Index

AATPase(s)

AAA-type, 279DnaA, 94P-type, 229, 231, 232, 304partitioning, 17, 19, 25, 74, 313RhcN, 126

abp/Abp, 319–321abrB/AbrB, 191, 194, 195acc/Acc, 142Acetaldehyde, 39, 62, 318Acetaldehyde/alcohol dehydrogenase(s), 318Acetaldehyde dehydrogenase(s), 63Acetoacetate, 101Acetosyringone, 139Acetyl-CoA, 39, 45, 286, 318Acetyl-CoA acetyltransferase(s), 21Achromobacter xylosoxidans, 43Acidovorax facilis, 240Aconitase(s), 22acpA/AcpA, 198, 199acs/Acs, 138Actinobacillus actinomycetemcomitans, 192Actinomycetales, 48acv/Acv, 141, 143Acylated homoserine lactones, 121Acyl Carrier Protein (ACP) domain, 286Addiction systems

pHG1, 243pTi-SAKURA, 143Shigella virulence plasmids, 155, 162, 163

Adenosine-5′-phosphosulphate (APS) kinase(s), 107

Adenylyltransferase(s), 279Adhesins, 175, 176Adhesion

of L. salivarius, 320of S. meliloti, 100

of Y. pestis, 179of Y. pseudotuberculosis, 177

α-galactoside(s), 101agp/Agp, 101Agrobacterium, 134Agrocinopine synthase(s), 138Agropine synthase(s), 138ags/Ags, 138Alanine, 317Alanine dehydrogenase(s), 317Alanine permease(s), 317Alcaligenes hydrogenophilus M50, 240Aldehyde dehydrogenase(s), 101α-methylacyl-CoA racemase(s), 301ami/Ami, 41, 199Amidase(s), 21, 22, 199, 275Amine oxidase(s) (AOs), 277, 2785-Amino-imidazole-4-carboxamide riboside

(AICAR), 109amq/Amq, 49Anaerobic class III ribonucleotide

reductase(s), 255and/And, 42, 79ant/Ant, 71–74Anthracene, 57, 58, 63Anthranilate, 42, 48, 49, 73, 79Anthranilic acid, 67Antimonite, 15Antisense RNA, 162Antisigma factors, 227AO. See amine oxidases (AOs)Aquaspirillum autotrophicum SA32, 240Arabinose, 101arc/Arc, 15, 109Archaea

alkaliphilic, 6genome organization, 4

Arginine, 15, 109, 263

327

328 Index

Arginyl-tRNA synthetase(s), 25ARS. See autonomously replicating sequence

(ARS)ars/Ars, 15Arsenate reductase(s), 12, 24Arsenic resistance, 12, 15Arsenite, 12, 15, 18, 24, 193Arsenite(III)-methyltransferase(s), 15Arthrobacter

catabolic plasmids in, 35degradation of aromatics, 39

Arthrobacter aurescens, 272Arthrobacter keyseri, 48Arthrobacter nicotinovorans, 272Arthrobacter nitroguajacolicus, 48Arthrobacter sp. strain FB24, 272, 273asn/Asn, 109ATP sulfurylase(s), 107Atrazine, 67, 298attI recognition site, 63, 65atxA/AtxA, 190, 191, 195, 196, 199Autoflavinylation, 275Autolysin, 199Autonomously replicating sequence (ARS), 94Avermectin, 285Azohydromonas lata, 240Azorhizobium caulinodans, 120azu/Azu, 97, 109

Bbacillary dysentery, 152Bacillus, 57Bacillus anthracis

abr gene, 191, 194, 195capsule, 188, 190, 197, 198germination of spores, 188, 191prs genes, 190sporulation, 191, 195, 196taxonomic position, 188toxin production, 188–192, 198, 199type IV secretion systems, 192, 199

Bacillus cereusabr gene, 194, 195as an opportunistic pathogen, 188conservation of chromosomal

sequences, 202toxin production, 194, 196

Bacillus schlegelii, 242Bacillus subtilis, 198Bacillus thuringiensis, 188, 197, 199, 201, 202Bacteriocins, 34, 179–181, 312, 319–321bad/Bad, 42bcl/Bcl, 195

bed/Bed, 41, 43ben/Ben, 42Benzaldehyde, 41, 45Benzamide, 41Benzene, 39, 41, 42, 45Benzo[a]pyrene, 58Benzoate, 39, 41, 42, 45, 255Betaine(s), 100, 102, 105β-ketoacyl synthase(s), 107, 288β-glucans, 103, 104β-glucosidase(s), 274β-glucosyltransferase(s), 102, 104bhb/Bhb, 101Bile salt hydrolase(s) (BSHs), 320Binome(s), 227Biphenyl, 41, 43, 47, 48, 66β-ketoacyl synthase(s), 107, 288β-ketoadipate(s), 42, 102β-Ketoadipate pathway(s), 42, 67, 73,

79, 102β-Ketoadipyl-CoA, 42box/Box, 42bph/Bph, 41, 43, 47, 486b protein, 138Bradyrhizobium japonicum, 241, 259Bubonic plague, 173Burkholderia

degradation of aromatics, 39, 41degradation of PAHs, 57

Burkholderia cepaciadegradation of 2,4-D, 43

Burkholderia glumae, 182Burkholderia vietnamiensis, 42, 210, 219, 221,

227Burkholderia xenovorans

genome size, 34degradation of polychlorinated

biphenyls, 41, 43multiple degradation pathways, 41

Buruli ulcer, 284–286, 288

Ccad/Cad, 303–305Cadmium resistance

pKB1, 304, 305Cadmium/zinc/cobalt resistance

pMOL30, 210, 212, 223, 224, 228, 229, 231, 232

caf/Caf, 177, 178, 181Calvin-Benson-Bassham cycle, 251, 257, 263Camphor, 43, 58CAM plasmid, 43, 58cap/Cap, 198, 199

Index 329

CapsuleB. anthracis, 188, 190, 197, 198B. cereus, 188Y. pestis, 177, 178

Carbamoyl phosphate, 249Carbazole, 57, 65, 67, 70, 73, 74, 79Carbon monoxide

concentration in the atmosphere, 242ligand in hydrogenase active site, 247, 249production via photochemical degradation

of marine Organic matter, 259Carbophilus carboxydus, 242Carboxidotrophs, 242car/Car

car-IIKA1 gene cluster, 79car-IKA1 gene cluster, 79pCAR1, 70–73P. resinovorans CA10, 67Sphingomonas, 79

Caseinolytic cell-surface protease(s), 320Catabolite repression

of A. nicotinovorans nicotine catabolism, 280of the O. carboxidovorans OM5 cox

genes, 263of the R. eutropha H16 hox genes, 251

cat/Cat, 42, 73, 79Catechol(s), 39, 41, 42, 45, 49, 58, 63, 67, 69,

79, 102Catechol 1,2-dioxygenase(s) (C12Os), 39, 255Catechol 2,3-dioxygenase(s) (C23Os), 39, 63Cation diffusion facilitators (CDFs), 17, 227,

231cbb/Cbb, 243, 251–253, 258, 259, 273CcdA/CcdB toxin/antidote system, 151, 162C4-dicarboxylate transport system, 101Cell septa localization/formation, 96Cellulase(s), 274Cereulide, 196Chaperones

in A. tumefaciens, 140in B. anthracis, 190, 192in Halobacterium sp. NRC-1, 20, 21in M. ulcerans, 287in the maturation of MBH in R. eutropha

H16, 248in S. meliloti, 107in Yersinia, 176–178

Chitooligosaccharide deactylase(s), 107Chlorobenzene(s), 43Chlorobenzoate(s), 42, 43Chlorocatechol, 42, 43Chlorocatechol 1,2-dioxygenase(s), 42Chloromuconate cycloisomerase(s), 43chr/Chr, 210, 212, 223, 227, 237, 238

Chromate resistance, 211, 218, 227, 229Chromosome II of H. marismortui

gatA, 21genes for penicillin synthesis, 22megaplasmid status, 21orc, 21parA genes, 21rrnB, 21trn49, 21

Chrysene, 57chvE/ChvE, 139clc/Clc, 43cnr/Cnr, 210–212, 223, 227, 233Coagulases, 179CoA ligase(s), 42Cobalt/nickel resistance, 210–213, 227CO dehydrogenase(s) (CODHs)

attachment to the inner membrane, 264[CuSMoO

2], 261, 262

FAD, 261, 262gas channels, 261genetic determinants, 259, 261–263iron-sulfur clusters, 261, 262maturation and assembly, 262molybdopterin-cytosin dinucleotide

