Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
pair change ...Figure 3.9 Removal of deaminated cytosine (uracil) from DNA. (A) Comparison of...Figure 3.10 Missense mutation. A mutation that changes T to C in the DNA templ...Figure 3.11 Nonsense mutation. Changing the CAA codon, encoding glutamine (Gln...Figure 3.12 Frameshift mutation. The wild-type mRNA is translated as glutamine...Figure 3.13 Slippage of DNA at a repeated sequence (for example, a series of A...Figure 3.14 Ectopic recombination between directly repeated sequences can caus...Figure 3.15 Formation of a long tandem-duplication mutation does not Inactivat...Figure 3.16 Recombination between inverted repeats can cause inversion mutatio...Figure 3.17 The pathway to galactose utilization in E. coli and most other org...Figure 3.18 Formation of a nonsense suppressor tRNA. (A) Gene X (turquoise) an...Figure 3.19 Selection of a His+ revertant. A sample of a His– mutant cul...Figure 3.20 Replica plating. (A) A few hundred bacteria are spread on a nonsel...Figure 3.21 A simplified diagram of recombination between two genetic markers....Figure 3.22 Different consequences of recombination between linear and circula...Figure 3.23 Using recombination to introduce an antibiotic resistance cassette...Figure 3.24 Using marker rescue to locate a mutation In the physical map of th...Figure 3.25 Complementation tests for allellsm. Four mutations, hisA1, hisA2, ...Figure 3.26 E. coli lacZ α intragenic complementation. (A) The lacZ∆M15 deleti...Figure 3.27 Identification of clones of the thyA gene of E. coli by complement...Figure 3.28 Use of marker rescue to identify a clone containing at least part ...Figure 3.29 Selected versus unselected markers In a bacterial cross. Replaceme...Figure 3.30 Example of generalized transduction. A phage Infects a Trp+ bacter...Figure 3.31 Cotransduction of bacterial genetic markers. (A) Two-factor cross....Figure 3.32 Generic test for reversion versus suppression. (A) The mutation ha...Figure 3.33 Using transduction to distinguish reversion from suppression. If t...Figure 3.34 Transfer of chromosomal DNA by an Integrated plasmid. Formation of...Figure 3.35 Partial genetic linkage map of E. coli showing the positions (blac...Figure 3.36 Mapping by Hfr crosses. The phenotypes and positions of the marker...Figure 3.37 Mapping by gradient of transfer during an Hfr cross. The ordinate ...
5 Chapter 4Figure 4.1 Supercoiling of a covalently closed circular plasmid. (A) A break i...Figure 4.2 Some common schemes of plasmid replication. (A) Unidirectional repl...Figure 4.3 Coexistence of two plasmids from different Inc groups. (A) After di...Figure 4.4 Genetic map of plasmid ColE1. The plasmid is 6,646 bp long. On the ...Figure 4.5 Regulation of the replication of ColE1-derived plasmids. RNA II mus...Figure 4.6 Pairing between an RNA and its antisense RNA. (A) An antisense RNA ...Figure 4.7 Regulation of replication of the IncFII plasmid R1. (A) Locations o...Figure 4.8 Regulation of plasmid ColIb-P9 copy number by antisense RNA inhibit...Figure 4.9 Regulation of plasmid pT181 copy number by antisense RNA regulation...Figure 4.10 The ori region of pSC101. R1, R2, and R3 are the three iteron sequ...Figure 4.11 The “handcuffing” or “coupling” model for regulation of iteron pla...Figure 4.12 The Xer functions of E. coli catalyze site-specific recombination ...Figure 4.13 Model for partitioning of the R1 plasmid. (A) Structure of the parFigure 4.14 Model for partitioning by par systems on P1, F, and RK2. (A) Struc...Figure 4.15 Finding the origin of replication (ori) in a plasmid. Random piece...Figure 4.16 pUC expression vector. A gene cloned into one of the restriction s...Figure 4.17 pBAC cloning vector for cloning large pieces of DNA. The multiple ...Figure 4.18 Shuttle plasmid YEp13. The plasmid contains origins of replication...
6 Chapter 5Figure 5.1 A simplified view of conjugation by a self-transmissible plasmid, t...Figure 5.2 Partial genetic map of the ~100-kilobase pair (kbp) self-transmissi...Figure 5.3 Representation of the F transfer apparatus. The pilus is assembled ...Figure 5.4 Mechanism of DNA transfer during conjugation, showing the Mpf funct...Figure 5.5 Reactions performed by the relaxase. (A) The relaxase nicks the DNA...Figure 5.6 Fertility Inhibition of the F plasmid. Only the relevant tra genes ...Figure 5.7 Gene arrangements of type IV secretion loci. Genes with homologs in...Figure 5.8 Mechanism of plasmid mobilization. The donor cell carries two plasm...Figure 5.9 Integration of the F plasmid by recombination between IS2 elements ...Figure 5.10 Generation of a prime factor by recombination. Recombination may o...Figure 5.11 Self-transmissible and mobilizable elements are found with integra...Figure 5.12 Fluorescence micrograph of Bacillus subtilis cells showing the loc...Figure 5.13 Self-transmissible Integrating conjugative elements (ICE) can carr...Figure 5.14 Genetic map and diagram of the integration and excision process of...
