key":"ppat.1014543.ref033","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/978-1-0716-1653-6_9","article-title":"Complexome Profiling of Plant Mitochondrial Fractions","volume":"2363","author":"L Schr\u00f6der","year":"2022","journal-title":"Methods Mol Biol"},{"key":"ppat.1014543.ref034","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/978-1-0716-0834-0_19","article-title":"Mitochondrial Complexome Profiling","volume":"2192","author":"H Giese","year":"2021","journal-title":"Methods Mol Biol"},{"issue":"5","key":"ppat.1014543.ref035","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2020.09.011","article-title":"A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions","volume":"28","author":"K Barylyuk","year":"2020","journal-title":"Cell Host Microbe"},{"issue":"1","key":"ppat.1014543.ref036","doi-asserted-by":"crossref","first-page":"6192","DOI":"10.1038\/s41467-026-73664-2","article-title":"The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles","volume":"17","author":"SA Chisholm","year":"2026","journal-title":"Nat Commun"},{"key":"ppat.1014543.ref037","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00614-21","article-title":"A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology","volume":"6","author":"SL van Esveld","year":"2021","journal-title":"mSphere"},{"issue":"2","key":"ppat.1014543.ref038","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1104\/pp.16.01675","article-title":"SDH6 and SDH7 Contribute to Anchoring Succinate Dehydrogenase to the Inner Mitochondrial Membrane in Arabidopsis thaliana","volume":"173","author":"C Schikowsky","year":"2017","journal-title":"Plant Physiol"},{"issue":"11","key":"ppat.1014543.ref039","doi-asserted-by":"crossref","first-page":"7255","DOI":"10.1074\/jbc.M806623200","article-title":"Novel mitochondrial complex II isolated from Trypanosoma cruzi is composed of 12 peptides including a heterodimeric Ip subunit","volume":"284","author":"J Morales","year":"2009","journal-title":"J Biol Chem"},{"issue":"7954","key":"ppat.1014543.ref040","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/s41586-023-05817-y","article-title":"Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex","volume":"615","author":"A M\u00fchleip","year":"2023","journal-title":"Nature"},{"issue":"6595","key":"ppat.1014543.ref041","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1126\/science.abn7747","article-title":"Structures of Tetrahymena\u2019s respiratory chain reveal the diversity of eukaryotic core metabolism","volume":"376","author":"L Zhou","year":"2022","journal-title":"Science"},{"issue":"2","key":"ppat.1014543.ref042","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2019.12.013","article-title":"Identification of a Master Regulator of Differentiation in Toxoplasma","volume":"180","author":"BS Waldman","year":"2020","journal-title":"Cell"},{"issue":"1","key":"ppat.1014543.ref043","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/s41598-018-37671-8","article-title":"An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats","volume":"9","author":"C Ramakrishnan","year":"2019","journal-title":"Sci Rep"},{"key":"ppat.1014543.ref044","doi-asserted-by":"crossref","first-page":"42746","DOI":"10.1038\/srep42746","article-title":"Mitochondrial behaviour throughout the lytic cycle of Toxoplasma gondii","volume":"7","author":"J Ovciarikova","year":"2017","journal-title":"Sci Rep"},{"issue":"37","key":"ppat.1014543.ref045","doi-asserted-by":"crossref","first-page":"19335","DOI":"10.1074\/jbc.M116.725069","article-title":"The Import of Proteins into the Mitochondrion of Toxoplasma gondii","volume":"291","author":"GG van Dooren","year":"2016","journal-title":"J Biol Chem"},{"issue":"5","key":"ppat.1014543.ref046","article-title":"ATP synthase-associated coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing proteins are critical for mitochondrial function in Toxoplasma gondii","volume":"14","author":"MM Usey","year":"2023","journal-title":"mBio"},{"key":"ppat.1014543.ref047","article-title":"DeepLoc 2.1: multi-label membrane protein type prediction using protein language models","volume":"52","author":"MT \u00d8dum","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"ppat.1014543.ref048","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1021\/acsinfecdis.4c00450","article-title":"Biogenesis of Cytochromes c and c1 in the Electron Transport Chain of Malaria Parasites","volume":"11","author":"AE Garc\u00eda-Guerrero","year":"2025","journal-title":"ACS Infect