(X-amylase 252-3, 290, 294, 389 acquired immune deficiency syndrome

(AIDS) 311, 407 act genes 299 adaptor 71-3

conversion 72 preformed 71 single-stranded 72-3

adh gene 357 Aeromonas spp. 389 affinity chromatography 254 afsA, afs8 gene 300 Agrobacterium spp. 25, 185

recombination-deficient 346 A. radiobacter 366 A. rhizogenes 348-9 A. tumefaciens 111, 334-48, 366,

371 alcohol tolerance 273-4 alkaline phosphatase

as fused polypeptide 253 dephosphorylation of DNA 74-5,

94 promoter regulation 223

allele replacement 207-9, 319-21 Alteromonas espejiana BAL31 64 Ames test 400-2 Anabaena azo/lae 370 Anabaena 7120373 Anacystis nidulans 359 antibiotic

ampicillin 402 chloramphenicol for plasmid amplification 78, 147,237 cloning biosynthesis genes 293-4 ensuring plasmid stability 242 inactivating enzyme 273, 324 mitomycin C 84, 223, 403 modified 281-2 nystatin enrichment 213 penicillin enrichment 82,213 spectinomycin for plasmid

Index

amplification 78 streptomycin dependence 242

antibiotic production actinomycins 281 actinorhodin 293-4, 299-300 aminocyclitols 281 ~-lactams 281; cephalosporins 271,

275, 277, 291; cephamycin 277, 280; nocardicin 273; penicillins 271-2,275-7,284,291

candicidin 281 carbapenems 292 6 deoxyneomycin B 282 dihydrogranatirhodin 299-300 granaticin 299 herbicidins 365 herbimycins 365 kanamycin 291 medermycin 299-300 mederrhodin A, B 299-300 milbemycin 363 narasin 103 neomycin 291 novobiocins 281 paromomycin 291 rifamycins 281, 291 streptomycin 300 tetracyclines 271, 280-1 tylosin 103 yield improvement 271-7, 280-5, 291-4

antibiotic resistance ampicillin 5, 24, 79, 112, 150, 180,

239,322,342 carbenicillin 99 chloramphenicol 5, 81, 100, 112, 151-2 erythromycin 5 gentamicin 320, 375 G418 5, 112, 180; in animal cells 110;

in plant cells 347; in yeast 108 kanamycin 5,24, 112,319-21,342,

345 neomycin 103-4, 375

411

INDEX

nocardicin 273 spectinomycin 99, 343 streptomycin 5, 84, 99, 343 sulphonamide 99, 112 tetracycline 5,24,81-4,99,112,186,

271,315,342 thiostrepton 103-4 trimethroprim 5, 115 viomycin 103, 116

antimutator 211,301 anti-sense RNA 226 antitrypsin

gene 307, 328 site-directed mutagenesis 307-8

ARG region 107 aroA gene 315, 358-9 Arthrobacter 61, 397 aspartame 408 aspartate kinase 275 Aspergillus nidulans 109 Aspergilluy niger 285 Aspergillus oryzae 389 auxotroph

ensuring vector stability 242 improving amino acid production

275-6,292 improving antibiotic production 277 revertants 280,291 selection of recombinants 115

avidin 121 Azotobacter vinelandii 370

Bacillus 244,276-8,290,361-89,397 B. amyloliquejaciens 252-3,297 B. cereus 363 B. megaterium 363 B. stearothermophilus 299, 306 B. subtilis 31, 148, 180, 249, 363, 389;

a.-amylase 294; exoprotease­deficient 253; gene insertion in 244; minicell-producers 321; producing foreign proteins 257-8; promoter probe vectors 232; promoters 220-1, 223, 258; ribosome-binding sites 229; secretion vectors 252-3; transduction 31; transformation 14-17

B. thuringiensis 359,361-3 p-exotoxin 362 6-endotoxin 359, 362

Bacteroides amylogens 389 bacteriophage

fl87 F116L 31 Mu 4, 26,183-7

412

A gene 187; B gene 185; C gene 185; kit gene 84; mini-Mu 185, 187; Mu d 149-51; Mu-Pl hybrids 185; Mu-t.. hybrids 35,150-1

