Download Archaea

20
The Archaea
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Outlines
• 20.1 What is archaea: an overview
• 20.2 Phylum Crenarchaeota 熱泉古菌
• 20.3 Phylum Euryarchaeota 寬廣古菌
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20.1 Overview of the Archaea
1. Some common habitats of archaea
2. The debate that surrounds archaeal taxonomy
3. Three key metabolic pathways that are central to
archaeal physiology
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Archaea
• Many features in common with Eukarya (真核)
– genes encoding proteins for replication, transcription,
translation
• Features in common with Bacteria
– genes encoding proteins for metabolism
• Other elements are unique to Archaea
– unique rRNA gene structure
– capable of methanogenesis
• Highly diverse with respect to morphology, physiology,
reproduction, and ecology
• Best known for growth in anaerobic, hypersaline, pH
extremes, and high-temperature habitats
• Also found in marine arctic temperature and tropical
waters
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Archaeal Taxonomy
• 5 major physiological and morphological groups
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Archaeal Taxonomy
• Two phyla based on
Bergey’s Manual
– Euryarchaeota (寬廣古菌)
– Crenarchaeota (熱泉古菌)
• Metagenomic analysis
reveals additional species
(some are not culturable)
• 16S rRNA and SSU rRNA
analysis also shows
– Group I are Thaumarchaeota
(奇古菌)
– Group II are Korachaeota (初
古菌)
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Archaeal Metabolism
• Great variation among the different archaeal
groups
• Autotrophy, organotrophy, and phototrophy have
been observed
• Differ from other groups in glucose catabolism,
pathways for CO2 fixation, and the ability of some to
synthesize methane (甲烷)
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Archaeal Metabolism: Autotrophy
• Carbon fixation pathways include
– Reductive acetyl-CoA pathway
– 3-hydroxyproprionate/4-hydroxybutyrate (HP/HB) cycle
– Dicarboxylate/4-hydroxybutyrate (DC/HB) cycle
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Archaeal Metabolism: Autotrophy-1
• Reductive acetyl-CoA pathway
– Most energy efficient (1 ATP burned/pyruvate formed)
– 2 CO2 molecules incorporated into 1 acetyl group
– Acetyl group combined with additional CO2 to form pyruvate
– Used by methanogens both for carbon fixation and for energy
conservation
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Archaeal Metabolism: Autotrophy-2 & 3
– 5 ATP/pyruvate
formed
– Found in
anaerobic and
microaerobic
members
HP/HB cycle
DC/HB cycle
– Some of its
enzymes are
sensitive to
oxygen
– Steps are similar
to a reversal of
the TCA cycle
– 9 ATP/
pyruvate
synthesized
– Can be
operated
under aerobic
conditions
– Has less of a
demand for
metal
cofactors
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Acetyl-CoA Assimilation: Glyoxylate
(red lines) and Methylaspartate
Pathways (black lines)
Autotrophic
archaea and some
haloarchaea use
the glyoxylate
pathway
Haloarchaea lack
ICL and use the
methylaspartate
pathway
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Archaeal Metabolism
Chemoorganotropy-1:
modified EmbdenNo net ATP
generation on
Meyerhof
archaea
• Similarities in eukaryotes
and bacteria
• 3 pathways unique to
Archaea
– modified Embden-Meyerhof
pathway
– 2 modified Entner-Duodoroff
pathways
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Chemoorganotropy-2:
2 modified
Entner-Duodoroff
pathways
No ATP generation
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20.2 Phylum Crenarchaeota
1. The major physiological types among crenarchaea
2. The importance of crenarchaeol in the discovery of
new crenarchaeotes
3. Hyperthermophilic and thermoacidophilic growth
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Phylum Crenarchaeota
• Most are extremely thermophilic
– hyperthermophiles (hydrothermal vents)
• Most are strict anaerobes
• Some are acidophiles
• Many are sulfur-dependent
– for some, used as electron acceptor in anaerobic
respiration
– for some, used as electron source
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Parasitic
Nanoarchaeum
attaches to
Ignicoccus
The outer membrane of Ignicoccus
house H2:sulfur oxidoreductase and
ATP synthase complex, making it the
only micro to have an energized outer
membrane.
Nanoarchaeum equitans forms tiny
cells (350-500 mM) that attach to
Ignicoccus.
