Bacterial Genomes: Physical Structure and Analysis

Front Matter....Pages i-xxix
Front Matter....Pages 1-1
Structure and Sizes of Genomes of the Archaea and Bacteria....Pages 5-11
Chromosomal Organization: Nucleoids, Chromosomal Folding, and DNA Topology....Pages 12-22
Prophages and Cryptic Prophages....Pages 23-29
Insertion Sequences and Transposons....Pages 30-37
Interspersed Repetitive Sequences in Bacterial Genomes....Pages 38-48
Chi Sites and Their Consequences....Pages 49-66
Origins of Chromosome Replication....Pages 67-77
Restriction Modification Systems: Where They Are and What They Do....Pages 78-92
Genome Ploidy....Pages 95-102
Segregation of the Bacterial Chromosome....Pages 103-111
Chromosomal Rearrangements....Pages 112-118
Mechanism of Avoidance of 5-methylcytosine to Thymine Mutations in Bacteria....Pages 119-129
Conjugative Transposons....Pages 130-139
Phase Variation....Pages 140-152
The Dynamic Genome of Rhizobium ....Pages 153-161
Programmed DNA Rearrangements in Cyanobacteria....Pages 162-173
Evolution of the E. coli Genome....Pages 177-186
E. coli Genes: Ancestries and Map Locations....Pages 187-195
Prokaryotic Genome-Wide Comparisons and Evolutionary Implications....Pages 196-212
Insertion Sequences and their Evolutionary Role....Pages 213-220
Front Matter....Pages 1-1
Multiplicity of Ribosomal RNA Operons in Prokaryotic Genomes....Pages 221-229
Genome Evolution in the Salmonellae....Pages 230-239
Structure and Evolution of Escherichia coli Rhs Elements....Pages 240-248
Front Matter....Pages 249-249
Physical Mapping and Fingerprinting of Bacterial Genomes using Rare Cutting Restriction Enzymes....Pages 253-311
One-dimensional Pulsed-field Gel Electrophoresis....Pages 312-325
Two-dimensional Pulsed-field Gel Electrophoresis....Pages 326-336
Use of Bacteriophage Mu-P22 Hybrids for Genome Mapping....Pages 337-347
Encyclopedias of Bacterial Genomes....Pages 348-361
Localizing Genes by the Introduction of Rare Restriction Sites....Pages 362-369
Towards a Cosmid-derived Physical Map of the Synechococcus PCC 7002 Genome....Pages 370-380
Fingerprinting Bacterial Genomes using Restriction Fragment Length Polymorphisms....Pages 383-398
Use of Endogenous Repeated Sequences to Fingerprint Bacterial Genomic DNA....Pages 399-413
Applications of DNA and RNA Fingerprinting by the Arbitrarily Primed Polymerase Chain Reaction....Pages 414-436
Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes....Pages 437-454
Organization of the European Bacillus subtilis Genome Sequencing Project....Pages 457-467
Sequence Features of the Genome of a Unicellular Cyanobacterium Synechocystis sp. strain PCC6803....Pages 468-477
A Minimal Gene Complement for Cellular Life and Reconstruction of Primitive Life Forms by Analysis of Complete Bacterial Genomes....Pages 478-488
Resources for the Escherichia coli Genome Project....Pages 489-497
The Mycobacterial Database MycDB and the Mycobacterial Genome Sequencing Project....Pages 498-507
Mycoplasma genitalium....Pages 508-519
Front Matter....Pages 249-249
Other Mycoplasma sp.....Pages 520-525
 Mycoplasma capricolum Genome Project....Pages 526-540
Sequence Skimming of Chromosome II of Rhodobacter sphaeroides 2.4.1 T....Pages 541-551
Sequencing the Genome of Sulfolobus solfataricus P2....Pages 552-558
MAGPIE: A M ultipurpose A utomated G enome P roject I nvestigation E nvironment for Ongoing Sequencing Projects....Pages 559-566
Integrated Genome Informatics....Pages 567-582
Front Matter....Pages 583-597
 Anabaena sp. Strain PCC 7120....Pages 599-604
Aquifex pyrophilus....Pages 605-607
Bacillus cereus/Bacillus thuringiensis....Pages 609-612
 Bacillus subtilis 168....Pages 613-615
Bordetella pertussis Strain Tohama I....Pages 617-619
 Borrelia burgdorferi and the Other Lyme Disease Spirochetes....Pages 621-624
 Bradyrhizobium japonicum strain 3I1b110....Pages 625-628
 Brucella melitensis 16M (ATCC 23456)....Pages 629-632
 Campylobacter jejuni TGH9011 (ATCC 43431)....Pages 633-636
 Caulobacter crescentus CB15....Pages 637-639
 Clostridium beijerinckii NCIMB 8052 Chromosome....Pages 641-644
 Clostridium perfringens CPN50....Pages 645-647
Enterococcus faecalis....Pages 649-650
Escherichia coli....Pages 651-653
Front Matter....Pages 583-597
 Haemophilus influenzae Rd....Pages 655-657
 Haloferax volcanii DS2 and Halobacterium salinarium GRB....Pages 659-664
 Helicobacter pylori CH19....Pages 665-667
 Lactococcus lactis subsp. lactis ILI403 and Lactococcus lactis subsp. cremoris MG1363....Pages 669-671
Leptospira interrogans....Pages 673-678
Listeria monocytogenes....Pages 679-680
 Methanobacterium thermoautotrophicum Marburg....Pages 681-683
Mycobacterium leprae....Pages 685-687
 Mycoplasma genitalium G-37 (ATCC 33530)....Pages 689-693
Myxococcus xanthus DK 1622....Pages 695-701
Neisseria gonorrhoeae MS11-N198 (ATCC 49759)....Pages 703-705
Planctomyces limnophilus DSM 3776 T ....Pages 707-708
Burkholderia (Pseudomonas) cepacia Strain ATCC 17616 and 25416; Pseudomonas aeruginosa Strain C and PAO (DSM 1707)....Pages 709-717
Rhizobium meliloti....Pages 719-721
 Rhodobacter capsulatus SB1003....Pages 723-727
 Rhodobacter sphaeroides 2.4.1 T ....Pages 729-731
Salmonella typhi....Pages 733-735
Salmonella typhimurium....Pages 737-739
Serpulina hyodysenteriae B78 T ....Pages 741-742
Staphylococcus aureus....Pages 743-753
Front Matter....Pages 583-597
 Streptococcus pneumoniae R6....Pages 755-757
 Sulfolobus tokodaii 7....Pages 759-761
 Synechococcus PCC 7002....Pages 763-770
 Thermus thermophilus HB8....Pages 771-772
 Treponema pallidum subsp. pallidum (Nichols)....Pages 773-774
Back Matter....Pages 775-793