Index

AACA. See Adenylyl cyclaseacaA. See Adenylate cyclase AACC. See 1-aminocyclo-propane-1-carboxylic

acidAcinetobacter baumannii, 10Acrasid cellular slime molds, 220, 224Acrasidae, 231, 233

A. rosea, 231, 232Heterolobosea, 231, 232molecular phylogenetic analyses, 232, 233P. flagellata, 231

Acrasis granulata (A. granulata), 226, 231Acrasis rosea (A. rosea), 227, 231, 233

life cycle of, 232morphotype of, 233

Actin cytoskeleton, 12–14, 60Actin polymerisation, 53, 54

effect on pseudopod formation, 52in lamellipodia formation, 55

Acytostelium leptosomum, 149Acytostelium subglobosum (A. subglobosum),

140Adenylate cyclase A (acaA), 93Adenylyl cyclase (ACA), 56, 73, 75Aggregation, 56–59, 201

centres, 57optical density waves, 59periodic cAMP synthesis, 56signals, detection and amplification, 58

AgnA–E. See ArgonautesALC. See Anterior-like cellsAllovahlkampfia kona (A. kona), 233ALS14. See Amyotrophic lateral sclerosisAlzheimer’s disease, 19, 20

American Type Culture Collection (ATCC),234

1-aminocyclo-propane-1-carboxylicacid (ACC), 134

Amoebozoa. See CopromyxidaeAMP-activated protein kinase (AMPK), 20, 21AMPK. See AMP-activated protein kinaseamtA, 100amtC, 100Amyloid precursor protein (APP), 19Amyotrophic lateral sclerosis (ALS14), 19Ankyrin B (AnkB), 13Anterior-like cells (ALC), 31, 63, 96APP. See Amyloid precursor proteinArgonautes (AgnA–E), 119ATCC. See American Type Culture

CollectionAutophagy, 15

Atg9, 16ER and mitochondria, 16, 17microautophagy, 15, 16PI3Kinase complex, 16, 17by starvation conditions, 16Vmp1, 16

Axenic liquid broth medium, 6

BBacterial artificial clones (BAC), 37BamHI, 8Basic leucine zipper (bZIP), 96Biogeography of protists, 177, 178Biomedical research, in Dictyostelium dis-

coideum. See Dictyosteliumdiscoideum

M. Romeralo et al. (eds.), Dictyostelids,DOI: 10.1007/978-3-642-38487-5, � Springer-Verlag Berlin Heidelberg 2013

243

Bipolar disorders, 22Li treatment, 24

Burkholderia cenocepacia, 10Butterfly woods, 159Bystander effect, 207BzpF, 101

CC-module binding factor A (CbfA), 93–94Caenorhabditis elegans (C. elegans), 2, 4, 12,

91, 119, 125Calcineurin (CN), 101cAMP. See Cyclic adenosine monophosphatecAMP receptors (cARs), 73

Dictyostelium, 74heterotrimeric G proteins, 79structure, 74

cAMP response element binding protein(CREB protein), 101

cAR1 transcription factor (Crtf), 94, 95cARs. See cAMP receptorsCbfA. See C-module binding factor ACell density sensing factors, 92Cell migration, 14Cell motility, 2, 13

actin cytoskeleton, 14–15DCX, 14GPCR, 14LIS1, 14–15lissencephaly, 14pathobiology, 13–14SDS, 15

Cell movement, 50actin cytoskeleton, 14from aggregation, 6230-50 cyclic AMP use, 49to cytoskeleton

actin filament network, 51cell-substrate contacts, 50, 51class I myosins, 51–52non-stimulated cells, 52in response to cAMP gradient, 51

in eukaryotic cells, 5interaction with signalling, 61

Cell–cell repulsion, 194Cell–cell signalling, 49, 50, 56Cellular behaviours, 50

during chemotaxis, 52–53Cellular slime molds (CSM), 183, 193, 210,

220behavioural modification, 210–211characteristic feature, 194

diversification, 174–177ecology, 177–178evolution, 167–170exceptions, 185fruiting body shapes, 189–190heterodox, 190intercellular interactions, 203–207microorganisms morphology, 186molecular phylogenies, 184morphology versus molecular data,

170–174natural selection for dispersal, 187–188null hypothesis, 195patches of bacteria, 187pre-aggregation cells, 202–203slugs migration, 188social selection, 196, 198

evolutionary consequences, 207–210fitness consequences, 199P. pallidum, 197, 198phenotypic variation, 197sexual reproduction, 196–197social groups, 198

sociality development, 199–200stochastic factors, 202–203temporal expression, 211traits, 200–202unimodal phenotype, 204

