Subject Index. 2D, analyses, 173, electrophoresis, 166

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1 Subject Index 2D, analyses, 173, electrophoresis, 166 acetate/succinate CoA transferase (ASCT), 8, 9, 104, 115, 116, 118, 119, 126, 128 acetyl, CoA, 104, 119, 121, CoA hydrolase, 126, CoA synthase, 102 adenylate kinase, 119, 127 ADP/ATP carrier, 115, 157, 221 aerobic, resistance, 185, respiration, 256 aerobic eukaryotes, 6 alcohol dehydrogenase E, 151 alpha-ketoglutarate dehydrogenase, 103 alternative oxidase (AOX), 223, 243 amitochondriates, 204, 205 Amoebozoa, 266 Amylovorax,98 anaerobic, chytrids, 151, eukaryotes, 1, 3, 5 7, 10, 11, resistance, 187 Andalucia incarcerata, 277 Antonospora,32, locustae, 44, 211, 219, 256 apicomplexans, 232 apicoplast, 233 apoptotic body, 258 Arabidopsis, 164 archaebacteria, 5, 239 Archaeplastida, 266 Archezoa, 204 arginine, 135, biosynthesis, 165, deiminase, 136, dihydrolase pathway, 136 articulin, 245 ATP:AMP phosphotransferase, 127 ATP, production, 165, synthase, 223, synthesis, 2, 8 10, 12 ATP/ADP translocase, 164 autophagy, 88 axostyle, 76, 78, 93 Blastocystis, 256 bongkrekic acid, 115 Bradyrhizobium,11 Breviata anathema, 278 butyryl-coa, 104 calcium, 81, 86 Canfield oceans, 3, 7, 9 11, 13, 14 carbamate kinase, 136 cardiolipin, 115, 214 Carpediemonas membranifera, 274 catalase, 129 cellulose, 151 chaperone, 58, 157, 216 chaperonin 60, 205 Chilomastix cuspidata, 274 Chlamydomonas reinhardtii,9 Chromalveolata, 266 chytridiomycete, 10, 148 ciliates, 76, 78 citrulline, 136 class A flavodiiron protein, 131 cleavage site, 41, 56 CO 2, 115, 118, 128 coenzyme A (CoA), 115, 126, 128 coenzyme Q, 125 complex I, 103, 120, 125, 165 complex II, 165

2 284 Subject Index confocal, 240 costa, 76, 78, 93 Cpn10, 43 Cpn60, 42, 43, 232 cristae, 236, 258 cryo-electron tomography, 239 crypton, 203 Cryptosporidia, 256 Cryptosporidium, 51, 54, 57, 58, 204, 213, parvum, 32, 121, 124, 174, 205, 207, 219, sp., 23 crystalline core, 84 cyanide, 128 Cyclidium porcatum,80 cyclosporine A, 259 cysteine desulfurase (IscS), 43, 132, 133, 205, 215, 217, 219 cytochalasin, 78, 87 cytochrome, 127, 261, P450 reductase, 121, 124, c oxidase, 209 Dasytricha, 98, 103 Desulfovibrio vulgaris, 131 Dictyostelium discoideum, 212 dihydrofolate reductase, 135 diplomonads, 174 Diploplastron affine, 103, 107 division, 86, 88, 91, 212 dynamin, 92 electron, transfer, 164, transport, 122, 165, 220, 221 Encephalitozoon cuniculi, 2, 32, 44, 54, 57, 58, 173, 211, 256 endobiotic bacteria, 270, 275 endoplasmic reticulum, 24, 87, 88 endosymbiont, 1, 4, 5, 13, 106 endosymbiotic theory, 4 6 Entamoeba, 2, 10, 32, 35, 42, 54, 57, 132, 220, 256, histolytica, 23, 122, 174, 204, 206 Entodinium simplex, 103, 107 epibiotic bacteria, 277 Epidinium, 98, 103 Eremoplastron bovis, 103, 107 ethanol, 9, 151, 191 Eudiplodinium, 98, 103 Euglena gracilis, 8, 10, 121, 124, 164, 174, 260 eukaryote evolution, 1, 3, 7, 13 eukaryotic supergroups, 266 Euplotes, 102 evolution, 22, 107, 174, 202 Excavata, 213, 266 F o F 1 -ATP synthase, 103, 120, 127 Fasciola hepatica, 260 fatty acids, 261 [FeFe] hydrogenase, 123, 124 ferredoxin, 31, 35, 43, , 125, 132, 180, 187, 189, 217, 219, 222, genes, 194 ferritin, 223 FeS (see iron-sulfur) flavodiiron protein, 131, 186 flavoprotein, 129 FMN, 125, 131 formate, 9, 152 frataxin, 132, 133, 216, 218, 219 freeze-fracture, 79, 81, 83 FtsZ, 92, 212 Fugu, 164 fumarase, 260, 262 fumarate, 107, hydratase, 260, 262, reductase, 8 fungi, 76, 213 futile cycling, 185 geological model, 6 Giardia intestinalis, 10, 23, 31, 35, 43, 54, 57, 122, 132, 204, 212, 213, 217, 256 glucose, 101, 103 glutaredoxin, 216, 217 glycerol-3-phosphate dehydrogenase (G3PDH), 57, 222 glycine, 135, decarboxylase complex (GDC), 134, 135 glycolysis, 116, 202, 240 H cluster, 123, 124 H protein, 134 heat shock protein 70 (see Hsp70) heme, 133 Heterolobosea, 275 hidden Markov model, 33, 173 Hmp31, 45, 115, 137