Boiling
temperature
and rich in
sulfur
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Hyperthermophilic Crenarchaeote
• Pyrodiciaceae is
hyperthermophilic as
it can survive
autoclaving for an hour
• Strictly anaerobic
• Use H2/formate as a
electron donor and
Fe3+ as an electron
acceptor
• Under anaerobic
condition, Fe(III) is
reduced to Fe3O4
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Crenarchaeota…
• Include organotrophs and lithotrophs (sulfuroxidizing and hydrogen-oxidizing)
• Contains 25 genera
– two best studied are Sulfolobus and Thermoproteus
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Genus Thermoproteus
• Long thin rod, bent or branched
– cell walls composed of glycoprotein
• Thermoacidophiles
– 70–97 °C
– pH 2.5–6.5
• Anaerobic metabolism
– lithotrophic on sulfur and hydrogen
– organotrophic on sugars, amino acids, alcohols, and organic acids
using elemental sulfur as electron acceptor
• Autotrophic using CO or CO2 as carbon source
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Genus Sulfolobus
• Irregularly lobed, spherical shaped
– cell walls contain lipoproteins and carbohydrates
• Thermoacidophiles
– 70–80°C
– pH 2–3
• Metabolism
– lithotrophic on sulfur using oxygen (usually) or ferric iron as
electron acceptor
– organotrophic on sugars and amino acids
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Genome Construction of Sulfolobus
Sulfolobus grows
at pH 2-4, but
maintains a
cytoplasmic pH at
approximately 6.5.
The pH gradient
allows for ATP
generation by
ATPase and at least
15 secondary
transporter for
organic solute
uptake.
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Phylum Crenarchaeota
• Group I archaea
– archaeal unique membrane lipid, crenarchaeol is widespread in
nature
• marine waters
• rice paddies, soil, freshwater
• Recent growth of mesophilic archaea
– capable of nitrification (ammonia to nitrate)
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20.3 Phylum Euryarchaeota
1. Methanogenesis: process and its importance in carbon
flow and energy production
2. The physiology and ecology of anaerobic methane
oxidation
3. How halophiles cope with osmotic stress
4. Rhodopsin-based phototrophy as used by halophiles
5. The habitats of methanogens and halophiles
6. List one unique feature for Thermoplasma, Pyrococcus,
and Archaeoglobus
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Phylum Euryarchaeota
• Consists of many classes, orders, and families
• Often divided informally into five major groups
1. methanogens
2. halobacteria
3. thermoplasms
4. extremely thermophilic S0-metabolizers
5. sulfate-reducers
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1. Methanogens
• All methanogenic microbes are Archaea
– called methanogens: produce methane
• Methanogenesis
– last step in the degradation of organic compounds
– occurs in anaerobic environments (only when O2 and
most other electron acceptors are unavailable)
• e.g., animal rumens
• e.g., anaerobic sludge digesters
• e.g., within anaerobic protozoa
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Methanogens
• 26 genera, largest group of cultured archaea
– differ in morphology
– 16S rRNA
– cell walls
– membrane lipids
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Methanogens
• Unique anaerobic production of methane
– hydrogen, CO2 oxidation
– coenzymes, cofactors
– ATP production linked with methanogenesis
• What are the
potential
mechanisms by
which methanogens
are thought to
couple CO2 reduction
to ATP generation?
Two mechanisms are
hypothesized currently, which
are not exclusive. One is that
protons are generated on the
outside of the membrane in
step 5, which would build the
proton motive force, in turn
allowing ATP synthesis via
ATP synthase. The other is
that step four drives uptake of
Na+ ions, and releasing those
back across the membrane
could drive either H+ export or
ATP synthesis directly.
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Ecological and Practical
Importance of Methanogens
• Important in wastewater treatment
• Can produce significant amounts of methane
– can be used as clean burning fuel and energy source
– is greenhouse gas and may contribute to global warming
• Can oxidize iron
– contributes significantly to corrosion of iron pipes
• Can form symbiotic relationships with certain bacteria,
assisting carbon/sulfur cycling
Sulfate-reducing bacteria
Methanogens
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2. Halobacteria
• Order Halobacteriales; 17 genera in one family,
Halobacteriaceae
• Extreme halophiles (halobacteria)
– require at least 1.5 M NaCl
• cell wall disintegrates if [NaCl] < 1.5 M
– growth optima near 3–4 M NaCl
• Aerobic, respiratory, chemoheterotrophs with
complex nutritional requirements
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Strategies to Cope with Osmotic Stress
• Increase cytoplasmic osmolarity
– use compatible solutes (small organics)
• “Salt-in” approach
– use Na+/H+ antiporters/K+ symporters to increase concentration
of KCl and NaCl to level of external environment
• Acidic amino acids in proteins
– Acidic aa on the surface of the folded protein attract cations, which
form a hydrated shell on the protein
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e.g., Halobacterium salinarium (H.