Dis"},{"issue":"2","key":"ppat.1014543.ref049","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1002\/bies.200800164","article-title":"Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology","volume":"31","author":"RF Waller","year":"2009","journal-title":"Bioessays"},{"issue":"6324","key":"ppat.1014543.ref050","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1126\/science.aal2415","article-title":"The structure of the yeast mitochondrial ribosome","volume":"355","author":"N Desai","year":"2017","journal-title":"Science"},{"issue":"6230","key":"ppat.1014543.ref051","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1126\/science.aaa1193","article-title":"Ribosome. The structure of the human mitochondrial ribosome","volume":"348","author":"A Amunts","year":"2015","journal-title":"Science"},{"key":"ppat.1014543.ref052","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens8020047","article-title":"ApiAP2 Transcription Factors in Apicomplexan Parasites","volume":"8","author":"MD Jeninga","year":"2019","journal-title":"Pathogens"},{"issue":"13","key":"ppat.1014543.ref053","doi-asserted-by":"crossref","first-page":"8271","DOI":"10.1093\/nar\/gku500","article-title":"The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems","volume":"42","author":"J Oberstaller","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"ppat.1014543.ref054","doi-asserted-by":"crossref","first-page":"3170","DOI":"10.1093\/molbev\/msab090","article-title":"Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria","volume":"38","author":"J Pyrih","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"12","key":"ppat.1014543.ref055","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1038\/s41594-019-0339-2","article-title":"Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution","volume":"26","author":"K Tucker","year":"2019","journal-title":"Nat Struct Mol Biol"},{"issue":"8","key":"ppat.1014543.ref056","doi-asserted-by":"crossref","first-page":"412","DOI":"10.3390\/genes9080412","article-title":"Protein Import into the Endosymbiotic Organelles of Apicomplexan Parasites","volume":"9","author":"N Mallo","year":"2018","journal-title":"Genes (Basel)"},{"issue":"15","key":"ppat.1014543.ref057","doi-asserted-by":"crossref","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","article-title":"A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core","volume":"430","author":"L Zimmermann","year":"2018","journal-title":"J Mol Biol"},{"issue":"9","key":"ppat.1014543.ref058","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/nsmb.3273","article-title":"An atomic structure of the human 26S proteasome","volume":"23","author":"X Huang","year":"2016","journal-title":"Nat Struct Mol Biol"},{"issue":"5","key":"ppat.1014543.ref059","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.tcb.2019.01.007","article-title":"The Role of EMC during Membrane Protein Biogenesis","volume":"29","author":"PJ Chitwood","year":"2019","journal-title":"Trends Cell Biol"},{"key":"ppat.1014543.ref060","doi-asserted-by":"crossref","first-page":"624","DOI":"10.12688\/f1000research.6944.1","article-title":"The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?","volume":"4","author":"JG Wideman","year":"2015","journal-title":"F1000Res"},{"issue":"5","key":"ppat.1014543.ref061","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009717","article-title":"The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei","volume":"18","author":"A Iyer","year":"2022","journal-title":"PLoS Pathog"},{"issue":"6","key":"ppat.1014543.ref062","article-title":"ER membrane complex (EMC): Structure, functions, and roles in diseases","volume":"38","author":"Q Zhu","year":"2024","journal-title":"FASEB J"},{"issue":"5","key":"ppat.1014543.ref063","doi-asserted-by":"crossref","DOI":"10.1002\/bies.202100258","article-title":"Eukaryotic cellular intricacies shape mitochondrial proteomic complexity","volume":"44","author":"M Hammond","year":"2022","journal-title":"Bioessays"},{"issue":"8","key":"ppat.1014543.ref064","doi-asserted-by":"crossref","first-page":"2173","DOI":"10.1093\/molbev\/msaa061","article-title":"A Uniquely Complex Mitochondrial Proteome from Euglena gracilis","volume":"37","author":"MJ Hammond","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"1","key":"ppat.1014543.ref065","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1186\/s12864-025-12233-1","article-title":"The mitochondrial proteome of diplonemids: from conventional pathways to eccentric RNA editing and transcript processing","volume":"26","author":"MW Gray","year":"2025","journal-title":"BMC