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Chapter 2 : General Characteristics and Important Model Organisms

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Abstract:

This chapter provides an overview of the and some of their morphological, physiological, biochemical, and molecular properties. It introduces model organisms and systems that have been used to study fundamental properties and principles of archaeal biology, in addition to those that have served as models for understanding the biology of more complex eucaryal cells. The chapter describes phylogeny of and the origin of life, and gives an overview of the characteristic properties of archaeal cells. Rather than one model organism, a broad range of archaea have proven useful for studying morphology, physiology, molecular mechanisms of adaptation, and so forth. These include , , and spp. for methanogenesis; for proteolysis; for light-driven proton translocation, gene regulation, chemotaxis, and gas vesicles synthesis; for sulfate reduction; and for inorganic sulfur metabolism; , , , and the methanogens for electron transport chains; and for DNA replication and transcription; , , and for translation. The chapter also describes the properties of major archaeal taxa according to their ecology and molecular similarity. Important characteristics of some of the key organisms are also included in this chapter. , , and are the most well studied methanogens and are important model organisms for studies on acetoclastic methanogenesis, transcription, and chaperonins.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2

Key Concept Ranking

Environmental Microbiology
0.95504004
Bacteria and Archaea
0.8311506
Type II NADH Dehydrogenase
0.45387098
Bacterial Proteins
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0.95504004
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Figures

Image of FIGURE 1.
FIGURE 1.

16S rDNA phylogenetic dendrogram of the . Branches representing cultivated strains (boldface lettering and dark polygons); branches representing sequences determined from molecular ecology studies (white polygons). Alternative branch points of and (dashed lines) ( ). Reproduced with modifications from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 2.
FIGURE 2.

Subunit composition and phylogenetic dendrogram of RNA polymerase amino acid sequences. (A) Virtual SDS-polyacrylamide gel showing the subunit sizes of the subunits of the different RNA polymerases. Homologous subunits are shown in identical shading. Reproduced with modifications from ( ) with permission of the publisher. (B) Phylogenetic dendrogram of concatenated RNA polymerase amino acid sequences and presence of a single subunit or two-subunit B homologs. Reproduced with minor modifications from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 3.
FIGURE 3.

Hypothetical scenario for the origin of living cells from (in)organic precursors. Archaeal and bacterial cells are shown escaping from within naturally formed inorganic metal sulfide-based compartments in a 3.8-Ga-old hydrothermal vent. The compartments (1 to 100 mm in diameter) and vent structures are schematic and not drawn to scale. LUCA, last universal common ancestor. Reproduced with modifications from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 4
FIGURE 4

Cell shapes of various archaea. (A) Scanning electron micrograph of cells within a network of extracellular cannulae ( ). (B) Phase-contrast micrograph of with gas vesicles. Photograph courtesy of T. Hechler, Darmstadt. (C) Electron micrograph of a freeze-etched cell showing the hexagonal lattice of the S layer ( ). (D) Ultrathin section of a cell ( ). (E) Ultrathin section of cells ( ). (F) Ultrathin section of cells Bars, 1 μm. Panels A and C to E reproduced from with permission of the publisher. Panel F reproduced from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 5.
FIGURE 5.

The S-layer protein tetrabrachion. (A) Electron micrograph of the negatively stained tetrabrachion-protease complex. (B) Schematic model of the complex with dimensions. (C) Schematic model of the cell surface of . (D) Proposed folding topology with cysteine residues and the unique proline residue separating left- and right-handed supercoils. Figure compiled and reproduced from ( ) and the ( ) with permission of the publishers.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 6.
FIGURE 6.

Flagellated archaea. (A) Reproduced from ( ) with permission of the publisher. (B) Reproduced from the ( ) with permission of the publisher. (C) PHH4. Photograph courtesy of T. Hechler, Darmstadt.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 7.
FIGURE 7.

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, 4μm. (G) Pt-shadowed electron micrograph of a single SM1 cell with appendages. Figure compiled, modified, and reproduced from ( ) and ( ) with permission of the publishers.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 8.
FIGURE 8.

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 ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 9.
FIGURE 9.

Chemical structures of diphthamide and hypusine. Modifications (bold type) of the amino acids histidine and lysine to form diphthamide and hypusine, respectively. ADP ribosylation site catalyzed by diphtheria toxin (arrow).

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 10.
FIGURE 10.

(.) Three-dimensional structure of the 50S subunit of the ribosome. The ribosome arm around ribosomal protein L1 was omitted (for a more complete picture see reference ). Figure drawn from the coordinates from PDB entry 1QVF ( ); 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: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 11.
FIGURE 11.

() Haloarchaea in liquid cultures and within salt crystals. (A) Cultures of and first flask (front), WFD11 wild type; second flask, WFD11 gas vesicle Δ>D 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: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 12.
FIGURE 12.

Morphology of haloarchaea. (A) Negative stain image of aerobically grown PHH1 with gas vesicles. (B) Negative stain image of aerobically grown with gas vesicles. (C) Phase-contrast micrograph of WFD11 gas vesicle ΔD mutant (see Fig. 14 ). (D) Phase-contrast micrograph of with gas vesicles. (E, F) Negative stain electron micrographs of cells showing pleomorphic shape. (G) Phase-contrast micrograph of WFD11 wild type. Photographs courtesy of T. Hechler, Darmstadt.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 13.
FIGURE 13.

