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Color Plates

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Figures

Image of Figure 5 (Chapter 23)

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Figure 5 (Chapter 23)

Uptake of fluorescent archaeosomes by phagocytic cells. Archaeosomes composed of total polar lipids were prepared either by incorporating a small amount of the fluorescent lipid rhodamine-phosphatidylethanolamine (62) or by entrapping 1.5 mM carboxyfluorescein (66). Uptake was performed in 1 ml of RPMI medium added to 0.5 million adhered cells (62). Panels show 30-min uptakes: (A) rhodamine-archaeosomes (100 μg) by thioglycollate-activated mouse peritoneal macro-phages; (B) uptake of rhodamine-archaeosomes (25 μg) by bone marrow-derived DCs; (C) uptake of carboxy-fluorescein-archaeosomes (40 μg) by macrophages culture J774A.1; and (D) uptake of rhodamine-archaeosomes (100 μg) by thioglycollate-activated mouse peritoneal macrophages.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 7 (Chapter 2)

The euryarchaeon SM1 and its extracellular appendages (“hami”). (A) Electron micrograph of a “hamus.” (B) Enlargement of the hook region. (C) Simplified model of a hamus with the three filaments shown in different colors and 3D reconstruction from cryoelectron microscopy. (D) “String of pearls,” archaeal/bacterial community in cold, sulfurous spring water. (E) Hamus model with dimensions. (F) Natural biofilm hybridized with an SM1-specific fluorescent probe; circle diameter, 4 μm. (G) Pt-shadowed electron micrograph of a single SM1 cell with appendages. Figure compiled, modified, and reproduced from (264) and (265) with permission of the publishers.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 8 (Chapter 2)

Three-dimensional structures of archaeal Argonaute proteins. (A) 3D structure of Ago with the PAZ domain (blue) and the PIWI domain (green/yellow) (PDB code 1U04). (B, C) Similarity of the PIWI domain (B) with the catalytic core of the RNase H1 (C) (PDB code 1RDD) with the catalytic DDE triad and bound Mg ion highlighted. The PIWI domain has a putative, similar catalytic DDE triad and a conserved Arg (position 627). (D, E) 3D structure of the PAZ domain (D) and comparison with the homologous domain of human Ago1 bound to an siRNA mimic (E) (PDB code 1SI3). (F) Domain structures of Ago proteins, including N-terminal, linker (L1 and L2), PAZ, Mid, and PIWI domains and of human dicer comprising a DEXH helicase, a PAZ, two RNase III, and dsRBD domains and a conserved domain of unknown function (DUF). Panels A to E reproduced with modifications from (241) with permission of the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 10 (Chapter 2)

Three-dimensional structure of the 50S subunit of the ribosome. The ribo-some arm around ribosomal protein L1 was omitted (for a more complete picture see reference 200). Figure drawn from the coordinates from PDB entry 1QVF (200); ribosomal RNAs are displayed in red (backbone) and gray (bases), proteins are displayed as yellow backbone ribbons. Top left, crown view; top right, back view; bottom, bottom view; the circle indicates the position of the polypeptide exit tunnel.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Image of Figure 11 (Chapter 2)

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Figure 11 (Chapter 2)

Haloarchaea in liquid cultures and within salt crystals. (A) Cultures of and first flask (front), WFD11 wild type; second flask, WFD11 gas vesicle ΔD mutant (see Fig. 14); third flask, WFD11 gas vesicle ΔD mutant complemented with the gene; fourth flask, wild type. (B) Himalayan rock salt (“Eubiona”; Claus, GmbH, Baden-Baden, Germany). (C, D) Crystals formed from dried cultures (cells trapped within). Bars, 1 cm. Crystals courtesy of F. Pfeifer, Darmstadt, Germany. Photographs by F. Pfeifer, Darmstadt, Germany (panel A), and A. Kletzin (panels B to D).

