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Color Plates

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Figures

Image of Color Plate 1 (chapter 4).

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Color Plate 1 (chapter 4).

Cell cycle-regulated expression profiles. (A) The temporal gene expression profiles of 34 flagellar genes are shown on the left. Yellow indicates increased level of expression; blue indicates decreased level of expression. The flagellar genes are expressed in a transcriptional cascade of four classes (see text). The order of assembly and gene expression is indicated by the large arrow next to the schematic of s polar flagellum structure. Class II genes encode the export apparatus and inner ring structures (black), class III genes encode the rest of the basal body and hook (dark gray), and class IV genes encode the flagellar filament proteins (light gray). (B) The expression profiles of cell cycle-regulated genes associated with several DNA replication and metabolic functions. Timing of the expression profiles is indicated in minutes above each set of profiles and by a corresponding cell cycle diagram. (Modified from reference 14, with permission of the publisher.)

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 2 (chapter 4).

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Color Plate 2 (chapter 4).

Tracking DNA replication fork progression in using microarrays. Replication was synchronized using a temperature-sensitive initiation mutant strain. Shifting this strain to the restrictive temperature for 90 min allowed completion of replication, but with no additional initiations. Shifting this strain back to the permissive temperature then produced synchronized initiations. Samples of partially replicated DNA and fully replicated DNA were collected, labeled, and competitively hybridized on a whole-genome microarray (Fig. 1). Spots for genes that have been replicated are expected to have fluorescence ratios near 2, compared with a ratio of 1 for unreplicated genes. This information could be mapped back to the chromosome, drawn as a gray-and-red circle, with red indicating genes that have been replicated. The limits of the red area thus indicate the replication fork location. The concentric circles at the bottom show how executing this assay at different time points—0, 1, 7, and 20 min—allowed measurement of replication fork progression. (Modified from reference 13, with permission of the publisher.)

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 3 (chapter 15).

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Color Plate 3 (chapter 15).

Model of RNAP structure and function. (A) The transcription cycle. Core RNAP is blue, the initiation factor s is orange, the DNA template is black, and the nascent RNA transcript is red. (B) Model of the TEC. The incoming NTP and an arrow showing its path into the TEC through the secondary channel are green. (C) The nucleotide addition cycle. The and + sites are shown as two joined circles. (Inset) Two Mg ions (red circles) catalyze phosphodiester bond formation between the 3′ end of the nascent transcript and an incoming NTP.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 4 (chapter 15).

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Color Plate 4 (chapter 15).

Structure of core RNAP. (A) The downstream face of core RNAP. The model is based on the coordinates of the holoenzyme (PDB [Protein Data Bank] ID 1IW7 [97]), with the s subunit and a nonconserved region not present in β′ (amino acids 164 to 448) removed and the RNAP conformation adjusted to that observed in the core RNAP (PDB ID 1I6V [109]) by movement of RNAP mobile modules (23). Sequence insertions present in (23) are not depicted. The path of the secondary channel is illustrated by a dashed line. The a-carbon backbone is shown as a worm inside a semitransparent surface. Subunits are color-coded as follows: β′, pink; b, cyan; αI, green; αII, yellow; ω, gray. The β′ bridge helix and trigger loops are depicted as green and orange worms, respectively. Zn and Mg atoms are depicted as yellow balls. The aCTDs are shown in arbitrary positions 43Å from the core. They are shown as isolated domains but may be present as a dimer in RNAP (7). The boxed inset depicts the upstream face of core RNAP, illustrating the "crab-claw" shape of the enzyme. (B) The active-site channel. The RNAP model in panel A is shown rotated 908 to the right. The subunits are shown as solid surfaces except that the ZBD, β′ Mg-binding loop, rudder, lid, and zipper are shown as pink worms in a semitransparent surface, and the b flap domain is shown as a dark blue worm in a semitransparent surface. The β′ bridge helix is depicted as a green worm. The antibiotic rifampin (labeled Rifampicin in the figure) is depicted in red (b is rendered semitransparent in front of rifampin to reveal the antibiotic nestled in its binding pocket.) The clamp, protrusion, and lobe are outlined in black. (C) Two αCTDs bound to UP element DNA. This model is based on the crystal structure of aCTD, DNA, and catabolite activator protein (PDB ID 1LB2 [6]). Nontemplate DNA is light green; template DNA is dark green. Two residues involved in recognition of the UP element (Arg-265 and Asn- 294) are shown as red sticks. The CAP interaction determinant is indicated by the blue space-fill valine residue at position 287. Asp-259 and Glu-261, two residues that interact with s region 4, are shown as orange sticks. Only one of each symmetric pair of residues is labeled.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 5 (chapter 15).

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Color Plate 5 (chapter 15).