Chaperone-mediated autophagy (CMA), 15Chemoattractant, 52

binding of, 72, 75cell’s Gb lacking effect, 79cells measuring, 5230-50 cyclic AMP, 49D. discoideum response, 73quorum sensing, 201temporal responses to, 77–78

Chemokines, 6, 14, 52Chemokinesis, 52Chemotactic compass, 71

cAMP and folic acid, 73–74chemotaxis, 71–73polarity in migration

gradient sensing and switching, 78pseudopods, 79

signalingcAMP oscillations, 77chemoattractants, 75evolutionary model, 76Ras D expression, 76

Chemotaxis, 2, 13actin cytoskeleton, 14cellular behaviours

244 Index

in Dictyostelium, 52pseudopod extension process, 53starving Dictyostelium cells, 52

cytoskeleton, 72DCX, 14–15Dictyostelium sp., 73GPCR, 14LIS1, 14–15lissencephaly, 14migration of cells, 71pathobiology, 13–14SDS, 15signalling

actin polymerisation, 55cAMP gradients, 53cAMP signalling activation, 57G heterotrimeric proteins, 54LEGI model, 53–54molecular mechanisms, 55–56phospholipases, 54–55PI3 kinase, 54quantitative characterization, 56Rac activation, 55

Chronic obstructive pulmonary disease(COPD), 14

CI. See Complex ICienkowsky’s description, 226ciPCR. See Culture-independent PCRCisplatin, 22CMA. See Chaperone-mediated autophagyCMF. See Conditioned medium factorCN. See CalcineurinComplex I(CI), 21

of oxidative phosphorylation chain, 5Conditioned medium factor (CMF), 92COPD. See Chronic obstructive pulmonary

diseaseCopromyxa, 139Copromyxa arborescens (C. arborescens), 228Copromyxa protea (C. protea), 228

life cycle of, 229mature fruiting bodies of, 228, 229

Copromyxella sp., 230–231Copromyxidae, 2, 228

C. arborescens, 228C. protea, 228, 229–230Copromyxella sp., 230–231tubular mitochondrial cristae effect, 230

Cortexillin, 78cotA, 100cotB, 94, 100cotC, 95, 99, 100

cotD, 100cprB, 95CRAC. See Cytosolic regulator of adenylyl

cyclaseCrc protein, 12CREB protein. See cAMP response element

binding proteinCrtf. See cAR1 transcription factorCSM. See Cellular slime mouldsCulmination and fruiting body formation,

99–102, 201cotC, 100distal promoter, 101MADS-box transcription factor, 100–101MybC, 99–100pspA, 100pstA cells, 99pstO cells, 99putative TF PadA, 100TacA, 101–102temperature influences, 99

Culture-independent PCR (ciPCR), 174Cyclic adenosine monophosphate (cAMP), 6,

52, 73, 135cells moving in response to, 51chemoattractant 30-50, 52D. discoideum cells treatment with, 23external, 59periodic regulation, 73signaling, 49, 57waves, 58

30-50 cyclic AMP, 49Cytosolic regulator of adenylyl cyclase

(CRAC), 57

DDCX. See Double-cortinDicer proteins (DrnA), 119DictyBase, 9, 44, 91Dictyostelia

diversificationage for dictyostelids’ crown node,

175–176fossil calibration, 174, 176molecular dating of protest, 175Myxogastrea, 168, 177reconstructions of divergence times,

175terrestrialization, 176–177

within soil, 178species, 169, 170, 172

Index 245

See also Sex in DictyosteliaDictyostelid cellular slime molds. See Dicty-

ostelids, in North American forests;Cellular slime molds (CSM)

Dictyostelid social amoebas, 2, 168, 170diversification, 174–177morphology vs. molecular data, 170

ciPCR, 174Dictyostelia species, 170, 172Dictyostelids groups, 172, 173molecular tools, 174nrITS suitability, 170position of root, 172, 174

species complexes, 169Dictyostelids, in North American forests

dispersalbats, 151dictyostelid propagules, 150, 151

diversitydirect positive relationship, 155distribution types, 153species and absolute densities, 154in tropical and subtropical environ-

ments, 152ecological individuality

D. mucoroides, 158environmental responses and adapta-

tions, 157soil pH, 159

genomes, 140, 142global distribution

D. deminutivum, 162D. septentrionalis, 161deciduous forest, 160NSF PBI, 159

haploids, 131molecular phylogeny, 139optimum habitat, 155relative abundance

D. mucoroides, 152in Ohio, 151

sex determination, 138Dictyostelium, 51

aggregationcAMP receptor, 56cAMP relay and chemotaxis, 57counting factor, 58CRAC, 57detection and amplification, 58gene expression and distribution, 57optical density waves reflect cAMP

waves, 59cAMP receptors, 74during chemotaxis in, 52–53

pseudopod extension process, 53starving Dictyostelium cells, 52

development, 56differentiation

ACA, 63–64ammonia concentration, 64cAMP pulses control, 62cell types and cell type proportioning,