(MCD), 261, 262regulation, 263structure, 261, 262

Coenzyme A (CoA) thioesters, 42Coiled-coil domains, 10, 192Colicins, 181Collagens, 177Comamonas, 57Conjugative transfer

cupriavidus strains, 212IncP-9 plasmids, 62mycobacterial plasmids, 292pAO1, 273pAW63, 201pCAR1, 72, 73pHCG3, 259pHG1, 243pHV4, 18pKB1, 304pMOL28, 218–220pMOL30, 222pMP118, 321, 322pNG600, 23pNGR234a, 121pSymA, 94, 95pSymB, 94, 95pXO2, 201pYpsIP31758.2, 182Shigella virulence plasmids, 162

330 Index

Conjugative transfer (cont.)Ti and Ri plasmids, 143Yersinia plasmids, 180

cop/Cop, 14, 18–20, 155, 162, 210, 221, 224, 229–233

Copy number controlTi plasmids, 142

Core proteins of lactobacilli, 318CO sensing, 263cox/Cox, 259, 261–263, 279CpxA/CpxR system, 157Cresol(s), 39, 41, 42, 45, 46CRISPR sequences, 18, 23Cryptic plasmids

of A. tumefaciens, 142of mycobacteria, 284of Yersinia species, 181

Crystal protein, 188ctr/Ctr, 96Cupriavidus

in clean rooms, 218growth on organic solvents, 218

Cupriavidus metalliduranslithotrophy, 240taxonomical position, 212transcriptome, 232, 233

Cupriavidus metallidurans genomic islands

CMGI-2, 222CMGI-3, 222CMGI-28a, 223, 227CMGI-30a, 223–225, 228CMGI-28b, 220, 223CMGI-30b, 223, 224, 229, 231CMGI-28c, 223

Cupriavidus taiwanensis, 219cyc/Cyc, 109, 263cyd/Cyd, 8, 12cys/Cys, 317Cysteine, 317Cytochrome a

1, 263

cytochrome b, 247, 264cytochrome b

6, 19

Cytochrome b558

, 264Cytochrome b

561, 262, 264

cytochrome b563

, 264Cytochrome c, 254, 263, 264, 302, 303Cytochrome oxidase(s), 8, 298, 412Cytochrome p450, 141, 288Cytokine production, 152, 153, 176Cytotoxins

Shigella, 152czc/Czc, 210, 212, 218, 223, 227–229,

231, 232

D2,4-D. See 2,4-dichlorophenoxyacetic acid

(2,4-D)dct/Dct, 101Dead Sea, 4Deethylsimazine, 298Dehydratase(s), 101, 286, 317, 318Denitrification

R. eutropha H16, 243, 253, 254, 257S. meliloti, 97, 109

De-ubiquinating cysteine protease(s), 176DHPH. See 2,6-dihydroxypyridine

hydroxylase(s) (DHPHs)D-hydroxynicotine, 276, 277Diazotrophs

H2 oxidation by, 241, 242

Dibenzofuran, 67, 80Dibenzo-p-dioxin, 67Dibenzothiophene, 41, 67, 2982,4-Dichlorophenoxyacetic acid

(2,4-D), 35, 43, 81Dienelactone hydrolase(s), 431,2-Dihydroxynaphthalene

dioxygenase(s), 622,6-dihydroxy-pseudo-oxynicotine, 2752,6-dihydroxy-pseudo-oxynicotine

hydrolase(s) (PONHs), 2752,6-dihydroxypyridine, 2752,6-dihydroxypyridine hydroxylase(s)

(DHPHs), 2753,4-Dimethylphenol, 39, 42, 43, 58, 62, 63,

79, 255Dioxygenase(s), 39, 42, 43, 58, 62, 63, 79, 255Dioxygenation, 58, 67, 79DL-mesodiaminopimelic acid, 198dmp/Dmp, 39, 45, 47dnaA/DnaA, 94, 162DNA polymerase(s), 15, 17, 22, 139dnk/Dnk, 318D-nornicotine, 271Domain swapping, 289dsb/Dsb, 22, 222dTDP-rhamnose, 104

EEctoine(s), 101, 102Edema factor (EF), 190, 195EF. See edema factor (EF)ehu/Ehu, 102Electrophoresis in Eckhardt gels, 120, 124Embden-Meyerhof-Parnas pathway, 318Endonuclease(s) III, 21Enterobacteriaceae, 81, 172

Index 331

Enteroinvasive Escherichia coli (EIEC), 152

envZ/EnvZ, 157Epoxidation, 303Epoxide hydrolase(s), 298, 303EPR spectroscopy

of O. carboxidovorans OM5 CODH, 261

of the R. eutropha H16 SH, 250Erythromycin, 2853-Ethylpyridine, 298Ethyl t-butyl ether (ETBE), 298eut/Eut, 102EXAFS, 261Excinuclease(s), 18Exopolysaccharides (EPSs), 92, 101, 103, 110,

120, 298

FFlavin adenine dinucleotide (FAD), 28, 261,

262, 275, 277F1 antigen, 178, 179Far east scarlet-like fever (FESLF)

Y. pseudotuberculosis, 182FB24-1, 273FB24-2, 273FB24-3, 273F1 capsular antigen, 177F1 capsule anchoring protein, 177F1 capsule chaperone protein, 177F1 capsule regulatory protein, 177fdrI/FdrI, 79fdrII/FdrII, 79fdx/Fdx, 79, 108, 125[Fe(CN−)

2CO] complex of the R. eutropha

H16 MBH, 248, 249Fermented goods, 312Ferredoxin, 58, 62, 63, 79, 125Ferrulic acid, 141ΦH, 11FHA domains. See forkhead-associated

(FHA) domainsfhp/Fhp, 254Fibronectin, 177FISH, 94fix/Fix, 98, 105, 108, 125, 127Flavin mononucleotide (FMN), 250Flavoenzyme(s), 275Flavohemoprotein(s), 254Flavonoid(s), 104, 105, 124–127Flavoprotein oxidoreductase(s), 109Flavoproteins, 261, 262Fluorene, 41, 79

Foldingof S. meliloti Nod proteins, 107of Y. pestis F1 antigen, 178

fol/Fol, 277Folylpoly-γ-glutamate ligase(s), 198F1 operon, 178, 279, 280Forkhead-associated (FHA) domains, 291Formimidoyltetrahydrofolate

cyclodeaminase(s), 21Formyltetrahydrofolate deformylase(s), 277Formyltetrahydrofolate synthetase(s), 21Fructose-1,6-bisphosphatase(s), 252, 263, 319Fructose-1,6-bisphosphate aldolase(s), 252, 263Fructose-6-phosphate, 319fts/Fts, 15, 18, 95, 96Fumarate, 101fur/Fur, 158

GGalactoglucan (EPS II), 103, 104Galactosyltransferase(s), 104GALLS gene, 141γ-aminobutyrate, 273, 275, 277, 278Gastroenteritis, 173Gas vesicles, 4, 9, 10, 12gat/Gat, 21Gene 6b. See tml/TmlGenetic colonization, 138Genome reduction, 315Genomic islands, 34, 47, 56, 72, 221, 222,

227, 233Genomic rearrangement, 121, 123, 124, 220Gentisate(s), 39, 42ger/Ger, 191glg/Glg, 97Gluconeogenesis, 319Glucosamine synthase(s), 107Glucose-1-phosphate, 103, 104Glucose-6-phosphate, 103Glucosyltransferase(s), 104Glutamine-dependent asparagine

synthetase(s), 109Glutamyl-transpeptidase(s), 198Glyceraldehyde-3-phosphate

dehydrogenase(s), 252, 263Glycogen metabolism, 97Glycolipids, 274GMP synthase(s), 21γ-N-methylaminobutyrate, 275, 277,

278, 280γ-N-methylaminobutyrate oxidase(s)

(MABOs), 277, 278Gordonan, 298

332 Index

Gordoniabiodegradation, 298, 299taxonomy, 298

Gordonia alkanivorans, 305Gordonia amicalis, 298Gordonia jacobaea

production of carotenoids, 298transformation of, 301

Gordonia nitida, 298, 305Gordonia polyisoprenivorans, 298, 299

isolation, 299transformation of, 300, 301

Gordonia rubropertincta, 298Gordonia terrae, 298Gordonia westfalica

insertion sequences (IS), 300isolation, 299

Great Salt Lake, 4groEL/GroEL, 98, 107Group II introns, 99, 257gsp/Gsp, 225GTPase-activating proteins, 176GTPases, 15, 18, 191gtr/Gtr, 223, 224, 229gvp/Gvp, 12, 15

