The adaptation of eukaryotic cells to anaerobic conditions is reflected by substantial changes to mitochondrial metabolism and functional reduction. Hydrogenosomes belong among the most modified mitochondrial derivative and generate molecular hydrogen concomitant with ATP synthesis. The reduction of mitochondria is frequently associated with loss of peroxisomes, which compartmentalize pathways that generate reactive oxygen species (ROS) and thus protect against cellular damage. The biogenesis and function of peroxisomes are tightly coupled with mitochondria. These organelles share fission machinery components, oxidative metabolism pathways, ROS scavenging activities, and some metabolites. The loss of peroxisomes in eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in the anaerobic, hydrogenosome-bearing protist Mastigamoeba balamuthi We found a conserved set of peroxin (Pex) proteins that are required for protein import, peroxisomal growth, and division. Key membrane-associated Pexs (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles distinct from hydrogenosomes, the endoplasmic reticulum (ER), and Golgi complex. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) identified 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed specific targeting to peroxisomes. The matrix proteins identified included components of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of peroxisomes, named "anaerobic" peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxisomes in anaerobic organisms.

Department of Parasitology Faculty of Science BIOCEV Charles University 25242 Vestec Czech Republic

Department of Parasitology Faculty of Science BIOCEV Charles University 25242 Vestec Czech Republic;

Institute of Parasitology Biology Centre Czech Academy of Sciences 370 05 České Budějovice Czech Republic

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Gabaldón T., Peroxisome diversity and evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 765–773 (2010). PubMed PMC

Schlüter A., et al. , The evolutionary origin of peroxisomes: An ER-peroxisome connection. Mol. Biol. Evol. 23, 838–845 (2006). PubMed

De Duve C., Baudhuin P., Peroxisomes (microbodies and related particles). Physiol. Rev. 46, 323–357 (1966). PubMed

Smith J. J., Aitchison J. D., Peroxisomes take shape. Nat. Rev. Mol. Cell Biol. 14, 803–817 (2013). PubMed PMC

Pieuchot L., Jedd G., Peroxisome assembly and functional diversity in eukaryotic microorganisms. Annu. Rev. Microbiol. 66, 237–263 (2012). PubMed

Bolte K., Rensing S. A., Maier U. G., The evolution of eukaryotic cells from the perspective of peroxisomes: Phylogenetic analyses of peroxisomal beta-oxidation enzymes support mitochondria-first models of eukaryotic cell evolution. BioEssays 37, 195–203 (2015). PubMed

Speijer D., Evolution of peroxisomes illustrates symbiogenesis. BioEssays 39, 1700050 (2017). PubMed

de Duve C., The origin of eukaryotes: A reappraisal. Nat. Rev. Genet. 8, 395–403 (2007). PubMed

Gabaldón T., A metabolic scenario for the evolutionary origin of peroxisomes from the endomembranous system. Cell. Mol. Life Sci. 71, 2373–2376 (2014). PubMed PMC

Gabaldón T., Evolutionary considerations on the origin of peroxisomes from the endoplasmic reticulum, and their relationships with mitochondria. Cell. Mol. Life Sci. 71, 2379–2382 (2014). PubMed PMC

Schrader M., Costello J., Godinho L. F., Islinger M., Peroxisome-mitochondria interplay and disease. J. Inherit. Metab. Dis. 38, 681–702 (2015). PubMed

Fransen M., Nordgren M., Wang B., Apanasets O., Role of peroxisomes in ROS/RNS-metabolism: Implications for human disease. Biochim. Biophys. Acta 1822, 1363–1373 (2012). PubMed

Menendez-Gutierrez M. P., Roszer T., Ricote M., Biology and therapeutic applications of peroxisome proliferator- activated receptors. Curr. Top. Med. Chem. 12, 548–584 (2012). PubMed

Sugiura A., Mattie S., Prudent J., McBride H. M., Newly born peroxisomes are a hybrid of mitochondrial and ER-derived pre-peroxisomes. Nature 542, 251–254 (2017). PubMed

Gentekaki E., et al. , Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol. 15, e2003769 (2017). PubMed PMC

Gabaldón T., Ginger M. L., Michels P. A. M., Peroxisomes in parasitic protists. Mol. Biochem. Parasitol. 209, 35–45 (2016). PubMed