63cell–cell signalling mechanisms, 64DIF spreads, 62myosin II, 63–64prespore and prestalk cell types, 51

Dictyostelium discoideum (D. discoideum), 1,35, 90, 156, 157

A and T nucleotides, 36animal-like proteins in, 4chemotactic molecule, 2comparative genomics in, 4DIRS elements, 38functional categories, 91in human diseases, 2life cycle, 3MidA, 4–5molecular genetics

central resource, 9BamHI-sites, 8DpnII-sites, 8in experimental systems, 7insertional mutagenesis in, 8, 9phosphoinositide signaling, 7REMI, 8

molecular pharmacology, 23blind genetic screening, 22ERK, 22, 23GSKA-independent mechanism, 23through inositol depletion, 24Li, 22mammalian cell lines, 21–22phosphoinositide pathway, 24PO mutants, 24VPA, 22

multicellular structure, 2parallelisms with animal cells, 3pathogen–host interactions in, 10–13SH2 domain-containing proteins, 3social amoebae genome properties, 37from soil to laboratory

aggregative movement, 5cell movement in eukaryotic cells, 5complex regulation, 7dictyostelids, 5enzyme activities, 6–7mysterious chemotactic molecule, 6

246 Index

NC4 isolation, 6transcription factors in, 102Vmp1, 4–5See also Modeling human disease

Dictyostelium giganteum (D. giganteum), 174genetic variation, 174heterothallic strains, 137

Dictyostelium lacteum (D. lacteum), 39–42,44, 149, 151, 162, 211

Dictyostelium minutum (D. minutum), 131ancestral slime mold, 184group 3 species, 158macrocyst, 131

Dictyostelium mucoroides (D. mucoroides),131, 168, 224

aggregation, 131growth, 162sorocarpic amoebae, 224sorocarpic protists species, 171

Dictyostelium polycephalum (D. polyceph-alum), 142, 158, 189

Dictyostelium purpureum (D. purpureum), 90genetic variation, 174heterothallic, 140northern hardwood deciduous forest, 162

Dictyostelium rosarium (D. rosarium), 150,190

Differentiation inducing factor (DIF), 62, 206deficient mutants, 96, 97hexaphenone, 62lipid-soluble polyketides, 206morphological defects, 98putative TF PadA, 100

dimA- mutant, 97dimB- mutant, 97DimB proteins, 97Dimmers, active, 3, 4Dipeptide glorin, 184Diplophrys stercorea (D. stercorea), 236DNA, 7

alignments of coding, 39damage by UV, 176DNA-methyltransferase, 43exogenous, 7methylation, 43microarray, 101modification, 110surveys, 177transposons, 37

Double-cortin (DCX), 14Double-stranded RNA (dsRNA), 119DpnII, 8, 9DrnA. See Dicer proteinsDrosophila melanogaster, 2, 91

dstA- mutants, 98

EecmA, 94, 96–98, 100, 102ecmB, 95–101Endoplasmic reticulum (ER), 13, 118

autophagosome membrane, 16, 17eukaryotes, 118Legionella sp., 13Vmp1, 18

Everything is everywhere (EiE) hypothesis,177

Excavata. See AcrasidaeExtracellular calcium, 133Extracellular chemotactic molecule, 2Extracellular signal-regulated kinase (ERK),

22, 23

FFA. See Folic acidFeeding cells, 200–201Filopodia, 55

F. alba life cycle, 234gradient sensing or force generation, 55

Fluorescence recovery after photobleaching(FRAP), 79

Fluorescence resonance energy transfer(FRET), 54

Folic acid (FA), 73chemoattractant, 77mediated signaling, 79stimulation, 77, 78

Fonticula alba (F. alba), 233images of, 235life cycle of, 233–234type culture, 234–235