HHaloarchaea, 4–6, 12, 25–27Haloarcula marismortui, 4, 20Halobacterium sp. NRC-1

DNA rearrangements, 4gas vesicle-deficient mutants, 9, 10gas vesicle genes, 9genome organization, 11horizontal gene transfer, 26megaplasmid evolution, 25orc genes, 15, 16transcription factors, 16

Haloferax volcanii, 4, 11, 15, 16, 19Haloperoxidase(s), 98Haloquadratum walsbyi, 6, 10, 24Helicase(s), 18, 19, 22, 23, 25hem/Hem, 97Heme(s), 97, 247, 254, 259Heteroaromatics, 67Heterologous expression studies, 262Hexose oxidation, 2746HLNO. See 6-hydroxy-L-nicotine oxidase(s)

(6HLNOs)hmg/Hmg, 42H-NS, 156

binding sites, 156–158MvaT family, 74, 75

interaction with VirB, 163silencing of imported genes by, 161structure, 157suppression of Shigella genes by, 157, 159

hod/Hod, 49Homogentisate, 42Horizontal gene transfer

in Burkholderia xenovorans LB400, 41of car genes, 67between haloarchaeal megaplasmids,

18, 26of heavy metal resistance genes, 223, 231of meta-cleavage pathway genes, 63of nic genes, 273pNGR234a, 122of S. meliloti genes, 95, 99, 100, 122in S. meliloti, 95, 101, 125of Shigella virulence factors, 155, 161, 180

hox/Hox, 243, 247–251, 259, 264hsn loci, 125htl/Htl, 12hup/Hup, 264Hydratase(s), 63, 101Hydrogenophaga pseudoflava, 242Hydrogenotrophs, 241, 242Hydrolase(s), 43, 63, 193, 196, 255, 274, 275,

298, 303Hydroperoxidase(s), 98Hydroquinone, 39Hydroxybenzalpyruvate hydratase-

aldolase(s), 622-Hydroxychromene-2-carboxylate

dehydrogenase(s), 626-Hydroxy-D-nicotine, 275, 2806-Hydroxy-D-nicotine oxidase(s), 275Hydroxylation, 39, 42, 45, 2756-Hydroxy-L-nicotine, 275, 2806-Hydroxy-L-nicotine oxidase(s)

(6HLNOs), 275, 281Hydroxymethyltransferase(s), 317Hydroxymuconic semialdehyde

dehydrogenase(s), 63Hydroxymuconic semialdehyde

hydrolase(s), 63Hydroxynitrocarbazole, 676-Hydroxy-N-methylmyosmine, 2752-Hydroxypenta-2,4-dienoate, 796-Hydroxy-pseudo-oxinicotine, 275hyp/Hyp, 249, 250, 264, 277

Iiaa. See tms/Tmsici/Ici, 42

Index 333

ics/Ics, 159IHF. See Integration Host Factor (IHF)IL-10, 175Immunoblotting analysis, 10incA cis-acting untranslated RNA, 94Inc groups. See Incompatibility groupsIncompatibility

of catabolic plasmids, 35determinants on pNGR234a, 421determinants on pTi-SAKURA, 142fusion of incompatible Ti plasmids, 142of haloarchaeal plasmids, 26, 57of pSymA and pSymB, 94

Incompatibility groupsin the genus Pseudomonas, 57IncFII plasmids, 155, 161, 162IncN plasmids, 62IncP-1 plasmids, 35, 39, 43, 47, 57, 62, 81IncP-2 plasmids, 35, 43, 45, 66IncP-7 plasmids, 35, 57, 65, 66, 72, 73IncP-9 plasmids, 35, 57, 58, 60–62, 65, 66,

73, 81IncW plasmids, 62of Shigella virulence plasmids, 154, 155,

157Ti and Riplasmids, 142

Injectisomes, 175Insertion sequences (IS),

and mls expression in Mycobacterium ulcerans, 287

of A. nicotinovorans pAO1, 273of Burkholderia, 41of R. metallidurans genomic islands,

223, 224of catabolic plasmids, 35, 68of G. westfalica pKB1, 300, 301of haloarchaeal plasmids, 4, 7, 9–11, 18,

24–26of M. ulcerans pMUM plasmids, 287,

291, 315of R. eutropha H16 pHG1, 255, 257of Rhizobium sp. NGR234

pNGR234a, 127of Rhodococcus catabolic plasmids, 68of Shigella virulence plasmids, 154of S. meliloti, 95, 99of Y. pestis pMT1, 181

Integrase(s), 20, 23, 24, 25, 63, 66Integration host factor (IHF), 47Integrins, 175Interferon-γ, 175Interposon mutagenesis, 262int/Int, 66, 223–225, 229Intron-encoded proteins (IEPs), 257

Inversion isomers, 7–9, 25inv/Inv, 159, 163ipa/Ipa, 155, 159, 162ipb/Ipb, 48ipg/Ipg, 155, 159ipt/Ipt, 138Iron-sulfur cluster(s)

in CODH, 262in nicotine dehydrogenase, 275in the periplasmic nitrate reductase

of R. eutropha H16, 254in the R. eutropha H16 MBH, 247in the R. eutropha H16 RH, 251in the R. eutropha H16 SH, 250

Ironregulation of Shigella virulence

genes, 158uptake in S. meliloti, 102, 103

IS100, 181IS881, 255, 257IS1071, 210, 223–225, 227IS1086, 224IS1473, 273IS1627, 190IS2404, 291IS2606, 291IS3 family, 15IS5 family, 24IS30 family, 15ISH2, 9ISH3, 9, 19ISH4, 9, 19, 24ISH6, 24ISH8, 9, 19ISH9, 24ISH11, 19Isopropylbenzene, 483-Isopropylcatechol, 48ISPre1, 73ISPre4, 73IS Rm2011-2, 99ISRme3, 224ISRme10, 224ISRtr1, 123Iterons, 80

KKDH. See ketone dehydrogenase(s)

(KDHs)kdh/Kdh, 276, 281Ketone dehydrogenase(s) (KDHs), 275,

278–280kla/Kla, 71

334 Index

LLactic acid bacteria (LAB), 312Lactobacillus

core proteins, 318production of BSHs by strains of, 320taxonomy, 312

Lactobacillus plantarum, 314, 317Lactobacillus salivarius

amino acid metabolism, 317genome organization, 313gluconeogenesis, 319homofermentative metabolism, 318isolation of, 312probiotic properties, 319

Laminins, 177Large variable region (VAR), 137, 141

aspartate, 101, 220, 317LcpK30, 301lcr/Lcr, 174–176ldh/Ldh, 317Lead resistance, 210, 221, 228, 229Leghemoglobin, 259Lethal factor (LF)

binding to protective antigen, 190encoded by pBC218, 196encoded by pBCXO1, 195function, 196lef gene, 190

Leucine-rich repeats, 159Leucine zippers, 192LF. See lethal factor (LF)14-3-3-Like proteins, 138Linear plasmids, 48, 284Linker scanning mutagenesis, 9, 11Lipase(s), 274lip/Lip, 274Lipochitooligosaccharides, 105Lipopolysaccharide(s), 103, 174Lithotrophs, 240, 241, 250lon/Lon, 263Low calcium response, 175, 176Lower pathway(s), 39, 41, 43, 48,

49, 62L-rhamnose isomerase(s), 319L-serine dehydratase(s), 317, 318lsp/Lsp, 320LytTR DNA-binding domain, 263

Mmab/Mab, 277, 280, 281MABO. See γ-N-methylaminobutyrate

oxidase(s) (MABOs)Major facilitator superfamily (MFS)

permeases, 19, 229, 254, 274

Major intrinsic proteins (MIPs), 194, 196Malate, 101Malonyl-CoA, 286Mandelate, 39mao/Mao, 277, 278, 280MAO. See monoamine oxidases (MAOs)mas1/Mas1, 138mas2/Mas2, 138MCD. See molybdenum cytosine dinucleotide

(MCD)M cells, 152mcm/Mcm, 23mcr/Mcr, 301Melamine, 298Melibiose, 101Membrane-bound hydrogenase(s) (MBHs)

diatomic ligands of the R. eutropha H16 enzyme, 247, 249

[Fe(CN−)2CO] complex of the R. eutropha

H16 enzyme, 248, 249gas channels in the R. eutropha H16

enzyme, 247iron-sulfur clusters of the R. eutropha H16

enzyme, 247maturation and assembly of the

R. eutropha H16 enzyme, 248, 249[NiFe] center of the R. eutropha H16

enzyme, 247, 249of Oligotropha carboxidovorans OM5,

259, 264Merbromin, 225Mercury chloride, 225Mercury resistance

determined by Tn4378 and Tn4380, 225pIJB1, 47pMOL28, 225of Tn5046, 65

mer/Mer, 13, 15, 17, 19, 21, 47Mesorhizobium loti, 99Meta-cleavage pathway(s)