Three-dimensional model of the sensory rhodopsin highlighting α-helices and retinal (black) and chemical structure of the all- form of retinal (PDB code 1H2S).

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 14.
FIGURE 14.

Gas vesicle operons in genes are shown as boxes above or below according to their direction of transcription, and promoter regions are denoted by arrows; plasmid-encoded region; chromosomally encoded region; chromosomally encoded region of ΔD, in-frame deletion mutant of the region, leading to gas vesicle-overproducing transformants; chromosomally encoded region of (formerly ISH30, insertion element; chromosomally encoded region from the genome of GvpE and GvpD, transcriptional activator and repressor, respectively. Modified from a figure provided by F. Pfeifer, Darmstadt, with reference to several sources ( ) and the genome sequence (GenBank NC_007355).

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 15.
FIGURE 15.

(.) 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: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 16.
FIGURE 16.

Electron micrograph of . Reproduced from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 17.
FIGURE 17.

Genome rearrangements in species. (A, B) Pairwise genome dot plots: (A) solid arrows with capital letters indicate large synteny segments conserved between and (B) shaded arrows represent the location and relative orientation of synteny segments conserved in all three species; small squares denote position of IS elements in the genome. (C to E) Genome organization and synteny segments in the three species. Location and orientation of the major syntenic genome fragments conserved between and are marked as above; 10 smaller syntenic fragments conserved also with are marked with medium arrows. Dashed arrows represent the two replichores defined by the origin of replication () and the putative terminus of replication at the bottom of the arrows; LCTR1 and 2, two families of long conserve tandem repeats occurring in all species ( ). Reproduced with modifications from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 18.
FIGURE 18.

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

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 19.
FIGURE 19.

( 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) a-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 ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 20.
FIGURE 20.

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) ( ). Panels A to E reproduced from ( ) with permission of the publisher. (F) Ultrathin 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 probes (green). Panels F to H reproduced from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 21.
FIGURE 21.

Electron micrographs of and . (A, B) cells with branched form. (C, D) with golf club structure. Reproduced from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 22.
FIGURE 22.

Morphology and ultrastructure of and . (I) : (a) Ptshadowed showing the outline of the cell shape; (b) ultrathin section of cytoplasmic membrane (cm) and S layer (sl); (c) negatively stained individual cell; (d) ultrathin section showing pleomorphic morphology. (II) : (a) ultrathin section of showing irregular cell shape; chr, translucent chromatoid region; (b) enlargement of the cell envelope with cytoplasmic membrane (cm) and no cell wall; (c) Pt-shadowed cells showing cytoplasmic lobes (cl) protruding from the surface. Reproduced from ( ) with permission from the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 23.
FIGURE 23.

( 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) ( ). (B) Top view of the 20S proteasome core particle showing the sevenfold symmetry (PDB code 1PMA) ( ). (C) Top view of the homohexameric tricorn protease complexed with a tridecameric peptide derivative (PDB code 1N6E) ( ).

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 24.
FIGURE 24.

Electron micrographs of (Left) Phase-contrast micrograph; bar 10 μm. Photograph courtesy of K. Lauber, Darmstadt, Germany. (Right) Transmission electron micrograph of thin section; bar 1 μm. Photograph courtesy of W. Zillig, Martinsried, Germany.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 25.
FIGURE 25.

Phylogenetic dendrogram of the based on 16S rDNA sequences. Scale bar, 10 estimated exchanges within 100 nucleotides. Reproduced with minor modifications from ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 26.
FIGURE 26.

The bioinorganic sulfur cycle. Sulfur cycle depicted with enzyme reactions involving sulfur compounds. Enzymes: 1, polysulfide reductase; 2, sulfur reductase; 3, sulfide:quinone oxido-reductase or sulfide:cytochrome oxidoreductase; 4, sulfur oxygenase; 5, sulfite:acceptor oxidoreductase (the acceptor is cytochrome in most bacteria) or sulfite oxidase; 6, ATP sulfurylase or adenylylsulfate:phosphate adenylyltransferase (APAT); 7, ATP sulfurylase; 8, adenylylsulfate (APS) reductase; 9, sulfite reductase; 10, tetrathionate reductase; 11, thiosulfate:acceptor oxidoreductase; 12, Sox complex; 13, sulfur oxygenase reductase; 14, thiosulfate reductase; 15, tetrathionate hydrolase (there is also a trithionate hydrolase in addition); 16, -acetylserin or -phosphoserine sulfhydrolases; 17, cysteine desulfurase; 18, APS kinase; 19, 3′-phosphoadenylylsulfate (PAPS) reductase. Gray circles denote disproportionation reactions. Reactions of cysteine breakdown are omitted. Compiled from several sources ( ) with permission of the publishers.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 27.
FIGURE 27.

() 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 κT/e; white, neutral; blue, ≥-10 ± 1 κT/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 ( ) with permission from the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 28.
FIGURE 28.

(.) 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; C P, 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: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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Image of FIGURE 29.
FIGURE 29.

Hypothetical scheme of the modular evolution of complex I from an ancestral hydrogenase. Bacterial, archaeal, and cyanobacterial complexes emerged by acquisition of specific modules. Dark gray, hydrogenase module; light gray, transporter module. Reproduced and modified from the ( ) with permission of the publisher.

Citation: Kletzin A. 2007. General Characteristics and Important Model Organisms, p 14-92. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch2
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References

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