chapter 17 archaea. i. phylogeny and general metabolism 17.1 phylogenetic overview of archaea 17.2...
TRANSCRIPT
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Chapter 17
Archaea
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I. Phylogeny and General Metabolism
17.1 Phylogenetic Overview of Archaea
17.2 Energy Conservation and Autotrophy in Archaea
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17.1 Phylogenetic Overview of Archaea
Archaea share many characteristics with both
Bacteria and Eukarya
Archaea are split into two major groups
Crenarchaeota
Euryarchaeota
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Detailed Phylogenetic Tree of the Archaea
Figure 17.1
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17.2 Energy Conservation and Autotrophy in Archaea
Chemoorganotrophy and chemolithotrophy
▪ With the exception of methanogenesis, bioenergetics
and intermediary metabolism of Archaea are similar to
those found in Bacteria
- Glucose metabolism
: EMP or slightly modified Entner-Doudoroff pathway
- Oxidation of acetate to CO2
: TCA cycle or some slight variations of TCA cycle
: Reverse route of acetyl-CoA pathway
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- Electron transport chains with a, b, and c-type
cytochromes present in some Archaea
: use O2, S0, or some other electron acceptor (nitrate or
fumarate)
: establish proton motive force
: ATP synthesis through membrane-bound ATPase
- Chemolithotrophy
: H2 as a common electron donor and energy source is well
established
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▪ Autotrophy via several different pathways is widespread
in Archaea
▪ acetyl-CoA pathway in methanogens and
most hyperthermophiles
▪ Reverse TCA cycle in some hyperthermophiles
▪ Calvin cycle in Methanococcus jannaschii and a Pyrococcus
species (both are hyperthermophiles)
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II. Euryarchaeota
17.3 Extremely Halophilic Archaea
17.4 Methane-Producing Archaea: Methanogens
17.5 Thermoplasmatales
17.6 Thermococcales and Methanopyrus
17.7 Archaeoglobales
17.8 Nanoarchaeum and Aciduliprofundum
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II. Euryarchaeota
Euryarchaeota
Physiologically diverse group of Archaea
Many inhabit extreme environments
E.g., high temperature, high salt, high acid
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17.3 Extremely Halophilic Archaea
Haloarchaea
Extremely halophilic Archaea
Have a requirement for high salt concentrations
Typically require at least 1.5 M (~9%) NaCl for growth
Found in solar salt evaporation ponds, salt lakes, and
artificial saline habitats (i.e., salted foods)
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Hypersaline Habitats for Halophilic Archaea
Figure 17.2a
Great Salt Lake, Utah
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Figure 17.2b
Seawater Evaporating Ponds Near San Francisco Bay, California
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Figure 17.2c
Pigmented Haloalkaliphiles Growing in pH 10 Soda Lake in Egypt
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Figure 17.2d
SEM of Halophilic Bacteria
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17.3 Extremely Halophilic Archaea
Extremely hypersaline environments are rare
Most found in hot, dry areas of world
Salt lakes can vary in ionic composition, selecting
for different microbes
Great Salt Lake similar to concentrated seawater
Soda lakes are highly alkaline hypersaline environments
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Ionic Composition of Some Highly Saline Environments
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Haloarchaea
Reproduce by binary fission
Do not form resting stages or spores
Most are nonmotile
Most are obligate aerobes
Possess adaptations to life in highly ionic environments
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Some Genera of Extremely Halophilic Archaea
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Some Genera of Extremely Halophilic Archaea
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Micrographs of the Halophile Halobacterium salinarum
Figure 17.3
Dividing cell
Glycoprotein subunit structure
on the cell wall
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Water balance in extreme halophiles
Halophiles need to maintain osmotic balance
This is usually achieved by accumulation or synthesis of
organic compatible solutes
Halobacterium species instead pump large amounts of
K+ into the cell from the environment