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 15 (Chapter 2)

Solfatara and Pisciarelli fumaroles. (Left) Fumaroles in the Solfatara caldera (Pozzuoli near Naples, Italy) with deposition of sulfur, mercury, and arsenic salts. (Right) Fumarole-heated hole with boiling water, typical of habitats for (Pisciarelli, near Naples, Italy). Photos taken by A. Kletzin.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 18 (Chapter 2)

Three-dimensional structures of tungsten-containing aldehyde:ferredoxin oxidoreductases from (A) Cartoon of the formaldehyde:ferredoxin oxidoreductase (FOR), homotetrameric holoenzyme (150). (B) Cartoon of the aldehyde:ferredoxin oxidoreductase (AOR) homodimeric holoenzyme (53). (C) Peptide chains of AOR (cyan) superimposed on FOR (magenta) showing close structural similarity (150). (D) Active-site cavity of the FOR with surrounding residues and glutarate shown (150). (E) [4Fe-4S] cluster and the W-(bis-tungstopterin) cofactor of the AOR (53). FOR images reproduced from the with permission of the publisher (150); AOR images reproduced from (53) with permission of the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 19 (Chapter 2)

Model of the voltage-gated K-channel KvAP and comparison with the KcsA K channel. (A) Stereo view of the KvAP pore with electron density map contoured at 1.0 Δ_ carbon (yellow), nitrogen (blue), oxygen (red), potassium (green). (B, C) α-Carbon traces of the KvAP pore (blue) and the KcsA K channel (green) shown as a side view (B) and end-on from the intracellular side (C); S5, S6, outer and inner helices; glycine-gating hinges (red spheres). (D, E) Models of the closed (D) and open (E) KvAP structures based on the positions of the paddles (red), the pore and the S5 and S6 helices of KcsA. Reproduced with modifications from (168, 169) with permission of the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 20 (Chapter 2)

Electron micrograph and fluorescence images of and (A) Transmission electron micrograph of thin-sectioned cell with broad periplasmic space (P) and budded vesicles; OM, outer membrane, C, cytoplasm, bar, 1 μm. (B) Negative stained outer membrane, highlighting power spectra of image field (C to E) (275). Panels A to E reproduced from (275) with permission of the publisher. (F) Ul-trathin section of cells attached to the outer membrane of sp. KIN/4. (G) Platinum shadowing of cell with several cells attached (left side of photograph). (H) Confocal laser-scanning micrograph using (red) and specificprobes (green). Panels F to H reproduced from (152) with permission of the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 23 (Chapter 2)

Three-dimensional structures of the proteasome and tricorn protease. (A) Side view of the 26S proteasome/activator particle with the two sets of seven terminal PA26 subunits and the two αββα rings (PDB code 1YA7) (93). (B) Top view of the 20S proteasome core particle showing the sevenfold symmetry (PDB code 1PMA) (245). (C) Top view of the homohexameric tricorn protease complexed with a tride-cameric peptide derivative (PDB code 1N6E) (195).

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 27 (Chapter 2)

Three-dimensional structure of the sulfur oxygenase reductase. (A) The SOR holoenzyme. Cartoon representation viewed along the crystallographic fourfold axis; cyan, α-helices; purple, β-sheets; red spheres, Fe ions. (B) Molecular accessible surface representation in the same orientation of inner surface of the sphere, color-coded according to the calculated electrostatic potentials: red, ≤ — 10 ± 1 KT/e; white, neutral; blue, ≥ + 10 ±1 KT/e. (C) Cavity surface representation of the catalytic pocket, with conserved cysteines and iron highlighted; gray arrow, cavity entrance. (D) Effect of mutants on SOR activity; †, zero activity; ↓ reduced activity; ⇓ strongly reduced activity. The core active site composed of the Fe site and the persulfide-modified Css31 is highlighted within ellipsoids. Reproduced with minor modifications from (411) with permission from the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 28 (Chapter 2)

Canonical respiratory chain in bacteria and mitochondria. Scheme based on 3D structures with the exception of the membrane domain of complex I, for which a structure is not available. Domains that have not been identified in are shown in black. PP, periplasm; CM, cytoplasmic membrane; CP, cytoplasm; Q, quinols/quinones. The figure was prepared from the coordinates of PDB entries 1FUG (complex I, ), 1NEK (complex II, ), 1KYO (complex III, ), 1EHK (complex IV, ), and 2CCY (cytochrome ).

