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Index
415
2 micron yeast plasmid 69 bulge-helix-bulge introns 122, 129–130 adaptive mutation 169, 354 homing endonuclease 130 AddAB 15 AddAB polygenetic tree of 20 Cag protein translocation 170 amitochondrial protests 400 Campbell type recombination 5 antigenic variation 235, 278, 373–374 Campylobacter fetus 284 in Borrelia hermsii 290–292 catenane 84 mediated by homologous Chi site 10, 17, 18, 285 recombination 363–365 chloroplast 401 Bordetella pertussis 364 Chromosome balance 360 group A Streptococc M protein 374 CodY 255 group B Streptococci 373 com box (cin box) 243 in Haemophilus influenzae 363 combination (concatenation) of conserved Neisseria gonorrhoeae porin 374 proteins 393 in Streptococcus pyogenes 364 competence (for genetic transformation) in Neisseria 287–289, 293 [see also transformation] 235, 372–373 anti RBS sequence 179 biological role of 235–237 anti restriction proteins 218 bi stability in 256 Arabidopsis thaliana 401 escape from 254–255 AraC 61 escape from; role of comGA 255 ArcA (SfrA) 185 in Neisseria gonorrhoeae 235 purine repression of 259–260 Bacillus subtilis 15, 20, 21, 22, 23, 68 regulation of 241–260 Hbsu 100 regulation of in Bacillus subtilis 244–257, bacterial endosymbiont 400 260 biofilm formation 299 regulation of in B. subtilis and S. Bordetella phage retroelement 137–138 pneumoniae role in phage interconversion 137 regulation in H. influenzae 257–258, 259, β-recombinase 99 260 activity in mammalian cells 109 regulation of in Streptococcus BPP-1 phage 137 pneumoniae 242–244, 260, 373
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competence (cont.) CTnBst 222 role of camp 258–259 CTnDOT 221 role of peptidoglycan 260 excision 221–222 role of Sxy-1 (TfoX) 259 integrase int 221 stimulating peptide (CSP) 242 tet(Q) 221 sporulation factor (CSF) 245, 246–247 CTnERL 221 ComK CTnGERM1 222 box 253 CTnscr 224, 336 induced K state 256–257 CTnR391 223 regulation 255 CTnR391 insertion site 223 regulation at PcomK 253–254, 256 CTXφ phage 332, 334 regulation of stability 249–253, 254 cyanobacteria 401 regulation of stability role of ClipC 249, 416 254, 255 dam- 186 regulation of stability role of ClipP 249, Dam methylation 186, 299 254 Darwinian threshold 396 regulation of stability role of MecA 249, D. radiodurans 21, 23
index 254, 255 DinB 177 regulation of stability role of Spx 252 DinI 13 ComP/ComA two component Din invertase 285 system 248–249 DNA as food 237, 260 ComS 255 gyrase 182 ComQ 247–248 in hypothesis 93 ComX 243–244 inversion 279–281 ComX pheromone 245, 247–248 invertase 101–105 conjugative genomic island 342 out hypothesis 93 conjugative pore (of F) 173 polymerase III 13 conjugative transposition; mechanisms restriction 237 of 209 triple-stranded (H-DNA) 293 conjugative transposon 66, 207, 342 uptake mechanisms 238–241 from Bacteroides 221–223 uptake mechanisms related to type II from Enterobacteriaceae 223–224 secretion 238–240 Conservative site-specific recombinases uptake mechanisms related to type IV 35–36 secretion and conjugation 238, constins 66, 342 240–241 contingency genes 292 uptake sequences 238 corynephage β of Corynebacterium DnaB 12 diptheriae 324 DnaC 12 coupling protein (of F) 171 DnaT 12 cpx∗ 187 domain swap model 52 Cpx pathway 178 Dot/Icm genomic island 171 Cpx regulon 186 double cross over 5 Cre 46, 49, 56, 57, 69 RNase activity 62 early cells 396 recombination complexes 42, 48 ectopic recombination 4 CRP (camp repressor protein) 185 endonuclease (homing) 126 CTn7853 222 endosymbiosis 395 CTn12256 221–222 enhancer site 102
