j689

Index

a acute/chronic pulmonary Acanthamoeba castellanii 152 histoplasmosis 567 acid-fast staining 327 ACV trafficking 248 acquired immune deficiency syndrome adaptive immune system 217 (AIDS) 330, 329, 357 – antigen processing 225–230 acquired/secondary mutualistic – B cells, antibodies and immunity 553–554 224–225 þ -associated 131 – CD4 TH1 217–220 actin-based motility system 440, 435 – cells of 217–225 þ – process 435 – cytotoxic CD8 T 221–222 actin-binding proteins (ABPs) 126, 127 – natural killer T lymphocytes 222–223 – coronin 337 – regulatory T cells 223–224 – filamin 130 – T receptors 225 – SipA 379 – ab T cells 217 actin 126, 135 – gd TCRT lymphocytes 222 – background 126 – TH2 lymphocytes 217–220 – – – disruption 135 TH17 lymphocytes 220 221 actin-dependent process 132 adaptive virulence mechanisms 27 – 289 adenylate kinase 133 actin depolymerization factor (ADF) 127 ADP-actin 129 actin filament 129 ADP-Pi-bound monomers 126 actin interactions 128 ADP-ribosylation factor 1(Arf1) 71 – binding 128 ADP transporter 133 – nucleation 128 Aerobacter aerogenes 21 actin monomers 127 Afipia felis 237, 239, 240, 242, 248, see also cat actin nucleation assay, schematic scratch disease presentation 130 – containing 240, 241, 242, 249, actin polymerization process 116, 129, 243, 251 247 – immunology 251–252 – inhibitor 399 – intracellular bacterium 239 – machinery, lipophosphoglycan (LPG)- – intracellular fate determination 246–248 mediated retention 590 – low-efficiency uptake pathway 242–243 actin-recruiting 277 – macrophages 246 actin-remodeling proteins 118 – uptake/intracellular compartmentation actin-rich -containing membrane, model 240, 248 formation 402 Agrobacterium tumefaciens 311, 575 actin system 126 – Cre recombinase reporter assay 311

Intracellular Niches of Microbes. Edited by Ulrich E. Schaible and Albert Haas Copyright 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32207-7 690j Index

– mediated transformation, ankyrin-repeat 305, 404, 557 characterization 575 – containing protein 305 AIDS see acquired immune deficiency anthrax toxin 179 syndrome antiapoptotic pathways 623 Akt autophosphorylation 663 – c-FLIP 619 algal symbionts 537 – c-IAP1 619 – endosymbionts 537, 542 – c-IAP2 619 / 527, 542–543 – -linked IAP 619 – endosymbiosis 538 – proteins 619 amastigotes 584–585 antibacterial peptides 342 Amblyomma maculatum 470 antibiotics 200 amino acid biosynthetic pathways 154 antibodies 366 amitochondrial organisms 7 – maternal 366 – Entamoeba 7 – role 366 – Giardia 7 antigen discovery techniques 147 – Microsporidia 7 – antigen microarrays 147 amoeba-associated bacteria 239 – immunoblotting/autodisplay 147 Amoeba proteus 14 antigen-enzyme complex 101 amoeboid cells 125 antigenic protein, VapA 362 Anaplasma phagocytophilum 301, 303, antigen-presenting cells 210, 211, 217, 579 304, 306 – MHC molecules 217 – acidic markers 305 antigen processing 225 – annexins 309 – antibody generating 225 – autophagosome markers 308 – B cells 225 – cation-independent mannose-6-phosphate – CD1-mediated antigen presentation 308 226–227 – caveolae/lipid raft 303 – cross-presentation 227–228 – clathrin 309 – granuloma formation 228–229 – endosomal markers 306 – immunological memory 229–230 – genomes 310 – vaccination 229–230 – golgi-plasma membrane pathway 307 anti-inflammatory , transforming – GPI-anchored proteins 303 223 – host cell compartmentalization, antimicrobial drugs 191 characterization 302 antimicrobial peptide (AMP) 332 – host intracellular compartments 303 – cathelizidin LL37 332 – inclusions 307 – 332 – lysosomal membrane markers 305 – hepcidin 346 – membrane-bound inclusions 302 antioxidant enzyme systems 477 – myeloperoxidase localization 305 antituberculosis vaccines 229 – NADPH oxidase components 309 apical complex, compartments, role 597 – phorbol-12-myristate-13-acetate (PMA) 310 parasite 597, 613, 636 – phospholipase Cg2 (PLCg2) activation 304 – Babesia 597 – proliferation 304 – protozoa 152, 153, 597 – protein tyrosine phosphorylation 304 apoptosis 347, 348, 619, 621 – replicative inclusions 303, 304 – apoptotic cell 37, 39, 42, 51, 163 – rough endoplasmic reticulum-Golgi – death receptor-induced 619, 621 pathway 307 – Fas-induced 619 – transcytosis process 304 – pathways 556 – vesicle-associated membrane protein 2 Arabidopsis 18, 29 (VAMP2) 309 – genome 29 – Western blotting 310 – model 18 annexin 1 348 arabinose assimilation operon 399 – N-terminal domain 348 ATP accumulation 133 – proteolysis 348 AT-hook proteins 624 Index j691

ATP/ADP translocases, energy exchange 476 bacterial cell wall protein, internalin 437 ATPase inhibitor 420 bacterial effector proteins 373 ATP-binding transmembrane receptor 133 bacterial 154, 531 ATP depletion actin 134 – aphidicola 154 attenuated strains 257 bacterial lumazine synthase 266 autoimmune diseases 330 183, 184 – antibody infliximab treatment 330 – symbionts 183 – rheumatoid arthritis 330 bacteriophages 27 autophagocytic process 290, 496 bacteriostatic/cidal elements 291 – interactions 290 Bartonella-containing 241, 249 – marker 290 Bcl-2-like proteins 294 autophagosomes 15, 216 Bdellovibrio bacteriovorus 7 autophagy 216, 308, 450 BimA cells 403, 404 – Atg6 308 – protein-protein interactions 403, 404 – Atg8 308 – transient expression 403 – markers LC3 450 blood-brain barrier 433 – pathway, Atg5-dependent conjugation bloodstream trypomastigotes, acidified systems 643 medium 662 – types of 216 bone marrow-derived macrophages avidin-biotin binding system 99 (BMDMs) 120, 405, 579 avidin-horseradish peroxidase (HRP) 100 Bradyrhizobium strains 515 Brill–Zinsser disease 471 b Brucella 258, 266 Babesia species 597 – DC activation inhibition 267 – Babesia divergens 597 – intra-host cell compartmentation 258–262 – Babesia gibsoni 597 – role of proinflammatory cytokines – Babesia microti 597 267–268 – binary fission 598 – role of VirB 268 – erythrocytic stages 601 – stealth 266 – genome 607 Brucella BvrS/BvrR system 263 – host cell invasion 601 Brucella-containing phagosome 247, 259, 260 – host cell modification 602 – schematic view 260 – infected cells 603 Brucella Tir-protein 267 – intra-host compartmentation Brucella virulence factors, schematic characterization, relationship to representation 264 virulence 600 Brucellosis, see Malta fever – morphological description 600–601 Brugia malayi, pathogenic filarial nematode 8 – nutritional aspects 604 Burkholderia pseudomallei 150, 210, 495 – parasite cell biology/genomics to drug – actin-based motility 401–404 targets 607 – adherence 396 – apicoplast 607 – cell contact 396 – food vacuole 608 – cell fusion 404 – novel permeation pathways 608 – cellular mechanisms 407 – relationship to virulence 603 – escape 400 – transmitting agents 597 – flagellin 397 – virulence factors 606 – transcription, microarray babesiosis, symptoms 600 analysis 405 bacille Calmette–Guerin (BCG) vaccine 328, – genome sequences 395, 396, 400 345 – genome structure 395 – attenuation, genomic regions of difference – host cell interactions 394, 406 (RD) deletion 328 – immunology 406 bacilli transcriptome analysis 345 – induced actin tails, confocal Bacillus anthracis 198, 208 micrographs 402 bacterial camouflage 264 – induced MNGC formation 400 692j Index