NAH7 plasmid, 63pCAR3, 79pEST1026, 39pVI150, 45pWW0, 74

Methionine, 97, 161, 317Methylamine, 278, 280Methylase(s), 18Methylenetetrahydrofolate, 21, 277Methylene-tetrahydrofolate dehydrogenase/

cyclohydrolase(s), 2775, 10-Methylenetetrahydrofolate

reductase(s), 214-Methylmuconolactone, 255Methylmuconolactone isomerase(s), 255

Index 335

Methylmuconolactone methyl isomerase(s), 255

3-Methylpyridine, 2982-Methylquinoline, 48Methyl t-butyl ether (MTBE), 298met/Met, 161MFS permeases. See Major facilitator

superfamily (MFS) permeasesMHYT domain, 262, 263mia/Mia, 158Microarray analysis, 73, 228, 232min/Min, 96MIP proteins. See Major intrinsic proteins (MIPs)mis/Mis, 138Mixotrophy, 241mls/Mls, 286–289, 290, 292mml/Mml, 255mmr/Mmr, 224, 229, 232moa/Moa, 276, 278mob/Mob, 95, 279, 281mod/Mod, 279moe/Moe, 279Molybdate uptake, 279Molybdenum cofactor, 254, 273, 275, 278, 279Molybdenum cofactor biosynthesis, 254, 273,

275, 278, 279Molybdoenzyme(s), 254, 263Molybdoproteins, 261, 262Molybdopterin (MPT), 254, 261, 263, 279Molybdopterin-cytosin dinucleotide

(MCD), 261, 262, 279Molybdopterin guanine dinucleotide cofactor

(MGD), 254Monoamine oxidase(s) (MAOs), 277, 278Monooxygenase(s), 39, 42, 275moq/Moq, 49Mosaic elements (MS), 122mox/Mox, 275mpf/Mpf, 61, 62MPT. See Molybdopterin (MPT)mrr/Mrr, 22, 24mrs/Mrs, 62Muconate cycloisomerase(s), 43, 255Muconolactone isomerase(s), 255Multimer resolvase(s), 25, 243MvpT/MvpA toxin/antidote system, 155,

162, 163mxi/Mxi, 155, 159, 161Mycobacterium

degradation of PAHs, 57degradation of rubber, 299

Mycobacterium abscessus, 284Mycobacterium avium, 284Mycobacterium avium-intracellulare, 284Mycobacterium branderi, 284

Mycobacterium celatum, 284Mycobacterium chelonae, 284Mycobacterium fortuitum, 284, 292Mycobacterium marinum, 287, 288, 289, 292Mycobacterium peregrinum, 284Mycobacterium scrofulaceum, 284Mycobacterium smegmatis, 287, 292, 301,

304, 305Mycobacterium ulcerans

distribution of plasmids in, 288genome reduction, 292infection, 284insect hosts, 293insertion sequences (IS), 291transposons, 288in fish hosts, 288

Mycobacterium vanbaalenii, 57, 58Mycobacterium xenopi, 284Mycolactone(s)

biosynthesis of, 287, 288of Mycobacterium ulcerans subsp.

liflandii, 288properties, 285structure, 285types, 285

Mycolic acid(s), 48Myosin-like repeats, 192

NN-acetyl-glucosamine, 107, 180N-acetylmuramoyl-L-alanine amidase(s), 199N-acyl-homoserine lactone, 121, 143N-acyltransferase(s), 107, 303NAD(P)H:ferredoxin oxidoreductase(s), 79NAD(P)H-nicotine blue oxidoreductase(s),

275, 277NADP+-dependent succinic semialdehyde

dehydrogenase(s), 277nah/Nah, 41, 60, 61, 62, 63, 66NAH7 plasmid, 58

backbone, 61evolution of, 66incompatibility, 58nah genes, 62organization, 60origin of, 65Tn4655, 63

Naphthalene, 35, 39, 41, 57, 58, 60, 62, 63, 65, 66, 71

Naphthalene cis-dihydrodiol dehydrogenase(s), 62

Naphthalene dioxygenase(s), 62Naphthalene 1,2-dioxygenase ferredoxin, 62Naphthalene 1,2-dioxygenase reductase(s), 62

336 Index

Naphthalene sulfonate, 66nap/Nap, 97, 109, 254Natronomonas pharaonis, 4, 6ncc/Ncc, 6, 14, 18, 211, 212, 224, 229ndh/Ndh, 275, 278, 279, 281NDH. See Nicotine dehydrogenase(s) (NDHs)nep/Nep, 277, 279, 280N-(2-hexylamino-4-phenylimidazol-1-yl)-

acetamide, 298Ni-chelating chromatography, 279nic/Nic, 272, 276, 281, 304Nicotine

availability in natural habitats, 271, 272catabolism, 275, 276, 277, 278extrusion of catabolic end products, 280regulation of genes for catabolism, 280, 281uptake, 279

Nicotine blue, 275Nicotine dehydrogenase(s) (NDHs), 275, 280[NiFe] center(s)

of the O. carboxidovorans OM5 MBH, 264of the R. eutropha H16 MBH, 247, 249of the R. eutropha H16 RH, 251of the R. eutropha H16 SH, 250

nif/Nif, 98, 99, 120, 122–124, 144, 254nir/Nir, 109, 254nit/Nit, 275Nitrate reductase(s), 19, 97, 109, 253, 254, 257Nitric oxide reductase(s), 97, 254Nitrilase(s), 275Nitrite reductase(s), 97, 254, 257Nitrogenase(s), 100, 105, 108, 125, 127Nitrogen fixation

in Rhizobium sp.NGR234, 120, 122, 124, 125, 127, 134

in S. meliloti, 92, 96, 99–101, 103, 105, 107–110

Nitrous oxide reductase(s), 21, 22N-methylaminopropyl-(6-hydroxypyridyl-3)-

ketone, 275N-methylhydantoinase(s), 24nnr/Nnr, 97, 107, 109Nocardia, 298, 299noc/Noc, 142nod boxes, 107, 125, 127Nod factors, 94, 104, 105, 107, 120, 124, 125nod/Nod, 98, 100, 101, 104, 105, 107, 109,

120, 122, 124, 125, 127Nodulation

Rhizobium sp. NGR234, 120, 122, 124, 125S. meliloti, 92, 96, 98–101, 104, 105,

107, 109noe/Noe, 98, 124nol/Nol, 98, 124, 125Nopaline synthase(s), 138

nop/Nop, 126, 127N

2O reductase(s), 109, 257

NO reductase(s), 109, 257nor/Nor, 97, 109, 254nos/Nos, 21, 97, 109, 138, 254Novosphingobium, 29, 56, 57, 70Novosphingobium aromaticivorans, 41,

65, 66nox/Nox, 142nrd/Nrd, 254, 257nre/Nre, 211, 224, 229nrt/Nrt, 97NtSIP1, 138Nuclear localization signals (NLSs), 140

OO-antigen, 174ocs/Ocs, 138Octane, 43Octopine synthase(s), 138OCT plasmid, 43Oligotropha carboxidovorans OM5, 264omp/Omp, 141, 142, 157, 179, 229Opines, 135–138, 141–143orc/Orc, 12, 15–17, 19–25oriM, 292oriR, 162oriT (mob) sites

pKB1, 304pNGR234a, 241pSymA, 94pSymB, 94Ti and Ri plasmids, 143

oriVpAW63, 26pCAR1, 71, 72pCAR3, 80pHCG3pKB1, 300pMT2, 62pMT118, 313pNGR234a, 121pNRC100, 11pNRC200, 11pPCP1, 181pSymB, 95pXO1, 191–193pXO2, 201, 202

Ortho-cleavage pathway(s), 39, 41–43, 49, 67, 255

ots/Ots, 96Overdrive sequence, 139, 1404-Oxalocrotonate decarboxylase(s), 63Oxalocrotonate tautomerase(s), 63

Index 337

Oxidase(s), 4, 8, 12, 109, 264, 275–278, 280, 298, 302

3-Oxoacid CoA-transferase(s), 243-Oxoadipate enol-lactone hydrolase(s), 2552-Oxo-4-hydroxypentanoate aldolase(s), 632-Oxopent-4-enoate hydratase(s), 63