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eukaryote to bacteria transfer structure 153–167 (glutaminyl-rRNA synthase) 399 transfer 168 ExoV 10 transfer in natural environments 189–190 φC31 106 transfer initiation 188 integrase 106 transfer regulation 178 integrase activity in mammalian cells transfer region (tra) 167, 170–174 109 vegetative and conjugative φR73 336 replication 188–189 F-sex factor 153 fertility inhibition 168, 178 F’ strains 167, 168 (FinOP) system 178–182 FRT 57, 69 fim operon 279 Gam 24 switch 300 GATC site 186 417 role of DNA gyrase 281 gene conversion 4, 8, 286–292 role of DNA topology 281 in Borrelia hermsii 291 index fimA promoter 280 in Neisseria 286–290, 363 fimB gene dosage 360 regulation by RpoS 300 genetic mosaic 352 fimbrins 279 genome reduction 358 FinO structure 180 genome simplification 397–399 FinP structure 181 genomic islands (genetic island) 324, Fis 54, 59, 102, 183, 282, 301 342–344, 352, 366–367 Fis structure 104 metabolic island 342 fitness island 334 microbial evolution (role in) 342–344 flagella of Salmonella typhimurium phase resistance island 342 variation in 281–283 symbiosis island 342 Flp 46, 51, 56, 57, 69 GFP:lacI fusion: for lacO binding assay recombination complex 42, 48 188 site-specific RNA cleavage 62 Gin 41, 52, 54, 68, 84, 101–105 F’lac 176, 186, 355–356 gix 54, 101 F-pilus 173 group I ribozymes 70 specific phages 168 group I introns 122–128 F-plasmid 151 mobility 126–128 derepressed 168 splicing 124–126 DNA metabolism 174–176 structure and distribution 122–124 DNA metabolism and adaptive Tetrahymena 128 mutation 176–178 transposition 128 history of 151–153 group II intron 70, 122, 219 induced recombination 176 evolution of 134–135 integration 169 L1.ltrB 133 leading region 166 maturase 133 replicons 166 retrohoming 133–134 response to extracytoplasmic retrotransposition 134 stress 186–188 RmInt1 134 role in dynamic genome 190 RNP particle 133 role of host factors in tra splicing 132–133 regulation 182–186 structure and distribution 131–132
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γδ 41, 69, 98 between E. coli and Salmonella resolvase 41, 84–88 typhimurium 390 activated mutants (activity in between eukaryotes and bacteria 395, mammalian cells) 109 399–402 structure 88 between hyperthermophilic Archaea and res I 41, 99 bacteria 390 between low G+C Gram positives and H. influenzae 21 Archaea 389 Helicase IV 10 between thermophilic bacteria and Archaea Helicase role in F-transfer 174 389 Helicobactor pylori 15, 21 between Spirochetes and Archaea 389 heteroduplex 8 between Wolbachia and insects 394 HexAB 21 detection of 387 418 Hfr strains 167, 168 effect on tree topologies 394 Hfr gradient of transmission 170 eukaryotes 385 high frequency of transfer or HFT (of F) 178, extent of 390–391 181 mechanism for transfer across