– infected HeLa cells, scanning electron – Drosophila phagocytes, infection of 73–74 microscopy 398 – Legionella-containing phagosome 68, 69 – intracellular life 394–395 – Legionella-directed phagosome biogenesis – intracellular replication 405 70–72 – invasion 398 – phagocytic host cells 65 – median lethal dose 395 cellular nucleation-promoting factors, – polysaccharide biosynthesis Wiskott–Aldrich syndrome protein (WASP) clusters 397 family 402 – T3SS-associated gene clusters 399 cellular trafficking 263, 265 Burkholdria thailandensis, virulence-associated central nervous system (CNS) 433 loci 396 Chagas disease 655 – clinical stages 655 c – digestive megasyndromes 655 calcium binding protein 574 – drugs, treatment of 656 calmodulin-activated adenylate cyclase 296 – meningoencephalitis 655 Camponotus floridanus 548 chaperonin-containing T complex 117 capsular polysaccharides, rhizobial 516 chemical mediators 38 – carboxysomal CO2-concentrating mechanism 38 (CCM) 532 – cytokines 38 cardiomyopathy, see Meningoencephalitis receptor 335 casein kinase II enzyme (CK2) 623 – CCR7 335 catalase-peroxidase 407 – DCs 335 cationic bactericidal peptides 263 chemotherapeutics 331 – defensin-like antibiotic polymyxin B 263 – isoniazide 331 – lactoferrin 263 – streptomycin 331 – lysozyme 263 chicken embryo fibroblast, transmission cation-independent mannose-6-phosphate electron micrograph of 470 receptor 308 Chlamydia-containing vacuole 4, 84, 85 cat scratch disease 237, 238, 239 Chlamydia-derived branched-chain fatty – bacterium 237 acid 275 – self-limiting lymphadenopathy 237 Chlamydia pneumoniae 198 caveolar trafficking system 304 Chlamydia trachomatis 25, 151, 273, 276, 279, CCM see carboxysomal CO2-concentrating 282 mechanism – developmental cycle 274 þ CD8 282 – inclusion 273, 274, 279, 281 cell cycle 398 – characterization 273–275 – regulatory proteins 557, 672 – immunology 281–282 retinoblastoma protein 672 – infections 276, 279 – target gene 620 – recombination types 25 cell death, -independent type 348 – vegetative/replicative stages 151 cell-free fusion assays 102, 103, 104 chlamydial protease activity factor (CPAF) 282 cell-free system 99, 102, 104, 311, 336 Chlorella/hydra endosymbiosis 538–541 – ATPase 311 Chlorella vulgaris 539, 541 – endosome-endosome fusion systems 99 Chlorochromatium aggregatum 9 – NADH dehydrogenase-like proteins 311 chlorophyte-derived gene 540 – nuclear proteins 311 cholera toxin B (CTB) 246 – tyrosine phosphatase 311 cholesterol-dependent bacteria, cell junction formation 437 Ehrlichia/Anaplasma spp. 312 cell plasma membrane 449, 601 cholesterol-dependent cytolysins (CDCs), cell-to-cell adhesion receptor 493 pore-forming 441 cellular model systems 65 cholesterol oxidase 363 – animal model Drosophila melanogaster 72–73 chromatin-binding proteins 556 – bacterial species 67 chromatophore 531, 532 – Dictyostelium cells 66 c-Jun NH2-terminal kinases 622 Index j693

– AP-1 transcription factors 622 d – ATF-2 transcription factor 622 DAMP assay 82, 306 CK2 see casein kinase II enzyme dendritic cells 159, 206, 212, 255, 416, 434, clathrin-mediated machinery 579 438 – microbial death 159 CNS see central nervous system de novo protein synthesis 472, 602 colony-stimulating factor (CSF)-activated density gradient centrifugation analysis 87 macrophages 573 detergent resistant membranes (DRMs) 245 community-acquired pneumonia 273 diacylglycerol 449 confocal immunofluorescence microscopy diatom, Climacodiun frauenfeldianum 533 241 Dictyostelium cells 66 COPI complex 50 Dictyostelium discoideum 10, 65, 457, reef ecosystem 530, 537 458, 459 Coxiella-containing phagosome 289 – free-living amoeba 37 – maturation 289–290 – host model for 67 Coxiella-infected cells 294, 296 – macrophages 70 – growth cycle 290 – phagocytic potential of 66, 70, 71 Coxiella intrahost compartment 288 – slime mold 10 – characterization 288–294 – social amoeba 459 Coxiella metabolism 293 – transcriptional host cell 67 Coxiella (PV) differential in-gel electrophoresis 111 model 290, 294, 297 dimorphic fungal pathogen, Histoplasma – immunology 297 capsulatum 567 Coxiella-specific interactions 295 Diphtheria 179 cyanobacteria 5, 532 diverted phagosome maturation/compartment – CCM-microcompartments 532 maintenance 262, 295, 586 – genome 9 – factors 262–266 – heterocyst-forming 528 – genes 295–297 – symbionts 6, 13 – involving Leishmania molecules 586–592 Cyanophora paradoxa, living fossil 535 DNA-binding protein 382 Cyanothece-like N2-fixing endosymbiont 533 – domains 624 cystic fibrosis 26 DNA-fragments 311 16, 366 – repair 24 – 16, 40, 206, 321, 331, 417, 477 – replication 618 – production profiles 366 – synthesis 616, 623 – 16 dormancy-associated genes, Rv3133 345 cytokine-inducible Src homology 2-containing DosR-mediated hypoxic response 154 protein 406 Dot/Icm system 317, 321 cytolethal distending toxin (cdtB) 554 – dependent mechanism 321 Cytophaga-Flexibacter-Bacteroides (CFB) 554 – Legionella. pneumophila proteins cytoplasmic incompatibility 555, 556 translocation 317 – phenotype 556 – virulent Legionella pneumophila 321 cytoplasmic iron pool 345 Drosophila melanogaster 65, 72, 73, 458, 557 cytoplasmic pathogens 128 – cellular and humoral immune cytoplasmic signaling mechanism 450 responses 72 cytoplasmic streaming 542 – host-pathogen interaction 72, 73 cytoskeleton elements 9 – macrophage-like phagocytes 73 cytoskeleton-pathogen interaction 125 – RNA interference systems 74 cytosol 420, 439 – S2 cells, RNA interference screens 448 – host cell replication 439 drug delivery systems 348 – phagosome replication 420 drug design 191 – proteins 225 – infectious diseases 197 cytotoxic T lymphocytes 217, 221 – parasitic infections 198 – associated antigen 4 (CTLA-4) 223 drug-resistant malaria 256 694j Index

drug screening 199 – vesicle-associated membrane protein 2 – in vivo imaging systems 199 (VAMP2) 309 drugs 196 – vs. Anaplasma phagocytophilum 307 – uptake and loss 196 Ehrlichia granulosum 210 eicosapentanoic acid 132 e electron microscopy 137 early endosomal antigen 1 (EEA1) 161, 259, elementary bodies 273, 274, 278, 295 359, 419, 658 – endocytosis 277 – association 306 – microtubule-mediated trafficking 278 – endosome-endosome docking/fusion 306 Ena/vasodilator-stimulated early endosomal markers 315, 359, 377, phosphoprotein 438 448 endocytic organelles 137 – endosomal antigen 1 (EEA1) 377 endocytotic membrane 616 – -associated membrane protein 1 endomycorrhization signaling pathways 511 (LAMP1) 183, 241, 304, 315, 339, 359, 377, endoplasmic markers 261 448, 460 – BiP 261 – Rab5 241, 315, 339, 359, 377, 448 – ribophorin 261 – Rab7 86, 109, 138, 177, 241, 315, 448, 460, endoplasmic reticulum (ER) 47, 66, 78, 166, 513 241 – transferrin receptor 377 – Brucella trafficks 179 east coast fever, macroschizonts 614 – calcium-binding proteins 70 ectoparasites, of mammal 17 – caveosome 179 Ehrlichia chaffeensis 301, 303, 304 – Chlamydia 179 – acidic markers 305 – cis-Golgi network 185 – annexins 309 – eukaryotes, secretory pathway of 178 – autophagosome markers 308 – Legionella-containing 179 – brefeldin A treatment 307 – proteins 109, 116 þ – Ca2 -calmodulin inhibitors sensitivity 309 – Toxoplasma 180 – cation-independent mannose-6-phosphate – trans-Golgi network 179 receptor endosome/lysosome markers 48, 367, 377, – caveolae/lipid raft 303 448 – clathrin 309 – fluorescent dextrans 377 – detrimental systemic illnesses 312 – LBPA/BMP 367 – dual-infected cells, replicative – LGPs 377 inclusions 303 – lysosomal hydrolases/cathepsins 377 – genomes 310 – lysosome-associated membrane protein 1 – Golgi-plasma membrane pathway 307 367, 377 – GPI-anchored proteins 303 – mannose 6-phosphate receptors 377 – host cell compartmentalization, – Rab7 367, 448 characterization 302 – vacuolar ATPase (v-ATPase) 377 – host intracellular compartments 303 endosomal system 192 – immune defense phagocytes 302 – remodeling 119 – inclusions 307 endosome-endosome fusion systems 99 – infected HL-60 cells 303, 306, 307 endosymbiotic algae 539, 540 – myeloperoxidase localization 305, 306 endosymbiotic organelles 6 – NADPH oxidase components 309 endosymbiont theory 5, 534 – phospholipase Cg2 (PLCg2) activation Enterococcus faecali 26, 215 304 enteropathogenic bacteria 119 – proliferation 304 enzymatic/fluorometric quantification – protein tyrosine phosphorylation 304 technique 97 – replicative inclusions 304 epidemic typhus agent 302, 471 – rough endoplasmic reticulum-Golgi – Rickettsia prowazekii 302, 471 Pathway 307 epithelial Caco-2 cell 182 – transcytosis process 304 epithelial cell lines 259, 488 Index j695