Embley T. M., Martin W., Eukaryotic evolution, changes and challenges. Nature 440, 623–630 (2006). PubMed

Nývltová E., et al. , Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Mol. Biol. Evol. 32, 1039–1055 (2015). PubMed PMC

Nývltová E., et al. , NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of Mastigamoeba balamuthi. Proc. Natl. Acad. Sci. U.S.A. 110, 7371–7376 (2013). PubMed PMC

Hayashi H., Suga T., Some characteristics of peroxisomes in the slime mold, Dictyostelium discoideum. J. Biochem. 84, 513–520 (1978). PubMed

Pánek T., et al. , First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Mol. Phylogenet. Evol. 98, 41–51 (2016). PubMed

Neufeld C., et al. , Structural basis for competitive interactions of Pex14 with the import receptors Pex5 and Pex19. EMBO J. 28, 745–754 (2009). PubMed PMC

Koch J., Brocard C., PEX11 proteins attract Mff and human Fis1 to coordinate peroxisomal fission. J. Cell Sci. 125, 3813–3826 (2012). PubMed

Otera H., et al. , Mff is an essential factor for mitochondrial recruitment of Drp1 during mitochondrial fission in mammalian cells. J. Cell Biol. 191, 1141–1158 (2010). PubMed PMC

Williams C., van den Berg M., Sprenger R. R., Distel B., A conserved cysteine is essential for Pex4p-dependent ubiquitination of the peroxisomal import receptor Pex5p. J. Biol. Chem. 282, 22534–22543 (2007). PubMed

Goto S., Mano S., Nakamori C., Nishimura M., Arabidopsis ABERRANT PEROXISOME MORPHOLOGY9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes. Plant Cell 23, 1573–1587 (2011). PubMed PMC

Kalel V. C., Mäser P., Sattler M., Erdmann R., Popowicz G. M., Come, sweet death: Targeting glycosomal protein import for antitrypanosomal drug development. Curr. Opin. Microbiol. 46, 116–122 (2018). PubMed

Galiani S., et al. , Super-resolution microscopy reveals compartmentalization of peroxisomal membrane proteins. J. Biol. Chem. 291, 16948–16962 (2016). PubMed PMC

Barlow L. D., Nývltová E., Aguilar M., Tachezy J., Dacks J. B., A sophisticated, differentiated Golgi in the ancestor of eukaryotes. BMC Biol. 16, 27 (2018). PubMed PMC

Bauer S., Morris J. C., Morris M. T., Environmentally regulated glycosome protein composition in the African trypanosome. Eukaryot. Cell 12, 1072–1079 (2013). PubMed PMC

Banerjee S. K., Kessler P. S., Saveria T., Parsons M., Identification of trypanosomatid PEX19: Functional characterization reveals impact on cell growth and glycosome size and number. Mol. Biochem. Parasitol. 142, 47–55 (2005). PubMed

Krause C., Rosewich H., Woehler A., Gärtner J., Functional analysis of PEX13 mutation in a Zellweger syndrome spectrum patient reveals novel homooligomerization of PEX13 and its role in human peroxisome biogenesis. Hum. Mol. Genet. 22, 3844–3857 (2013). PubMed

Dunkley T. P., Watson R., Griffin J. L., Dupree P., Lilley K. S., Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 3, 1128–1134 (2004). PubMed

Rucktäschel R., Girzalsky W., Erdmann R., Protein import machineries of peroxisomes. Biochim. Biophys. Acta 1808, 892–900 (2011). PubMed

Moyersoen J., Choe J., Fan E., Hol W. G., Michels P. A., Biogenesis of peroxisomes and glycosomes: Trypanosomatid glycosome assembly is a promising new drug target. FEMS Microbiol. Rev. 28, 603–643 (2004). PubMed

Helm M., et al. , Dual specificities of the glyoxysomal/peroxisomal processing protease Deg15 in higher plants. Proc. Natl. Acad. Sci. U.S.A. 104, 11501–11506 (2007). PubMed PMC

Watkins P. A., Ellis J. M., Peroxisomal acyl-CoA synthetases. Biochim. Biophys. Acta 1822, 1411–1420 (2012). PubMed PMC

Annoura T., Nara T., Makiuchi T., Hashimoto T., Aoki T., The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions. J. Mol. Evol. 60, 113–127 (2005). PubMed