PI 31-2, 35 P291 P495 P22 184-6,315 SP6122-4 SPP131,101 T3125 T4246-7 T5 92, 246 T6116 T7 125, 194, 227, 246 cp 80 88 cp 105 101 cp 434 88 cp C31103-5 cp C31.KC400 103, 112, 116-17 cp SV1 31 see also lambda, M13 phage

barriers to genetic exchange 46-7 Beauveria bassiana 364 bioA gene 32 bioconversion 268, 385 biomass conversions 385-9

cellulose 387-9 hemicellulose 389 lignin 386-7 starch 389

biosensors 384, 408 bla gene 80, 125, 150, 230, 321, 324 Brevibacterium lactojermentum 292 brewing

improvement of yeasts 273, 287-90, 292,297

phenolic off-flavour 287-9 see also POF gene

5-bromo-4-chloro-3-indolyl-P-D­galactoside (Xgal) 85; 91, 93, 200, 346

carboxypeptidase B 254-5 cat gene 151, 230, 347 catabolite repression 280, 388 cellulase 385, 387-9 Cellulomonas fimi 387-8 cellulose 280, 387-9 Cephalosporium acremonium

(Acremonium chrysogenum) 275-7, 291, 294

cerlocus 235, 241-4 chi sequence ( site) 91-2, 325 chloramphenicol acetyl transferase (CAT)

cat gene cartridge 151-2, in assaying gene expression 80, 232 mediating chloramphenicol-resistance

80-1,232 chromosome mobilisation ability (Cma) 20,

23-6,291 Citrobacter jreundii 185 Clostridium butyricum 102

Clostridium spp. 387, 389 Clostridium thermocellum 102, 387-8 codon usage 131, 229-30 competence 13 complementation 115, 234 comutation 176-7 conjugation 20-6, 290-1

clumping-inducing agents 31 conjugative transposon 31 definition 20 F system 20-3 FinOP fertility inhibition 22 Gram-positive bacteria 30-1 transfer (tra) operon 20-2 see also plasmid

copA, copB gene 237 copy DNA (cDNA) 57, 82, 257

cloning 57, 82, 310 definition 57 library 114 vectors 82, 87

Corynebacterium glutamicum 275-7 cosmid 93-5

c2XB 95 definition 93 gene libraries 113 pJB893 pKT25899

cotransformation 19-20, 111 crown gall disease 335-9

opine 335 see also Agrobacterium, Ti plasmid

ctx operon 319-21 cyanobacteria 369 cytoduction 287, 289

dam methylase (DNA adenine methylase) 7,62, 165, 211

dcm methylase (DNA cytosine methylase) 62

denaturation mapping 130 Devoret test see inductest dhfr gene 110 dideoxynucleotide 133, 136 dihydrofolate reductase 110, 115, 352 direct selection ofrecombinants 82-4, 91-

2,101,115 dnaA gene 180 DNA adenine methylation see dam

methylase DNA glycosylase 166, 176 DNA gyrase 7 DNA ligase 66-7, 74, 166

E. coli 57,66,82 T4 66-7,137,238,293

DNA polymerase E. coli DNA polymerase I 63, 78,167,

183, 189, 234; in ColEl replication 183; Klenow fragment (enzyme) 63,

INDEX

122, 133-7, 201; nick translation reaction 121, 132,200; proofreading exonucleolytic activity: 3' -+5' 63 164-5 201 5'-+3' 63 121, 201' " ,

E. coli DNA polymerase III 170-1 Micrococcus luteus 196 T4 57, 63,121-2, 132

DNA probe see probe DNA repair 165-73

error-prone (mutagenic) 169-71, 179 excision 167-9, 179 mismatch 165,203 photoreactivation 165-7 post-replication recombinational

( daughter-strand gap) 169 SOS 169, 176-7,224,246,402

DNA replication 26, 164-5, 234-7 DNA sequencing

genomic 141, 143-4 kilosequencing 137, 140-1 Maxam and Gilbert 132-4, 143 M13 133-5, 137-42,201

plasmid 135 primers 133-6 Sanger-chain termination 133-41 see also M13 phage, primer DNase see nuclease

ELISA 118, 145, 298 end-product inhibition see feedback

inhibition endorphin 253, 257,407 endotoxin 257-8 enhanced oil recovery 397-8 5-enolpyruvylshikimate 3-phosphate

synthase (EPSP) 315, 358-9 envA mutation 400 Erwinia herbicola 366 ethidium bromide 127, 137, 198 expression vectors see vectors

feedback (end-product) inhibition 267, 275-7,388 end-product analogues and 275

fimbriae see pili fix genes 374-6

galactokinase 298 ~-galactosidase 83, 88, 91-3

ex-peptide 83-5, 200 galE gene 32,315 galK gene 298 gdh gene 295 gel electrophoresis of DNA 127-9, 131,