– in vitro challenge 488 Fenton reaction 330 – HeLa 259 filament systems 125 – Vero 259 – actin 125 epithelial growth factor (EGF) 196 – filamentous hemagglutinin 40 ER-associated protein degradation (ERAD) – intermediate filaments 125 pathway 74, 319 – microtubules 125 – component 319 fimbriae, electron microscopy 396 – function 319 flavonoids 514, 518 – machinery 117 F-like conjugative transfer system 28 – Npl4 319 fluorescence-activated cell sorting (FACS) 88, – Ufd1 319 100, 461 ER-Golgi intermediate compartment 318 – in phagosome research 88 erythrocyte membrane proteins 602 – use 88, 100 erythrocyte plasma membrane 602 fluorescence resonance energy transfer Escherichia coli 21, 215 (FRET) 80, 99, 199 eukaryotic cells 172, 441 fluorescent lipid derivatives 85 – membrane-bound compartments 172–176 – NBD-glucosylceramide 86 – membrane, cholesterol-containing 441 – NBD-sphingomyelin 86 eukaryotic domains 296 fluorescent metal ion indicators 84 – ankyrin repeats 296 follicle-associated epithelium (FAE) 487 – coiled-coil domains 296 food-borne pathogens 26 – F-box domains 296 – Listeria 26 – leucine-rich repeats 296 – Salmonella 26 – tetratricopeptide repeats 296 Forkhead box transcription factor 223 eukaryotic protein degradation pathway, see Francisella pathogenicity island (FPI) 423 N-end rule pathway – genes, mechanisms of action 423 exocytic pathway/secretory pathway 179 Francisella tularensis 182, 415, 417 expressed sequence tag (EST) data 111 – antigens 425 expression profiling techniques 146–147, – clinical isolates 419 149 – compartment 420, 421 – biological inferences 149 – lifecycle 416, 417 extracellular matrix (ECM) 40, 41 – 418 – fibronectin 41 – pathogenicity island 420 – laminin 41 – phagocyte interactions 425 – molecules 41 – phagocytosis receptors 418 extracellular polysaccharides (EPS) 516 – phagosome maturation 416 extracellular signal-regulated kinases – neutrophil respiratory burst (ERKs) 622 inhibition 421 ezrin radixin moesin (ERM) protein – phagocytosis receptors 417–418 family 131, 133 – virulence factors 422 – AcpA 423 f – lipopolysaccharide/capsule 422 F-actin filaments 45 – phagocyte function disruption 422 F-actin network 398 free-living protozoa 17 facultative symbionts 548 – amoebae, Acanthamoeba 394 fatty acids 150 fungal hyphae 509 – metabolism fusion reconstituting assays 98 – b-oxidation 150 fusogenic machinery components 47, 49 Fcg receptors (FcgR) 41 – N-ethylmaleimide-sensitive factor – classes 41 (NSF) 49 – FcgRIIA 41 – NSF-attachment proteins (SNAPs) – FcgRIIIA 41 49 – mediated phagocytosis 44, 45, 46, 50, 244, – soluble N-ethylmaleimide-sensitive factor- 248 attachment protein (SNARE) 49 696j Index

g guanosine triphosphatase (GTPase) 317, 337, gemfibrozil 197 398, 447, 584, 621 145, 152, 343 – early vesicle formation 317 – control 152 – Rab5 337 – patterns 145, 154 – Rab14 337 genetic recombination 21 – ras-related 621 – conjugation 22 – mechanisms 22 h – transduction 22 Hamiltonella defensa 551, 554 – transformation 22 – secondary endosymbiont 551, 554 gene transfer 21, 22 haploid genome 458 – frequency 22 haploid social amoeba Dictyostelium, – types 21 features 68 genome directed primers 148 heat-killed pathogens 135, 361, 434, 579 genomic islands 24, 395 heat shock protein expression 344 gentamicin, in drug efficacy 194 Helicobactor pylori 25 glaucocystophyte cyanelles 533 hemozoin formation 608 gliding motility 601, 636 heparin-bearing glycoprotein 675 gluconeogenesis 182 hepatocyte growth factor (HGF) receptor glycerophospholipid 44 437 – phosphatidic acid 44 heterotrimeric G protein-linked signal – phosphatidyl serine 44 transduction 70 glycolipid-enriched microdomains (GEMs) heterotrophic/photosynthetic eukaryotes 6 622 heterotrophic secondary host cell 535 glycoprotein 209 high-affinity iron-binding protein, glycosphingolipids 226 lactoferrin 345 glycosylated transmembrane proteins, high-performance liquid chromatography lysosome membrane-associated (HPLC) 111 protein 78 high-throughput protein sequencing 117 glycosylphosphatidylinositol (GPI)-anchored histidine acid phosphatase 423 proteins 40, 111, 180, 269, 304, 600, Histoplasma capsulatum 567, 568, 574, 577 625 – conidia 568 Golgi apparatus 166 – genome 574, 577 – matrix proteins 318 – immune serum 569 – vesicles 291 – intracellular survival 573 granulocyte-macrophage colony stimulating – involving genes 573–579 factor 571 – yeasts, phagocytosis 570 granulocyte- colony-stimulating histoplasmosis, murine model 574 factor 213 homologous recombination 551 granulocytic ehrlichiosis, see human horizontal gene transfer 9, 22, 23, 24, 30 granulocytic anaplasmosis – S-adenosylmethionine (SAM) 23 granuloma 191, 225, 229 – DNA gyrase A/B subunits 23 – formation 191, 225 – indicator, genomic islands 24 – tissue reaction 228 Abscisic acid 638 GRAS domain proteins 512 hormone-like peptide 346 green fluorescent protein (GFP) 86, 308 host cell apoptosis, inhibition 294 – in vivo localization 110 host cell compartment remodeling – tagged actin 128 671–679 – tagged Beclin1 308 – by Trichinella 671–679 – tagged LC3 308 host cell-derived transporters 531 – tagged proteins 110 host cell factors, pathogen-directed phagosome green hydra, see Hydra viridissima biogenesis 70 GTP-binding protein, Rac2 310 microtubules 616, 617 GTP exchange factors 378, 398 host cytoplasm 439 Index j697

þ þ host defense functions 341 – CD4 /8 T cells 480 – intracellular GTPases 341 – innate immune system 320, 366 – nitric oxide synthase (NOS2) 341 – toll-like receptors 320 endothelial cells, infection of 477 – natural killer (NK) cells 206 host-microbe interactions 3, 10, 22, 146, 148, – schizont-infected cell 625 149, 154, 275 – -stimulating virulence factors 331 – insights 148, 154 – zebrafish 458 host-parasite interactions 15, 27, 149, 258, immunity-related GTPases 215 295, 348, 557, 607 – GTP-binding proteins 215 host-recognition systems 108 – natural resistance-associated macrophage host-symbiont interactions 549, 551 protein 215 host-symbiont specificity 537 immunity-specific genes 268 housekeeping genes 28 immunoassays 257 human cerebral endothelial cells, Rickettsia immunoblot maturation profiles 110 rickettsii 478 immuno-electron microscopy 419 human food-borne pathogen, see Listeria immunofluorescence microscopy 86 monocytogenes immunoglobulin receptor human granulocytic anaplasmosis 301 – mediated phagocytosis 240 human granulocytic ehrlichiosis agent, see – mediated uptake 242 Anaplasma phagocytophilum immunoreceptor tyrosine-based activation human-Histoplasma capsulatum yeasts, motif (ITAM) 41, 43 in vitro interaction 570 in vitro assays 101, 130 human immunodeficiency virus (HIV) 330 in vitro phagosome human listeriosis, schematic steps 433 – lysosome fusion 99 human macrophages 570, 571, 572, – motility 138 577, 578 in vivo expression technology (IVET) 405 – anti-histoplasma activity, activation 572 in vivo microbial transcriptomics 148 310, 569 inclusion membrane interactions 278 – derived macrophages 569 – chlamydial control 278–281 – lipopolysaccharaide pretreatment 310 – genes encoding proteins 279 neutrophil peptides 210 indoleamine 2,3-dioxygenase (IDO) 15, human Q fever 287 282 human rickettsial infections 478 inducible nitric oxide synthase (iNOS) 364, – respiratory distress syndrome 478 381 – spotted fever 478 – induction 407 – typhus fever 478 infectious diseases 4 humoral immunity 252 inflammatory cytokine genes 51, 365 Hydra viridissima 538 – g 365 hydrogenosomes, ATP-producing – interleukin-1b 51 organelles 7 – interleukin-6 51 hypertranscription 558 – tumor necrosis factor a 51, 365 hypertrophic mature nurse cell, inflammatory immune responses 330, 685 morphology 676 influenza-like illnesses 301 hyphal germ tube 509 – febrile illness 433 – HGA 301 i – HME 301 IkB kinase complex 620, 626 inlAB operon, InlA/InlB 437 Imd-signaling pathway 553 innate effector mechanisms 214–216 immune deficiency signaling pathway 16 – acute phase proteins 215 immune-modulating pathogens 330 – 214, 215 – helminthes, role 330 – granulysin 214 immune system(s) 16, 203, 320, 330, 366, – humoral innate immunity, cardinal 433, 434, 625 feature 215 – adaptive 203, 434 – immunity-related GTPases 215 698j Index