FonticulaceaeF. alba, 233–235Holomycota, 234

Form spores, 129–130, 226Förster resonance energy transfer (FRET), 79Fosmids. See Bacterial artificial clones (BAC)Fossil

calibration, 174, 176living fossils, 190metasequoia, 185record, 170, 186

FRAP. See Fluorescence recovery afterphotobleaching

FRET. See Fluorescence resonance energytransfer; Förster resonance energytransfer

Index 247

Fruiting bodies, 56, 200, 203Fruiting bodies (cont.)

amoebae, 194asexual, 129, 131–133, 136BzpF, 101by calcineurin, 101, 102cellular aggregation, 220, 224of Copromyxa protea, 228–230formation, 56, 99–102fungus-like, 220MADS-box transcription factor, 100–101multicellular formation, 89–90MybC, 99–100non-aquatic, 178in plasmodial slime molds, 220in Protostelia, 168putative TF PadA, 100shapes, 189–190single sorocarp, 235stages, 74stalk and spore mass, 193temperature influences, 99

Fungal models, 2Fungal traits, 2‘‘Fungus-like’’ fruiting body, 220

GG-box binding factor (GBF), 95G-protein coupled receptor (GPCR), 14GAP. See GTPase activating ProteinsGBF. See G-box binding factorgbfA, 95, 99, 103GDP. See Guanosine diphosphateGEFs. See Guanine nucleotide Exchange

FactorGenomics

future directions, 44–45social amoebae, 35–36

GFP. See Green fluorescent proteinGiant cell

Dictyostelid sexual and parasexual cycles,130

enlarged nucleus, 131–132haploid amoebae, 135macrocyst tertiary wall, 136

Global distributionD. deminutivum, 162D. septentrionalis, 161deciduous forest, 160NSF PBI, 159

GPCR. See G-protein coupled receptorGreen fluorescent protein (GFP), 75

autophagosome marker protein, 19

cAR1, 75pseudopods, 15

gtaC-mutant, 97GTP. See Guanosine triphosphateGTPase activating Proteins (GAP), 54, 75Guanine nucleotide Exchange Factor (GEFs),

75Guanine Nucleotide Exchange Factor activat-

ing Ras (RasGef), 54Guanosine diphosphate (GDP), 75Guanosine triphosphate (GTP), 75Guttulina protea. See Copromyxa protea (C.

protea)Guttulinopis clavata (G. clavata), 236Guttulinopis Guttulinopis (G. stipitata), 236Guttulinopis nivea (G. nivea), 236Guttulinopis vulgaris (G. vulgaris), 235, 236Guttulinopsidae, 236

HHD. See Huntington’s diseaseHereditary spastic paraplegia (HSP), 19Heterolobosea, 231, 232

Acrasis, 232lobose amoebae, 231Naegleria, 232

Heterothallism, 140Heterotrimeric G proteins, 79

cytosol and plasma membrane, 80Ga-subunit, 79immobile fraction, 81

Hexaphenone, chlorinated, 62, 95Histones, 110

methylation, 43modification, 110modifiers, 90, 91, 103

Holomycota, 234Homothallism, 140HSP. See Hereditary spastic paraplegiaHuntington’s disease (HD), 18

IImmune system, 14Individual amoebas, 2Individuality, ecological

D. mucoroides, 158environmental responses and adaptations,

157soil pH, 159

Inositol phosphate pathway, 23, 24Inositol-regulatory genes, 24Inositol synthase 1 (INO1), 24

248 Index

Internal Transcribed Spacer (nrITS), 168Dictyostelid phylogenetics, 170marker, 175

Internal transcribed spacer 1 (ITS1), 117

JJAK kinases, 4JAK receptors, 3

KKlebsiella aerogenes, 136Knock-out strains (KO strains), 7, 23

LLamins, 4LegC3, 13Legionella, 13Legionella pneumophila, 13, 113Legionnaires’disease, 13Lissencephaly 1 (LIS1), 14, 15Lithium (Li), 22lncRNAs, 111, 113

D. discoideum, 113genomic regions, 111

Lobosea, 230Local excitation global inhibition model

(LEGI model), 53, 54Long non-coding RNAs. See lncRNAsLumbricus terrestris (L terrestris), 156

MMacrocyst formation, 132, 202

cell fusion, 134–135cells of sexual cycle, 136cycloheximide, 137D. discoideum, 135extracellular calcium, 133germination, 137giant cell, 136haploid cells, 135–136humid or moist conditions, 133level of light, 132–133nutrient availability, 132temperature, 133–134

