Tina M. Henkin - Snyder and Champness Molecular Genetics of Bacteria

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 p R’ 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 c II and c III 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 λd gal 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 DNA between ...Figure 8.6 R factors, or plasmids containing many resistance genes, may have b...Figure 8.7 Some examples of noncomposite transposons. The positions of the tra...Figure 8.8 Example of a mating-out assay for transposition. See the text for d...Figure 8.9 The DDE transpose has been adapted in multiple ways for different f...Figure 8.10 Replicative transposition of Tn 3 (orange) and formation and resolu...Figure 8.11 Model for single-strand DNA transposition with IS 608 . IS 608 moves ...Figure 8.12 Regulation of Tn 5 transposition. Two similar IS 50 elements flank t...Figure 8.13 Transposition after DNA replication facilitates DNA repair. (A and...Figure 8.14 Transposon Tn 7 uses an element-encoded heteromeric transposase and...Figure 8.15 Random transposon Tn 5 mutagenesis. Random transposon mutagenesis o...Figure 8.16 Cloning genes mutated by insertion of a transposon. A transposon u...Figure 8.17 Assembly of integrons. The primary transposon carries an integron ...Figure 8.18 Example of a superintegron from Vibrio cholerae . More than 100 cas...Figure 8.19 Regulation of Salmonella phase variation and some other members of...Figure 8.20 Domain structure of tyrosine recombinases (Cre, XerCD, etc.; λ Int...Figure 8.21 Model for the reaction promoted by the Cre tyrosine (Y) recombinas...Figure 8.22 Structures of some sites recognized by tyrosine (Y) recombinases. ...Figure 8.23 Domain structure of serine (S) recombinases. The conserved catalyt...Figure 8.24 Model for the reaction promoted by the γδ recombinase. (A)Four re...Figure 8.25 How successive attacks by nucleophilic hydroxyl groups of serine (...Figure 8.26 Excision of a group II mobile intron from an mRNA. (A)After trans...Figure 8.27 Integration of a group II mobile intron into double-stranded DNA b...

10 Chapter 9Figure 9.1 Replication forks initiated at oriC can collapse when there are nic...Figure 9.2 Model for promotion of recombination Initiation at a χ site by the ...Figure 9.3 Model for how χ sites can help RecBCD load RecA to direct DNA repli...Figure 9.4 Models for recombination Initiation by the RecF pathway on substrat...Figure 9.5 Model for how DNA substrates with various types of DNA breaks are p...Figure 9.6 Model for synapse formation and strand exchange between two homolog...Figure 9.7 Holliday junctions can form through the action of RecA. The movemen...Figure 9.8 Model for the mechanism of action of the Ruv proteins. (1)One or t...Figure 9.9 A synthetic Holliday junction with four complementary strands. The ...Figure 9.10 Model for how linear fragments are recombined Into the chromosome ...Figure 9.11 Recombineering: in vivo DNA modification in E. coli using λ phage-...Figure 9.12 Migration of Holliday junctions. By breaking the hydrogen bonds ho...Figure 9.13 Repair of a mismatch in a heteroduplex region formed during recomb...Figure 9.14 Repair of mismatches can give rise to recombinant types between tw...

11 Chapter 10Figure 10.1 Survival of cells as a function of the time or extent of treatment...Figure 10.2 (A)Modified bases created by deaminating agents, such as nitrous ...Figure 10.3 Repair of altered bases by DNA glycosylases. (A)The specific DNA ...Figure 10.4 (A)Structure of 8-oxoG. (B)Mechanisms for avoiding mutagenesis d...Figure 10.5 Alkylation of guanine to produce O 6-methyiguanine. The altered bas...Figure 10.6 (A)The adaptive response. (B)Regulation of the adaptive response...Figure 10.7 Two common types of pyrimidine dimers caused by UV irradiation. In...Figure 10.8 Photoreactivation. The photoreactivating enzyme (photolyase) binds...Figure 10.9 Base analogs 2-amlnopurlne (2-AP) and 5-bromouracll (5-BU). The am...Figure 10.10 Mutagenesis by incorporation of the adenine analog 2-AP into DNA....Figure 10.11 Mutagenesis by a frameshift mutagen. Intercalation of a planar ac...Figure 10.12 The methyl-directed mismatch repair system. The newly replicated ...Figure 10.13 MutSLH DNA repair in E. coli . (A)One arm of a replication fork i...Figure 10.14 Colonies due to mut mutants have more papillae. A lacZ mutant was...Figure 10.15 Model for nucleotide excision repair by the UvrABC endonuclease. ...Figure 10.16 Model for transcription-coupled nucleotide excision repair. Mfd-d...Figure 10.17 Model for recombination-mediated bypass of DNA damage in the DNA ...Figure 10.18 Fork regression model for recombination-mediated replicative bypa...Figure 10.19 Models for how regressed replication forks can be repaired by mul...Figure 10.20 Repair of a DNA interstrand cross-link through the combined actio...Figure 10.21 Regulation of the SOS response regulon in Escherichia coli . About...Figure 10.22 Detection of a mutant defective in mutagenic repair. Colonies of ...Figure 10.23 Regulation of SOS mutagenesis in E. coli . (A)Before DNA damage o...