– macroautophagy 215 – infection 221 innate immune cells 214 – trafficking pathways 23 – blood basophils 214 – intracytoplasmic 23 – mast cells 214 – intraphagosomal 23 innate immune signaling pathways 416 intracellular life 14 – tumor necrosis factor a (TNFa) 416 – ecological view 14–16 innate immune system 267 – immunological view 16–17 innate immunity 203, 206 – public health view 17–18 – blood basophils 214 intracellular localization 191 – dendritic cells 212–213 – aminoglycosides 194 – innate effector mechanisms 214–216 – antibiotic classes, accumulation levels – innate receptors 206 of 193 – innate recognition, pathogens 207 – criteria 191–192 – mast cells 214 – drug concentrations 195 – microbes recognition 206 – fluoroquinolones 195 – natural killer cells 213–214 – b-lactam antibiotics 194 – phagocytic cells 212 – macrolides 195 innate immunity receptors 206 – transport vesicles 195 – NOD-like receptors (NLRs) 208 intracellular proteomes 147 – pattern recognition receptors (PRRs) 206, intracellular RNA profiling 145 209 intracytoplasmic replication 488 – toll-like receptors (TLRs) 207–208 – bacterial interaction 488 inner membrane complex (IMC) 636 – cell-to-cell spreading 492–493 insect immune system 550 – intracellular actin-based motility 492–493 – cellular immune response 550 – intracellular replication 492 – humoral immune response 550 – invasion, type III secretion system insect symbionts, introduction 547–550 effectors 491 insects carrying endosymbionts 550 – vacuolar lysis 492 interdigitated stichocytes 681 intraphagosome parameters 79 – morphology 681 – hydrolytic enzymes 79 – structure 681 – ions concentrations 79, 83–85 interferon g (IFNg) 184, 252, 364, 641 – micronutrients 79 – activated macrophages 406 – osmolarity 79 – gene expression 366, 645 – oxygen pressure 79 – macrophages 643, 644 – pH 79 – treatment 155 ipa genes 486 (IL-8) synthesis 397 IpaD oligomers, modeling of 490 interferon-induced GTPases 118 iron-binding internalin, role 437 – molecules 345 interspecies relationships 9 – transferrin protein 365 – commensalism 9 iron-capturing siderophore 84 – definitions 9 iron depletion 199 – mutualism 9 iron sequestration encoding genes 153 – 9 – pathogen 9 j – symbiosis 9 J774E macrophages 244, 245 intra-host cell compartmentation – confocal immunofluorescence analysis characterization 357–361 245 – virulence relationship 357 – transmission electronic micrograph 244 intracellular bacteria 23 – bacterial parasites 23 k – gene transfer 23–27 Kala-azar 583 – Chlamydiae 197 Klebsiella pneumoniae 73 – cyanobacteria 527 kleptoplastids 536 Index j699 knob-associated histidine-rich protein – bacterial virulence factors 316–317 (KAHRP) 603, 605 – infection host factors 317 knockdown efficiency 89 – Ipaf-mediated restriction 321 – in phagosome research 89 – legionnaires’ disease 315 – vs. knockout 89 – lysosomal markers 322 Koch’s postulates 238 – membrane transport 322 Kupffer cells 432, 434 – phagocytosis 71, 320 – protein synthesis 322 l – Rab proteins 318 lactoferrin 199, 210, 263, 332, 346, 498 – surrogate host for 67 Lageniastrum macrosporae 543 – type IV secretion, detection 321 LAMP1 see lysosome-associated membrane – vegetative/replicative stages 151 protein1 legionnaires’ disease 11, 26, 103, 239 lateral gene transfer 10 root hairs, invasion of 509 latex bead-containing (LBPs) 42, Leishmania 15, 583, 584 88, 108, 125, 129, 162 – containing phagosome membrane 590, – actin assembly assay 131, 132 593 – actin-binding assay 130–131 – infected macrophages 592 – lipid species 162 – intra-host cell compartmentation – maturation profiles 113 characterization 584–586 – phagosomal membranes 131 – introduction 583–584 latex bead system 127 – lifecycle 591 lectin/glycan interaction mechanism 541 – promastigotes 588 Legionella-containing vacuoles (LCVs) 71, 87, – purine auxotrophs 15 110, 120, 315 – surface phosphoglycans 587 – autophagic markers 320 – structure/diversity 587 – bacterial replication 69 lepromatous leprosy 220 – biogenesis 318, 320 Leucaena leucocephala 516 – Dictyostelium cells 71 leucine-rich repeats (LRRs) 66, 437 – vs. endoplasmic reticulum 315 – N-terminal domain-containing 437 – formation 317 – protein 296, 437 – host cell structures 69 ligand-coated beads 128 – intracellular interactions of 69 ligand recognition 42 – maturation 319, 320 – signaling events 42–46 – membrane 318, 319 – complement receptor-mediated – phagosome proteins of 71 phagocytosis 45–46 Legionella intracellular niche, iron – FcgR-mediated phagocytosis 42–45 homeostasis 69 lineage-specific basic helix-loop-helix 671 Legionella pneumophila 11, 12, 13, 17, 67, 151, lipids 43 185, 239, 261 – accessibility 85 – adaptive immunity 321 – biosynthesis 602 – antigens 321 – raft 246, 258 – biology 315 – roles 43 – cell-autonomous restriction 321 lipid microdomains 245–247 – characteristic 418 – dependent macropinocytosis 246, 247 – contaminate appliances 315 – molecules 227 – endocytic transport disruption 320 – role 245–246 – genome 12 lipid-soluble antibiotics 195 – immunity 315 – chloramphenicol/penicillin 195 – infection 315, 318, 320, 321 – rifampicin 195 – cytokine production 321 lipoarabinomannan (LAM) 336 – immune response 320 lipoate-protein ligase 405 – intracellular replication requirements lipophosphoglycan (LPG) 225, 227, 586, 316 584 700j Index

lipopolysaccharide (LPS) 268, 287, 383, 397, – mediated vacuolar escape 448 422, 516 – monomer 443 – -binding protein (LBP) 42, 209 – open reading frame 435 – biosynthesis 287 – molecular mechanism 444 – determinants 257 – PEST-like sequence 443 – free Gram-negative bacteria 222 – regulation activity 444 lipoprotein signal peptide 362, 446 – signal sequence 443 liquid chromatography/mass spectrometry – stabilizing residue 444 (LC-MS) techniques 117 – synthesis 443 Listeria innocua-containing phagosomes liver-stage malaria 220 241 LLO see listeriolysin O þ Listeria monocytogenes 12, 89, 150, 182, 432 – CD4 T cell 220 – antibodies 434 Lotus japonicus 510 – critical role 434 low-density lipoproteins (LDLs) 196, 209 – bacterial lipoproteins 445 death 664 – bacterial phospholipases, role 445 lymphogranuloma venereum (LGV) – clinical manifestations 432 strains 273 – glyceraldehyde-3-phosphate dehydrogenase LysM-type receptor kinases (LysM-RKs) 510 (GAPDH) 447 lysobisphosphatidic acid (LBPA) 420 – hematogenous dissemination 433 lysosomal acid phosphatase 673 – hemolysin-negative mutants 434 lysosomal glycoproteins (LGP) 373 – host cell cytoplasm 435 – enriched membrane tubules 373 – host cell entry 435–438 lysosomal hydrolases 289, 419, 570 – intracellular lifecycle stages 436, 438 lysosomal peroxidase 361 – electron micrographs 436 – transmission electron microscopic – schematic representation 436 analysis 361 – intracellular motility 439 30, 48, 78, 248, 592, 657 – lethal necrotizing hepatic infection 431 – -associated membrane proteins 48, 161, – listeriolysin O (LLO) 441, 450 183, 241, 260, 336, 394, 339, 448, 585 – dependent vacuole maturation delay – lysosomal marker 278 448 – fluid-phase markers 360 – independent vacuole maturation – lysosomal fusion 660 delay 447 lysosomotropic marker 242 – critical role 450 LysoTracker 82 – listeriosis 432 b-lactam antibiotics 194 – metalloprotease 445 – mimic d-alanyl-d-alanine 194 – pathophysiology 432 – phagosome escape mechanisms 449 m – phagosome maturation 446 macroautophagy 216 – PrfA-regulated virulence gene cluster 12 – cytoplasmic, vesicular transport of 216 – regulatory mechanism 444 macrophage (s) 4, 16, 47, 211, 240, 246, 336, – vacuole escape role 441 418, 568, 570, 571, 572, 577, 591, 678 – virulence determinants 439 – anti-histoplasma activity 571 – virulence factor 434, 435 – antigen-presenting function 347 Listeria pathogenicity island 1 (LAPI-1) 26 – culture 5 listeriolysin O (LLO) 434, 443, 448 – derived cells 329 – bacterial phospholipases 445 – derived complement components 569 – PC-PLC 445 – functions 615 – PI-PLC 445 – Fc receptor-mediated phagocytosis 615 – compartmentalization 443 – lipopolysaccharide-induced tumor necrosis – deficient mutant 448 factor a secretion 615 – degradation 444 – nitric oxide generation 615 – dependent perforation 448 – oxidative burst 615 – host role 444 – upregulation of procoagulant activity 615 Index j701