Macropinocytosis, 2, 21matA, 138, 140, 141matB, 139, 141matC, 139, 141

matD, 139Mating type sex, 132matS, 139matT, 139–141MDR. See Multidrug resistance transporterMedium-sized ncRNAs, 113–114

Class I RNAs, 114–115With unknown functions, 118non-coding RNAs, 117–118snoRNAs, 116–117spliceosomal RNAs, 115–116

Megabases (Mb), 9Messenger RNA (mRNA), 110

intron sequences, 115padA expression, 100transcriptional regulator genes, 92

Micro RNAs (miRNAs), 110, 119Microautophagy, 15–16Microbial models, 1–2Microcyst formation, 209MidA. See Mitochondrial dysfunction protein

AMitochondria, 20, 42

autophagosome membrane formation, 16,17

Copromyxella sp., 230Fonticula sp., 234mitophagy, 20organellar genomes, 41Pocheina sp., 231

Mitochondrial disease, 20AMPK, 20–21D. discoideum, 20MidA and CI, 21pathological phenotypes, 20yeast models, 21

Mitochondrial dysfunction protein A (MidA),5

Model organisms, 1, 2Modeling human disease

autophagy, 15Atg9, 16ER and mitochondria, 16, 17microautophagy, 15–16PI3Kinase complex, 17by starvation conditions, 16Vmp1, 16

cell motility and chemotaxis, 13actin cytoskeleton, 14DCX, 14–15GPCR, 14LIS1, 14–15

Index 249

lissencephaly, 14pathobiology, 13–14SDS, 15

genome analyses, 10mitochondrial disease, 20

AMPK, 20–21CI, 21D. discoideum, 20MidA, 21pathological phenotypes, 20yeast models, 21

pathogen–host interactionsAnkB, 13bacterial pathogens, 11D. discoideum cells, 10intracellular pathogens, 12–13Legionella, 10Legionella pneumophila, 13Mycobacterium, 10opportunistic bacteria in mammalian

models, 11–12Pseudomonas aeruginosa, 11virulence traits, 12

protein aggregation disordersALS14, 19amyloid precursor protein, 19Hirano body-like aggregation, 19HSP, 19Huntington’s disease, 18, 19in neurodegenerative diseases, 18–19PtdIns3P signaling, 18S. cerevisiae, 18

Moderate endemicity model, 177Molecular pharmacology, in D. dictyostelium,

23blind genetic screening, 22ERK, 22, 23GSKA-independent mechanism, 23through inositol depletion, 24Li, 22mammalian cell lines, 21–22phosphoinositide pathway, 24PO mutants, 24VPA, 22

Mounds, 59, 95and slug formation, 59–61

MrfA. See Myelin regulatory factormRNA. See Messenger RNAMS. See Multiple sclerosisMulticellular assembly, Dictyostelium cells, 95

bZIP, 96, 97complex gradients, 95, 96dgcA, 99DIF-1 functions, 97

DimB, 97evolution of organisms, 219–220MrfA, 98MybE, 98Psp cells, 96pst subtypes, 96in shaping cellular populations, 98–99STAT proteins, 97–98STATa, 97

Multicellularity, 220aggregative, 238Amoebozoa, 230prokaryotic and eukaryote life, 220rapid evolution, 195starvation, 129

Multidrug resistance transporter (MDR), 8Multiple sclerosis (MS), 14MybB protein, 93MybE protein, 98Myelin regulatory factor (MrfA), 98Myeloblastosis (MYB), 93Myxogastrea, 168

Dictyostelia, 175Mycetozoa, 168species-rich clade, 177

Myxogastrid slime molds, 226Myxomycetes. See Myxogastrid slime molds

NNational Science Foundation Plant Biodiver-

sity Inventory grant (NSF PBI), 159ncRNAs. See Non-coding RNAsNext generation sequencing technologies

(NGS technologies), 38NGS technologies. See Next generation

sequencing technologiesNon-coding RNAs (ncRNAs), 109

Dictyostelia, 111, 112gene expression, 109gene promoter element, 121–122medium-sized, 113

class I RNAs, 114–115D. discoideum, 118protein delivery and RNA processing,

117–118snoRNAs, 116–117spliceosomal RNAs, 115–116

RNP complexes, 110small RNAs

gene expression, 119microRNAs in D. discoideum, 120–121retrotransposon, 120

Non-dictyostelid sorocarpic amoebae, 226

250 Index

Acrasidae, 231, 233A. rosea, 231, 232Heterolobosea, 231, 232molecular phylogenetic analyses, 232,