index Hin 41, 52, 54, 68, 84, 101–105, 282, 301 domains 394–396 Hix site 41, 54, 101, 282 HSP70 394 HMG-1 100 Hs1VU protease/chaperone pair 187 H-NS 183, 281, 300, 335 HU 100, 103, 216 Holliday junction 8, 12, 24 hydrogen hypothesis 395 homing (by introns) 126 hydrogenosomes 400 homologous recombination 3, 33–35 hypermutators 277 biochemistry 8 deletion mediated by 356–359 illegitimate recombination Mycobacterium tuberculosis 356 homology directed 368 Ochrobacterium intermedium 356 IncH11 transfer system 171 Streptococcus mutans 356 Inc I plasmids 171, 283 definition 4 Inc J integrative phage/plasmids 171, 223 deletions and reductive evolution 357–359 IncP plasmids 170 foreign DNA acquisition 365–368 Int (from Tn916) 210, 212–216 and deletion 367–368 structure 213 inragenic; biological consequences Intλ 214 of 353–355 integrase 36 RecA independent 14 serine recombinase family 105–107 tandem duplication 353–355 integration host factor (IHF) 59, 172, 175, and divergence 355–356 183, 281, 300, 335 in E. coli 354 introns 121 resulting in antibiotic resistance 354 invertase 36 in Nostoc linckia 356 activating mutations 105, 108 in Salmonella typhimurium 353 FimB and FimE 280 horizontal gene transfer 151, 385 inversions 359–363 between Agrobacterium and Hela cells distribution of 361–363 394–395 fitness costs of 360–361 between Archaea and bacteria 397–399 Neisseria meningiditis 364 between Archaea and eukaryotes 396–397 Pseudomonas aeruginosa in 364
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synapse 104 mms 22 tuf genes in Salmonella typhimurium 360, mobiliseable transposons 219, 221 361 mosaic genes 369–372 invertasome 283 fluroquinolone resistance 371 IS3 180 penicillin resistance 355–370 IS3a 166 Neisseria cinera 371 IS3b 166 Neisseria flavescens penA 371 IS100 340 Neisseria gonorrhoeae 371 IS200 362 Neisseria meningitidis penA 370 IS481 364 Streptococcus mitis 371 IS605 337 Streptococcus oralis 371 IS607 transposase 107 Streptococcus pneumoniae 371 island probing 338 sulfonamide resistance ISXc5 resolvase 99 Neisseria meningitidis 372 419 iteration of strand exchange 95 TetM 371 IVS mosaicism in conjugative transfer index Leptospira 130 systems 169 helix 9 131 mouse transcription factor Zif268 109 rRNA 122, 130–131 msDNA 135 Salmonella 131 Mu 41, 63, 68, 101 Yersinia 131 MutL 11, 21 MutS 11 Lactobacillus acidophilus DNA inversion Muller’s ratchet 351 in 285 Mycoplasma agalactiae avg genes 286 lacZ 176 Mycoplasma bovis vsp genes 285 lambda 24 Mycoplasma pulmonis vsa genes 286 Int 46, 59, 66, 211 integrase family 286 NaeI61 Xis 59 NBUs (non replicating Bacteroides units) 221 leuX 339 nic site 174 LexA 13, 23 niche specialization 359, 363 LINE element 72, 135 non LTR retroelements 135 Listeria monocytogenes phase switching in nucleosome-like structure (in F) 172 302 Nucleotidyl transfer mechanism 39–41 loop-loop kissing interaction 179 loxP 57 Opa proteins from Neisseria 287, 293 Lrp (leucine-responsive regulatory origins of replication (of F) 166 protein) 185, 281, 297, 300 oriT (of F) 172, 174, 176 oriT (of Tn916) 210, 217, 218 mating pair stabilization 173 OxyR 299 merodiploid 6, 169 mini F-plasmids 166, 188 Parabaslids 400 mismatch repair genes from bacteria 366 pathogenicity island 323, 324 Hex system 373 α heamolysin 333, 339 MutSHL system 373 Bordetella pertussis 333 mitochondrial evolution 400 concept of 324 mitosome 400 cross-talk activation 335
