ADVANCES IN GENETICS

By C. HITID

1 STRUCTURE OF THE BACTERIAL CELL 1 11 THE CYTOPLASM COMPARTMENT 1 12 THE CYTOPLASMIC MEMBRANE COMPARTMENT 3 13 THE CELL WALL COMPARTMENT 8 14 THE OUTER MEMBRANE COMPARTMENT 9 15 THE PERIPLASMIC COMPARTMENT 15 16 EXTRACELLULAR MATRICES 19 17 APPENDAGES 21 2 ORGANIZATION OF THE BACTERIAL CHROMOSOME 29 21 STRUCTURE OF THE CHROMOSOMES 29 22 PRINCIPLES TO COMPACT THE BACTERIAL CHROMOSOME 31 221 SUPERHELICITY 31 HISTONE-LIKE PROTEINS IN E COLI 32 23 ORGANIZATION OF THE BACTERIAL CHROMOSOME INTO GENES AND REPETITIVE SEQUENCES 36 231 GENES 36 232 REPETITIVE SEQUENCES 37 24 LARGE REARRANGEMENTS WITHIN THE CHROMOSOME 44 241 DUPLICATIONS 44 242 DELETIONS 45 243 INVERSIONS 49 3 THE BACTERIAL CELL CYCLE: REPLICATION OF THE CHROMOSOME, PARTITIONING AND CELL DIVISION 51 31 REPLICATION 51 311 REPLICATION OF CIRCULAR CHROMOSOMES 51 312 REPLICATION OF LINEAR CHROMOSOMES AND PLASMIDS 67 32 PARTITIONING (SEGREGATION) OF THE DAUGHTER CHROMOSOMES 68 33 CELL DIVISION 73 PLASMID-AND CHROMOSOME-ENCODED TOXIN-ANTITOXIN MODULES 79 341 34 POSTSEGREGATIONAL KILLING OF PLASMID-FREE CELLS 80 342 4 CHROMOSOMAL TOXIN-ANTITOXINS 81 41 RECOMBINATION 83 411 HOMOLOGOUS RECOMBINATION 83 THE RECBCD PATHWAY OF HOMOLOGOUS RECOMBINATION 85 412 THE RECF PATHWAY OF HOMOLOGOUS RECOMBINATION 90 413 ADDITIONAL HOMOLOGOUS RECOMBINATION FUNCTIONS 91 414 RECOVERY OF REPLICATION AT A BLOCKING DNA LESION 92 42 421 INTEGRATION/EXCISION SYSTEMS 99 SEQUENCE-SPECIFIC RECOMBINATION 97 422 RESOLVASE SYSTEMS 100 423 INVERSION SYSTEMS 103 424 SHUFFLONS 107 425 INTEGRONS 107 426 HOMING ENDONUCLEASES 110 43 ILLEGITIMATE RECOMBINATION 112 431 INSERTION SEQUENCE ELEMENTS 113 432 433 TRANSPOSONS 114 TRANSPOSING BACTERIOPHAGES 115 434 MECHANISMS OF TRANSPOSITION 116 435 CONJUGATIVE AND INTEGRATIVE ELEMENTS 118 436 NONHOMOLOGOUS ENDJOINING (NHEJ) 119 5 51 ORIGIN OF MUTATIONS AND REPAIR OF DNA LESIONS 121 52 CLASSES OF MUTATIONS 121 521 ORIGIN OF MUTATIONS 124 522 SPONTANEOUS MUTATIONS 124 523 INDUCED MUTATIONS 126 DETECTION SYSTEMS FOR MUTATIONS 128 524 ADAPTIVE MUTATIONS 129 53 REPAIR OF DNA LESIONS 131 531 THE METHYL-MEDIATED MISMATCH REPAIR SYSTEM 132 532 VERY SHORT PATCH REPAIR 133 533 THE NUCLEOTIDE EXCISION REPAIR SYSTEMS 534 PATHWAYS OF BASE EXCISION REPAIR 136 535 134 536 REPAIR OF OXIDIZED NUCLEOTIDES 138 PHOTOREACTIVATION OF CYCLOBUTANE DIMERS 140 537 538 TRANSCRIPTION-COUPLED NUCLEOTIDE EXCISION REPAIR 141 539 THE ADAPTIVE RESPONSE 141 5310 THE SOS RESPONSE 143 REPLICATION AND REPAIR 148 5311 REPAIR OF INTERSTRAND CROSSLINKS IN DNA 150 5312 DEINOCOCCUS RADIODURANS 151 PRINCIPLES OF GENE REGULATION 153 6 61 REGULATION AT THE LEVEL OF DNA 153 611 ALTERATIONS OF THE STRUCTURE OF THE DNA 154 612 GATC METHYLATION AND GENE EXPRESSION 157 613 PROGRAMMED DNA REARRANGEMENTS WITHIN THE CHROMOSOME 159 614 TRANSCRIPTIONAL SILENCING AND CRYPTIC GENES 159 62 REGULATION AT THE LEVEL OF TRANSCRIPTION 162 621 THE DNA-DEPENDENT RNA POLYMERASE 162 622 REGIONS OF THE PROMOTER 168 623 INITIATION OF TRANSCRIPTION 170 624 ELONGATION OF TRANSCRIPTION 173 625 TERMINATION OF TRANSCRIPTION 175 626 ANTI-SIGMA