PPA. See Protective antigen (PA)paa/Paa, 42pAC27

clcABD operon, 43pAD1, 199, 201pagA/PagA, 190, 191PAGI2-C island, 223PAHs. See Polycyclic aromatic hydrocarbons

(PAHs)pAL1

degradation of anthranilate, 49pAL5000, 284pAMβ1, 199, 201pAO1

carbohydrate catabolism genes, 274conjugative transfer, 273γ-N-methylaminobutyrate catabolism

genes, 277, 278hexose oxidation genes, 274molybdenum cofactor synthesis genes,

273, 275, 278, 279nep genes, 277, 279, 280nicotene catabolism genes,

275–277nicotine uptake, 279nic regulon regulators, 280, 281organization, 272relatives, 273

PAPS. See 3′-phosphadenosine-5′-phosphosulphate (PAPS)

Paracoccus pantotrophus, 240par/Par

mycobacterial plasmids, 292pCAR1, 71, 72, 75–77pCAR3, 80pHV1, 19pHV4, 17pL47, 25pL131, 24pMOL28, 219, 220pMOL30, 222pMT2, 62pMP118, 313, 314pNG400, 23pNRC100, 12Shigella virulence plasmids, 163

Partitioningmycobacterial plasmids, 292pAO1, 273pCAR1, 75pCAR3, 80pHCG3, 259pHG1, 243pHV1, 19pHV3, 19pHV4, 17pKB1, 300, 301pL47, 25pMP118, 313pMT2, 62pNG200, 15, 23pNG300, 23pNG400, 23pNG600, 22pNRC100, 11, 12pSymA, 93pSymB, 93Shigella virulence plasmids, 159, 163

pAtC58, 142, 143Pathogenicity islands (PAIs), 190, 191, 194,

195, 198, 202P1-ATPase-mediated efflux systems, 229,

231, 232pAW63, 197, 201pBBR1MCS-2, 300pBBR1MCS-5, 300, 305pBC218, 196, 197pBc10987, 193–195, 197pBCXO1, 193, 195, 197pBD2, 48pBN6, 66pbr/Pbr, 210, 212, 223–225, 228, 229, 232 pBT9727, 197, 201, 202pBVIE01, 42, 221, 222pBVIE02, 42, 219, 220, 230pBVIE04, 42pca/Pca, 42, 73, 102pCAR1

conjugative transfer, 72, 73, 75evolutionary relationships, 71, 72incompatibility, 72mobile genetic elements, 72, 73plasmid-chromosome interactions,

73–75oriV, 72, 74partitioning, 72, 74–76regulation of anthranilate degradation

genes, 73, 74replication, 72tra/Tra, 72

pCAR2, 73

338 Index

pCAR3, 66, 70, 77–80PCBs. See Polychlorinated biphenyl(s) (PCBs)pCD1. See pYVpCER270, 193, 196–197pCF10, 201pch/Pch, 41pCLP, 284pColE1, 181pDBMCS-2, 301pDBMCS-5, 301pDK1, 39pDTG1, 61, 63, 65, 66p42e, 96pem/Pem, 243penicillin(s), 22penicillin acylase(s), 22pentose phosphate pathway, 251, 317–319peptidyl-prolyl cis-trans isomerase(s), 21Periplasmic dissimilatory nitrate

reductase(s), 97pEST1026, 39pEST4011, 43, 47pesticin, 179, 180, 181pExo, 92Peyer’s patches, 173pgsB/PgsB, 198pha/Pha, 41PHB. See polyhydroxybutyrate (PHB)pHCG3

cbb genes, 263cox accessory genes, 262, 263cox genes, 259, 261cycH, 263gene for a b-type cytochrome, 264hox genes, 264hyp genes, 264lon, 263megaplasmid-chromosome interactions, 264repB-repC intergenic region, 259rep genes, 259tra/trb genes, 259

pHCM2, 181Phenanthrene, 57, 58, 63Phenol(s), 35, 39, 42, 45Phenol hydroxylase(s) (PHs), 39Phenylacetyl-CoA, 42Phenylalkanoate(s), 41phe/Phe, 39pHG1

cbb genes, 251, 252conjugative transfer, 243gene for a b-type cytochrome, 247gene for a MBH-specific C-terminal

endopeptidase, 249

gene for a SH-specific C-terminal endopeptidase, 250

genes for degradation of aromatics, 255genes hoxA,hoxB, hoxC and hoxJ, 250, 251hyp genes, 249IS881, 255, 257junkyard region, 255, 257MBH gene cluster, 246, 247megaplasmid-chromosome

interactions, 257, 258mobB, 254nap genes, 254nar genes, 253, 254nifM gene, 254nor genes, 254nos genes, 254organization of the hox regulon, 243, 248parA and parB genes, 242pemI and pemK genes, 242repA, 242SH gene cluster, 249, 250similarity to pMOL28, 242similarity to pSym of Cupriavidus

taiwanensis, 242xerC and xerD genes, 242

phl/Phl, 39pHMT112, 41pho/Pho, 102Phoshoenol pyruvate (PEP), 2533′-Phosphoadenosine-5′-phosphosulphate

(PAPS), 107, 120Phosphatase(s), 176, 191, 252, 263, 319Phosphate uptake, 102Phosphoglucomutase(s), 103Phosphoglycerate kinase(s), 252, 263Phosphoglycolate phosphatase(s), 252, 263Phospholipase D (PLD), 177, 178Phosphorelay signal transduction systems

B. anthracis, 191C. metallidurans, 231L. salivarius, 319Shigella, 157R. eutropha H16, 250, 251S. meliloti, 101, 108, 109

5-Phosphoribosyl-1-pyrophosphate (PRPP), 317

Phosphoribulokinase(s), 252, 263Phosphotransferase system (PTS)

transporters, 319Phosphotyrosine phosphatase(s)176pH stress, 24Phthalate(s), 41, 48, 79pht/Pht, 48pHV1, 5, 16, 19, 20

Index 339

pHV2, 6, 11, 16pHV3, 5, 16, 18, 19pHV4, 5, 16–20, 23pIB1. See pYVpIJB1, 43, 47pim/Pim, 180PIN domain, 143pINV A, 154, 155pINV B, 154, 155pINV-2457T, 154pIP501, 199, 201pJP4, 43, 47pKB1

analysis of gene expression by RT-PCR, 303

cadmium resistance, 303conjugation frequency, 304conjugative transfer, 304construction of vectors from, 300, 301curing of, 301derivatives, 305genes for c-type cytochromes, 302genes for rubber degradation, 302identification by pulsed field gel

electrophoresis (PFGE), 299oriV, 300tra genes, 304transformation frequency, 304

pKB2, 306pkc/Pkc, 275pkn/Pkn, 291PKSs. See Polyketide synthase(s)

(PKSs)pL23, 6, 24, 25pL47, 6, 25pL131, 6, 24pla/Pla, 179–181Plasminogen activator, 173, 179, 181pLCR. See pYVplcR/PlcR, 195PLD. See phospholipase D (PLD)pM3, 62pmf/Pmf, 280pMOL28

backbone, 220bimA1B1, 227chr genes, 211, 223, 227cnr genes, 210, 227conjugative transfer, 218, 225evolution of metal resistance genes, 233induction of cnr genes, 233IS elements, 223par genes, 220pil genes, 220

similarity to pHG1, pBVIEO2 and pRALTA, 219, 220

TnCme2 insertion, 223, 225, 227trb genes, 220

pMOL30backbone, 221bimA2B2, 227conjugative transfer, 225cop genes, 224, 229, 230czc genes, 223, 228evolution of metal resistance genes,

233, 234induction of heavy metal resistance

genes, 231–233IS elements, 224ncc/nre genes, 211, 224, 229pbr genes, 223, 224, 228peculiarity of the copB gene, 229similarity to pBVIE01, 221TnCme2 insertion, 225

pMOL50, 224pMP118

bacteriocin genes, 320, 321bile salt hydrolase gene, 319, 320copy number, 314distribution of pMP118-like plasmids

in Lactobacillus strains, 321GC content, 314genes for core proteins, 318genes for sorbitol and rhamnose utilization, 319genes for surface proteins, 320genes of amino acid metabolism, 316, 317genes of carbohydrate metabolism, 318genes of purine and pyrimidine anabolism, 317identification of, 313IS elements, 315ori, 313pseudogenes, 315repA and repE, 313, 314tra genes, 321, 322GC content, 314

pmr/Pmr, 74–77pMT1, 177, 178, 181pMT2, 62pMUM001

backbone, 292mycolactone locus, 286–288non PKS-coding regions, 290, 291

pMUM002backbone, 292genes for serine/threonine protein kinase(s)