3 Subject Index 285 Hmp35, 46, 115, 137 Hsp70, 43, 54, 70, 205, 232 HydE, 124, 137 HydF, 124 HydG, 124 hydrogen, 76, 115, 153, 166, 256, peroxide, 128, 129, 175 hydrogenase, 107, 119, 121, 123, 174, 189, 214, maturase, 124, 174 hydrogenosomal, targeting motif, 137, terminal oxidase, 186 hydrogenosome, 23, 30, 35, 44, 76, 181, 203, 206 hydroxyurea, 78 Hymenolepis diminuta, 221 immunolabeling, 93 import, 22, machinery, 173, motor, 53 inner membrane, 232 inner membrane protease, 26 intestinal tract, 202 invasion, 246 invertebrates, 8, 9, 12 iron storage, 245 iron sulfur (FeS), 113, 116, 119, 122, 123, 125, 129, 131, 137, cluster (ISC), 121, 132, 133, 215, 237, cluster assembly, 11, 215, protein, 133 IscA, 132 IscS (see cysteine desulfurase) IscU, 132, 215 Isd11, 218 isopycnic centrifugation, 138 Isotricha, 98, 103 Janus green, 258 karyokinesis, 93 2-keto acid oxidoreductase, 116, 121, 193 Krebs cycle, 119, 260, 262 L protein, 134 lactate, 9, 191, dehydrogenase (LDH), 128, 191, 243 latency, 125 lateral gene transfer, 2 Leishmania, 260 Lyromonas vulgaris, 276 lysosome, 88, 136, 138 malate, 116, 128 malic enzyme, 116, 119, 124, 125, 136, 138, 189 mass spectrometry, 166 Mastigamoeba, balamuthi, 132, 206, 220, 270, punctachora, 270, simplex, 270 Mastigella commutans, 270 matrix, 81, 84 membrane, 79, 114, 115, 125, potential, 220, 244 Metamonada, 273 Methanobacterium formicicum, 106, 270, 275, 276 methanogenic symbiont, 106 Methanoplanus endosymbiosus, 106 methyl viologen, 119 methylmalonyl-coa, 8 Metopus, 98, contortus, 80, 106, striatus, 106 metronidazole, 79, 116, 118, 122, 180, 257, anion radicals, 181, 185, 189, resistance, 184 microaerophile, 128 microsporidia, 23, 32, 44, 57, 204, 207 microtubule, 93 mitochondrion, 24 mitochondrion-like organelle, 232 MitoLight, 258 mitosis, 93 mitosome, 23, 30, 42 44, 116, 203, 204 MitoTracker Green, 258 Monocercomonas, 114, sp., 78 Monocercomonoides, 275 Monopylocystis visvesvarai, 276 Mycoplasma,4 N 5,N 10 -methylene tetrahydrofolate, 135 N-acetyl glucosamine, 83 NAD(P)H nitroreductases, 194 NAD-dependent malic enzyme, 182 NADH