7 Chapter 6Figure 6.1 The Griffith experiment. (A) Type R (rough) nonencapsulated bacteri...Figure 6.2 Structure of DNA uptake competence systems. (A) Firmicutes. (B) Pro...Figure 6.3 Visualization of DNA uptake using fluorescent labels. Competent B. ...Figure 6.4 Sequence logos showing conservation of uptake sequences for natural...Figure 6.5 Transformation by plasmid DNA. DNA is linearized outside the cell (...Figure 6.6 Import of multiple DNA fragments into a single cell by congression....Figure 6.7 Regulation of competence development by quorum sensing. (A) In Baci...Figure 6.8 Comparison of competence regulatory mechanisms. Green arrows indica...Figure 6.9 Repair of DNA damage by transforming DNA. Thymine dimers (T residue...
8 Chapter 7Figure 7.1 Electron micrographs and plaques of some bacteriophages. (A) A phag...Figure 7.2 A typical bacteriophage multiplication cycle. After the phage injec...Figure 7.3 Transcriptional regulation by a regulatory cascade during developme...Figure 7.4 Genetic map of phage T7. The genes for the RNA polymerase used for ...Figure 7.5 Regulation of SP01 gene expression by a cascade of σ factors. Early...Figure 7.6 (A) Genomic map of phage T4. From Karam JD (ed), Molecular Biology ...Figure 7.7 Sequence of T4 middle-mode and late promoters. Only the sequences i...Figure 7.8 Model for T4 DNA replication and activation of a replication-couple...Figure 7.9 Genetic map of λ cyclized by pairing at the cos sites, shown at the...Figure 7.10 Antitermination of transcription in phage λ. (A) Before the N prot...Figure 7.11 Sequences of the nutL and nutR regions of bacteriophage λ. Box A, ...Figure 7.12 Formation of the Q protein antitermination complex at the pR’ prom...Figure 7.13 Infection cycle of the single-stranded DNA phage f1. Steps 1 throu...Figure 7.14 Schematic representation of the filamentous bacteriophage M13. The...Figure 7.15 Replication of the circular single-stranded DNA phage M13. First, ...Figure 7.16 Overview of replication of phage λ. See text for details.Figure 7.17 Replication of phage T7 DNA. Replication is initiated bidirectiona...Figure 7.18 Initiation of replication of phage T4 DNA. In stage 1, replication...Figure 7.19 T4 DNA headful packaging. Packaging of DNA longer than a single ge...Figure 7.20 Timing of phage lysis by activation of holins. The antiholin keeps...Figure 7.21 Overview of the fate of λ DNA in the lytic and lysogenic pathways....Figure 7.22 Genetic map of phage λ. The locations of key genes and transcripts...Figure 7.23 Formation of lysogens after λ infection. (A) The cII and cIII gene...Figure 7.24 Integration of λ DNA into the chromosome of E. coli. (A) The Int p...Figure 7.25 Regulation of repressor synthesis in the lysogenic state. The dumb...Figure 7.26 Cro prevents repressor binding and synthesis by binding to the ope...Figure 7.27 Induction of λ. Accumulation of single-stranded DNA (ssDNA) due to...Figure 7.28 Retroregulation. (A) After infection, the xis and int genes cannot...Figure 7.29 Competition determining whether phage will enter the lytic or lyso...Figure 7.30 Recombination between two phage mutations. The two different mutan...Figure 7.31 Tests of complementation between phage mutations. Phages with diff...Figure 7.32 Generalized transduction. A phage infects one bacterium, and in th...Figure 7.33 Formation of a λdgal transducing particle. A rare mistake in recom...Figure 7.34 Induction of the λdgal phage from a dilysogen containing both λdga...Figure 7.35 Lysogenic conversion. (A) Shiga toxins encoded by close relatives ...Figure 7.36 Use of phage T7 for phage display. (A) A randomized protein-coding...
9 Chapter 8Figure 8.1 Overview of transposition. See the text for details.Figure 8.2 Steps in transposon excision. Inverted repeats (IRs) (shown as oran...Figure 8.3 Steps in transposon insertion. The transposon inserts into a target...Figure 8.4 Structures of some composite transposons. The left (L) and right (R...Figure 8.5 Two insertion sequence (IS) elements can transpose any