Acosta-Virgen K., et al. , Giardia lamblia: Identification of peroxisomal-like proteins. Exp. Parasitol. 191, 36–43 (2018). PubMed

Ludewig-Klingner A. K., Michael V., Jarek M., Brinkmann H., Petersen J., Distribution and evolution of peroxisomes in alveolates (Apicomplexa, Dinoflagellates, Ciliates). Genome Biol. Evol. 10, 1–13 (2018). PubMed PMC

Vaidya A. B., Mather M. W., Mitochondrial evolution and functions in malaria parasites. Annu. Rev. Microbiol. 63, 249–267 (2009). PubMed

Žárský V., Tachezy J., Evolutionary loss of peroxisomes–Not limited to parasites. Biol. Direct 10, 74 (2015). PubMed PMC

Müller M., et al. , Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76, 444–495 (2012). PubMed PMC

Cross L. L., Ebeed H. T., Baker A., Peroxisome biogenesis, protein targeting mechanisms and PEX gene functions in plants. Biochim. Biophys. Acta 1863, 850–862 (2016). PubMed

Gonzalez N. H., et al. , A single peroxisomal targeting signal mediates matrix protein import in diatoms. PLoS One 6, e25316 (2011). PubMed PMC

Motley A. M., Hettema E. H., Ketting R., Plasterk R., Tabak H. F., Caenorhabditis elegans has a single pathway to target matrix proteins to peroxisomes. EMBO Rep. 1, 40–46 (2000). PubMed PMC

Grou C. P., et al. , Members of the E2D (UbcH5) family mediate the ubiquitination of the conserved cysteine of Pex5p, the peroxisomal import receptor. J. Biol. Chem. 283, 14190–14197 (2008). PubMed

Skrede S., Halvorsen O., Mitochondrial pantetheinephosphate adenylyltransferase and dephospho-CoA kinase. Eur. J. Biochem. 131, 57–63 (1983). PubMed

Tahiliani A. G., Neely J. R., Mitochondrial synthesis of coenzyme A is on the external surface. J. Mol. Cell. Cardiol. 19, 1161–1167 (1987). PubMed

Reumann S., et al. , In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes. Plant Physiol. 150, 125–143 (2009). PubMed PMC

Pracharoenwattana I., Cornah J. E., Smith S. M., Arabidopsis peroxisomal malate dehydrogenase functions in β-oxidation but not in the glyoxylate cycle. Plant J. 50, 381–390 (2007). PubMed

Güther M. L. S., Urbaniak M. D., Tavendale A., Prescott A., Ferguson M. A. J., High-confidence glycosome proteome for procyclic form Trypanosoma brucei by epitope-tag organelle enrichment and SILAC proteomics. J. Proteome Res. 13, 2796–2806 (2014). PubMed PMC

Antonenkov V. D., Dehydrogenases of the pentose phosphate pathway in rat liver peroxisomes. Eur. J. Biochem. 183, 75–82 (1989). PubMed

Annoura T., Nara T., Makiuchi T., Hashimoto T., Aoki T., The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions. J. Mol. Evol. 60, 113–127 (2005). PubMed

Nagy M., Lacroute F., Thomas D., Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts. Proc. Natl. Acad. Sci. U.S.A. 89, 8966–8970 (1992). PubMed PMC

Hines V., Keys L. D. 3rd, Johnston M., Purification and properties of the bovine liver mitochondrial dihydroorotate dehydrogenase. J. Biol. Chem. 261, 11386–11392 (1986). PubMed

Andersen P. S., Jansen P. J. G., Hammer K., Two different dihydroorotate dehydrogenases in Lactococcus lactis. J. Bacteriol. 176, 3975–3982 (1994). PubMed PMC

Michels P. A., Hannaert V., Bringaud F., Metabolic aspects of glycosomes in trypanosomatidae–New data and views. Parasitol. Today (Regul. Ed.) 16, 482–489 (2000). PubMed

Makiuchi T., Nara T., Annoura T., Hashimoto T., Aoki T., Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene 394, 78–86 (2007). PubMed

Cabrera R., Babul J., Guixé V., Ribokinase family evolution and the role of conserved residues at the active site of the PfkB subfamily representative, Pfk-2 from Escherichia coli. Arch. Biochem. Biophys. 502, 23–30 (2010). PubMed

Opperdoes F. R., Szikora J. P., In silico prediction of the glycosomal enzymes of Leishmania major and trypanosomes. Mol. Biochem. Parasitol. 147, 193–206 (2006). PubMed