134,138-43 gene

hybrid 118, 280, 298, 343-5 split (exon/intron) 55-6,130-1

413

INDEX

tandem 238 see also gene fusion, operon fusion

gene cartridge 151-2 gene cloning

cDNA 57-8, 82 definitions 54-5 direct selection of clones 82-4 directional (forced) 73-4 host strains: B. subtilis 100-1; E. coli

77-8,83-4,91-2; S. cerevisiae 105 in animal cells 109 in filamentous fungi 109-11 in plants 111, 334-46 in Streptomyces 102-7 insertional inactivation 80 open reading frame (ORF) 118-20 primary 55 properties of cloning vectors 76 shotgun 137 subcloning 55 see also ligation, plasmid, restriction

enzyme, vector gene dose optimisation 232-46

autoregulated/lethal genes 232 by vector copy number 237-8 by vector stability 241-4 tandem genes 238-40

gene fusion 92-3, 118-20, 149-52, 298 gene libraries

amplification and stability 115 cDNA 114 formulae for estimating representation

113-14,116 genomic 113-14, 125-7, 407

gene synthesis 58-9, 206-7 genetic instability 241-6, 301 genome walking 152 ~-glucanase 297 glutamate dehydrogenase 295 glutamate synthase 295 glutamine synthetase 295 gIycosylation of proteins 258-9 gptgene 112 growth hormone 249, 407

haemolysin (HLY) 257, 319 haploidisation 40-2, 284 helicase II 167 hemicellulose 385 heteroduplex 130, 191, 198

mapping 130 mismatched 200-6

heterokaryon 40, 283 hilA gene 93 Hfr 20, 23 HO gene 38-9 homogenotisation see allele replacement homologous recombination 207-11

see also recA gene, recombinational rescue

414

homopolymer tailing 67,73,82 hsdR, hsdS gene 77 hsn genes 374, 376 human immune-deficiency virus (HIV) 407 hybrid antibiotic 299-300 hybrid arrested translation (HART) 148 hybrid released translation (HRT) 147 hybridisation (nucleic acid) 121-6

colony/plaque 125-6,324 diagnosis of disease 324-8, 360 in situ 125 Northern transfer 130 probe 114, 121-6, 152,324,328,373;

biotinylation 121; nick translation 121-3; radiolabelling 121-5; random priming 122-3

Southern transfer 128-9, 143, 324-5 see also M13 phage, primer

hydrogenase 369, 372

ice-minus bacteria 366-7 ice region 366-7 ilv gene 180 immunogen 309 immunoglobulin 116-18, 246, 254 immunological screening

enzyme-linked immunosorbent assay (ELISA) 118

oo..gtll plaques 93 of ORF vector recombinants 118-20 radioimmunoassay 116-18

inaZ gene 366 incD, incG gene 241 inclusion body 247-8,256,258 incompatibility (fungal) 37-9 incompatibility (plasmid) 2, 234-7

group IncP( -1) plasmid 98-100 group IncQ plasmid 99-100 group IncW plasmid 98-9 inc determinants 234, 237, 241 mechanism 234-7, 241

inductest 402 insertion sequence (IS) 4, 23-8

IS15 IS2 5, 23 IS323 ISS 23 IS21 5, 25, 28

insulin 59, 252 integrative suppression 26 interferon

ex (leucocyte) 208, 240, 258-9 ~ (fibroblast) 247,307 "( (immune) 258 hybrid 208-10

interleukin-2 307, 407 in vitro phage packaging 96-8, 105

kar gene 287, 290

killer strains of yeast killer toxin plasmids 107-8, 290, 292 in strain improvement 289-90,292

Klebsiella pneumoniae 25,372-3

lac operon lacI gene 244 lacZ gene 83, 91, 118, 149,231,249,298 lacZ.lM15 deletion 77, 83

~-lactamase detection 143, 324 secretion 229 OXA-2324 TEM 79,229,258,324

lambda (A) phage 31-6, 87-98 amber mutants 88, 90-2, 125 attB 32,225 attL 32, 225 attP 32-3, 98, 184, 225 attR 32,225 b2 deletion 98 cI (immunity) gene 31, 87-8 cI repressor 145 cIm allele 95, 98, 116, 224, 238 chi sites 91-2 cos site 89, 93-8, 107 gam gene 91-2 gene A 96, 125 gene B 125 gene D96-7 gene E96-7 gene S 36, 90, 93, 97 intgene 184 Int protein 33, 224-5 in vitro packaging 96-8, 105 life cycle 187 A bio 33-4 A gal 33-4 nin5 deletion 90 red gene 91-2 size selection of recombinants 89 Spi+ phenotype 91-2 stuffer fragment removal 89-90 xis gene 184 Xis protein 33, 224-5 vectors 87-98