(STPKs), 291mycolactone locus, 286–288non PKS-coding regions, 290, 291

340 Index

pMUM003backbone, 292genes for serine/threonine protein kinase(s)

(STPKs), 291non PKS-coding regions, 290, 291

pNC903, 301pND6-1, 65, 66, 71, 72Pneumonic plague, 173, 180pNG100, 20, 23pNG200, 20, 23pNG300, 20, 23pNG400, 18, 20, 23pNG500

orc genes, 22pNG600, 22, 23pNG700, 21pNGR234a

curing of, 120G+C content, 121, 122genes for a type III secretion

system, 126nif and fix genes, 124, 125nod, nol and noe genes, 124, 125oriT, 121oriV, 121rearrangements, 123repABC, 121replicon fusion, 124tra genes, 121ttsI, 126

pNGR234b, 120, 125pNL1

bph, xyl, pch, 41, 80incompatibility, 80nah genes, 66rep genes, 80

pNL2, 41pNod-Nif, 92pNRC100

arsADRC and arsR2M, 15arsenic-resistance genes, 12A+T-rich segment, 11cydA and cydB, 8, 12evolution of, 25, 26gvp genes, 9, 10housekeeping genes, 12htlD, 12inverted repeat (IR) sequence,

11, 25mobile genetic elements, 4orc genes, 12oriV, 10, 11par genes, 12repH, 11

tbp genes, 12trxAB, 8

pNRC200arcRABC gene cluster, 15argS, 15, 25, 26cydA and cydB, 12ftsZ5, 15gvp genes, 15housekeeping genes, 12htlD, 12inverted repeat (IR) sequence, 11, 12orc genes, 15oriV, 11polB2, 15repH, 12tbp genes, 12, 15, 16trxA and trxB, 12

pnt/Pnt, 274pol/Pol, 15, 17, 22Polychlorinated biphenyl(s) (PCBs),

41, 48Polycyclic aromatic hydrocarbons (PAHs), 48,

57, 58, 65, 80Poly-γ-D-glutamate, 188, 198Polyhydroxybutyrate (PHB), 101Polyketide(s), 285, 286Polyketide cyclase(s), 275Polyketide synthase(s) (PKSs), 285–287Polymorphonuclear leukocytes, 152, 176PONH. See 2,6-Dihydroxy-

pseudo-oxynicotine hydrolase(s) (PONHs)

Porins, 229pP51, 41, 43pPCP1, 179, 181pPER272, 193, 196–197pPGH1, 39(p)ppGpp, 45pRA500, 41pRALTA, 219, 220pRE1, 48pREA250, 304pREA400, 304Precursor Z, 278Prenyl transferase(s), 141pRHL1, 48pRHL2, 48pRHL3, 48pRi1724, 135, 137, 138, 141pRi2659, 135, 141pRmeSU47a, 92pRmeSU47b, 92Probiotics, 312, 313, 320, 322Propane, 299

Index 341

Protective antigen (PA)encoded by pBC218, 196encoded by pBCXO1, 195encoded by pXO1, 188, 189pagA gene, 190proteolytic processing, 190secretion of, 190

Protein phosphorylation, 291Proteolytic processing

of B. anthracis protective antigen, 190of R. eutropha H16 hydrogenase large

subunits, 249, 250of Yersinia pre-Pla protein, 179

Proteomelactobacilli core proteins, 318

Protocatechuate(s), 39, 41, 42, 48, 58, 79, 102prsA/PrsA, 190prt/Prt, 320pSD25, 259Pseudomonas resinovorans, 67, 70, 72, 73Pseudoappendicitis, 181Pseudogenes, 48, 177, 291, 313, 315, 320Pseudomomas sp. CF600, 45Pseudomonas

carbazole degradation, 67car genes, 67, 70CO-oxidizing strains, 242degradation of aromatics, 39degradation of benzene, 41, 43degradation of naphthaline, 58, 65, 66, 71degradation of PAHs, 57incompatibilty groups, 57IncP-9 plasmids, 58, 61mvt genes, 75

Pseudomonas carboxydohydrogena, 242Pseudomonas chlororaphis, 73Pseudomonas fluorescens, 73Pseudomonas putida

degradation of naphthalene, 58degradation of toluene, 58transcriptome, 73–75degradation of benzene, 41degradation of carbazole, 73degradation of 3-chlorobenzoate, 42degradation of p-cresol, 41degradation of phenols, 39

Pseudomonas resinovorans, 67, 70, 72, 73Pseudomonas sp. ND6, 71Pseudomonas sp. strain P51, 43Pseudomonas stutzeri, 73Pseudomonas thermocarboxidovorans, 242pSF118-20, 313, 314pSF118-44, 313, 314pSmeSM11a, 92

pSmeSM11b, 92pSOX, 300pst/Pst, 180pSymA, 66

curing of, 98, 99DnaA binding sites, 94GC content, 92gene expression in bacteroids, 98genes for betaine catabolism, 102genes for nitrogen fixation, 98genes for stress responses, 98host-specificity genes, 105housekeeping genes, 98incα2, 94incγ, 94mobile genetic elements, 99mob sites, 94napEFDABC cluster, 109nirKV, 109nnrR and nnrS genes, 97, 109nod genes, 98, 104, 105, 107nol and noe genes, 98nor genes, 97, 109nos genes, 97parAB genes, 93plant growth inhibitory genes, 98repABC genes, 93, 94rhbABCDEF operon, 102, 103sel genes, 98tRNA genes, 97

pSymBaraABCDEF cluster, 101autonomously replicating sequence

(ARS), 94chromosomal and plasmid features, 95coding capacity, 95dct genes, 101dinucleotide signature, 95DnaA binding sites, 94ehu and eut genes for ectoine catabolism, 102evolutionary history of, 95exo genes for succinoglycan synthesis,

103, 104exp genes for galactoglucan synthesis, 104ftsK2, 96GC content, 92, 95gene expression, 96genes expressed under salt stress, 96, 97genes for catabolism of short-chain fatty

acids, 101genes for PHB degradation, 101, 102incα1, 94minCDE genes, 95, 96mob sites, 94

342 Index

pSymB (cont.)parAB genes, 93pcaDCHGB and pcaIJF operons, 102pho genes for phosphate uptake, 102repABC genes, 93, 94synthesis of polysaccharides, 97thiamine biosynthesis genes, 101

pTB1, 259pTiBo542, 135, 141, 142pTiC58, 135, 141, 142pTiS4, 142pTi-SAKURA, 135, 137, 141–143pTOM, 42pTOM9, 211pTV1, 43Pulse-field gel electrophoresis (PFGE), 8,

120, 313pur/Pur, 277, 279, 280Putrescine, 24pVI150, 39, 45, 47pWR100, 154, 163pWR501, 154pWW0, 39, 41, 43, 58, 61, 65,

72, 74pWW53, 39, 71pXO1, 188–193

abRB, 191, 194atxA, 190, 191backbone, 189copy number, 197ger genes, 191organization, 198oriV, 191, 192Rap/Phr phosphatase, 191relatives, 193–197repX, 191, 192SLH proteins, 102sporulation, 191topX, 192toxin genes, 190type IV secretion system, 192

pXO2AcpA and AcpB, 198, 199autolysin, 199atxA gene, 190backbone, 197, 198capBCADE, 198–199capsul synthesis genes, 198conjugative transfer, 199, 201copy number, 197PAI, 198PgsB, 198relatives, 201replication, 199

repS, 199topoisomerase gene, 199tra genes, 201type IV secretion system, 199

pXO14, 199pYpsIP31758.1, 182pYpsIP31758.2, 182Pyrene, 57Pyruvate, 39, 45, 62, 253, 280, 317Pyruvate kinase(s), 318pYV

distribution in Yersinia strains, 173yadA, 176, 177ysc, 175

Qqox/Qox, 49

RRaffinose, 101Ralstonia eutropha H16

methylmuconolactone utilization, 255organoautotrophic growth on formate, 252synthesis of deoxynucleotides under

anoxic conditions, 254, 255, 257Ralstonia eutropha JMP134, 43, 47Ralstonia oxalatica, 47Ralstonia pickettiiRapamycin, 286Rap/Phr system, 191Recombinase(s), 122, 220, 223–225, 227, 229,

233, 234, 255Recombination hot spot (RHS) elements, 220Reductive pentose phosphate pathway

in R. eutropha H16, 251Regulators

AbpK/AbpR, 319AbrB, 191, 194, 195Acp, 198, 199of anthranilate degradation genes of

pCAR1, 73, 74AraC/XylS family, 74, 102, 157–159AtxA, 190, 191, 195, 196, 199B. anthracis Rap/Phr system, 191Caf1R, 177, 178of capsule synthesis in B. anthracis, 198, 199of carbohydrate metabolism in

