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Color Plates

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Figures

Image of Color Plate 1 (chapter 1)

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Color Plate 1 (chapter 1)

Stage- and compartment-specific gene expression during sporulation. Sporulating cells harboring fluorescent fusions to forespore- and mother-cell-specific promoters were visualized by fluorescence microscopy. In the top panels, the cells (from hour 2 of sporulation) contained σ- and σ- responsive promoters fused to (false-colored green) and (false-colored red), respectively. Note that all sporangia that have σ- dependent expression of also have σ- dependent expression of . In the middle panels,the cells (from hour 3 of sporulation) contained σ- and σ- responsive promoters fused to (blue) and (yellow), respectively. Note that some sporangia that have σ-dependent expression of do not yet have detectable σ-dependent expression of . In the bottom panel, the cells (from hour 4 of sporulation) contained σ- and σ- responsive promoters fused to (false-colored purple) and (false-colored green), respectively. Note that some sporangia that have σ- dependent expression of do not yet have σ- dependent expression of . Schematic diagrams to the right show the three signal transduction pathways that comprise the conversation between the mother cell and forespore. The membrane dye (TMA-DPH) stains the double membrane that surrounds the forespore more intensely prior to the completion of engulfment.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 2 (chapter 1)

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Color Plate 2 (chapter 1)

Activation of σ in the mother cell is controlled by a signal transduction pathway emanating from the forespore under the control of σ. Schematic diagram of the signal transduction pathway. Proteolytic activation of pro-σ in the mother cell requires the putative membrane-tethered aspartyl protease GA. GA localizes to the septal membrane and is inactive in its default state. The signaling protein R is produced in the forespore compartment under the control of σ and is secreted into the space between the forespore and mother cell membranes, where it activates the GA processing enzyme. Both pro-σ and GA are synthesized in the predivisional cell and are therefore present in both the mother cell and forespore compartments. Pro-σ is degraded by an unknown mechanism in the forespore. It is hypothesized that the signaling protein R activates GA by promoting its dimerization. Fluorescence micrographs of wild-type cells harboring a functional pro-σgreen fluorescent protein (GFP) fusion. Early during sporulation pro-σ localizes to all the membranes of the sporangia. Cell-cell signaling results in proteolytic processing and release of σ-GFP into the mother cell cytosol, where it localizes to the nucleoid and directs gene transcription. Pro-σ processing requires forespore gene expression under the control of σ. Pro-σ and σ were visualized by immunoblotanalysis of wole cell lysates from wild-type and σ mutant () cells in a sporulation time course.Time (in hours) is indicated.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 3 (chapter 1)

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Color Plate 3 (chapter 1)

Two models for the activation of σ in the forespore by σ in the mother cell. σ in the mother cell directs the synthesis of several engulfment proteins as well as the locus. In the first model, the IIIA proteins monitor the engulfment process. Upon completion of engulfment, they transduce a signal that triggers σ activation. In the second model, the IIIA complex is involved in transducing an unknown mother cell signal. In this second model, the requirement for engulfment must also be satisfied to activate σ, and this need not require IIIA.The engulfment protein IIQ localizes to the septal membrane on the forespore side and anchors IIIAH in the septal membrane on the mother cell side.The interaction between these two proteins has been established biochemically and cytologically. Fluorescence micrographs of a sporulating cell harboring and fusions.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 4 (chapter 1)

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Color Plate 4 (chapter 1)

The activation of σ in the mother cell is controlled by a signal transduction pathway emanating from the forespore under the control of σ. Schematic diagram of the signaling pathway. Proteolytic activation of pro-σ in the mother cell requires the putative membrane-embedded metalloprotease B. B resides in a multimeric membrane complex with A and BofA. A anchors the complex in the mother cell membranes that surround the forespore and serves as a platform to bring B and BofA into close proximity, wherein BofA holds B inactive. Two signals from the forespore under the control of σ trigger pro-σ processing. Both signaling proteins (IVB and CtpB) are serine proteases, and both target the regulatory protein A. Cleavage of A triggers activation of the B metalloprotease and pro-σ processing. It is hypothesized that cleavage of A results in a conformational change in the complex that allows pro-σ access to the caged interior of the membrane-embedded protease.The putative pro-σ processing enzyme B localizes to the engulfing septal membranes and is anchored there by the regulatory protein A. Wild-type and A mutant cells harboring a B-GFP fusion were visualized during sporulation by fluorescence microscopy. Pro-σ processing requires forespore gene expression under the control of σ. Pro-σ and σ were visualized by immunoblot analysis of whole cell lysates from wild-type and σ mutant () cells in a sporulation time course. Time (in hours) is indicated.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 5 (chapter 7)

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Color Plate 5 (chapter 7)

Extracellular complementation of HU261 () by conditioned spent medium. When grown on medium to which its own spent medium has been added, HU261 displays a bald phenotype after 4 days of growth (A). However,when grown on R5YE medium to which the conditioned spent medium of J660 () has been added, HU261 makes both aerial hyphae and pigment, as noted by the white periphery and darkening of the surrounding medium, respectively (B).