insertion 88-9 phasmid 95 replacement 89 Charon 4A 88 Charon 30 91 Flac:: A hybrids 36 1.105988,92 Agt11 88, 92-3 AgtWES.T562288 AL47.1 88, 91-2 ANM64188 ANM78188 MU::A hybrids 35

see also lysogen, promoter, synchronous site specific recombination

leu gene 105-7 lexA gene 169 ligation (of DNA molecules) 64-75

blunt termini 66-7, 70 cohesive termini 66

INDEX

partialy-filled termini 64-6 prevention of self-ligation 66, 73-5

Lignobacter 371 linker 70-1, 193 Ion gene 246 Lon protease see protease lopll locus 191 lpp gene 226, 230, 240 lysogen

1.32-4 Mu 187 see also lambda, Mu phage

lysozyme (T4) 297

Ml3 phage 83-7 in oligonucleotide mutagenesis 201-7 life cycle 83 Ml3K19 203, 205 Ml3mp785 Ml3mp887 Ml3mp987 Ml3mp10 203-4 Ml3mp1886-7 Ml3mp1986-7 mWB2341140 polylinkers 85-7 primers 133-6, 201

maxicell 145-6 mcrA, merB gene 78 metal recovery 399-400 metallothioneins 399-400 methyl transferase 166 methylation of DNA

in vitro 63, 71 in vivo 60, 71, 78

Methylophilus methylotrophus 257,294-7 microbial mining 398-9 Micrococcus 196, 397 microinjection 111, 147,335 minicells 145-6, 321 mob genes 27, 235 mobilisation

of chromosome 20-6 of nonconjugative plasmid 26-7

Moraxella bovis 61 mRNA stability 230 Mu phage, see bacteriophage mucA, mucB gene 400 mutagen 163-77

chemical 171-7; acridine orange 175-7; 2-amino-purine 175-7; bisulphite

415

INDEX

173-4,195-9; 5-bromouraciI175-7; ethylmethane sulphonate 174, 176; hydrazine 173-4; hydroxylamine 173, 193; methylmethane sulphonate 174; N-ethyl-N­nitrosourea 174; N-methyl-N'­nitro-N -nitrosoguanidine 174-6, 187,193,319; N-mustard 174, 194; S-mustard 174; nitrous acid 173-4; proflavine 175, 177

physical 177-8 specificity 163 transposon 180-5 usage 178-9

mutagenesis 163-207 antimutagenesis 211, 301 directed in vitro 188-207, 270, 306-8,

360; deletion by nucleases 188-92; deletion loop 196-9, 203; displacement (D) loop 196-8; insertional 193, 203-4; linker 193; nucleotide misincorporation 199-200; oligonucleotide 201-7, 297, 306-8; segment-directed bisulphite 195-7; shotgun gene synthesis 206-7

localised in vivo 36, 181, 187, 193 mechanisms 163-4, 169-71 site-directed in protein engineering:

ex -antitrypsin 307-8; interferon 307; interleukin-2 307; tyrosyl tRNA synthetase 297-8, 306

transposition 11-13, 179-87,315,373-5

see also mutational cloning mutant

antibiotic-blocked (idiotroph) 281-2 deletant 36, 188, 196 enrichment for: starvation 213; suicide

213 permeability 280 phosphate deregulated 281 resistant to: alcohol 273; antibiotics

271-3,294; catabolite repression 280; phage 274; toxic analogues 275-9

revertant 280 screens: random 212, 270-8; rational 212,

271-8; selective methods for 212,271-81

see also auxotroph mutasynthetic 281 mutasynthon 281 Mutatest see Ames test mutation 163-80, 270-81

amber 88, 125, 203 base substitution 163-4, 193-206 comutation 176-7 deletion 185, 187-92, 203

416

frameshift 163, 193 induced 163 insertion 180-5, 193, 203 novel product 281 polar 11, 180 spontaneous 163, 270 temperature-sensitive 26, 95, 237-8,

295 mutational biosynthesis (mutasynthesis)

281-2 mutational cloning 105, 115-17 mutator 211, 400 mutL gene 203 Mycobacterium 397 Myrothecium verricaria 389