A. nicotinovorans, 274CbbR of O. carboxidovorans OM5, 263CbbR of R. eutropha H16, 253, 258CopR/CopS two-component system,

229, 231

Index 343

CpxA/CpxR two-component system of Shigella, 157

Crp/Fnr family, 109CtrA, 96DctB/DctD of S. meliloti, 101, 101DmpR, 45, 47EnvZ/OmpR two-component system of

Shigella, 157ExpG, 104Fis, 158FixK, 108, 109FixL/FixJ, 108, 109Fur, 158GntR family, 274H-NS, 74, 156–159, 161, 163HoxA/HoxJ, 250, 251, 264IclR family, 102LacI family, 274LuxR-type, 281LysR family, 63, 102, 105, 106, 124,

252, 263MarR family, 18, 104MpfR, 62MvaT family, 74, 75, 77MxiE, 155, 159, 161NahR, 63NarX/NarL of R. eutropha H16, 254of nicotine catabolism in

A. nicotinovorans, 280, 281NifA of S. meliloti, 108, 109NifA of Rhizobium sp. NGR234, 125, 127NikR family, 264NnrR/NnrS, 97NodD1 of Rhizobium sp. NGR234,

124, 125NodD2 of Rhizobium sp. NGR234, 124NodD1 of S. meliloti, 105, 107NodD2 of S. meliloti, 105NodD3 of S. meliloti, 101, 105, 107NorR1, 254NorR2, 254NtrC/XyIR family, 45, 74, 250, 264, 280PbrR, 229PcaQ, 102PcaR, 102PmfR, 280Pmr, 74, 75, 77quorum-sensing regulators of Rhizobium

sp. NGR234, 121quorum-sensing regulators of Ti/Ri

plasmids, 143repressor RepB of Shigella, 162response regulator Spo0F of B. anthracis, 191RhrA, 102

of secreted protein genes in Shigella, 159Spo0A of H. marismortui, 23SyrA of S. meliloti, 101, 109SyrM of S. meliloti, 101, 105, 107SyrM1 of Rhizobium sp. NGR234, 124SyrM2 of Rhizobium sp. NGR234, 124TetR family, 280TfdR, 43of toxin gene expression in B. anthracis,

190, 191transcriptional activator VirF of Shigella,

157–159, 161TtsI, 126of virulence factor production in

B. cereus, 195, 196of virulence genes in Shigella, 157of virulence plasmid copy number in

Shigella, 162VirB of Shigella, 159Xre family, 74

Regulatory hydrogenase(s) (RHs), 251R.e.I1, 257Replication

of H. volcanii plasmids, 16, 19, 20iterons, 80of mycobacterial plasmids, 292NAH7, 61origin recognition complex, 12, 15,

19–21, 23pAO1, 273pAW63, 201pBT9727, 202pCAR1, 71, 72pCAR3, 80pHCG3, 259pHG1, 243pIJB1, 47pKB1, 300, 301pMOL28, 219, 220pMOL30, 222pMP118, 313, 314pMT2, 62pNG300, 23pNG400, 23pNG600, 22pNG700, 20pNGR234a, 121, 127pNL1, 80pNRC100, 10–12, 15pPCP1, 181pSymA, 93pSymB, 93, 94pXO1, 191pXO1-like plasmids, 193, 196

344 Index

Replication (cont.)pXO2, 199pXO2, 199repABC-type replicons, 80, 93–95, 121,

142, 259role of DnaA in replication of pSymA

and pSymB, 94of Shigella virulence plasmids, 161, 162of Ti plasmids, 136, 142

rep/Rep. See ReplicationResistance nodulation division (RND) efflux

systems, 210, 211, 220, 223, 224, 227–231

Resistance to nickel, cobalt and cadmium, 211, 212, 224, 239

Resolvase(s), 25, 243Restriction/modification systems

mycobacterial plasmids, 284pHV3, 19pHV4, 18pL47, 25pL131, 24pM118, 315pNG600, 22pNRC100, 12pNRC200, 15

Rhamnose, 319Rhamnulokinase(s), 319Rhamnulose-1-phosphate aldolase(s), 319rhb/Rhb, 102rhc/Rhc, 126Rhizobactin 102, 103Rhizobiaceae

genomic rearrangements in, 123mobile genetic elements, 99

Rhizobium sp. NGR234, 120, 125Rhizobium etli, 96, 121, 123Rhizobium tropici, 123, 124Rhodobacter capsulatus, 241,

263, 279Rhodococcus

degradation of aromatics, 48degradation of PAHs, 57degradation of rubber, 303linear plasmids, 35mixotrophy, 34

Rhodococcus erythropolis, 48, 291, 304Rhodococcus opacus, 240Ribose-5-phosphate isomerase(s), 318Ribulose-1,5-bisphosphate carboxylase/

oxygenase(s), 252, 263Ribulose-phosphate 3-epimerase(s), 252,

263, 318Rieske non-heme iron oxygenase(s), 58

Ri plasmidsclassification, 135evolutionary relationships, 137GALLS gene, 141incompatibility, 142genes for opine utilization, 142opine type, 135organization, 136rol genes, 138TSS, 140virulence genes, 139–141

RmInt1, 99RNaseH, 18, 21rol/Rol, 138Roseobacter denitrificans OCh 114, 259ros/Ros, 138, 139rox/Rox, 301R1 plasmid, 162R100 plasmid, 161–163rpoD/RpoD, 96rpoN/RpoN, 73, 74, 125RT-PCR, 72, 79, 232, 257Ruegeria sp. PR1b, 259ryh/Ryh, 158

SSalicylaldehyde dehydrogenase(s), 62Salicylate, 39, 41, 58, 62Salicylate hydroxylase(s), 63Salmonella enterica, 157, 161, 181SAL plasmid, 58Secretion

of B. anthracis toxins, 190, 192, 193

ESAT-6/WX100 proteins, 190of ExpE1 in S. meliloti, 104of galactoglucan in S. meliloti, 104of Nops by Rhizobium sp. NGR234, 126in L. salivarius, 320of succinoglycan in S. meliloti, 104type II secretion systems of

C. metallidurans, 225type III secretion system of Rhizobium sp.

NGR234, 126, 127type III secretion systems of Shigella, 152,

153, 155, 159type III secretion systems of Yersinia,

174–176, 178, 182type IVB secretion systems of

Y. pseudotuberculosis, 182type IV secretion systems of B. anthracis,

192, 193, 199Sedoheptulose-1,7-bisphosphatase(s), 252

Index 345

Sedoheptulose-1,7-bisphosphate aldolase(s), 252

Selenocysteine synthase(s), 98sel/Sel, 98Serine, 317Serine/threonine protein kinase(s) (STPKs), 291Shigella

invasion strategy, 152relationship to EIEC, 152sub-groups, 152subversion of host immune response, 153

Shigella boydii, 152Shigella dysenteriae, 152Shigella flexneri, 152Shigella sonnei, 152Shigella virulence plasmids

addiction systems, 162conjugative transfer, 162control of gene expression, 155control of virF expression by Fis, 158control of virulence factor expression by

iron, 158entry region, 155, 157H-NS and gene regulation, 156–158incompatibility, 155, 162initiation protein RepA, 162instability, 161integration into host chromosome, 161interactions between plasmid and

chromosomal genes, 159mobile genetic elements, 154mxi and spa genes, 155, 159oriR, 162partitioning, 163physilogical conditions for expression of

virulence factors, 157regulation of genes by VirF and VirB, 157regulation of virB by VirF, 159replication, 161, 162tra genes, 162transcriptional slippage, 161type III secretion system, 152, 153, 155, 159virB expression and DNA supercoiling, 159

Shigellosis, 152Siderophores

S. meliloti, 102Yersinia, 180

sigA/SigA, 287Sigma factors

sigma70ECF

, 17, 227sigma54, 125

sil/Sil, 224, 227, 229–231Sinorhizobium fredii NGR234. See Rhizobium

sp. NGR234

Sinorhizobium melilotidegradation of aromatic compounds, 102denitrification, 109genome organization, 92, 98, 99host range, 105, 120mobile genetic elements, 99plasmids in S. meliloti, 92

Site-specific resolution systems, 63, 66, 96S-layer gene(s), 190, 199SLH proteins. See Surface-layer homology