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 6 (chapter 9)

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Color Plate 6 (chapter 9)

The acyl-homoserine lactone signaling circuitry in . The schematic emphasizes the acyl-HSL signals, genes, and corresponding protein components for each quorum-sensing system. Small circles designate acyl-HSL signals. LasR, RhlR, and QscR control the expression of overlapping regulons.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 7 (chapter 9)

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Color Plate 7 (chapter 9)

Model of the interaction of LuxR-type proteins with their cognate acyl-HSL signals. (A) Class 1 QS receptors: acyl-HSL (diamonds) associates with the nascent polypeptide during ribosomal translation. The mature protein dimer with tightly bound signal activates transcription of target genes. (B) Class 2 QS receptors: acyl-HSL (circles) is also required for proper folding, but once folded,the mature protein binds its ligand reversibly. (C) Class 3 QS receptors: acyl-HSL (triangles) is not required for folding of apo-protein, and it reversibly binds to the mature protein.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 8 (chapter 11)

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Color Plate 8 (chapter 11)

Structure and activity of the AIP. At the right is a computer-predicted structure for AIP-II determined by an energy-minimizing algorithm, kindly provided by G. Lyon (personal communication). Residues belonging to the macrocycle are shown in green, those to the linear tail portion in magenta. At the left are diagrammatic representations of the four known AIP structures.The conserved essential cysteine is in red, and the S-C=O of the thiolactone bond is shown. Ring residues whose conserved hydrophobicity is thought to mediate generalized receptor binding are enclosed by gray circles. Residues that are critical for receptor activation are enclosed by colored circles; their replacement by alanine generates universal inhibitors for . The N terminus of AIP-III is marked with an asterisk to signify its importance for this peptide’s activity, as additional amino acids on the N terminus abolish receptor activation, while the same does not hold true for AIP-I.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 9 (chapter 11)

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Color Plate 9 (chapter 11)

RNAIII secondary structure (adapted from Y. Benito, F.A. Kolb, P. Romby, G. Lina, J. Etienne, and F. Vandenesch, :668-679, 2000). Computer-predicted structure was confirmed by enzymatic and chemical analyses. Numbers 1 to 14 refer to hairpins; A, B, and C indicate long-distance interactions (see Y. Benito, F. A. Kolb, P. Romby, G. Lina, J. Etienne, and F. Vandenesch, :668-679, 2000, for details). Regions of complementarity with the mRNA leader are highlighted in red (E. Morfeldt, :4569-4577, 1995; R. P. Novick, H. F. Ross, S. J.Projan, J. Kornblum, B. Kreiswirth, and S. Moghazeh, :3967-3975, 1993.) and the mRNA translation initiation region is in green (unpublished data); the region of complementarity to the SA1000 mRNA, which also centers on hairpin 13, overlaps with that to the mRNA (S. Boisset,T. Geissmann, E. Huntzinger, P. Fechter, N. Bendridi, M. Possedko, C. Chevalier, A. C. Helfer, Y. Benito, A. Jacquier, C. Gaspin, F. Vandenesch, and P. Romby, :1353-1366,2007). RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.). The coding sequence and potentially translatable regions upstream are outlined in blue, solid and dashed respectively; its SD sequence (70–4) and start (85–7) and stop (163–5) codons are in bold. C-rich loop sequences in hairpins 7, 13, and 14 complementary to the rot mRNA are also noted in bold.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 10 (chapter 11)

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Color Plate 10 (chapter 11)

Global regulation of the staphylococcal virulon–black-box model. See text for description.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 11 (chapter 18)

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Color Plate 11 (chapter 18)

(A) A TraR dimer complexed with OOHL bound to box DNA. Alpha helices involved in dimerization are shown in red, while those required for decoding box DNA are shown in orange. Residues that contact RNAP are shown in yellow. One molecule of OOHL, shown in CPK colors, is bound to the N-terminal domain of each monomer. (B) Hydrogen bonding between OOHL and four TraR residues:Trp57 bonds with the ring oxo group of OOHL,Asp70 bonds with the amine of OOHL, Tyr53 bonds with the 1-oxo group of OOHL, and Thr129 makes a water-mediated hydrogen bond with the 3-oxo group of OOHL (A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. Cortese, R. De Francesco, P. Neddermann, and S. D. Marco, :4393–4401,2002; R. G. Zhang, T. Pappas, J. L. Brace, P. C. Miller, T. Oulmassov, J. M. Molyneaux, J. C. Anderson, J. K. Bashkin, S. C. Winans, and A. Joachimiak, :971–974, 2002).

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 12 (chapter 22)

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Color Plate 12 (chapter 22)

Organization of gene clusters in the early, late, and delayed regulons of the CSP response. Pentagons and triangles indicate orientation of each open reading frame. Border colors indicate phenotype of deletion mutant: red = transformation defective; green = transformation proficient; black = not known. Fill colors indicate functional class of protein, as indicated to the right. Narrow triangles, genes possibly subject to transcriptional readthrough; R, CAxTT-16-CAxTT direct repeats; C, combox (TACGAATA). Bent hollow arrow, apparent promoter; lollipops, stem-loop terminators at early and late operons. Open reading frames are identified by common name or by designation in the genomic sequence of strain TIGR4 (H. Tettelin et al., :498–506, 2001).