Neurospora crassa 15, 19, 109, 115 nick-translation see DNA polymerase nif genes 360, 372-6 nitrogen fixation 360, 368-76 Nocardia mediterranea 291 Nocardia uniformis 273 nocardicin A 273 nod genes 371-6 passim nodulation of leguminous plants 374 Northern transfer 130 nos genes 339,343-6

nos-cat 348 nos-nptlI 343-7

nuclease AP endonuclease 166 BAL31 nuclease 64, 137, 191,319 exonuclease III 135, 137, 141, 191,

201 exonuclease V 91, 148, 191 exonuclease VII 130 A exonuclease 191 mung bean nuclease 64, 69 pancreatic deoxyribonuclease (DNase I)

121, 137, 191 restriction endonuclease see restriction

enzyme SI endonuclease 57, 64, 69, 130, 191;

in cDNA cloning 57-8; in mapping 130-2,328; in site-directed mutagenesis 196-8

UvrABC endonuclease 166-8

oligonucleotide mutagenesis 201-7 primer 141-3, 201 probe 114, 121,328 synthesis 58-9

ompA gene 230 ompF gene 257 open reading frame 6, 118, 131,351

in CaMV 351-3 ORF cloning 118-20

operon fusion 149,402

opine 335-9 origin of transfer ( ori1)

Co1E126-7 F 20-2 RP424

origin of vegetative replication ( ori V) ColE 1 234-7 F24 M13 85 pSC101 238-9 RP424

ovalbumin 252

par locus 241-2, 244 parasexual cycle 3, 40-2, 283-5

haploidisation 40-2, 284 heterokaryosis 40 in breeding programmes 283-5 nondisjunction 40 parental genotype (genome)

segregation 42 see also heterokaryon

Penicillium chrysogenum 271-2,275-7, 280,284-5,291

peptidase 246 leader 251 lipoprotein signal 251

Peptococcus 397 pest-resistant plants

herbicide 358-9 insect 359

phage see bacteriophage Phanerochaete chrysosporium 386 phasmid 95 pheSgene 84 phosphatase see alkaline phosphatase photolyase 165-7 pili 21, 314

CFAIIII 310 F 21-2, 83 gonococcal 119,314 K88310 K99310

pin gene 247 plasmid

amplification 78, 147,237 broad host range 25, 98-100 cointegrate 27-9 conjugative 20-6 copy number control 234-7 copy number mutant 80, 237 degradative 390-4 isolation of DNA 127 low copy 82 mobilisation 26-7, 79, 319-20 multicopy 78, 267 nonconjugative 20, 26, 79-80 regulation of replication 234-7 runaway replication 237-9, 267

stability 183, 241-4 suicide 183 see also incompatibility, par locus

plasmid (specific) CAM-Ocr 392 CloDF13 241-2

INDEX

CoIE1: cea gene 27,235; cerlocus 241-3; chloramphenicol amplification 78, 147, 237; cop mutants 234, 237; exc region 235; imm gene 27,235; mob genes 26, 235; nic(bom) site 26; RNA 1234-7; RNA II 234-7; rom gene 235-7 Collb 92 ColK 79,234 F 20-5,27-8,36,77,237 NAH392 NTP299 p3125 pAC25393-6 pAC27394-7 pACYC184 80-1, 241, 244 pAL4404 340, 342 pALS-II09 pAS8Rep-l 184 pAT153 80, 93, 241 pBC16101 pBD214101 pBR322: as cloning vector 78-81;

hybrid with other plasmids 100, 103,111,201,241,310,358

pBR325 80, 109 pBPV-~1112 pClI1313 pC194100-1 pCOS 101 pDVI00I109 pE194100 pEMBL series 87 pFG799 pFJ105103 pGJ5384 pHE384 pHV23112 pU28112 pU61103 pU63104 pIJ101 29, 103-4 pIJ643104 pIJ922294 pJDB219 107-8, 112 pJM209.211 320 pKB730 224-5 pKM101400 pKN8084 pKT23578 pKT25899 pKY228984 pLA784 pLG33882

417

INDEX

pLV21112 pLV5784 pLV5984,146 pMG411 238 pMP78107 pN0752384 pPHlJI::Mu::Tn5183 pRK290 99, 339, 342, 370 pRK2013 99, 320-1 pR016499 pSa74799 pSC101 82, 237-9, 244 pSV2-gpt 112 pSVT18682 pTB70295 pTJS75KrnS 346 pTR26284 pUBll0 100-1, 252-3 pUC886 pUC9 82, 86, 312 pUC19Cm 346 pWWO (TOL) 390-1 pYR12GR 112 1tVX 125 R1237 R6K237 R68.4525-6 R300B 99-100 Ri 334, 348-9 RPl/RP4/RK2 23-4, 99-100, 184,