– inflammatory protein (MIP) 213 MAPKs see mitogen-activated protein kinases – interferon marker proteins 359 – activated LRG47 knockout 341 mass spectrometry 109 – activated Mycobacterium tuberculosis 345 Masson’s trichrome reagent 677, 681 – activated phagolysosomes 344 Maurer’s clefts 602, 603, 605 – macrophages, activation of 347 – role 605 – mannose receptor 335 MCD see methyl-b-cyclodextrin macropinocytic ruffling 119 microbe-containing phagosomes/vacuoles macropinocytosis 84, 195, 245, 249 (MCVs).108, 110, 119–121 – reminiscent 243 Medicago truncatula 510 – uptake process 243–245 – DMI3 mutant 512 macropinosome(s) 162, 243, 247 – calcium/calmodulin-dependent protein – biogenesis 251 kinase 512 – progression model 251 mediterranean spotted fever (MSF) 477 macroschizont-infected cell lines 617 melioidosis 393, 395 – initial establishment 617 – clinical features 395 magnetic immuno-separation 110 – clinical management 393 major facilitator superfamily transporters membrane-associated actin assembly 131 293 membrane-bound proteins 600 major histocompability complex (MHC) 38, – glycosyl phosphatidylinositol moiety (GPI) 212, 321 600 – class I 38, 605, 616 membrane-bound regulators 132 – antigen 626 membrane-bound siderophores 345 – pathway 282, 347 membrane-delineated complexes 536 – class II 38, 297, 321, 346, 383 membrane fusion 47, 95, 102, 161, 280, 309, – bound peptides 226 318, 338, 400, 448 – mediated antigen 593 membrane glycoproteins 305 – peptide-specific 346 – CD63 305 – processing pathways 269, 347 membrane integrity 200 – polymorphic types 346 membrane protein, Rv3671c 344 malaria 600 membrane ruffling 245, 259 – antimalarial drugs 600 meningoencephalitis 655 – by Spiroplasma 558 merozoite surface protein 1 (MSP-1) 606 – cytoadherence 600 metacyclic trypomastigotes 656 – rosetting 600 methanogen 29 – symptoms 600 – Methanococcus jannaschii 29 Malta fever 255 methyl-b-cyclodextrin (MCD) 246, 303, 494 mammalian nucleation-promoting methyl citrate dehydratase deletion factors 440 mutant 343 mammalian pathogen 12 mice lacking genes 480 MAMPs see microbe-associated molecular microarray hybridization methods 148 patterns microautophagy 216 manganese-superoxide dismutase 446 – lysosomes invagination 216 mannose-binding lectin (MBL) 41, 42 microbe-associated molecular patterns – circulating opsonin 42 (MAMPs) 206, 332 mannose-binding protein 358 – bacterial flagellins 206 mannose-capped lipoarabinomannans – 206 (manLAM) 337 microbe-containing vacuoles 113 mannose receptor 417 – comparative proteomics 113–121 – blocking agents 417 microbial genomes 155 – 6-phosphate receptor 420 microbial growth 223 mannosylated lipoarabinomannan microbial ligands 208 (manLAM) 209 – TLR4/5/9 208 – mycobacteria 209 microbial RNA extraction 147 702j Index

– protein 147 – type III secretion system (T3SS) – RNA stabilization 147–148 substrates 486 – technique 149 Myc factors 510 lipopolysaccharide 184 Mycobacterium 224, 327, 338, 339 Micrococcus melitensis 255 – acid-fast staining 327 microdissection techniques 156 – activated macrophage, IFNg-activated 341 – bacterial RNA amplification 156 – antigens 347 microinjection 280 – cell wall lipids 211, 336, 339 microneme proteins 639 – LAM 336 microscopic/biochemical assays 97–99 – phosphatidylinositol mannosides microtubules 136 (PIMs) 336 – associated protein kinases 51, 136, 138 – trehalose dimycolate (TDM) 336 – cytoskeleton 136, 139 – containing phagosomes 82, 89, 103, 104 – interactions 136 – counteract proton influx 338 – motors 136, 137, 139 – expression profiling 342 – dynactin 137 – dormancy 344 – dynein 137 – intracellular environment 342, 343 Midichloria mitochondrii 185 – proteome 342–343 mitogen-activated protein kinases – regulatory genes 344 (MAPKs) 444, 477, 621 – transcriptome profiling 343 Mixotricha paradoxa 9 – genomes 327, 328, 338 monocyte colony-stimulating factor (M-CSF) – growth, control of 225 572 – host cell, resting macrophage 332, 333 monocyte-derived macrophages (MDM) 417, – infections 455 420 – leprosy 455 – high-resolution electron micrographs 420 – tuberculosis 455 mouse macrophages – intracellular compartment 332, 333 – anti-histoplasma activity 572 – intracellular niche, nutritional benefit 345 – IGTP 643 – leprosy 328, 331 – infection of 644 – affects 331 mRNA microarray analysis 209 – spectrum subtypes 331 mucocutaneous leishmaniasis 583 – MAC infections 332 multi-locus sequencing typing (MLST) 395 – phagocytes 332 – clinical features 395 – C-type lectins 335 multidrug resistance proteins (MRPs) 192 – DCs 332 – efflux transporters of 195 – polymorphonuclear neutrophils – gemfibrozil 192 (PMNs) 332 multinucleated giant cells (MNGCs) 395 – phagocytosis process 335 – formation 395 – phagosome(s) 200, 336, 337, 341 multiplicities of infection (MOI) 335 – characteristics 348 murine macrophages 578, 642 – early endosomal characteristics 337 – categories 642 – intracellular peculiarities 340 – cells 154, 240 – maturation inhibition 337 murine pulmonary melioidosis model 400 – murine bone marrow-derived muscle fiber compartment 673 macrophages 341 – parasite-induced remodeling 673–676 – RAW/J774 murine macrophage-like muscle-specific gene (MSG) expression cells 341 – loss of 678 – resting macrophage 336 – program 672 – transferrin receptor pathway 337 mutualism 14, 27 – transferrin travels 200 – associations 547 – protein transport systems 338 mutualistic/parasitic scenarios 145 – tuberculosis-like lesions 328 mutualistic primary endosymbionts 550–553 – urease-generating ammonia 338 mxi-spa locus 486 – virulence properties 332 Index j703

Mycobacterium avium 204 – virulence, isocitrate lyase function 343 – containing vacuoles pattern 120 – virulent strains 418 – intracellular complex 328 mycolic acid-containing lipids/ – Johne’s disease 328 lipoglycans 356 – paratuberculosis (MAP) 328 – mannosylated lipoarabinomannan 356 Mycobacterium bovis 89, 229, 327, 328, 337 – trehalose dimycolate 356 – antituberculosis vaccine 328 mycosporine-like amino acids 542 – BCG phagosome 337 MyD88-dependent pathway 266 – cattle tuberculosis 327 myosin 128, 129 – vs. Mycobacterium tuberculosis 327 Mycobacterium marinum 68, 83, 455 n – amoeba Dictyostelium 460 NADPH oxidase enzyme 310 – bacterial proliferation 456 – components 309 – Erp protein 461 – cytochrome b558 309 – establishment of 457, 458 Natural killer cells 213, 434 – ESX-5 locus 462 – effector function of 213 – fish, pathogen of 68 – granular lymphocytes 213 – gene mag-24 462 – human cytotoxic T lymphocyte (CTL) – genome sequence 461 214 – illness 455 – interferon g (INFg) 434 – immunological aspects of 463, 464 – role 213 – infections caused 456 natural resistance-associated macrophage – intracellular growth of 70 protein 1 (NRAMP1) 365 – intra-host cell compartmentation, – NRAMP1 transcription 365 characterization of 458–460 Necrotic Peyer’s patches 614 – phagolysosome formation 460 N-end rule pathway 443 – phagosome maturation, genes N-ethylmaleimide-sensitive fusion involvement 461–463 protein 96 – RD1 region 462 Neisseria gonorrhoeae 120 – virulence 458, 460, 461 Neohartmanella hartmanellae 8 – water-borne Gram-positive 455 Neonatal cardiomyocytes 663 – zebrafish 456 neuraminidase 662 Mycobacterium smegmatis 135 neutrophil-derived lipochalins 346 Mycobacterium tuberculosis 84, 90, 145, 150, Neutrophils see polymorphonuclear cells 165, 288, 328–331, 335 newborn larvae 670 – BCG vaccine 331 NFkB activation pathways 620 – cell death 347 NFkB-dependent cytokines 384 – clinical isolates analysis 329 NFkB-dependent survival circuitry 621 – complex 327 NFkB signaling pathways 626 – deletion mutants 339, 344 nitric oxide synthase 397, 424 – genomes 327 – derived reactive nitrogen intermediates – immune response 346 (RNIs) 341 – infection 341, 347 nitrogen-fixing cyanobacteria 529 – infection switches 329 nitrogen starvation 539 – intracellular, transcriptome/proteome Nocardia asteroides 355, 356 analysis 343 – characterstics 355 – in vitro-derived low iron/oxygen 153 – compartment 358, 360 – phagocytosis 335 – diverted phagosome maturation genes – phagosomes 335, 336, 337, 460 363–364 – risk factor 330 – immune responses 367 – transcriptome analysis 335 – immunology 364 – T cell antigens 346 – infection, Parkinson’s disease 357 – transcriptome profiling study 343 – lysozyme resistance 356 – transmission 347 – rifampin/erythromycin therapy 356 704j Index