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pathogenicity island (cont.) pAD1 218 cytotoxic necrotizing factor 333 pAM373 218 distribution of 326–332 P fimbriae 279 encoded secretion systems 332 pGO1 226 type III 333 phase variation 277 type IV 333 by DNA methylation 297–300 Enterococcus faecalis 333 of antigen, 43 (Ag43) 299–300 Helicobacter pylori 332 epigenetic 297 cag-PAI 333, 337 in Campylobacter 297, 364 high pathogenicity island 334, 339 in ecological interactions 301–305 attP site 340 from host to free living 302–303 translocation of 341 in lipooligosaccharides 294 Hrp PAI 333 in Haemophilus 296 420 integrase in 332, 336 in Helicobacter pylori 296 integration 335–337 in Mycoplasma 295–296 into tRNA genes 335 in Neisseria 289–290, 293–294, 295 iron uptake systems 334 in opc locus 294
index LEE 333, 335, 336, 339 in P fimbriae 297–299 LPA 336 in porA 294 mobilization of 340–342 by slipped-strand mispairing 292–294, Neisseria gonorrhoeae 332 295
PAI II536 339 role of environmental conditions 300–301 pertussis toxin 333 phenotypic variation in biofilm regulation of island encoded formation 303–305 genes 334–335 by coagulase negative Staphylococcus SaPI1 mobilization by φ80α and φ13 341 epidermidis 304 SHI-1 339 role of IS256 304 SHI-2 336 by Pseudoalteromonas aeruginosa 305 SP-1 333, 335 by Pseudoalteromonas atlantica 304 SP-2 333 by Salmonella typhimurium 304 SPI-3 336 by Vibrio cholerae 303 stability 337–340 Photorhabdus phase switching in 302 stabilization of (homing) 340 Phylogenetic footprints 388 Streptococcus enterica 332 Phylogenetic profiling 391 Streptococcus pneumoniae (PPI-1) 332 Phylogenetic trees toxic shock syndrome toxin 334 based on small subunit rRNA 388 uropathogenic E. coli 332, 337 plasmids (conjugative) 189 vap of D. nodosus 340 plasmid transfer in biofilms 189 Vibrio cholerae 332 plastid endosymbiosis 401 ToxT 334 pili 278 VPI 342 pil loci 287 island mobilization 341 minicassettes 287 by CP-T1 341 pilin virulence factors encoded on 332–334 L-pilin 290 pathogenicity islets 325 soluble (S-pilin) 289 P1 69 pilus P+ 289 TCP 335 PS 289 conjugative type II assembly 171
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Piv recombinase 286 res III 54 primosomal cascade 22 res transposon targeting 108 pSK41 replication fork reversal 8, 12 pop in recombinant 6 replication slippage 14 PriA 12, 22 resolution synapse 104 PriB 12 resolvase 36 PriC 12 activating mutations 93, 97, 108 pRK100 184, 185 binding to res 88–91 protein splicing 72 catalyzed strand exchange 92–97 proto-eukaryote (chronocyte) 395 domain rotation 93 pSLT 185 large resolvase 219 Pseudomonas aeruginosa 21 subunit rotation 93 retroelements 121 quorum sensing; role in competence 238, retrons 122, 135–137 421 242, 243 in E. coli 136 quorum sensing; role in competence in EC73 mobility 136 index Bacillus subtilis 245–249 that are mutagenic 137 in myxobacteria 136 R(resistance) factors 153 from vibrio 137 R1 plasmid 179, 185 reverse transcriptase 122, 132 R64 plasmid 283 rhs sequences 11 R100 plasmid 182, 184 rimJ role in pap operon Rac prophage 14, 23 thermoregulation 301 RAG1/RAG2 recombinase 66 RNase III 130 Rci recombinase 283 RNase H 135 RecA 8, 11, 13, 15, 21, 34 RNA chaperones 126 RecA star 13 subunit exchange model 52 RecBCD 8, 11, 176 RuvABC complex 21 RecF 10 RuvABC 8, 9, 10, 12, 13, 15, 21 RecFOR 20 RecG helicase 21 S. pneumoniae 21, 22 RecG 12, 15 Salmonella 15, 21, 41, 68 RecH 23 sapA gene cassettes 285 RecJ 10 serine recombinase 36, 38, 41, 48, 52, 54, 83, RecN 10, 13 219 RecO 10 evolution 107–108 RecP 23 hybrids 108–109 RecQ 10 use in biotechnology 109 RecR 10 serotype switches 372–373 RecT 23 Streptococcus pneumoniae 372 Recombination short sequence repeats (SSRs) 292 anchor 368 shufflon 283 between linkage groups sigma H 246 within a linkage group 352 Sin resolvase 99 relaxase (from F) 171, 174 Sin synapse 100 relaxosome (of F) 172, 175, 184 single strand binding protein (SSB) 10 res I 54, 84, 91, 99 single stranded promoters 175 res II 54 sis site 102