Intracellular K+ concentration exceeds extracellular Na+
concentration and positive water balance is maintained
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Concentration of Ions in Cells of Halobacterium salinarum
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Proteins of halophiles
Highly acidic
Contain fewer hydrophobic amino acids and lysine
residues
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Some haloarchaea are capable of light-driven
synthesis of ATP
Bacteriorhodopsin
Cytoplasmic membrane proteins that can absorb light
energy and pump protons across the membrane
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Model for the Mechanism of Bacteriorhodopsin
Figure 17.4
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Other rhodopsins can be present in Archaea
Halorhodpsin
Light-driven pump that pumps Cl- into cell as an anion for
K+
Sensory rhodopsins
Control phototaxis
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17.4 Methane-Producing Archaea: Methanogens
Methanogens
Microbes that produce CH4
Found in many diverse environments
Taxonomy based on phenotypic and phylogenetic
features
Process of methanogensis first demonstrated over
200 years ago by Alessandro Volta
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The Volta Experiment
Figure 17.5
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Habitats of Methanogens
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Micrographs of Cells of Methanogenic Archaea
Figure 17.6a
Methanobrevibacterruminantium
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Micrographs of Cells of Methanogenic Archaea
Figure 17.6b
Methanobrevibacter arboriphilus
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Micrographs of Cells of Methanogenic Archaea
Figure 17.6c
Methanospirillum hungatei
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Micrographs of Cells of Methanogenic Archaea
Figure 17.6d
Methanosarcina barkeri
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Characteristics of Some Methanogenic Archaea
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Characteristics of Some Methanogenic Archaea
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Diversity of Methanogens
Demonstrate diversity of cell wall chemistries
Pseudomurein (e.g., Methanobacterium,
Methanobrevibacter)
Methanochondroitin (e.g., Methanosarcina)
- (N-acetylgalactosamine + glucuronic acid)n
Protein or glycoprotein (e.g., Methanocaldococcus)
S-layers (e.g., Methanospirillium)
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Micrographs of Thin Sections of Methanogenic Archaea
Figure 17.7a
Methanobrevibacter ruminantium
Methanosarcina barkeri
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Hyperthermophilic and Thermophilic Methanogens
Figure 17.8a
Methanocaldococcus jannaschii
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Substrates for Methanogens
Obligate anaerobes
11 substrates, divided into 3 classes, can be converted
to CH4 by pure cultures of methanogens
Other compounds (e.g., glucose) can be converted to
methane, but only in cooperative reactions between
methanogens and other anaerobic bacteria
(syntrophic metabolism)
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Substrates Converted to Methane by Methanogens
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17.5 Thermoplasmatales
Methanocaldococcus jannaschii as a model
methanogen Contains 1.66 mB circular genome with about 1,700
genes
Genes for central metabolic pathways and cell division
- Similar to those in Bacteria
Genes encoding transcription and translation
- More closely resemble those of Eukarya
Over 50% of genes
- Have no counter parts in known genes from Bacteria and
Eukarya
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Thermoplasmatales
Taxonomic order within the Euryarchaeota
Contains 3 genera
Thermoplasma
Ferroplasma
Picrophilus
Thermophilic and/or extremely acidophilic
Thermoplasma and Ferroplasma lack cell walls
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Thermoplasma
Chemoorganotrophs
Facultative aerobes via sulfur respiration
Thermophilic
Acidophilic
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Thermoplasma Species
Figure 17.9a
Thermoplasma acidophilum
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Thermoplasma Species
Figure 17.9b
Thermoplasma volcaniumIsolated from Hot Springs
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A Self-Heating Coal Refuse Pile, Habitat of Thermoplasma
Figure 17.10
Self-heats from microbial metabolism.