295,345 RP4::Mu::Tn7183 RSF1010 27, 99 SAL 394 SCP129 SCP229,102 SLP1.2103 SP62-PL 122 SRP129 TOL 390-2 YCp 107 YEp 19, 107-8, 258 YIp 19, 105, 109, 244 YRp 107 see also Ti plasmid

Podospora anserina 109 POFgene 287 polA gene 169, 178, 183

see also DNA polymerase I polyethylene glycol

as fusant 15, 18-19,42 as ligation enhancer 67

polypeptide cyanogen bromide treatment 249-50 domain 252, 298 export 250-4 fusion 118-20, 249, 290, 298 integration into·membrane 252 purification (recovery) 254-5

418

signal (leader) sequence 250-4 stability 246-54

polyploidy 39, 267, 285 primer

hybridisation-probe 135-6 mutant (mismatched) 201-7, 307 random 122 reverse sequencing 133-5 sequencing (universal) 133-6, 141, 201

probe hybridisation 114, 121-8, 152,324-8,

373 oligonucleotide 121, 324-5 recombination 152

promoter 219-26, 231-3 -10 region 219-21, 224 -35 region 219-21, 224 B. subtilis 220-1, 258 enhancer sequence 222 E. coli 219-26 eukaryotic 222-3 fusion 149 phage A 223 probe vector 149-52,231-2 S. cerevisiae 222-3, 258 sigma factors and polymerase specificity

220-1 Streptomyces 221, 223, 258 TATA box 222 upstream element/upstream activation

site 222 see also vector

promoter (specific) CaMV353 lac (UV5) 224, 256 Ipp226,240 ApL 224, 238 ApR 224 miLA 372-3 nod box 374 nos 347 ompF257 PGK258 reeA 224 SP6122 tac 223-4 tetA 223, 256 trp 223-4,231,321 TRP1258

protease Bacillus exoproteases 246 carboxypeptidase B 254-5 leukocyte elastase 307 Lon 93, 246-7 Serratia marcescens exoprotease 257 subtilisin 63, 297 trypsin 249

protein engineering 297-8, 306-8 protein export see polypeptide

protein purification strategies as inclusion bodies 247 C-terminal Arg-fusions 254-5 following export 249, 256-7 S. aureus protein A fusion 254

protoplast fusion 3, 42-7, 291-2 eIectrofusion 42 in plants 333 in strain improvement 291-2 mini protoplast fusion 45 non-viable protoplasts 45

psbA gene 359 Pseudomonas aeruginosa 25,98,371,399 Pseudomonas cepacia 394, 396 Pseudomonas fluorescens 275, 363 Pseudomonas putida 25,366,393-6 Pseudomonas spp. 185, 366, 390-7 Pseudomonas syringae 366-7, 409 pyrA gene 109

qa-2 gene 109

R-Ioop mapping 130 random (hexanucleotide) priming 122 rational selection see mutant rearrangement of cloned DNA 92, 101 recA gene 23, 28, 77, 145,224,238 RecA protein 169, 172, 196 recBCgene 91-2,148,191,238 recE gene 101 recombinant DNA see gene cloning recombinationalrescue 16-19.101,107,

244,340-1 relaxation complex 26 rennin (calf chymosin) 258 repair of DNA termini 63-6 restriction enzyme (endonuclease) 59-63,

188,293 cleavage/ recognition sites 60-2 isoschizomer 61 merA, merB restriction system 78 methylation of sites 62-3 star activity 63 Type I 59-60, 203-5 Type II 59-65 Type III 59-60

restriction fragment length polymorphisms (RFLPs) 325-8 DNA fingerprinting 327-8 in Cystic fibrosis 325 in Huntington's chorea 325 minisatellite 325

restriction mapping 127-8 reverse transcriptase 57, 64-5, 200 reversed genetics (mutagenesis) 111, 208,

318-21, 374 revertant see mutant rfa gene 400, 402 Rhizobium spp. 25, 185, 370-6

INDEX

Hup strains 372 R. japonicum 371-3 R. leguminosarum 371 R. meliloti 371, 373-6 R. phaseoli 371 R. trifolii 371