Structure of s and holoenzyme. (A) The structure of the s subunit. σ is depicted as a gray rod with the regions of sequence conservation (1.2 to 4.2) in different colored boxes. Black bars beneath s represent the segments of s crystallized. The s region 4-DNA cocrystal is shown (PDB ID 1KU7 [19]). The s region 1.2 to 3.1 crystallized fragment (19) is modeled with partially single-stranded promoter DNA and the coiled-coil domain from β′ with which it interacts in holoenzyme (shown in dark gray), based on the fork junction RNAP structure (PDB ID 19LZ [65]). DNA is colored as in Color Plate 4 . The regions of s are colored as depicted in the schematic shown above the structures. The sequence of promoter elements is shown in gray boxes above the DNA, and selected bases are indicated with dotted lines. An arbitrary sequence has been modeled into the DNA of the region 1.2 to 3.1 fragment, rather than the promoter sequence. (B) A model of the structure of holoenzyme. The model is based on the T. thermophilus holoenzyme crystal structure (PDB ID 1IW7 [97]) with a missing segment of s region 4 modeled based on the holoenzyme structure (PDB ID 1L9U [66]). The view of RNAP is similar to that in Color Plate 4B . Arrows indicate the movement of the clamp, flap, lobe, and protrusion domains in holoenzyme relative to core RNAP (66). Core subunits are colored as in Color Plate 4 . s is colored as in panel A. The box indicates the area magnified in panel C. (C) The path of the s 3.2 linker. Parts of the surface from b0 and b and s 2.3 to 3.1 have been cut away to make the path of the linker through the RNA-exit channel visible.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 6 (chapter 15).

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Color Plate 6 (chapter 15).

A model for RP formation. (A) The holoenzyme depicted as in Color Plate 5B , rotated to show the upstream face (the same as in the inset to Color Plate 4A ) and with s shown as an orange surface. The gate loop is shown as a blue worm, and s 1.2 helix is red (it lies behind σ in this view). The line across the RNAP depicts the plane at which RNAP would be cut to generate the view shown in panels B through D. (B) A cutaway view of RP. The core is gray, σ is orange, and the flap is blue. The DNA is dark and light green and lies along the surface of the upstream face of RNAP. The negatively charged s region 1.1 lies in the positively charged downstream DNA channel. The β lobe and gate loop would lie above the plane of the page, protruding into the downstream DNA channel above σ region 1.2. (C) RP, a possible intermediate in RP formation. A kink forms in the DNA within the –10 element. Aromatic residues in s region 2.3 interact with the nontemplate strand to assist DNA opening. The DNA moves into the downstream DNA channel, replacing region 1.1. The b gate loop prevents entry of double-stranded DNA into the active site and may assist in unwinding the DNA. (D) RP. The downstream DNA is inserted in the downstream DNA channel, and melting has extended from the –10 element to the transcription start site. The template strand is guided into the active-site channel by positive residues in σ regions 2.4 and 3.0. NTPs entering through the secondary channel can be incorporated into a nascent transcript (red), extension of which is blocked by the σ 3.2 loop, resulting in abortive initiation. Adapted from Fig. 3 of reference 64, with permission.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 7 (chapter 15).

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Color Plate 7 (chapter 15).

Structure of the TEC. (A) A TEC model based on the core RNAP model shown in Color Plate 4 with mobile modules (23) adjusted to the conformation of the RNA II TEC (PDB ID 1I6H [34]). The RNA-DNA hybrid and downstream DNA positions are those observed in the RNAP II TEC (34) with the scaffold dimensions and upstream DNA as modeled by Korzheva et al. (45). Subunits and DNA are colored as in Color Plate 4 . RNA is red. Active-site Mg ions are yellow. The trigger loop is depicted as an orange worm. The βD loop II is shown as a dark blue worm. The box encloses the portion of the active-site channel magnified in panels B and C. (B) The conformation of the active site in holoenzyme (97). A portion of the nontemplate strand of the DNA has been removed to allow a clearer view of the active center. Ovals represent the + , and E sites. The RNA 3′ end is depicted in the + site; however, the kinked bridge helix in this structure would sterically clash with the base in the + site. (C) The conformation of the active site in the yeast RNAP II TEC (34). The view is the same as that in panel B. In this conformation, the bridge helix is straight and there is no steric clash between the bases in the + site and residues from the helix.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 8 (chapter 15).

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Color Plate 8 (chapter 15).

Postinitiation events in transcription. The color code and orientation are the same as in Color Plate 6 . (A) The end of abortive initiation. Once the RNA transcript exceeds 8 nt, it has fully displaced the s 3.2 linker from the RNAexit channel. This weakens the interaction between s and the promoter, allowing promoter clearance. (B) Promoter clearance. Removal of the 3.2 linker from the RNA-exit channel destabilizes the interaction between the flap and region 4, and consequently the interaction with the –35 element. (C) The TEC. After promoter clearance, the remaining contact between s and the core is weakened, and σ is stochastically lost from the complex. Adapted from Fig. 3 of reference 64, with permission.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 9 (chapter 22).

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Color Plate 9 (chapter 22).

Comparison of the dimeric structure of RuvC (B) and Ydc2 (A), showing a solvent-accessible surface and secondary structure cartoon. The four conserved acidic residues that form the catalytic metal-binding pockets in each enzyme are highlighted in red. (C) Structure of the Holliday junction. The junction is presented in the open, fourfold symmetric form seen in the absence of metal ions. This corresponds closely to the global conformation of the junction when bound by RuvC, RuvA, or Cce1/Ydc2, and the positions of the paired nicks in the phosphodiester backbone introduced by these enzymes are indicated by arrows. Some distortion of the center of the junction from the idealized B-form DNA represented is expected when it is complexed with these proteins.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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Image of Color Plate 10 (chapter 22).

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Color Plate 10 (chapter 22).

A monomer of RuvC is shown, with conserved residues highlighted and labeled. The four acidic residues (pink) constitute the metal-binding site of the enzyme. Lys-107 and Lys-118 (blue) may play a role in stabilization of the transition state. The possible functions of the other residues are discussed in the text.

Citation: Higgins N. 2005. Color Plates, In The Bacterial Chromosome. ASM Press, Washington, DC.
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