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Anaerobic Peroxisomes in Mastigamoeba Balamuthi

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Anaerobic Peroxisomes in Mastigamoeba Balamuthi Anaerobic peroxisomes in Mastigamoeba balamuthi Tien Lea, Vojtech Žárskýa, Eva Nývltováa, Petr Radaa, Karel Haranta, Marie Vancováb, Zdenek Vernera, Ivan Hrdýa, and Jan Tachezya,1 aDepartment of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic; and bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceské Budejovice, Czech Republic Edited by Tom M. Fenchel, University of Copenhagen, Helsingor, Denmark, and approved December 12, 2019 (received for review July 3, 2019) The adaptation of eukaryotic cells to anaerobic conditions is reflected the ER in the evolution of peroxisomal β-oxidation has been by substantial changes to mitochondrial metabolism and func- proposed (9, 10). tional reduction. Hydrogenosomes belong among the most mod- In addition to fatty acid metabolism, there is a plethora of other ified mitochondrial derivative and generate molecular hydrogen metabolic, regulatory, and evolutionary links between peroxisomes concomitant with ATP synthesis. The reduction of mitochondria is and mitochondria (11, 12). For example, the glyoxylate cycle of frequently associated with loss of peroxisomes, which compart- peroxisomes of land plants, fungi, alveolates, and lower animals mentalize pathways that generate reactive oxygen species (ROS) uses acetyl-CoA as a substrate to produce succinate that can be and thus protect against cellular damage. The biogenesis and imported into mitochondria to replenish the tricarboxylic acid function of peroxisomes are tightly coupled with mitochondria. (TCA) cycle. Both peroxisomes and mitochondria divide by fission These organelles share fission machinery components, oxidative and share multiple components of the fission machinery (13). metabolism pathways, ROS scavenging activities, and some me- More recently, mitochondria appeared to be directly involved in tabolites. The loss of peroxisomes in eukaryotes with reduced peroxisome biogenesis as a source of peroxisomal membranes and mitochondria is thus not unexpected. Surprisingly, we identified membrane proteins (14). Because of this tight interplay between peroxisomes in the anaerobic, hydrogenosome-bearing protist peroxisomes and mitochondria and the dependence of key per- Mastigamoeba balamuthi. We found a conserved set of peroxin oxisomal oxidases on the presence of molecular oxygen, it is not (Pex) proteins that are required for protein import, peroxisomal surprising that peroxisomes are generally absent in anaerobic growth, and division. Key membrane-associated Pexs (MbPex3, unicellular eukaryotes (protists) (15, 16). These eukaryotes harbor MbPex11, and MbPex14) were visualized in numerous vesicles dis- highly reduced anaerobic mitochondria, such as hydrogenosomes tinct from hydrogenosomes, the endoplasmic reticulum (ER), and and mitosomes (17). Hydrogenosomes lack most mitochondrial EVOLUTION Golgi complex. Proteomic analysis of cellular fractions and predic- metabolic functions, including β-oxidation. ATP is generated at tion of peroxisomal targeting signals (PTS1/PTS2) identified 51 the substrate level using an anaerobic pathway that catabolizes putative peroxisomal matrix proteins. Expression of selected pro- pyruvate or malate to acetate, CO2, and molecular hydrogen. teins in Saccharomyces cerevisiae revealed specific targeting to Anaerobic conditions apparently prevent the use of oxygen- peroxisomes. The matrix proteins identified included components dependent β-oxidation of fatty acid metabolism in both peroxisomes of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA and mitochondria, as well as other oxygen-dependent catabolic biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of Significance peroxisomes, named “anaerobic” peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxi- somes in anaerobic organisms. It is generally accepted that peroxisomes are absent in anaerobic eukaryotes. These organelles have evolved to compartmentalize peroxisome | Mastigamoeba balamuthi | mitochodria | anaerobiosis oxidative pathways and prevent cellular oxidative damage, namely, the β-oxidation of fatty acids that utilizes molecular oxygen and produces hydrogen peroxide. Mitochondria possess eroxisomes are single membrane-bound organelles present in a parallel β-oxidation pathway coupled with the respiratory Pnearly all eukaryotes (1). They are defined by a conserved set chain. The adaptation of eukaryotes to anaerobiosis is reflected of proteins named peroxins (Pexs) that are required for peroxi- by the reduction of mitochondrial metabolism and, not surpris- somal biogenesis (2). Biochemically, most peroxisomes share the ingly, concomitant loss