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site specific recombination 33, 35 insertion and excision 210–212 evolution 60–61 insertion and excision regulation 216–218 topology and geometry 54–60 transcriptional analysis 216 S-layer of Campylobacter 283–285 transcriptional attenuation in 216 S-protein 284 Tn925 mobilization of chromosomal SOS regulon 13 genes 218 SOS response 11, 13, 23 Tn1000 166, 169 SP01 phage intron 126 Tn1545 66 SP82 phage intron 126 Tn1549 225–226 spliceosomal introns 134 Tn4451 106 SpoI recombinase 106 Tn5030 222 spontaneous mutation 277 Tn5251 225 Spo0A 249 Tn5252 225 422 srfA promoter regulation 249 Tn5253 225 SSCmec 106 Tn5276 226 Staphylococcus aureus 99 production of nisin by 226 Streptococcus pyogenes 99 Tn5397 106, 218–221
index supercoiling 182 DNA sequence 219 surface exclusion 169 in Clostridium difficile 218 SXT element 171, 224 insertion and excision 219–220 response to activated RecA 224 mini transposon 219 symbiotic island 336 regulation of transposition 220–221 synapse 86, 97 tndX (a serine site-specific synaptic complex (with res) 91–92 recombinase) 219 syntrophic hypothesis 395 transcriptional attenuation in 221 TndX 219 target primed reverse transcription 133 tra operon 167 Tc1 107 traJ 167 T4 bacteriophage 24 traM 167 thermophilic bacteria evolution of 389 transferosome 175 thymidylate synthase intron 126 transformation (by DNA) 235 Ti plasmid of Agrobacterium tumefaciens 170, of Bacillus subtilis 236, 238, 241 394 of Haemophilus influenzae 236, 240, 241 Ti plasmid VirB region 170 of Helicobacter pylori 236, 240 Tn3 41, 69, 83, 84, 98 of Neisseria gonhorreae 241 resolvase 84–88 of Neisseria meningitides 236, 240, 241 resolvase activating mutants 105, 108 of Streptococcus pneumoniae 236, 238, Tn5 63 241 Tn7 63 translocation 359, 363 Tn10 63 distribution of 361–363 Tn21 resolvase 84, 99 in Salmonella 361 Tn552 107 in Yerisnia 362 Tn916 66, 207, 221, 225, 226 fitness costs of 360–361 att sites 211 rrn operon 361 behavior in Clostridium difficile 210 Salmonella typhimurium histidine operon in conjugation 218 359 coupling sequences 210 rrn operon 359
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transposase (serine recombinase unequal crossing over 6 family) 105–107 uropathogenic E. coli (UPEC) 279, tree of life 387–389 297 Archaea 388 UvrD 10 Bacteria 388 Eucarya 388 vaccinia topoisomerase 62 universal 389 vancomycin resistance 225–226 TrwB from R388 (structure) 171 variable number of tandem repeats type I fimbriae 279–281, 299 (VNTRs) 292 type IV pili of Neisseria 287 vrs box 286 type IV pilin of Moraxella lacunata and M. bovis 286 Xenorhabdus phase switching in type IV pilus systems 238, 283, 332 302 type IV secretions systems 153, 170 XerC 38, 46, 48, 58, 69 423 type IV secretions systems core genes for XerD 38, 46, 48, 58, 69 F 171 Xis (from Tn916) 210, 212–216 index type IV secretions system transferosome XisF 106 171 Xisλ 214 tyrosine recombinase 36, 38, 41, 42, 49, 56, 61, 69, 83, 221 zygotic induction 182
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