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 2 (Chapter 4)

Sequences and structures of representative archaeal chromatin proteins. Primary sequences of HMfB from (A), Sul7d (Sac7d) from (B), Alba (Sso10b1) from (C), and MC1 from sp. CHTI55 (D) are shown below the corresponding protein structure. The figure was constructed using structures available from the Protein Data Bank (11). Regions with α-helical and β-strand structures are colored identically in the sequence and in the corresponding structure.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Image of Figure 3 (Chapter 6)

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Figure 3 (Chapter 6)

Subunit structure of RNAPs from the three domains of life. The largest subunit in the and β’ in the is split into two subunits, A1 and A2, in the In methanogens, subunit B is also split into two polypeptides, B’ and B″. Different parts of bacterial subunit α are encoded by the genes for the archaeal subunits D and L. Subunits E1, F, H, N, and P are only shared between the and The pattern shown is based on separation of subunits by polyacrylamide gel electrophoresis under denaturing conditions. The numbers in the subunits of the eucaryal RNAP A (I), B (II), and C (III) indicate the molecular mass.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 4 (Chapter 6)

Structural similarity of RNAP (A) and yeast RNAPII (B). Comparison of interactions of an archaeal RNAP inferred from Far-Western analysis with interactions of yeast RNAPII observed in the crystal structure of the enzyme. The width of the lines connecting subunits is a measure of the intensity of the interaction. Modified from (27) with additional data from (2).

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 3 (Chapter 8)

Organization of the main ribosomal protein gene clusters in archaeal genomes. H-sp sp. NRC1; The last line () shows for comparison the organization of the same genes in that is also present in most bacteria. Genes that are within 50 bp of each other, and may therefore be cotranscribed, are indicated in the same color. Domain-specific genes are underlined.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 4 (Chapter 9).

Crystal structure of the GatDE complexed with tRNA. The dimer of the heterodimeric GatDE (thus forming a heterotetramer) binds two tRNA molecules. The asparaginase active site of GatD and the kinase/amidotransferase active site of GatE are distantly separated, connected with a “molecular tunnel.”

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 3 Chapter10.

Structure of archaeal group II chaperonin from and The side view and top view of the crystal structure of chaperonin, respectively. The α subunits are shown in dark green, and the β subunits are shown in dark blue. The hexadecameric structure was drawn using MOLSCRIPT (48). (C) The subunit structure of chaperonin. Apical, intermediate, and equatorial domains are represented by green, blue, and red, respectively. The helical protrusion is highlighted by yellow. The figure was drawn with the Viewer Light 5.0 software (Accelrys).

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 16 (Chapter 14).

Transmission electron micrographs of (a) cells after freeze etching, exhibiting an S-layer with p6 symmetry. Bar = 0.5 μm. (b) Extracellular cannulae, a specific feature of the genus negative staining with uranyl acetate; bar = 0.1 μm. (c) 3D tomogram of a frozen-hydrated cell with two cannulae; bar = 0.2 μm. Modified from the (106) with permission of the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 3 (Chapter 17).

. Crystal structure of the Sec61 protein-conducting channel. Views from the top (a) and the front (b). Faces of the helices that form the signal-sequence-binding site and the lateral gate through which TMs of nascent membrane proteins exit the channel into lipid are colored. The plug, which gates the pore, is green. The hydrophobic core of the signal sequence probably forms a helix, modeled as a magenta cylinder, which intercalates between TM2b and TM7 above the plug. Intercalation requires opening the front surface as indicated by the broken arrows, with the hinge for the motion being the loop between TM5 and TM6 at the back of the molecule (5/6 hinge). A solid arrow pointing to the magenta circle in the top view indicates schematically how a TM of a nascent membrane protein would exit the channel into lipid. Structure and legend reprinted from (107) with permission from the publisher.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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Figure 8 (Chapter 18)

Overview of halobacterial signal transduction. Transducer proteins (Htr proteins) are depicted as dimers (brown) and shown in their expected topology. The Htr regions involved in adaptation (yellow) and in signal relay (dark gray) to the flagellar motor via various Che proteins are indicated. The actions of the Che-protein machinery are illustrated for only one of the Htr proteins, shown on the left, for which an interaction with a substrate-loaded, membrane-anchored binding protein is indicated. CheD and CheJ (CheC) proteins are omitted for clarity. Htr1 and Htr2 transduce light signals via direct interaction with their corresponding receptors SRI and SRII. Repellent light signals mediated by SRI and SRII elicit the release of switch factor fumarate from a membrane-bound fumarate pool. MpcT senses changes in membrane potential (Δψ) generated via light-dependent changes in ion transport activity of BR and HR. The relative sizes of receptors, binding proteins, transducers, and Che proteins approximately reflect their corresponding molecular masses. Reproduced from (54) with permission of the publisher and D. Oesterhelt.

Citation: Cavicchioli R. 2007. Color Plates, In Archaea. ASM Press, Washington, DC.
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