NOD see nucleotide oligomerization domain – lipopolysaccharide-binding protein (LBP) nodulation signaling pathways 511 41 – endomycorrhization signaling – mannose-binding lectin (MBL) 41 pathways 511 – SP-A 42 – GTP-binding proteins 513 organelle fusion vs. organelle targeting non-typhoidal salmonellosis (NTS) 375 100 nondegradative vacuoles 451 – SLAPs 450 p Nonospora macronucleata 184 paracytophagy endogenous process, nonpathogen-containing phagosomes 135 advantage 440 nonphagocytic cells 335, 478 parasitophorous vacuoles (PVs) 274, 288, – in vitro infection 335 584, 585, 605, 606, 636, 638, 658, 660 nonprofessional phagocytes 163 – as host-parasite interface 605 – fibroblasts 163 – electrophysiology measurements 638 – macrophages 163 – environment resistance 291–293 – macropinocytosis 164 – proteome analysis 606 – microorganisms, uptake of 164 – resident proteins 606 – receptor genes 164 – role 605, 606 novel antibiotics 199 pathogen(s) 151, 164, 199, 464 – development of 199 – co-infections 348 N-terminal signal peptides 640 – containing phagosomes 85, 295 nuclear proteome 681 – derived antigens 267 – laminin-containing fraction 681 – gene expression-derived metabolic nucleate actin 135 map 151 nucleotide oligomerization domain (NOD) – host cell systems 77 296 – induced actin polymerization 379 – factor 508 – induced alterations 107 – like receptor 336 – induced changes, proteomic analysis – proteins 518 119–121 – receptor family 424 – iron-binding host proteins 199 – signaling 510 – macrophages, zebrafish 464 – signaling cascade 519 – malaria parasite 165 nurse cell 669, 670, 679, 684, 685 – peroxisomal vacuoles 185 – antioxidant enzyme expression 685 – prototype, diseases descriptions 472–475 – immunology 684–686 – transcriptomes 151 – remodeling/maintenance 679–684 – virulence factors 458 – involving molecules 679–684 pathogen-associated molecular patterns nurse cell phenotype 680 (PAMPs) 38, 51, 262, 266, 407 – parasite regulation evidence 680–683 – lipoproteins 302 nurse cell polymorphism 677 – lipoteichoic acid (LTA) 38 – membrane-anchored o lipopolysaccharides 38 obligate intracellular bacteria 10 – Nod/CARD family proteins 407 – Chlamydiae 10 – peptidoglycans 38 – Mycobacterium leprae 10 pathogenicity islands, see genomic islands – Rickettsiae 10 pattern recognition receptors (PRR) 38, 262, octadecyl rhodamine B 82 267, 335, 550 oligo-dT labeled beads/columns 148 – C-type lectins 38 oligomeric pore complex 441–442 – germline-encoded 335 – CDC monomer 441 – glycosylphosphatidylinositol (GPI)-anchored oligopeptidase B pathway 657 glycoprotein 38 opsonin(s) 41, 42 – integrins 38 – complement-derived proteins 41 – scavenger receptors 38 – C-type lectin 42 – toll-like receptors 38 Index j705 peptidoglycan – compartment maintenance genes 361 – N-acetylglucosamine residues 446 – contents 77, 85 – armored plastids 534 – whole-cell assays 77–79 – N-deacetylase 446 – cytoplasmic granules, fusion 210 – deficient C3PO 589 – development 160 – recognition protein 553 – drugs, loss 196 peribacteroid space (PBS) 513 – dynamic organelle 118–119 – hydrolytic enzymes 513 – endocytic pathway 447 Peyer’s patches 432 – endosome fusion assays 96, 97, 589 phagocytes 228 – formation quantification 80 – cells 65, 151, 209–212, 436 – fusion 136 – macrophages cell 37, 211–212 – b-galactosidase activities 83 – neutrophils cell 37, 210–211 – genetic probes 86–87 – coevolution 65 – gram-positive/gram-negative bacteria 342 – fusion 160 – hydrolytic activities 82 – granuloma formation 228 – interaction, schematic presentation 127 – mammalian cells pathway, outline 161 – killing 255 – MHC II-bound antigens 226 – lipase/protease activities 83 – particle binding stages 37 – lipid rafts 265 – phagosome formation/maturation – lumen, acidic 160 stages 37 – lysosome 360 – receptors 37–39, 51, 163 – components 79 – red blood cell (RBC) colonization 163 – formation 360 phagocytosis 41, 46, 50, 65, 125, 132, 138, – fusion 79–81, 82, 100, 104, 240, 290 159, 184, 221 – inhibition targeting 103 – amoebal ancestors 209 – maturation 48–50, 95, 126, 162, 361, – cytoskeletal elements 162 588 – definition 159 – arrest 459 – dendritic cells 160 – LPG role in inhibition 588–589 – endosome 160 – Rab-GTPases proteins 49 – gentamicin assays 194 – schematic presentation 126 – in cytostome 608 – SNAREs proteins 49 – inflammatory signals 50–52 – Staphylococcus 342 – intracellular trafficking 11 – TDM-mediated inhibition 341 – membrane dynamics 46–48 – membrane – modes 539 – protein 133, 134, 382, 421 – protozoa, nutrients 65 – symbiosome 535 phagolysosome 48, 95, 160, 177, 200 – model building 113–118 – biogenesis 588 – particle-induced impact isolation 112–113 – formation 199, 361, 364 112 – microscopic analysis 199 – pH quantification 81–82 – fusion 149 – proteomics methods 108–112 – intracellular bacterium Coxiella delay 178 – bead-containing phagosomes 108–110 – Legionella 179 – microbe-containing vacuoles 110–111 – Leishmania 178 – phagosomal protein separation 111–112 phagosomes 107, 118 – quantification 79–81, 82–83 – aggregation 130 – endocytic tracer analysis 80 – antimicrobial mechanisms 184 – fluorescence resonance energy transfer 80 – binding 138 – marker protein analysis 79 – biogenesis 66, 77, 78 – Rab proteins 162 – Dictyostelium 66 – real-time microscopic imaging 86–87 – examination methods 78 – receptor-mediated endocytosis, – lipids roles 377 transportation 200 – bound myosin 128 – trafficking 90, 138 706j Index