Genomics"},{"issue":"12","key":"ppat.1014543.ref066","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.1016\/j.pt.2018.08.008","article-title":"Reinventing an Organelle: The Reduced Mitochondrion in Parasitic Protists","volume":"34","author":"HJ Santos","year":"2018","journal-title":"Trends Parasitol"},{"issue":"10","key":"ppat.1014543.ref067","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.cub.2016.03.053","article-title":"A Eukaryote without a Mitochondrial Organelle","volume":"26","author":"A Karnkowska","year":"2016","journal-title":"Curr Biol"},{"issue":"1","key":"ppat.1014543.ref068","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1146\/annurev-micro-041222-025305","article-title":"Inside the Host: Understanding the Evolutionary Trajectories of Intracellular Parasitism","volume":"78","author":"P Barto\u0161ov\u00e1-Sojkov\u00e1","year":"2024","journal-title":"Annu Rev Microbiol"},{"issue":"7","key":"ppat.1014543.ref069","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/nrg.2016.39","article-title":"Evolution by gene loss","volume":"17","author":"R Albalat","year":"2016","journal-title":"Nat Rev Genet"},{"key":"ppat.1014543.ref070","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.molbiopara.2016.02.007","article-title":"Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions","volume":"209","author":"A Z\u00edkov\u00e1","year":"2016","journal-title":"Mol Biochem Parasitol"},{"issue":"1","key":"ppat.1014543.ref071","doi-asserted-by":"crossref","first-page":"2542","DOI":"10.1038\/s41467-023-38158-5","article-title":"Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae","volume":"14","author":"F Han","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"ppat.1014543.ref072","doi-asserted-by":"crossref","first-page":"5342","DOI":"10.1038\/s41467-020-18993-6","article-title":"Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization","volume":"11","author":"RK Flygaard","year":"2020","journal-title":"Nat Commun"},{"issue":"5629","key":"ppat.1014543.ref073","doi-asserted-by":"crossref","DOI":"10.1126\/science.1083647","article-title":"Comment on \u201cA green algal apicoplast ancestor\u201d","volume":"301","author":"RF Waller","year":"2003","journal-title":"Science"},{"issue":"6595","key":"ppat.1014543.ref074","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1126\/science.abq0368","article-title":"Mitochondrial complex complexification","volume":"376","author":"MA Huynen","year":"2022","journal-title":"Science"},{"issue":"1","key":"ppat.1014543.ref075","doi-asserted-by":"crossref","first-page":"7176","DOI":"10.1038\/s41467-021-27200-z","article-title":"How to build a ribosome from RNA fragments in Chlamydomonas mitochondria","volume":"12","author":"F Waltz","year":"2021","journal-title":"Nat Commun"},{"issue":"6413","key":"ppat.1014543.ref076","article-title":"Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes","volume":"362","author":"DJF Ramrath","year":"2018","journal-title":"Science"},{"key":"ppat.1014543.ref077","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1146\/annurev.micro.091208.073424","article-title":"Mitochondrial evolution and functions in malaria parasites","volume":"63","author":"AB Vaidya","year":"2009","journal-title":"Annu Rev Microbiol"},{"issue":"1","key":"ppat.1014543.ref078","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.ajhg.2016.05.021","article-title":"Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype","volume":"99","author":"CL Alston","year":"2016","journal-title":"Am J Hum Genet"},{"key":"ppat.1014543.ref079","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.cmet.2016.09.002","article-title":"The assembly pathway of mitochondrial respiratory chain complex I","volume":"25","author":"S Guerrero-Castillo","year":"2017","journal-title":"Cell Metab"},{"issue":"7","key":"ppat.1014543.ref080","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.202201858","article-title":"The cytochrome b carboxyl terminal region is necessary for mitochondrial complex III assembly","volume":"6","author":"D Flores-Mireles","year":"2023","journal-title":"Life Sci Alliance"},{"issue":"7","key":"ppat.1014543.ref081","doi-asserted-by":"crossref","first-page":"148425","DOI":"10.1016\/j.bbabio.2021.148425","article-title":"Complexome profiling reveals novel insights into the composition and assembly of the mitochondrial ATP synthase of Arabidopsis thaliana","volume":"1862","author":"H R\u00f6hricht","year":"2021","journal-title":"Biochim Biophys Acta Bioenerg"},{"issue":"6","key":"ppat.1014543.ref082","doi-asserted-by":"crossref","DOI":"10.1093\/plcell\/koaf055","article-title":"Complexome profiling of the