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 13 (chapter 23)

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Color Plate 13 (chapter 23)

Overall structure of CprB, an ArpA homolog. CprB constitutes a dimer, each subunit of which contains a ligand-binding pocket in the C-terminal portion and a helix-turn-helix DNA-binding domain in the N-terminal portion. The receptor dimer binds the same face of the DNA by inserting the DNA-binding helices in the major groove. The A-factor molecule in the pocket is illustrated with a ball model. The binding of A factor so that it is embedded completely in the pocket relocates the DNA-binding domains (DBD) outside the molecule via the long helix-4, thus dissociating ArpA from the DNA. This computer-modeled structure was provided by R. Natsume (R. Natsume, Y. Ohnishi, T. Senda, and S. Horinuchi, : 409–419, 2004).

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 14 (chapter 25)

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Color Plate 14 (chapter 25)

Three-dimensional molecular simulations of OHHL (A) and of furanone compound 4(B) of the furan ring structure annotated with a selection of bond angles. (C) Furanones accelerate the QS receptor degradation. Panel shows Western blots following the decay of overexpressed LuxR protein (in an background) over time in the absence and presence of furanone 56.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 15 (chapter 25)

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Color Plate 15 (chapter 25)

The QSIS1 screening system in action. The screening bacteria are cast into an agar plate along with AHL, X-Gal, and growth medium. Wells are punched in the plate in which test compounds are added. The test compounds diffuse into the agar, and where in appropriate concentration, QS is blocked, allowing growth of the bacteria. This is indicated by a blue rescue ring as the growing bacteria produce β-galactosidase which turns over the X-Gal.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 16 (chapter 25)

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Color Plate 16 (chapter 25)

(A) A QS monitor: Rfp-tagged harboring the fusion. (B) The ability to suppress QS in vivo was tested by infecting mouse lungs with alginate beads containing 2 × 10 CFU of per lung equipped with the QS monitor (M. Hentzer, K. Riedel, T. B. Rasmussen, A. Heydorn, J. B.Andersen, M. R. Parsek, S. A. Rice, L. Eberl, S. Molin, and M. Givskov, :87-102, 2002). Mice were administered 2μg of furanone 30 per g of body weight or saline via injection. (C) Infected animals were sacrificed in groups of three; the lung tissue samples were examined by SCLM. Expression of green fluorescence was used for detection of cell-cell signaling; for detection of bacteria in tissue samples, red fluorescence was used. At the left (with inhibitor), cell-cell communication appears blocked, since no or very little green fluorescence can be recorded.At the right (saline without inhibitor), cells are communicating.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 17 (chapter 27)

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Color Plate 17 (chapter 27)

The three-dimensional structure of the rhomboid GlpG. The catalytic serine lies at the top of the fourth transmembrane helix, which is central and shorter than the others, making a hydrophilic indentation in the extracellular face of the enzyme. This allows water access to the active site. The loops L1 and L5 are thought to participate in substrate access/gating, although the precise mechanism remains uncertain (Y. Wang, Y. Zhang, and Y. Ha, :179–180,2006; Z. Wu, N. Yan, L. Feng, A. Oberstein, H. Yan, R. P. Baker, L. Gu, P. D. Jeffrey, S. Urban, and Y. Shi, :1084–1091,2006). There is also uncertainty about the exact position of the fifth transmembrane helix, which in other structures is tilted away from the core, providing a possible substrate access route (Z. Wu, N. Yan, L. Feng, A. Oberstein, H. Yan, R. P. Baker, L. Gu, P. D. Jeffrey, S. Urban, and Y. Shi, :1084–1091,2006). This diagram is based on the structure of Wang et al.(Y. Wang, Y. Zhang, and Y. Ha, :179–180, 2006).

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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Image of Color Plate 18 (chapter 27)

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Color Plate 18 (chapter 27)

Secretase rhomboids (left) and mitochondrial rhomboids (right) have opposite membrane orientations. rhomboid-1 typifies the secretase-type rhomboids. The helices containing the active site serine and histidine are oriented in an out-in direction, and it cleaves type I substrates. The released fragment carries the short transmembrane remnant. Pcp1/Rbd1 is the best studied of the PARL-type mitochondrial rhomboids. The helices containing the active site serine and histidine are orientated in an in-out direction, and Rbd1 cleaves mitochondrial substrates that correspond to type II orientation (the C terminus is in the intermembrane space, which is topologically equivalent to the luminal/extracellular compartment [Schatz and Dobberstein, :1519–1526, 1996]).The released fragment carries the long transmembrane remnant. N-terminal to C-terminal orientations of key helices are indicated with white arrowheads.

Citation: Winans S, Bassler B. 2008. Color Plates, In Chemical Communication among Bacteria. ASM Press, Washington, DC.
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