phosphatidylinositol 3-kinase (PI3K) 44, – choice 601 49, 112, 161, 244, 278, 319 – invasion 601 – activation 621 – modification 602 – chemical inhibitors 319 – illness caused 598–600 – deletion 320 – infected cells 604, 609 – mannosides 104, 337 – intra-host compartmentation – mutants 319 characterization 600 – pathway, E2F/c-Myc transcription – morphological description 600–601 factors 623 – nutritional aspects 604 – products 320 – parasite cell biology/genomics to drug – role 319 targets 607 – substrates 320 – apicoplast 607 – surface-exposed GPI-anchored proteins – food vacuole 608 removal 304 – novel permeation pathways 608 phosphatidylinositol 4-kinase (PI4K) 133 – relationship to virulence 600, 603 phosphatidylinositol 4-phosphate 5-kinase – schizogony 601 alpha (PIP5KIa)43 – specific enzymes, digestive vacuole 604 phospholipid analogs 99 – transmitting agents 597 – benzoxadiazole phosphatidylethanolamine – virulence factors 606 (NBD-PE) 99 pleckstrin homology (PH) domain 378 – lissamine rhodamine polymerase chain reaction (PCR) assays phosphatidylethanolamine (N-Rh-PE) 99 239 507 polymorphic immunodominant molecule – arbuscular mycorrhizae 508 (PIM), functions 624 – bacterial symbionts 507 polymorphonucelar neutrophils cells – genes 510 (PMNs) 206, 210, 219, 261, 332 – common signaling/symbiosis pathway – intracellular microbes, host cells 210 512 – residual function 332 – plant perception 510–512 – transforming growth factor b (TGFb) 211 – symbiosis initiation 510 polymorphonuclear cells 261 – symbiosome 513–514 primary endosymbiont 528, 549, 551, 552 – invasion 508–509 – SOPE/SZPE 549 – metabolic pathways 608 professional phagocytes 163 – type II fatty acid biosynthesis 608 proinflammatory cell death mechanism, – symbiosis 507, 528 role 424 plasma membrane 128, 197, 513 proinflammatory cytokines 267, 321, 347, – diffusion 197 664 – mediated invasion pathway 658 – interleukin types 321, 347 – SM, invagination 513 – interferon g (IFNg) production 321 plasmids 27, 30, 356, 361, 362, 482 – role 267–268 – characterization 483 – tumor necrosis factora (TNFa) 347 – virulence 360 prokaryotic type IV secretion system plasminogen activator inhibitor type 2 (T4SS) 311 (PAI2) 348 – inclusions biogenesis 311 Plasmodium falciparum 151, 597, 602 promastigotes 585–586 – cell biology 609 – containing phagosomes 585, 586 – human host lifecycle 598–599 a-proteobacteria 5, 8, 239, 287 – infected erythrocyte, transmission electron – Coxiella 287 micrograph 602, 603 – Ehrlichia 8 Plasmodium species 220, 224, 597 – Rickettsia 8 – cell biological enigma 605 – Wolbachia 555 – erythrocytic stages 601 – Wolbachia pipientis 8, 10 – hemoglobin degradation pathway 608 protein – host cell – biosynthesis 192 Index j707

– cytoskeleton interactions 12 – specific effector proteins, NopL/NopP 183, – domain analysis 310 518 – interaction network 117, 619 – symbiotic signal molecules 514, 515 – profiling techniques 152 Rho family proteins 131 – tyrosine kinases (PTKs) 622 – GTPases 44, 45, 589 protein kinase C (PKC) 46, 589 rhodamine 134 – isoforms 449 – actin 134 – role 450 – dextran 128 proteolytic processes 616 Rhodococcus equi 355 – protease inhibitors, role 616 – antibody-opsonized 358 proteome, intracellular 147 – characteristics 355 proteomics, derived model 107 – chromosomally encoded virulence Pulse-Chase protocol 80 factors 362–363 purified phagosomes assays 87–88 – high-temperature-requirement A protein – lipidomics 88 (HtrA) 363 – proteomics 87–88 – isocitrate lyase 363 pyruvate dehydrogenase (PDH) 439 – mycolic acid-containing glycolipids 363 – nitrate reductase, role 363 r – peptidase D 363 Rab proteins 162, 260 – compartments 358, 360 – GTPases 49, 96, 281 – complement receptor 358 – interacting lysosomal protein (RILP) – containing vacuole 359, 360, 365 expression 50, 138 – antigen presentation 365 – phagosome fusion, key regulators 160 – experimental infection models 357 reactive nitrogen intermediates (RNIs) 211, – illnesses caused 355, 356 642 – immunity 364, 365 reactive nitrogen species (RNS) 293, 382 – infection 366 reactive oxygen species (ROS) 382, 446 – host genes relevant 364 – – intermediates 293, 642 TH2 responses control 366 receptors – in horses 356, 357 – mediated endocytosis process 95, 112, 196 – rifampin/erythromycin therapy 356 – mediated phagocytic process 584 – phagocytosis 358 – specific interactions 112 – virulence animal model 357 recombinant DNA technologies 609 – virulence plasmid 360, 367 recombination detection programs 28 Rickettsia prowazekii 181, 479 – Geneconv/MaxChi 28 – Gimenez staining 470 red blood cells (RBCs) 163, 598 – human infections 479 – blood-sucking insects 165 – mouse leukocytes/macrophages 479 – colonization 163, 164 – vascular endothelium 479 – membrane 604 Rickettsia species 469, 471, 472, 480 – Plasmodium merozoites 165 – animal models/immunology 479–480 regulatory genes, WhiB genes 344 – feature 471 regulatory system 310, 363 – genomics/proteomics 480–482 reverse transcription polymerase chain – intracellular parasitic nature 481 reaction (RT-PCR) 146, 552 – intracytoplasmic behavior 472–477 Rhizobium 183, 513, 516 – lifecycle 471 – flavonoid/NodD1 dependent regulatory – ligands 472 cascade model 520 – plasmid 482 – legume plant 183 – rickettsial diseases 469–472 – legume symbiosis, membrane 77, 183 – salivary glands 471 – NGR234, 520 – transmission 470 – nodules formation 183 RNA – roles 516 – amplification techniques 149 – species 14, 508, 515 – interference (RNAi) targeting 574 708j Index

– polymerase sigma factors, role 406 selectively capture transcribed sequences – profiling experiment 146, 149 (SCOTS) 148 – purification techniques 147 self-limiting influenza-like syndrome – silencing data 575 567 Rocky Mountain spotted fever (RMSF) 477 semi-intact cells vs. cell-free assays 100 rough endoplasmic reticulum (RER) 68, serial analysis of gene expression (SAGE) 673 technique 147 severe combined immunodeficiency (SCID) s 366, 434 Saccharomyces cerevisiae 29 Shigella, host defense 496 – human homologs 308 – cellular innate immunity, role of Salmonella species 164, 221, 373, 375, 377, 496–498 378, 379, 382, 383, 514 – escaping autophagy 496–498 – antigens, 383 – immune response 497 – biogenesis 376, 384 – resistance 498 – factors affecting 378 Shigella species 485 – host response inhibition by T3SS2, 382 – bacterial invasion 494 – containing phagosomes 104 – cell-to-cell spread 493 – containing vacuole 87, 373, 376, 379, 382, – chicken embryo fibroblasts 492 384 – connexin-dependent intercellular – characterization 376 communication 493 – endosomal markers 377 – cytoskeletal reorganization 491 – immunology 383 – epithelial cells 487 – juxtanuclear positioning 379 – Gram-negative bacteria 486 – lysosome fusion 382 – host cell cytosol 494 – maturation model 373, 377 – IcsA/VirG protein 496 – membranes 381 – IFN production 497 – role in virulence 376 – IL-1 receptor 487, 498 – virulence factors regulation 382 – infections 497 – effector protein, SopB 377 – enteroinvasive bacteria 498 – gene expression 382 – HLA-B27 patients 497 – induced filaments 139 – intestinal 485, 498 – induced gastroenteritis 375 – intracellular lifestyle 492 – infections in animals 375 – introduction 485–488 – infections in humans 373–375 – invasion 490 – inflammatory surface molecules 383 – bacterial colonic mucosa 486–488 – invasion characteristic signature 378 – cellular and tissular strategies 490 – mutants 381 – in vitro epithelial cells 498 – persistent infection development 375 – IpaB/IpaC 491 – serovars 374, 375, 383 – lipopolysaccharide 487 – SipC translocator component 495 – phagosomal escape 494 – type III protein secretion system – rabbit ileal loops infection 493 (T3SS) 164, 380–382 – red blood cell hemolysis 494 – typhoid-like systemic disease 375 – Shigellosis 485 – virulence factors 147 – acute inflammation 487 scavenger receptor A (SR-A) 258 – bacterial dysentery 485 second messengers 43 – hemolytic uremic syndrome 486 – diacylglycerol 43 – transcriptomic analysis 498 – inositol 1,4,5-trisphosphate 43 – vacuolar lysis 494 secondary endosymbionts 529, 549, 559 – virulence factors 422 – types 549 Shine–Dalgarno sequence 439 secondary endosymbiosis process 8, 529, signal transducers and activators of 597 transcription (STATs) 621 – schematic presentation 529 signaling pathways 679 Index j709