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Thermoplasma (cont’d)
Evolved unique cytoplasmic membrane structure to
maintain positive osmotic pressure and tolerate high
temperatures and low pHs
Membrane contains lipopolysaccharide-like material
(lipoglycan) consisting of tetraether lipid monolayer
membrane with mannose and glucose
Membrane also contains glycoproteins but not sterols
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Structure of the Tetraether Lipoglycan of T. acidophilum
Figure 17.11
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Ferroplasma
Chemolithotrophic
Acidophilic
Oxidizes Fe2+ to Fe3+, uses CO2 as carbon source
Grows in mine tailings containing pyrite (FeS)
- Generates acid (acid mine drainage)
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Picrophilus
Extreme acidophiles
Grow optimally at pH 0.7
Have an S-layer
Model microbe for extreme acid tolerance
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17.6 Thermococcales and Methanopyrus
Three phylogenetically related genera of hyperthermophilic
Euryarchaeota
Thermococcus
Pyrococcus
Methanopyrus
Comprise a branch near root of archaeal tree
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Detailed Phylogenetic Tree of the Archaea
Figure 17.1
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Thermococcales
Distinct order that contains Thermococcus and
Pyrococcus
Thermococcus: organics + So, 55-95oC
Pyrococcus: organics + So, opt. 100oC, 70-106oC
** In the absence of So, form H2
Indigenous to anoxic thermal waters
Highly motile
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Spherical Hyperthermophilic Archaea
Figure 17.12a
Shadowed cells of Thermococcus celer
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Figure 17.12b
Dividing cell of Pyrococcus furiosus
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Methanopyrus
Methanogenic (CO2 + H2)
Isolated from hot sediments near submarine hydrothermal vents
and from walls of “black smoker”
Opt. temp. 100oC, max. temp. 110oC (the most thermophilic of all
known methangens)
Contains unique membrane lipids: unsaturated form
Contains 2,3-diphosphoglycerate in the cytoplasm (> 1 M)
Functions as thermostabilizing agent
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Methanopyrus
Figure 17.13a
Electron Micrograph of a cell of Methanopyrus Kandleri
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Methanopyrus
Figure 17.13b
Structure of novel lipid of M. kandleri
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17.7 Archaeoglobales
Archaeoglobales Hyperthermophilic
Couple oxidation of H2, lactate, pyruvate, glucose, or
complex organic compounds to the reduction of SO42- to
H2S
Archaeoglobus
Opt. temp. 83oC
Produce methane, but lacks genes for methyl-CoM
reductase
Ferroglobus
Opt. temp. 85oC
Fe2+ + NO3- → Fe3+ + NO2- + NO
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Archaeoglobales
Figure 17.14a
TEM of Archaeoglobus fulgidus
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Figure 17.14b
Freeze-etched Electron Micrograph of Ferroglobus placidus
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17.8 Nanoarchaeum and Aciduliprofundum
Nanorchaeum equitans
One of the smallest cellular organisms (~0.4 µm)
Obligate symbiont of the crenarchaeote Ignicoccus
Contains one of the smallest genomes known
(0.49 mbp)
Lacks genes for all but core molecular processes
Depends upon host for most of its cellular needs
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Nanoarchaeum
Figure 17.15a
Fluorescence micrographof cells of Nanoarchaeum
Ignicoccus
Nanoarchaeum
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Figure 17.15b
TEM of a thin section of a cell of Nanoarchaeum
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Aciduliprofundum
Thermophilic: 55-75oC
Acidophile: pH 3.3-5.8, lives in sulfide deposits in
hydrothermal vents
Oragnics + So or Fe3+
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III. Crenarchaeota
17.9 Habitats and Energy Metabolism of Crenarchaeota
17.10 Hyperthermophiles from Terrestrial Volcanic Habitats
17.11 Hyperthermophiles from Submarine Volcanic
Habitats
17.12 Nonthermophilic Crenarchaeota
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17.9 Habitats and Energy Metabolism of Crenarchaeota
Crenarchaeota
Inhabit temperature extremes
Most cultured representatives are hyperthermophiles
Other representatives found in extreme cold
environments
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Habitats of Crenarchaeota
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Habitats of Hyperthermophilic Archaea
Figure 17.16a
A typical Solfatara in Yellowstone National Park
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Figure 17.16b
Sulfur-rich hot spring
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Figure 17.16c
A typical boiling spring of neutral pH in Yellowstone Park; Imperial Geyser
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Figure 17.16d
An acidic iron-rich geothermal spring
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Hyperthermophilic Crenarchaeota
Most are obligate anaerobes
Chemoorganotrophs or chemolithotrophs with diverse
electron donors and acceptors
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Energy-Yielding Reactions of Hyperthermophilic Archaea
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Properties of Some Hyperthermophilic Crenarchaeota