FACTORS 177 627 ANTI-TERMINATION/ATTENUATION OF TRANSCRIPTION 179 628 REGULATORS OF THE DNA-DEPENDENT RNA POLYMERASE 188 63 POST-TRANSCRIPTIONAL REGULATION 220 631 PROTEIN-MEDIATED REGULATION 220 632 RIBOREGULATION 222 633 RIBOSWITCHES 227 634 MRNA DECAY 230 635 INTRONS 239 636 RNA-BINDING PROTEINS 242 244 64 REGULATION AT THE LEVEL OF TRANSLATION 641 INITIATION OF TRANSLATION 247 642 ELONGATION OF TRANSLATION 248 643 TERMINATION OF TRANSLATION 252 644 RIBOSOME RECYCLING 253 645 TRANSLATIONAL CONTROL 255 646 THE 21 AND 22 AMINO ACID SELENOCYSTEINE AND PYRROLYSINE 258 647 MECHANISMS TO CREATE MULTIPLE GENE PRODUCTS FROM A SINGLE CISTRON 259 65 POST-TRANSLATIONAL REGULATION 266 651 PROTEOLYSIS 266 652 PROTEIN SPLICING 266 653 PROTEIN GLYCOSYLATION 266 654 CIRCULAR POLYPEPTIDES 268 7 PROTEIN QUALITY CONTROL THROUGH MOLECULAR CHAPERONES, PROTEIN FOLDING CATALYSTS AND ATP-DEPENDENT PROTEASES 271 71 INTRODUCTION 271 72 MOLECULAR CHAPERONES 271 721 FOLDER CHAPERONES 272 722 HOLDER CHAPERONES 279 723 DISAGGREGATING CHAPERONES 287 724 INTRAMOLECULAR CHAPERONES 289 725 73 731 74 FOLDING OF NASCENT POLYPEPTIDE CHAINS 290 PROTEIN-FOLDING CATALYSTS 292 PEPTIDYL-PROLYL ISOMERASES 292 75 DISULFIDE BOND FORMATION 293 751 PROTEASES 297 752 8 ATP-DEPENDENT PROTEASES 298 ATP-INDEPENDENT PROTEASES 305 81 SECRETION OF PROTEINS 309 82 INTRODUCTION 309 PROTEIN SORTING SIGNALS FOR SUBCELLULAR LOCALIZATION 310 83 CYTOSOLIC TARGETING FACTORS 315 84 TRANSLOCASES MOVE NEWLY MADE PROTEINS INTO OR ACROSS MEMBRANES 316 841 THE SEC PATHWAY OF PROTEIN TRANSLOCATION THROUGH THE INNER MEMBRANE 317 842 THE TAT PATHWAY OF SECRETION PROTEINS THROUGH THE INNER MEMBRANE 321 843 INSERTION PROTEINS INTO THE INNER MEMBRANE 323 85 ANCHORING OF LIPOPROTEINS INTO THE OUTER MEMBRANE 324 86 PROTEIN TRANSLOCATION PATHWAYS THROUGH BOTH MEMBRANES OF 861 GRAM-NEGATIVE BACTERIA 326 THE TYPE I SECRETION PATHWAY 326 862 THE TYPE II SECRETION PATHWAY 327 863 THE TYPE III SECRETION PATHWAY 330 864 THE TYPE IV SECRETION PATHWAY 333 865 TYPE V SECRETION PATHWAY (AUTOTRANSPORTER) 335 866 VESICLE-MEDIATED EXPORT 336 87 CELL WALL-ANCHORED SURFACE PROTEINS 337 88 9 S-LAYERS 339 91 STRESS GENES AND THEIR REGULATION 341 THE STRESS RESPONSE PATHWAY 341 92 THE HEAT SHOCK RESPONSE 342 93 THE COLD SHOCK RESPONSE 349 94 THE OSMOTIC SHOCK RESPONSE 353 941 THE HYPEROSMOTIC SHOCK RESPONSE 354 942 THE HYPOOSMOTIC SHOCK RESPONSE 359 95 THE OXIDATIVE SHOCK RESPONSE 361 951 THE OXYR REGULON 361 952 THE SOXRS REGULON 362 96 PH-REGULATED GENES 364 961 ACID STRESS 367 962 ALKALINE STRESS 369 97 METABOLIC STRESS: THE STRINGENT RESPONSE 371 98 NUTRIENT LIMITATIONS (STARVATION STRESS) 373 99 ENVELOPE STRESS RESPONSE 376 10 EXCHANGE OF GENES: TRANSFORMATION, CONJUGATION AND TRANSDUCTION 381 101 TRANSFORMATION 381 1011 TRANSFORMATION OF GRAM-POSITIVE BACTERIA 384 1012 TRANSFORMATION OF GRAM-NEGATIVE BACTERIA 387 102 CONJUGATION 388 1021 GRAM-NEGATIVE BACTERIA 389 1022 GRAM-POSITIVE BACTERIA 396 1023 CONJUGATIVE TRANSPOSONS 398 103 TRANSDUCTION 398 1031 GENERALIZED TRANSDUCTION 400 1032 SPECIALIZED TRANSDUCTION 401 104 HORIZONTAL GENE TRANSFER 402