233P. flagellata, 231

Copromyxidae, 228C. arborescens, 228C. protea, 228, 229–230Copromyxella sp., 230–231tubular mitochondrial cristae effect, 230

Fonticulaceae, 233F. alba, 233–234, 235Holomycota, 234

Guttulinopsidae, 236life cycle, 227–228research history, 224–227Sordiplophrys, 236–237See also Sorocarpic amoebae

Non-stimulated cells, 52North American forests, dictyostelids,

149–150decline, 156dispersal, 150–151diversity, 152–155ecological individuality, 157–159ecology, 156–157global distribution, 159–162optimum habitat, 155relative abundance, 151–152

nrITS. See Internal Transcribed SpacerNSF PBI. See National Science Foundation

Plant Biodiversity Inventory grant

OOpisthokonta. See FonticulaceaeOpportunistic bacteria in mammalian models,

11–12Optical density waves, 59, 60Organellar genomes, 41Oxidative phosphorylation, 5, 20

PpadAts, 100Parasexuality, 132Parkinson’s disease, 18, 20Pathogen–host interactions, in D. discoideum

cells, 10AnkB, 13bacterial pathogens, 11intracellular pathogens, 12–13Legionella, 10

Legionella pneumophila, 13Mycobacterium, 10opportunistic bacteria in mammalian mod-

els, 11–12and Pseudomonas aeruginosa, 11virulence traits, 12

Pathological thresholds, 20PDE. See PhosphodiesterasePelomyxa palustris, 141Phagocytosis, 2

dictyostelids, 5and endocytic traffic, 10haploid cells, 135intracellular pathogens, interference, 12null mutants, 19

Phosphatidyl-(3,4,5)-phosphate (PIP3), 56Phosphatidylinositide 3 kinase (PI3 kinase),

53, 56Phosphatidylinositol 4-phosphate, 13Phosphatidylinositol-4,5-bisphosphate (PIP2),

24, 56Phosphodiesterase (PDE), 8, 135Phosphoinositides (PIPs), 75Phospholipases, 54PI3 kinase. See Phosphatidyl-inositide 3 kinasePIAS. See Protein inhibitor of activated STATPIP2. See Phosphatidylinositol-4,5-

bisphosphatePIP3. See Phosphatidyl-(3,4,5)-phosphatePIPs. See PhosphoinositidesPiwi-interacting RNAs ((pi)RNAs), 110, 119PKA. See Protein kinase APkbA. See Protein kinase BPKS. See Polyketide synthase familyPlasma membrane (PM), 75

biophysical approaches, 79Crasis, 226PI3K, 77protein heterotrimers cycle, 80proteins, 134

Plasmids, 41–42Plasmodia, 226

fruiting body formation, 220slime molds, 168

Plasmodial slime molds. See MyxogastreaPM. See Plasma membranePocheina flagellata (P. flagellata), 231

and P. rosea, 231sorocarpic amoeba taxon, 221–223

Pocheina rosea (P. rosea) See Copromyxaprotea (C. protea)

Polycarpum Complex Group, 171, 172Polyketide synthase family (PKS), 39

Index 251

Polysphondylium pallidum (P. pallidum), 197,198

dictyostelids with distribution types, 153domain’s function, 93killer factor, 210novel factors, 99species, 171

Polysphondylium violaceum (P. violaceum),158

D. mucoroides, 160densities, 161dictyostelids with distribution types, 153phylogenetic analyses, 174sorocarpic amoeba taxon, 221–223species, 151, 171

Pre-aggregation cells, 202–203, 204Prestarvation factor (PSF), 92Protein aggregation disorders, 15

amyloid precursor protein, 19Hirano body-like aggregation, 19HSP and ALS14, 19Huntington’s disease, 18, 19in neurodegenerative diseases, 18–19PtdIns3P signaling, 18S. cerevisiae, 18

Protein inhibitor of activated STAT (PIAS), 97Protein kinase A (PKA), 92

catalytic sub, 93overexpression, 100by pharmacological inhibition, 23

Protein kinase B (PkbA), 24, 77Protists

amoeboid species, 167–168convergent evolution, 168sorocarpic protists species, 171

ecology and biogeography, 177–178molecular data in, 178molecular dating, 175sorocarpic, 179