4 286 Subject Index, dehydrogenase, 120, 122, 125, 182, oxidase, 128, ubiquinone oxidoreductase, 125 NADP-specific malic enzyme, 116 NADPH oxidase, 128 Neocallimastix, 35, 41, 46, 54, 147, 150, 165, 260, frontalis, 78, 86, 91, sp., 23, 31 NIF, 215 Nim proteins, 194 nitric oxide, 131 nitro anion radicals, nitroimidazole, 179 nitrosative stress, 132 nucleus, 23 Nyctotherus, 54, 57, 58, 98, 104, 175, ovalis, 23, 126, 165 ocean geochemistry, 6, 13 Ohr protein, 131 Ophryoscolex caudatus, 103, 107 Opisthokonta, 266 organic hydroperoxide, 131 origin, 164, 173 ornidazole, 180 ornithine, 136, decarboxylase, 136 OsmC, 131, 175 Ostracodinium obtusum bilobum, 103, 107 OXA, 210 oxidative, decarboxylation of malate, 182, decarboxylation of pyruvate, 181, phosphorylation, 4, 128 oxygen, 3, 5, 6, 127, 128, 202, respiration, 4, scavenging enzymes, 186 P protein, 134 PAM, 27, 53, 210 Pam18, 43 pelobionts, 270 Pelomyxa palustris, 106, 270 PEP carboxykinase, 116 Percoll, 138 Percolomonas descissus, 275 peripheral vesicles, 81 permeability, 115 peroxide, 130 peroxiredoxin, 130, 175 peroxisomes, 4 phosphatidylcholine, 115 phosphatidylethanolamine, 115 phosphatidylserine, 115 phosphoenolpyruvate, 116 phospholipid, 115 photosynthesis, 6 Phytomonas, 260 Piromyces, 9, 147, 150, 175 Plagiopyla,98, nasuta, 106 Plasmodium, 173, 202, 209, 215, falciparum, 11, 164, 206 polyamines, 135 Polyplastron,98 Polytomella,10 Postgaardi mariagerensis, 277 preprotein, 53 presequence, 29, 34, 40, 42, 210 processing peptidase, 25, 34, 43, 55, 211 programmed cell death, 261 propionyl-coa, 8 protease, 245 protein, expression, 190, import, 28 30, 164, 238, trafficking, 22, 23 Psalteriomonas, 175, lanterna, 275, vulgaris, 106 putrescine, 136 pyridine, nucleotide, 115, 119, nucleotide transhydrogenase, 205, 221 Pyrsonympha, 275 pyruvate, 115, 116, 128, 260, decarboxylase, 192, dehydrogenase complex, 101, 121, 222, formate lyase, 9, 101, 102, 105, 151, 165, kinase, 116 pyruvate:ferredoxin oxidoreductase (PFOR), 10, 101, 102, 104, 118, 119, 121, 129, 153, 165, 174, 180, 189, 214, 260 pyruvate:nadp oxidoreductase (PNO), 121, 124, 240, 260 reactive oxygen species, 129, 137 Reclinomonas americana, 209 reductive evolution, 237

5 Subject Index 287 relict mitochondrion, 205 respiratory chain, 125, 128, 210 Rhizaria, 266 rhodamine 123, 258 rhodoquinone, 8 Rickettsia,28, prowazekii, 56 Rli1, 239 RNA polymerase II, 205 rotenone, 126, 128 rubredoxin, 131 rubrerythrin, 130, 175 rumen, 148, ciliates, 107 Saccharomyces cerevisiae, 164, 215, 219 SAM, 25, 46, 47, 211 Sawyeria marylandensis, 276 Schizosaccharomyces pombe, 164 segmentation, 88, 91 segregation, 212 serine, 135, hydroxymethyltransferase (SHMT), 134, 135 signal, peptidase, 24, sequence, 24 small subunit ribosomal RNA, 205 Spironucleus, 132, barkhanus, 274, elegans, 274, salmonicida, 212, 218, vortens, 274 subcompartments, 236 substrate-level phosphorylation, 116, 126, 128, 156 succinate, 8, 9, 119, 128, 260, CoA ligase, 126, dehydrogenase, 260, 262, thiokinase (STK, see succinyl-coa synthetase) succinyl, CoA, 126, CoA synthetase (SCS), 10, 103, 119, 126, 260, 262 succinyl-coa:acetate CoA transferase, 126 sucrose gradient, 138 SUF, 215 sulfate, 6, 11 sulfide,6,11, quinone oxidoreductase, 12 superoxide dismutase (SOD), 129, 186, 222 symbiosis, 4 T protein, 134 targeting, sequence, 124, 126, 130, 166, signal, 34, 116 terminal oxidase, 103 tetrahydrofolate, 135 Tetrahymena, 102 thiol-dependent peroxidase, 130 thioredoxin, 130, 175, reductase, 130, 131 TIM, 27, 46, 50 52, 210, 238 tinidazole, 180 Tiny TIMS, 238 TOM, 25, 47, 49, 210, 238 tomography, 232 Toxoplasma gondii, 42, 213 Trachipleistophora hominis, 32, 54, 206 translocase, 25, 34, 174, 211 translocation, 25 transporters, 173 treatment failure, 185 tricarboxylic cycle (TCA), 156, 165 Trichomonadida, 76 trichomonads, 78 Trichomonas, 2, 31, 35, 54, 57, 58, 104, 109, 166, gallinae, 115, vaginalis, 180, 191 Trimastix, marina, 274, pyriformis, 274 Trimyema, 98, 104 Tritrichomonas, foetus, 84, 114, 123, 166, 180, 191, augusta,91 Trypanaosoma, brucei, 41, 202, 212, 216, 260, cruzi,43 ubiquinone, 8, 115, 120 Vahlkampfia anaerobica, 276 valyl-trna synthetase, 205 vertebrates, 8, 11, 12