– proteins types 116 – Nod proteins 519 – raft-induced 265 – production 514 – TGFb/TNFa, 679 – rhizobial regulation 518–519 signature-tagged transposon mutants, – rhizobial surface polysaccharides, screening 405 roles 516–517 single particle reconstruction analysis 489 – secreted proteins 517–518 skeletal muscle 671 – TtsI and tts-boxes 519–520 – structural proteins 677 – stages 534 þ þ Slc11a1 / gene 375, 382 – genetically resistant 375 t – murine model 375 target particles recognition 38–42 – role 376 – cooperation between receptors 42 small interfering RNAs (siRNAs) 89, 317 – direct 38–41 smokescreen effect 607 – indirect 41–42 soluble N-ethylmaleimide-sensitive factor T cell 227, 366 attachment protein receptor (SNARE) 96, – bone marrow precursor cells 218 309, 318 – function 480 – interaction 318 – granulomas 219 – complexes 280, 281, 318 – intracellular pathogens 228 – proteins 47, 102, 116 – markers, de novo expression 615 – VAMP2 proteins 309 – mediated clearance mechanism 366 spacious Listeria-containing phagosomes – MHC I pathway 227 (SLAPs) 451 – phagosomal pathogens 228 specific cell-mediated immunity, – receptor 217, 346 development 568 – SCID deficiency,366 spotted fever Rickettsia 477–479 – target antigens 626 scavenger receptors (SRs) 38, 39 tetracycline-resistant genomic islands 25, 26 – classes 39 Theileria parasites 29, 613, 614, 626 stable isotopes labeling by amino acids in cell – antiapoptotic mechanisms 619 culture (SILAC) 111, 118 – east coast fever 613 subtelomere-encoded variable secreted – host cell proliferation 627 proteins (SVSPs) 624 – host-parasite interaction genes 623 – FAINT domains 624 – host cell cytoskeleton interactions 625 superoxide dismutases (SODs) 257, 293 – host cell released proteins 624 suppressor of cytokine signaling 3 (SOCS3) – schizont surface 624 406 – immune responses against schizont 625 surface polysaccharides (SPS) 516 – induced Hck activation 622 surface proteins 615, 624 – infection 615 – adhesions 258 – intra-host cell compartment – lectins 258 characterization 615 – matrix proteins 258 – casein kinase II 623 – schizont, PIM 624 – c-Myc activation 620 – types 615 – cytoplasm development 616 symbiont hypothesis 6 – entry 615 – host relationships 13 – host cell manipulation 619 – schematic drawing 6 – mitogen-activated protein kinases 621 – symbiont interaction 23 – NFkB activation 619 symbiosis 13, 538 – phosphatidylinositol 3-kinase 623 – associations goal 527 – Src family 622 – interactions 534 – infections 614 – maintenance 538 – JAK/STAT 621 – protist 531–535 – non-transforming species 613 – signals 514 – pathogenesis macrophage role 615 – Nod factors 514–516 – schizont 624 710j Index

– property 617 – STAT3, phosphorylation 645, 646 – proteins 624 – strain diversity 634 – sporogony 615 – tachyzoites replication 637 – transformed cells 619–622, 627 trafficking pathways 605 – transforming species 613 – proteins 448 – transmitting agents 614 transcription 90, 675 – vaccines 628 – phagosome environmental sensor 90 tissue glycolipids, solid-phase assays 396 – profiling 145 T lymphocytes, see T cells – reprogramming 675, 678 toll-like (TIR) 66, transferrin receptor 241 207 – expression 622 toll-like receptor (TLR) 16, 40, 51, 242, 262, – pathway 337 406 – transports 345 – classification 51 transforming growth factor b (TGFb) 211, – signals 332 497 – types 383, 557 – anti-inflammatory properties 497 toxins 65 trans-Golgi network (TGN) 308, 419 – inactivators 198 translocator protein, BipD 399 – production 67, 198, 223 transmembrane adhesion protein, E- Toxoplasma gondii 166, 261, 633, 642, 643 cadherin 437 – food-borne infection 633 transmission electron microscopy (TEM) 80, – hormone abscisic acid 638 672 – infections 633 – experiments 80 – humans 633 transport systems, ABC transporters 445, 446 – toxoplasmosis 634 trans-autophosphorylation, proximity- – intracellular compartment, induced 620 characterization 635 trehalose dimycolate 211, 338, 364 – actin-based motility 636–637 – mycobacterial glycolipid 338 – active entry 637 Trichinella species 677, 684 – intracellular cycle 635–636 – derived antigens localization 682 – intracellular compartment, – ecto-protein kinase activities 684 immunology 641 – induced changes 678 – CD40/lysosomal clearance 644 – secreted products 680 – cytokine production, disruption – Trichinella pseudospiralis 677 645–646 – histochemical analysis 677 – host cell signaling 644 – infected muscle tissue 679 – IFNg signaling, disruption 644–645 – nurse cells 677, 678 – immunity-related GTPases 643–644 – Trichinella spiralis nurse cell 675 – infection control 641–643 – development 675 – intracellular fate 639 – infected tissue images 675 – intracellular lifecycle 635 – Trichinellids 669, 670 – invasion 637 – Trichinellosis 669–670 – lipoic acid 641 Trypanosoma cruzi 655 – macrophages expressing CD40 644 – antigen presentation 665 – mitochondrial product 641 – blocking apoptosis 663 – nonfusigenic nature 639 – Bradykinin receptors 657 – pathogenic nature 644 – hemolytic toxin Tc-TOX/LYT1, 662 – phagocytosis 637 – HIV/AIDS patients 656 – protein secretion 639 – immunology 664 – dense granule proteins 639 – TLR4-competent cells 665 – microneme proteins 639 – infected cell, maintenance 663 þ – rhoptry proteins 639 – CD4 T-cells 664 – reverse genetics techniques 634 – host cell apoptosis, subversion 663 – secretory pathway 641 – infected fibroblasts, microarray analysis 660 Index j711

– intracellular compartmentation 657 v – invasion 657, 659 vaccines 229, 281 – lysosome-independent pathway 658 – tissue culture 618 – trypomastigote retention 658, 660 – typhoid fever 230 – life cycle 661 – viruses 229 – parasite/disease 655–657 vaccination strategies 256–257 – parasitophorous vacuole, escape 661 vacuolar ATPase 359, 360 – phagosomes 660 – catalytic subunit, A 576 – trypomastigote stages 660 – proton 336 – trypanosome 655, 657, 664 – paucity 336 – bloodstream 655 – pumping 359 – trans-sialidase 662 vacuolar lysis 488, 494 tuberculosis 340 vacuolar membrane 450 – hypoxic conditions 344 – LLO-dependent perturbations 450 – T cell activation, apoptotic blebs 228, 339, vacuole-free pathogens 181 340 – cytoplasmic ubiquitin/proteasome protein tularemia 415, 424 degradation 181 – clinical forms 415 – macrophage’s cytoplasm 181 – pathogenesis 424 – Mycobacterium marinum 183 tumor necrosis factor (TNF) 46, 184, 206, var genes 604, 606, 607 365, 567, 571, 600, 619, 642 – expression 604, 607 – cytokine storm, effects 645 – silencing 607 – formation 184 variant erythrocyte surface antigen 604 – LPS-treated macrophages 645 vascular endothelial growth factor 249, – receptor 2 (TNF-R2) 348 675 two-component system (TCS) 310, 382 vasodilator-stimulated phosphoprotein 402 – histidine sensor kinase 310 vesicle-associated membrane protein 309 – PhoP/PhoQ 382 vesicular trafficking pathways 288 – response regulator 310 virulence-associated proteins 328, 357, 362, – sensory system 399, 403, 406 399 – phosphate moiety 400 – classes 356, 357, 362 – signal transduction system 344 – encoding plasmids 362 – DosR/PhoP regulon 344 – function 362 two-dimensional gel electrophoresis 109, – types 356, 357 147, 683 virulence-relevant surface-located systems type III secretion system 398, 488, 550 85 – analysis 489 – protein secretion systems 85 – effectors 379, 381, 517 virulence factor 406, 420, 486 – proteins 376 – expression 382, 425 – erythrocyte lysis assays 489 virulence gene expression 382 – gram-negative bacteria 489 virulent mycobacteria 340 – red blood cell hemolysis 494 – cytoplasmic localization 340 – rhizobial, genomes 517, 520 visceral leishmaniasis, see Kala-azar – role 398 vitamin D receptor 214 – Shigella 489 – translocated effector proteins 383 w – transmission electron micrographs 488 Warthin–Starry silver stain 238 – TtsI regulates 520 Wayne culture model 344 type IV secretion system (T4SS) 258, 265, Western blotting analysis 87, 134 295, 550 whole-genome expression profiling 145 whole-proteome identification studies 113 u Wiskott–Aldrich syndrome protein ulceroglandular tularemia 415 (WASP) 43, 45, 402, 476, 585 urease-generating ammonia 338 – homology-2 (WH2) domains 403 712j Index

Wolbachia pipientis 10, 14, 28, 556 – opsonization 569 – infected arthropods 28, 29 – dsidA G186AR 578 – mutagenesis 14 – G217BSIDA-silenced 578 World Health Organization (WHO) 329, 330 – phase-specific protein 3 (YPS3) 575 – two-hybrid screening technology 4, x 280 xylem-feeding sharpshooters 551, 559 Yersinia pseudotuberculosis 278 – Baumannia cicadellinicola 551, 559 – type III protein secretion 197 – Sulcia muelleri 551, 559 z y Ziehl–Neelsen staining, see acid-fast staining yeasts zipper-type mechanism 436 – containing phagosomes 570, 571 zoonotic disease 256