Protostelia, 168Pseudomonas aeruginosa (P. aeruginosa), 11,

12Pseudomonas fluorescens, 10Pseudopod extension process, 53PSF. See Prestarvation factorPsp cells, 96

proximal promoter, 101stkA, 100

PTEN phosphatase, 7

QQuorum-sensing (QS), 11

amoebae sense, 201

intracellular events, 199in slime moulds, 50

RRas, 56, 75–76

activation, 54C/G double nulls, 77GTPase, 94RasB, 76RasC, 54RasD, 76RasG, 54

RasGef. See Guanine Nucleotide ExchangeFactor activating Ras

rDNA palindromes, 40–41, 42RdRP. See RNA-dependent RNA polymeraseRER. See Rough endoplasmic reticulumRestriction enzyme-mediated integration

(REMI), 8, 93Rhizaria. See GuttulinopsidaeRibonucleoprotein (RNP), 110, 117Ribosomal RNAs (rRNAs), 110, 111RISC. See RNA-induced silencing complexRNA interference (RNAi), 20, 119

Dictyostelium, 73DIRS-1, 123MidA, 21TacA expression, 102

RNA recognition motifs (RRM), 115RNA-dependent RNA polymerase (RdRP),

119, 121RNA-induced silencing complex (RISC), 119RNAi. See RNA interferenceRNase MRP, 117

(nc)RNAs, 112snRNA genes, 121

RNP. See RibonucleoproteinRough endoplasmic reticulum (RER), 231RRM. See RNA recognition motifsrRNAs. See Ribosomal RNAs

SSaccharomyces cerevisiae, 3, 4, 9, 17, 18, 21,

37, 91, 102, 117SAGE. See Serial analysis of gene expressionSalmonella typhimurium, 10SCAR/WAVE protein, 14SDF. See Spore differentiation factorSDS. See Shwachman-Bodian-Diamond

syndromeSerial analysis of gene expression (SAGE),

113

252 Index

Serum response factor (SRF) family, 94Sex in Dictyostelia, 129

altruism and conflict study, 142–143brownish particles, 143considerations

ecological, 141–142evolutionary, 139–140taxonomic, 140–141

cytophagic or giant cell, 131–132dictyostelid genomes, 142haploids, 131macrocyst formation

cell fusion, 134–135cells of sexual cycle, 136cycloheximide, 137D. discoideum, 135extracellular calcium, 133germination, 137giant cell, 136haploid cells, 135–136humid or moist conditions, 133level of light, 132–133nutrient availability, 132temperature, 133–134

parasexual geneticsin D. discoideum, 138mating orientation, 137regulatory proteins, 139type II version, 138–139

parasexuality, 132sexual and parasexual cycles, 130sexual and parasexual genetics

D. discoideum and P. album, 137diploids, 138homologous genes, 139mating orientation, 137regulatory proteins, 139sex determination, 138–139

Sexual reproduction, 36, 196–197Shwachman-Bodian-Diamond syndrome

(SDS), 15Signal recognition particle (SRP), 111, 118Signal transducers and activators of transcrip-

tion A (STATa), 97D. discoideum, 3Dd-STATa, 113key pst genes, 98transcription factor, 123

Signalling, 50cAMP mediated cell–cell, 49cAMP signalling activation, 57during chemotaxis

actin polymerisation, 55cAMP gradients, 53

G heterotrimeric proteins, 54LEGI model, 53–54molecular mechanisms, 55–56phospholipases, 54–55PI3 kinase, 54quantitative characterization, 56Rac activation, 55

to cytoskeletonactin filament network, 51cell-substrate contacts, 50, 51class I myosins, 51–52non-stimulated cells, 52

intercellular, 208tip cells, 60

Single nucleotide polymorphism (SNP), 38(si)RNAs. See Small interfering RNAsSlugs, 73

ACA activity, 59adhesion molecules, 60cARs 2 and 4, 74Dictyostelium, 60, 61D. discoideum, 209forces measurements in, 61migration, 188, 201model calculation, 62optical density waves, 60–61pstA-specific gene expression, 98

Small interfering RNAs ((si)RNAs), 110, 119Small nuclear RNAs (snRNAs), 110, 115

D. discoideum, 112genes for, 115ncRNAs, 122targets, 116

Small nucleolar ribonucleoprotein particle(snoRNP), 110, 116

Small RNAs, 119, 120gene expression, 119microRNAs in D. discoideum, 120, 121retrotransposon, 120from transposon DIRS-1, 120

SNP. See Single nucleotide polymorphismsnRNAs. See Small nuclear RNAsSocial amoebae, 35, 129

comparative sequencingchromosome structures and palin-

dromes, 41DIRS clusters, 40gene cdc123 DNA alignment, 40gene families analysis, 39NGS technologies, 38

genome analysis, 35mitochondria, 42nuclear genomes

D discoideum, 36–38

Index 253

in social amoebae, 41Social amoebae (cont.)