of peroxisomes. The free-living anaerobic function of fatty acid oxidation, which generates hydrogen protist Mastigamoeba balamuthi is an organism that contradicts peroxide, and hydrogen peroxide-degrading enzymes, namely, this paradigm. Although Mastigamoeba possesses hydrogenosomes, catalase, to prevent cellular oxidative damage (3). Additional an anaerobic form of mitochondria, it also harbors peroxisomes. peroxisomal pathways are highly variable, indicating the remark- These organelles contain the archetypical Pexs that are required able versatility of peroxisomal functions (4). This is reflected by for peroxisomal biogenesis; however, they lack the hallmarks of the various names of peroxisomal subtypes, such as glyoxysomes, peroxisomal metabolism, β-oxidation and catalase. glycosomes, and Woronin bodies (5). The need for the compart- Author contributions: J.T. designed research; T.L., V.Ž., E.N., P.R., K.H., M.V., Z.V., I.H., and mentalization of enzymes that produce reactive oxygen species J.T. performed research; and J.T. wrote the paper. (ROS) has been proposed as a driving force behind the evolution The authors declare no competing interest. of peroxisomes. Peroxisomes were most likely derived from the This article is a PNAS Direct Submission. endoplasmic reticulum (ER) and originated endogenously within Published under the PNAS license. eukaryotes (6, 7), although they were long thought to be endo- Data deposition: MaxQuant results were uploaded to the PRIDE partner repository symbiotic remnants similar to mitochondria and plastids (8). The (https://www.ebi.ac.uk/pride/archive/) with the dataset identifier PXD014205.These- β-oxidation of fatty acids is considered to be the earliest pathway quences reported in this paper have been deposited in the online resource for community annotation of eukaryotes (ORCAE, https://bioinformatics.psb.ugent.be/orcae/)andaregiven that resided in an ancestral peroxisomal proteome due to its in Dataset S1. widespread occurrence (6). Phylogenetic analysis suggested that 1To whom correspondence may be addressed. Email: [email protected]. this pathway was inherited from the endosymbiotic ancestor of This article contains supporting information online at https://www.pnas.org/lookup/suppl/ mitochondria, duplicated and retargeted to peroxisomes to mini- doi:10.1073/pnas.1909755117/-/DCSupplemental. mize the harmful effects of ROS (6, 7). However, a parallel role of www.pnas.org/cgi/doi/10.1073/pnas.1909755117 PNAS Latest Articles | 1of11 Downloaded by guest on September 29, 2021 and biosynthetic pathways in anaerobic protists. As a consequence, and peroxisome fission (Pex11-1 and Pex11-2) (Fig. 1A and SI peroxisomes may become dispensable for these organisms. Appendix, Fig. S1 and Table S1). Most M. balamuthi Pexs Mastigamoeba balamuthi is a free-living anaerobic amoeba of (MbPexs) were colinear or slightly shorter than the correspond- the Archamoebae lineage. The characteristics of the mitochondria ing orthologs, and all possessed the expected functional domains of M. balamuthi conform to those of hydrogenosomes (18). The (SI Appendix, Fig. S2). The C-terminal domain of Pex14 is anaerobic character of M. balamuthi emphasizes the presence of a markedly short; however, its N-terminal domain contains char- nitrogen-fixing (NIF) and oxygen-sensitive e-bacterial FeS cluster acteristic phenylalanine residues that are indispensable for its assembly machinery that replaced the standard mitochondrial iron– interaction with Pex5 (22) (SI Appendix, Fig. S2). The functional sulfur cluster (ISC) machinery (19). Moreover, oxygen-sensitive domains were identified using HHpred searches with high con- enzymes such as hydrogenases are present in M. balamuthi hydro- fidence (probability values ranged from 84 to 100) (SI Appendix, genosomes and in the cytosol, producing hydrogen from both Fig. S2), whereas the overall similarity of MbPex protein se- compartments (19). Archamoebae belongs to the group Conosa quences to their human orthologs ranged between 14% for Pex3 with the sister lineage Mycetozoa that inhabits aerobic niches and and 57% for Pex7 (SI Appendix, Table S2). The correct identi- contains oxygen-respiring mitochondria and standard peroxisomes fication of MbPexs containing domains that are present in var- (20, 21). Thus, it is likely that hydrogenosomes in M. balamuthi ious proteins with unrelated functions, such as ATPases evolved from aerobic mitochondria via secondary adaptation to associated with diverse cellular activities (AAA, Pex1, and Pex6), anaerobic environments, and we expected that an anaerobic lifestyle tetratricopeptide repeats (TPR and Pex5), WD40 repeats (Pex7), would lead to the loss of peroxisomes, as observed in other an- and proteins of the
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