Gill E. E., et al. , Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi. Mol. Microbiol. 66, 1306–1320 (2007). PubMed

Petrova V. Y., Drescher D., Kujumdzieva A. V., Schmitt M. J., Dual targeting of yeast catalase A to peroxisomes and mitochondria. Biochem. J. 380, 393–400 (2004). PubMed PMC

Leger M. M., Gawryluk R. M. R., Gray M. W., Roger A. J., Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii. PLoS One 8, e69532 (2013). PubMed PMC

Santos H. J., Makiuchi T., Nozaki T., Reinventing an organelle: The reduced mitochondrion in parasitic protists. Trends Parasitol. 34, 1038–1055 (2018). PubMed

de Souza W., Lanfredi-Rangel A., Campanati L., Contribution of microscopy to a better knowledge of the biology of Giardia lamblia. Microsc. Microanal. 10, 513–527 (2004). PubMed

de Souza W., Special organelles of some pathogenic protozoa. Parasitol. Res. 88, 1013–1025 (2002). PubMed

Chávez L. A., Balamuth W., Gong T., A light and electron microscopical study of a new, polymorphic free-living amoeba, Phreatamoeba balamuthi n. g., n. sp. J. Protozool. 33, 397–404 (1986). PubMed

Cáp M., Stěpánek L., Harant K., Váchová L., Palková Z., Cell differentiation within a yeast colony: Metabolic and regulatory parallels with a tumor-affected organism. Mol. Cell 46, 436–448 (2012). PubMed

Green S. R., Moehle C. M., Media and culture of yeast. Curr. Protoc. Cell Biol. Chapter 1, 1.6.1–1.6.12 (2001). PubMed

McCammon M. T., Veenhuis M., Trapp S. B., Goodman J. M., Association of glyoxylate and beta-oxidation enzymes with peroxisomes of Saccharomyces cerevisiae. J. Bacteriol. 172, 5816–5827 (1990). PubMed PMC

Sterck L., Billiau K., Abeel T., Rouzé P., Van de Peer Y., ORCAE: Online resource for community annotation of eukaryotes. Nat. Methods 9, 1041 (2012). PubMed

Neuberger G., Maurer-Stroh S., Eisenhaber B., Hartig A., Eisenhaber F., Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J. Mol. Biol. 328, 567–579 (2003). PubMed

Lazarow P. B., The import receptor Pex7p and the PTS2 targeting sequence. Biochim. Biophys. Acta 1763, 1599–1604 (2006). PubMed

Flynn C. R., Mullen R. T., Trelease R. N., Mutational analyses of a type 2 peroxisomal targeting signal that is capable of directing oligomeric protein import into tobacco BY-2 glyoxysomes. Plant J. 16, 709–720 (1998). PubMed

Mikolajczyk J., et al. , Small ubiquitin-related modifier (SUMO)-specific proteases: Profiling the specificities and activities of human SENPs. J. Biol. Chem. 282, 26217–26224 (2007). PubMed

Malínská K., Malínský J., Opekarová M., Tanner W., Visualization of protein compartmentation within the plasma membrane of living yeast cells. Mol. Biol. Cell 14, 4427–4436 (2003). PubMed PMC

Gietz R. D., Schiestl R. H., Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 38–41 (2007). PubMed

Schindelin J., et al. , Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). PubMed PMC

Bolte S., Cordelières F. P., A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006). PubMed

de Chaumont F., et al. , Icy: An open bioimage informatics platform for extended reproducible research. Nat. Methods 9, 690–696 (2012). PubMed

Makki A., et al. , Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biol. 17, e3000098 (2019). PubMed PMC

Kaurov I., et al. , The diverged trypanosome MICOS complex as a hub for mitochondrial cristae shaping and protein import. Curr. Biol. 28, 3393–3407.e5 (2018). PubMed

Smith J. J., et al. , Transcriptome profiling to identify genes involved in peroxisome assembly and function. J. Cell Biol. 158, 259–271 (2002). PubMed PMC

Štáfková J., et al. , Dynamic secretome of Trichomonas vaginalis: Case study of β-amylases. Mol. Cell. Proteomics 17, 304–320 (2018). PubMed PMC

Wang Y., et al. , Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019–2026 (2011). PubMed PMC

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