(SLH) proteinsSmall multidrug resistance (SMR) pumps,

277, 279SMR pumps. See Small multidrug resistance

(SMR) pumpsSoluble hydrogenase(s) (SHs), 249, 250Solute transport systems, 96Sorbitol, 319Sorbitol-6-phosphate 2-dehydrogenase(s), 319Sortases, 192, 320Southern hybridization, 8, 9, 72, 124, 301, 313spa/Spa, 155, 159Spermidine synthase(s), 24Sphingobium, 57, 66Sphingomonas

carbazole degradation, 67, 70, 78, 79car genes, 67, 79degradation of aromatics, 39

Sphingomonas xenophaga, 66Sphingomonas yanoikuyae, 58spo0F/Spo0F, 191Spores

germination of B. anthracis spores, 191germination of B. cereus spores, 196infectious state of B. anthracis, 188inhibition of sporulation by PlcR and

AtxA, 195sporulation of B. anthracis, 188, 191, 195sporulation of B. cereus, 196

5S rRNA, 21SsaDH. See Succinate-semialdehyde

dehydrogenase(s) (SsaDHs)ssd/Ssd, 277Staphylococcus, 57Staphylococcus aureus, 210, 272stb/Stb, 163Sterne strains, 189, 192STPKs. See serin/threonin protein kinase(s)

(STPKs)Streptomyces sp. 299, 301Streptomyces thermoautotrophicus, 242S-triazine hydrolase(s), 298Subtilisin protease domain, 279Succinate, 73, 74, 98, 101, 278, 280

346 Index

Succinate-semialdehyde dehydrogenase(s), 21, 278

Succinoglycan (EPS I), 103, 104Succinyl-CoA, 39Sucrose hydrolase(s), 274Superoxide dismutase(s) (SODs), 18, 227, 301Surface-layer homology (SLH) proteins, 192, 199Surface proteins, 315, 320syc/Syc, 176Symbiotic islands, 120sym loci, 99syr/Syr, 101, 105, 107, 109, 124

Tt-amyl methyl ether (TAME), 298TATA binding proteins (TBPs), 12, 15, 16, 19tbp/Tbp, 12, 15, 16, 19TC-1, 273TC-2, 273TCA cycle. See Tricarboxylic acid (TCA)

cycletcb/Tcb, 43T cell priming, 176T-complex, 139T-DNA, 137

covalent linkage to VirD2, 139entry into plant nucleus, 140formation of T-complex, 139genes for synthesis of opines, 135, 138genes for synthesis of phytohormones, 138of pRi1724, 138of pRiA4b, 137processing, 139rol genes, 138transfer by the VirB apparatus, 140

T-DNA transfer stimulator sequence (TSS), 140Tellurite resistance, 71tfb/Tfb, 15, 16, 19, 21, 22tfd/Tfd, 43, 47tgt/Tgt, 158Thioesterase(s), 286, 287Thiomersal, 225Thioredoxin, 4, 8, 12, 21, 22, 303Thioredoxin reductase(s), 4, 8, 12, 21thu/Thu, 97tiorf24/Tiorf24, 142, 143tiorf25/Tiorf25, 142, 143Ti plasmids

classification, 135copy number, 142curing of, 143genes for opine utilization, 142incompatibility, 142organization, 136

rep genes, 142tra genes, 143vir genes, 139–141

tml/Tml, 138tmr/Tmr, 138tms/Tms, 138Tn501, 154, 225Tn552, 272Tn554, 225, 272 Tn917, 199Tn4371, 47, 222Tn4378, 223, 225Tn4380, 223, 225, 227Tn4651, 72Tn4653, 65, 72Tn4655, 63, 65, 66Tn4676, 72Tn5046, 65Tn5280, 43Tn5530, 47Tn5542, 41TnBvie1, 227TnCme2, 223–225, 227, 229TnCme3, 15Tn501 family, 15tnm/Tnm, 225tnp/Tnp, 63–66, 72, 73, 223, 225tod/Tod, 43TOL plasmid, 58, 72Toluene, 41–43, 58, 63, 71–74, 81Toluene ortho-monooxygenase(s), 42tom/Tom, 42Topoisomerases, 192, 199topX/TopX, 192Toxins

B. anthracis, 188–192, 194, 196BCEA0165 and BCEA0203, 194B. cereus, 187–192, 194, 196, 198, 202B. thuringiensis, 201, 202Shigella, 152Yersinia, 177, 178, 181

Toxoflavin, 182TR1, 276, 281TR2, 276, 281tra-box, 142Transaldolase(s), 318Transaminase(s), 278Transcriptional slippage, 161Transcription factors (TFBs), 15, 16, 19, 21, 22Transcriptome

Cupriavidus metallidurans, 232, 233pNGR234a, 127Pseudomonas putida, 73–75

Transketolase(s), 252, 263, 318Translational coupling, 162

Index 347

Translation initiation factor IF-2, 19Transporters

for arabinose in s. meliloti, 101for arsenite efflux in H. volcanii, 18for arsenite efflux in N. pharaonis, 24for C

4-dicarboxylates in s. meliloti, 101

for cobalt and nickel in C. metallidurans, 227for ectoine in s. meliloti, 102for α-galactosides in s. meliloti, 101for heavy metals in N. pharaonis, 24for lead in C. metallidurans, 229for 4-methylmuconolactone in R. eutropha

H16, 23MFS permease for nitrate/nitrite in

R. eutropha H16, 255MFS permease in A. nicotinovorans, 274for molybdenum in A. nicotinovorans, 279for nickel in O. carboxidovorans, 264for polyglutamate in B. anthracis, 148for phosphate in s. meliloti, 102peptide transporters in H. volcanii, 19proteinase export in s. meliloti, 104solute transporters in S. meliloti, 96for sorbitol in L. salivarius, 319

Transposase(s), 16, 18–20, 22–24, 48, 63, 72, 73, 99, 122, 190, 225, 227, 233, 234, 255, 257, 287, 291, 315

Transposon mutagenesis, 263Transposons, 34, 35, 43, 47, 56, 63, 65, 66, 72,

98, 210, 225, 226, 229, 272, 273tra/Tra, 11, 12, 23, 27, 121, 162, 321

AW63, 201IncP-9 plasmids, 62Ti and Ri plasmids, 143

trb/Trb, 47, 136, 137, 143, 163, 220, 222, 259Trehalose, 96Trehalose 6-phosphate synthase(s), 96Trehalose synthase(s), 96Tricarboxylic acid (TCA) cycle, 45, 58, 79tRNA(s), 21, 95, 97, 98, 158, 316trx/Trx, 8, 12tryptophanyl-tRNA synthetase(s), 18tts/Tts, 126Tumour necrosis factor-α, 175tye/Tye, 175Type IV pilus, 100Tyrosinase(s), 194tzs/Tzs, 141

UUDP-galactose, 103UDP-glucosamine, 107UDP-glucose, 103UDP-glucose-4-epimerase(s), 103

Upper pathway(s), 39, 41, 43, 48, 62ura3-based gene knockout, 15

VV antigen. See lcr/Lcrvap/Vap, 143Variovorax paradoxus H-4, 240vir boxes, 139VirE2-interacting proteins (VIPs), 140vir/Vir, 163, 175

Agrobacterium, 136, 137, 139, 140, 141, 144

B. thuringiensis, 201Shigella, 157–159, 161–163Yersinia, 175

XXanthine dehydrogenase(s), 263, 279Xanthomonas, 301xdh/Xdh, 263, 279xer/Xer, 243Xylene(s), 35, 39, 41, 43, 66, 72xyl/Xyl, 39, 41, 43, 63, 73, 74

Yyad/Yad, 176, 177YD motifs, 220Yersinia, 172, 173Yersiniabactin, 180Yersinia enterocolitica, 176,

biogroups, 173contribution of plasmids to virulence,

174, 182pathogenesis, 173role of YadA in virulence, 177

Yersinia murine toxin, 177Yersinia outer membrane proteins (Yops),

174–176Yersinia pestis

acquisition of plasmids, 180anti-phagocytic activity, 179capsule, 178, 179colonization of flea digestive tract, 178contribution of plasmids to virulence,

181, 182lack of O-antigen, 174life cycle, 173mobile genetic elements, 181Pla and survival in the lungs, 180plasminogen activator, 179role of Ymt in virulence, 177, 178Yops, 174, 175

348 Index

Yersinia pseudotuberculosisbiotypes, 173contribution of plasmids to virulence,

181, 182role of YadA in virulence,

176, 177symptoms, 181

ymt/Ymt, 177, 178, 181yop/Yop, 174, 176

ypk/Ypk, 174–177, 179ysc/Ysc, 175y4xI, 126y4yS, 126

ZZavarzinia compransoris, 242zntA/ZntA, 231