Rhizopus arrhizus 399 Rhodopseudomonas spp. 25, 185 ribonuclease

inhibitors of 148 RNase H 57, 82, 234

ribosome-binding site 56, 227-9, 240, 253

RNA mRNA production 219-26 RNA I, RNA II 234-7 RNA-I, RNA-2 355 stability 230

RNA polymerase B. subtilis 220-1 E. coli 122, 220-1 eukaryotic 222 SP6122 Streptomyces 221 T3125 T7125

rom (rap) gene 22, 234-7, 244 rpsL gene 84 rusts in pest control 365

Sl endonuclease mapping 130-2 Saccharomyces

cloning in 105-8 improvement of industrial strains 287-

90 killer strains 289-90, 292 mating factors 38,258 mating-type switching 38-9 promoters 223, 258 rare mating 285-90 S. cerevisiae 258-9,287-8, 297, 399 S. diastaticus 287, 289 S. uvarum (car/sbergensis) 273-4, 287-

9 Salmonella 315-18,325

S. dublin 315 S. typhi 315 S. typhimurium 252, 315, 358-9, 400

scaffolding 244-6 scours 309 secretion vector 252-4, 257-8

see also polypeptide serB gene 242 Serratia marcescens 257-8, 290 sexual cycle in fungi 3, 36-9, 285 sfa locus 23 Shigella dysenteriae 185 Shigella sonnei 316 Shine-Dalgarno sequence 120, 151, 227-9

419

INDEX

signal sequence see polypeptide, secretion vector

single cell protein (SCP) 290, 294-7 site-directed mutagenesis see mutagenesis somatostatin 249-50 sopA gene 241 SOS chromotest 402-4 Southern transfer 128-9, 143, 324-5 Sporotrichum pulverulentum 386 Staphylococcus aureus 14, 100, 102, 148

plasmids as vectors 100-2 protein A 118-19, 254

Staphylococcus carnosus 102 strain improvement 28-9, 265-301-

gene transfer 281-92 in vitro recombinant DNA techniques

292-300 mutagensis 270-81 strain degeneracy 300-1 strategies 266-70

streptavidin 121 streptococci 10 1-2, 258 Streptococcus faecalis 30-1, 180

conjugation 30-1 transformation 14-16

Streptococcus pneumoniae 102 Streptococcus sanguis 14, 102 Streptomyces 29-30, 102-5,257-8,277,

389 antibiotics see antibiotic pock-formation 30 promoters 221-3, 258 promoter-probe vector 232 S. antibioticus 300 S. aureofaciens 103,271-3 S. avidini 121 S. coelicolor 29, 102-5, 221, 293-4,

299-300 S. erythreus 294 S. fradiae 280 S. granuloruber 103 S. griseus 281,292-3,300 S. hygroscopicus 294 S. kanam yceticus 291 S. lipmanii 280 S. lividans 148, 258, 300 S. parvulus 294 S. peuticus 294 S. rimosus 291 S. vinaceus 103 S. venezuelae 31 S. violacearuber 103, 299 S. viridifaciens 280 S. viridosporus 387

strM gene 242 subtilisin see protease suLA (sfiA ) gene 246-7, 402 Sulphobolus 398 supE gene 88, 91

420

supF gene 91, 125 synchronous site-specific recombination

224-5 synthetic gene 58-9

T4 DNA ligase 66-7,137,224-5,238,293 T4 DNA polymerase 57, 63,121-2, 132 T4lysozyme 297 T4 polynucleotide kinase 121, 132 T4 RNA ligase 66 terminal deoxynucleotidyl transferase 67-9,

121,132 tet genes 80-3, 125,244,256 p-thalassaemia 328 Thermomonospora spp. 387-8 thermophile 269 Thiobacillus 398 thr operon 293 thrombin 308 thy gene 101 thymidine kinase (tk) gene 110-11, 322-3 Ti plasmid 334-48

as cloning vector 339-48 binary vector 340-6 cointegrate vector 343-5 mini-Ti 340 nos gene 339, 343-6 T-DNA 335-46, 353 vir 336

Ti plasmid vectors (specific) pENK4K 345-6 pGV3850345 pMON120 345 pMON128 343-5 pMON200 345 pTiA6336 PTiAch5337 pTiB653 343-5 pTiC58337 pTiT37 338, 342 SEV (pTiB653::pMon128) 343-5 SEV (pTiB653-SE::pMON200) 344-5

toxin cholera 318-21 enterotoxin 309,318 LT 309-10,318 ST 309-10 see also B. thuringiensis

tra operon see conjugation transcription

attenuation 226 mutagenesis during 187 terminator 226-7,240,244 transcription fusion 149

see also gene fusion, promoter, RNA polymerase

transduction 31-6 generalised 32, 184 high frequency transducing lysate

(HFf) 34, 267 in genetic manipulation 35-6 in strain improvement 290 low frequency transducing lysate (LFf)