plasmids, 41–42rDNA Palindromes, 42transcription regulation

nucleosomes, 44RNAs, 43

Social behaviour, 193–194CSM, 196, 197DIF, 206evolution, 210

Social selection, 196, 198evolutionary consequences

aggregation, 208CSM, 207, 209–210microcyst formation, 209P. pallidum, 210

fitness consequences, 199intercellular interactions

bystander effect, 207cell-type differentiation, 205D. discoideum slugs, 205D. giganteum, 206–207diffusible chemical signals, 206fruiting body, 203negative feedbacks, 205, 206

P. pallidum, 197, 198phenotypic variation, 197sexual reproduction, 196, 197social groups, 198traits, 200–202

Sociality developmentevolutionary forces, 238fruiting body, 200quorum sensing, 199

SoilsciPCR for, 174in Costa Rica, 236Dictyostelia within, 178earthworms, 156in Java, 236from limestone, 150pH, 159University of Oregon, 183

Sordiplophrys, 236–237Sorocarpic amoebae, 220

acrasid cellular slime molds, 220, 224dictyostelids, 220eukaryotic tree of Life, 224life cycle, 227–228research history, 224

Cienkowsky’s description, 226D. mucoroides, 224, 226molecular data, 227

novel sorocarpic taxa, 227Tieghem’s observations, 226–227timeline of 140 years, 225

taxon, 221–223Sorodiplophrys stercorea (S. stercorea), 235

amoebae, 237species complexes, 169

Sorogen, 228, 234Sorogena, 224

eukaryotic tree, 224sorocarp, 227species complexes, 169

Sphingolipids, 22metabolizing enzymes, 22molecular pharmacology, 23

Spliceosomal RNAs, 115–116Spore differentiation factor (SDF), 99

key signal peptides, 100spore tissue, 206

SRP. See Signal recognition particleStarvation, 194, 208

autophagy, 16cAMP synthesis and secretion, 56cARs, 73congeneric amoebae, 90developmental program, 92environmental conditions, 202gbfA, 95gene expression programme, 56hospitable environments, 92

Starving Dictyostelium cells, 52STATa. See Signal transducers and activators

of transcription ASTATc, 98Stenotrophomonas maltophilia, 10Strict molecular clock, 175–176

TTATA-binding protein (TBP), 90TE. See Transposable elementTerrestrialization, 176–177TgrC1 gene, 93

cAMP gradient, 94TF modulation, 95

Tieghem’s observations, 226–227Tip cells, 60Tip-organizer, 99TKL. See Tyrosine-like kinasesTranscriptional machinery, 90, 91Transcriptional regulators, 90

conservation, 92D. discoideum and D. purpureum, 90, 91development

254 Index

8-Br-cAMP, 94–95acaA expression, 93cAMP by adenylate cyclases, 92–93carA expression, 93CbfA, 93, 94cell density sensing factors, 92Crtf, 94GBF, 95MADS-box transcriptional factors, 94MybB, 93physical cell–cell contact, 95

expression profile, 92functional categories, 91multicellular assembly

bZIP, 96–97complex gradients, 95–96dgcA, 99Dictyostelium cells, 95Dictyostelium STAT proteins, 97–98DIF-1 functions, 97DimB, 97MrfA, 98MybE, 98Psp cells, 96pst subtypes, 96in shaping cellular populations, 98–99STATa, 97

open questions and directions, 102–103regulations, 91

Transfer RNAs (tRNAs), 110D. discoideum, 111genome properties, 37ncRNAs, 112, 122RNase P, 117snoRNAs, 116vicinity, 38

Transposable element (TE), 37, 38Tubulinea. See LoboseaTyrosine-like kinases (TKL), 430-untranslated region (30 UTRs), 121

UUV-light, 6, 8

VVacuole, 18

amoebae, 230giant cell, 136Legionella, 13

Vacuole membrane protein 1 (Vmp1), 4–5autophagy, 16D. discoideum, 18

Valproic acid (VPA), 22cAMP, 23inositol phosphate pathway, 24treatment, 24

van Tieghem’s description, 231VASP protein, 19Vibrio cholera, 10‘‘Violaceum Complex’’ Group, 174

WWiskott-Aldrich syndrome, 14

XX chromosome inactivation, 111

YYersinia pseudotuberculosis, 10

ZZygote, diploid, 130, 136

Index 255