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17.10 Hyperthermophiles from Terrestrial Volcanos
Sulfolobales
An order containing the genera Sulfolobus and Acidianus
Sulfolobus
Grows in sulfur-rich acidic hot springs
Aerobic chemolithotrophs that oxidize reduced sulfur or iron
Acidianus
Also lives in acidic sulfur hot springs
Able to grow using elemental sulfur both aerobically and
anaerobically (as an electron donor and electron acceptor,
respectively)
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Acidophilic Hyperthermophilic Archaea, the Sulfolobales
Figure 17.17a
Sulfolobus acidocaldarius
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Figure 17.17b
Acidianus infernus
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Thermoproteales
An order containing the key genera Thermoproteus,
Thermofilum, and Pyrobaculum
Inhabit neutral or slightly acidic hot springs or
hydrothermal vents
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Rod-Shaped Hyperthermophiles, the Thermoproteales
Figure 17.18a
Thermoproteus neutrophilus
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Figure 17.18b
Thermofilum librum
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Figure 17.18c
Pyrobaculum aerophilum
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17.11 Hyperthermophiles from Submarine Volcanos
Shallow-water thermal springs and deep-sea
hydrothermal vents harbor the most thermophilic of
all known Archaea
Pyrodictium and Pyrolobus
Desulfurococcus and Ignicoccus
Staphylothermus
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Desulfurococcales with Temperature Optima > 100°C
Figure 17.19a
Pyrodictium occultum Thin-section electron micrograph of P. occultum
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Figure 17.19c
Thin section of a cell of Pyrolobus fumarii
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Figure 17.19d
Negative stain of a cell of strain 121,the most heat-loving of all known
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Desulfurococcales with Temperature Optima Below Boiling
Figure 17.20a
Thin section of a cell of Desulfurococcus saccharovorans
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Figure 17.20b
Thin section of a cell of Ignicoccus islandicus
Extremely large periplasm
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The Hyperthermophile Staphylothermus marinus
Figure 17.21
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17.12 Nonthermophilic Crenarchaeota
Nonthermophilic Crenarchaeota have been
identified in cool or cold marine waters and
terrestrial environments by culture-independent
studies
Abundant in deep ocean waters
Appear to be capable of nitrification
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Cold-Dwelling Crenarchaeota
Figure 17.22
Photo of the Antarctic peninsulaFlouresence photomicrograph of seawater treated with FISH probe
DAPI (diamidino-2-phenylindole) stained
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IV. Evolution and Life at High Temperatures
17.13 An Upper Temperature Limit for Microbial Life
17.14 Adaptations to Life at High Temperature
17.15 Hyperthermophilic Archaea, H2, and Microbial
Evolution
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17.13 An Upper Temperature Limit for Microbial Life
What are the upper temperature limits for life?
Laboratory experiments with biomolecules suggest
140–150°C
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Thermophilic and Hyperthermophilic Prokaryotes
Figure 17.23
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17.14 Adaptations to Life at High Temperature
Stability of Monomers
Protective effect of high concentration of cytoplasmic
solutes
Use of more heat-stable molecules
e.g., use of nonheme iron proteins instead of proteins that
use NAD and NADH
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Protein Folding and Thermostability
Amino acid composition similar to that of
nonthermostable proteins
Structural features improve thermostability
Highly hydrophobic cores
Increased ionic interactions on protein surfaces
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Chaperonins
Class of proteins that refold partially denatured proteins
Thermosome
A major chaperonin protein complex in Pyrodictium
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DNA Stability
High intracellular solute levels stabilize DNA
Reverse DNA gyrase
Introduces positive supercoils into DNA, which stabilizes DNA
Found only in hyperthermophiles
High intracellular levels of polyamines (e.g., putrescine,
spermidine) stabilize DNA and RNA
DNA-binding proteins (archaeal histones) compact DNA into
nucleosome-like structures
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Archael Histones and Nucleosomes
Figure 17.25
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SSU rRNA Stability
Higher GC content
Lipid Stability
Possess dibiphytanyl tetraether type lipids; form a lipid
monolayer membrane structure
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17.15 Hyperthermophilic Archaea, H2, and Evolution
Hyperthermophiles may be the closest descendants
of ancient microbes
Hyperthermophilic Archaea and Bacteria are found on
the deepest, shortest branches of the phylogenetic tree
The oxidation of H2 is common to many
hyperthermophiles and may have been the first energy-
yielding metabolism
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Upper Temperature Limits for Energy Metabolism
Figure 17.26