34 specialised 32

transfection 13, 96, 111 transformation (of animal cells) 109 transformation (of microorganisms) 3, 13-

20 bacterial 13-18 competence 14-18 cotransformation 19-20 deletion formation in 191, 257 efficiency in cloning 96, 105-7 fungal 18, 109 in strain improvement 290 liposome 15, 18 plant 335 protoplast 15-19, 105 specificity of DNA uptake 18

transit peptide 347 transit sequence 359 transketolase 276, 278 translation

coupled transcription/translation (Zubay) 148

hybrid arrested 148 hybrid released 147 in vitro 143, 147 in vivo 147,227-31,250 RRUUURR sequence 228-9 Shine-Dalgamo sequence 120, 151,

227-9 termination 231 translational reading frame 93, 118,

231 transposable genetic elements 3-13

in plants 357-8 in prokaryotes 3-13, 179-87 Ty4 See also insertion sequence, Mu,

transposon transposition

cointegrate formation 7-11, 27-9 direct 9-10 immunity 6 models for 6-13 mutagenesis 11-13, 179-85,315,373-

5; deletion 11, 180,267; insertion 11,185-7; translocation of adjacent genes 11, 267

transposon complex 4-6 compound (composite) 4-6 conjugative 31 resolvase 10-11 transposase 5, 10

transposon (specific)

Tn1 /Tn3 4-9, 150, 180 Tn~ 180,211,347,373 Tn 7 5, 180, 183, 343 Tn95, 151,232

INDEX

Tn106, 11-13, 186,211,256,315 Tn5015,26 Tn5515 Tn 903 (601) 5,108,110,180,211,

345 Tn 917180 Tn 1 000 (yfJ) 4-5, 9-11, 23, 28, 182 Tnl7215

Trichoderma reesei 280,387-8 Trichoderma spp. 367 trp genes 107, 231, 242, 310 trypsin see protease tyrosyl t-RNA synthetase 297-8, 306

umuCgene 169,171,178 umuD gene 169, 171 ung gene 198 URA3 gene 112 ~-urogastrone 254-5 ush gene 84 uvrA gene 145, 167,402 uvrR gene 167, 400, 402 uvrC gene 167 uvrD gene 167 UvrABC nuclease 166-8

vaccine 308-23, 407 antimalaria 314,323 live attenuated 315-23; anticholera

318-21; salmonellosis 315-17; typhoid 315

minicell 321 subunit 308-11; E. coli-related disease

309-10; foot and mouth disease 310-11; hepatitis 311; herpes simplex 311

synthetic peptide 311 toxoid 309,319 vaccinia virus recombinants 321-3

vector animal virus 109-11 binary 345-6 cosmid 93-5 direct selection 82-4, 101, 115 dual origin 238-9 expression 223-46, 267, 293, 310 fusion 149 insertion 321-3 intermediate 339-40 kilosequencing 149 mitochondrial plasmid 109 open reading frame 118-20 phasmid 95 plant: from components of plant

genome 357; viroid 334; virus 334

421

INDEX

properties for cloning 76 secretion 252-4, 257 shuttle 103, 111-112, 340 translational reading frame 231 see also bacteriophage, lambda, Mu,

plasmid, Ti plasmid Verticillium lecanii 364 Vibrio cholerae 319-21 viroid 334, 356 virus

adenovirus 110-11 Baculovirus: granulosis virus (GV)

364-5; nuclear polyhedrosis virus (NPV) 364-5

Caulimovirus 111, 349-54; CilMV 111, 349-54; promoter 353-4; ORF 351-3

Geminivirus 349, 354-5; bean golden mosaic virus (BGMV) 354; cassava latent virus (CLV) 354

papillomavirus 111 retrovirus 111 SV40109-1O tobacco mosaic virus (TMV) 368 tobacco necrosis virus satellite 355-6 tobacco rattle virus (TRV) 355 vaccinia 110, 321-3

422

see also bacteriophage, lambda, M13 phage

vph gene 103

Western blotting 120, 145

xer gene 242-4 Xgal see 5-bromo-4-chloro-3-indolyl-~-D­

galactoside xylanase 389

yeast 258-9, 273-4, 285-90, 389 ARS (autonomously replicating

sequence) 107, 112,258 ciro / cir+ strains 107 gene cloning in 105-8 Kluyveromyces lactis 198 protoplast fusion 19, 292 2 ~m plasmid 107 YCp 107 YEp 19,107,258 YIp 19, 105-6, 244 YRp 107 see also plasmid, Saccharomyces

Zubay system see transcription, translation Zymomonas mobilis 273