Chlamydomonas psb28 mutant reveals TEF5 as an early PSII assembly factor","volume":"37","author":"J Lang","year":"2025","journal-title":"Plant Cell"},{"issue":"2","key":"ppat.1014543.ref083","doi-asserted-by":"crossref","first-page":"149035","DOI":"10.1016\/j.bbabio.2024.149035","article-title":"The mitochondrial respiratory chain from Rhodotorula mucilaginosa, an extremophile yeast","volume":"1865","author":"P Casta\u00f1eda-Tamez","year":"2024","journal-title":"Biochim Biophys Acta Bioenerg"},{"issue":"5","key":"ppat.1014543.ref084","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1111\/j.1365-313X.2005.02577.x","article-title":"Histochemical staining and quantification of plant mitochondrial respiratory chain complexes using blue-native polyacrylamide gel electrophoresis","volume":"44","author":"M Sabar","year":"2005","journal-title":"Plant J"},{"issue":"8","key":"ppat.1014543.ref085","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1038\/nprot.2007.261","article-title":"Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips","volume":"2","author":"J Rappsilber","year":"2007","journal-title":"Nat Protoc"},{"key":"ppat.1014543.ref086","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"J Cox","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ppat.1014543.ref087","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Galaxy Community","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ppat.1014543.ref088","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1093\/bioinformatics\/btu623","article-title":"NOVA: a software to analyze complexome profiling data","volume":"31","author":"H Giese","year":"2015","journal-title":"Bioinformatics"},{"issue":"11","key":"ppat.1014543.ref089","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evae231","article-title":"LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins","volume":"16","author":"\u0141F Sobala","year":"2024","journal-title":"Genome Biol Evol"},{"issue":"4","key":"ppat.1014543.ref090","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"15","key":"ppat.1014543.ref091","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"ppat.1014543.ref092","doi-asserted-by":"crossref","DOI":"10.32942\/X2P62N","article-title":"IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models","author":"T Wong","year":"2025"},{"key":"ppat.1014543.ref093","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"I Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"ppat.1014543.ref094","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002392","article-title":"A systematic screen to discover and analyze apicoplast proteins identifies a conserved and essential protein import factor","volume":"7","author":"L Sheiner","year":"2011","journal-title":"PLoS Pathog"},{"issue":"9","key":"ppat.1014543.ref095","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/emboj\/21.9.2149","article-title":"Toxoplasma gondii myosin A and its light chain: a fast, single-headed, plus-end-directed motor","volume":"21","author":"A Herm-G\u00f6tz","year":"2002","journal-title":"EMBO J"},{"issue":"2","key":"ppat.1014543.ref096","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/0166-6851(96)02598-4","article-title":"A novel epitope tag system to study protein targeting and organelle biogenesis in Trypanosoma brucei","volume":"77","author":"P Bastin","year":"1996","journal-title":"Mol Biochem Parasitol"},{"issue":"7","key":"ppat.1014543.ref097","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"},{"key":"ppat.1014543.ref098","article-title":"UCSF ChimeraX: Tools for structure building and analysis","volume":"32","author":"EC Meng","year":"2023","journal-title":"Protein Sci"},{"issue":"8016","key":"ppat.1014543.ref099","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"J Abramson","year":"2024","journal-title":"Nature"},{"key":"ppat.1014543.ref100","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"AM Waterhouse","year":"2009","journal-title":"Bioinformatics"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1014543","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:22:08Z","timestamp":1790702528000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1014543"}},"subtitle":[],"editor":[{"given":"Michael L","family":"Reese","sequence":"first","affiliation":[{"name":"UTSW: The University of Texas Southwestern Medical Center","place":["UNITED STATES OF AMERICA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,29]]},"references-count":100,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1014543","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,29]]}}}