halobium)
• Has unique type of photosynthesis
– not chlorophyll based
– uses modified cell membrane (contains bacteriorhodopsin)
– absorption of light by bacteriorhodopsin drives proton
transport, creating PMF for ATP synthesis
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Features of Halobacterium
Rhodopsins
• Bacteriorhodopsin: light-driven ion pumps
– chromophore similar to retinal
– seven membrane spanning domains
– purple aggregates in membrane
• Halorhodopsin: light-driven ion pumps
– light energy to transport chloride ions
• 2 sensory rhodopsins: photosensory receptors
– flagellar attached photoreceptors
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Genomic Reconstruction of of
Halobacterium NRC-1
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Proteorhodopsin
• Now known to be widely distributed among
bacteria and archaea
– found in marine bacterioplankton using DNA sequence
analysis of uncultivated organisms
– also found in cyanobacteria
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3. Thermoplasms
• Class Thermoplasmata
• Three different genera
– Thermoplasmataceae
– Picrophilaceae
– Ferroplasmataceae
• Thermoacidophiles
• Lack cell walls
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Genus Thermoplasma
• Thermoacidophiles; grow in refuse piles of coal
mines at 55–59°C, pH 1–2, FeS
• Cell structure
– shape depends on temperature
– may be flagellated and motile
– cell membrane strengthened by diglycerol tetraethers
(caldarchaeol), lipopolysaccharides, and glycoproteins
– nucleosome-like structures formed by association of DNA
with histone-like proteins
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Genus Picrophilus
• Irregularly shaped cocci, 1 to 5 M diameter
– large cytoplasmic cavities that are not membrane bound
– no cell wall
– has S-layer outside plasma membrane
• Thermoacidophiles
– 47–65°C (optimum 60°C)
– pH <3.5 (optimum 0.7)
• Aerobic
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4. Extremely Thermophilic S0-Reducers
• Class Thermococci; one order, Thermococcales
• One family containing three genera, Thermococcus,
Paleococcus, Pyrococcus
• Motile by flagella
• Optimum growth temperatures 88–100°C
• Strictly anaerobic
• Reduce sulfur to sulfide
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5. Sulfate-Reducing Euryarchaeota
• class Archaeoglobi; order Archaeoglobales; one family
with one genus, Archaeoglobus
• irregular coccoid cells
– cell walls consist of glycoprotein subunits
• extremely thermophilic (optimum 83°C)
– isolated from marine hydrothermal vents
• metabolism
– lithotrophic (H2) or organotrophic (lactate/glucose)
– use sulfate, sulfite, or thiosulfite as electron acceptor
– possess some methanogen coenzymes
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Aciduliprofundum
• Newly characterized thermophilic euryarchaeote
– acidophile, requires pH 3.3 to 5.8
– thermophile, 60–75oC for growth
– inhabit hydrothermal vents
– sulfur- and iron-reducing heterotroph
• First thermoacidophile in sulfide rich areas
• May be important in iron and sulfur cycling
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5/9/2017 Homework
1. Define ‘organotrophy’, ‘lithotrophy’, ‘autotrophy’, and ‘phototrophy’.
2. Why do methogens use the reductive acetyl-CoA pathway for carbon
fixation (Figure 20.3)? Given that the DC/HB pathway uses far less ATP
per pyruvate synthesized than the HP/MB pathway, why do some archaea
use the HP/HB pathway instead? Explain why the fixation of CO2 by
Thermoproteus spp. using the DC/HB cycle is not photosynthesis (Figure
20.4).
3. Why do haloarchaea use the methylaspartate rather than the glyoxylate
cycle for the incorporation of acetate? Why might the production of
glutamate as an intermediate be beneficial for some haloarchaea (Figure
20.5)?
4. Discuss the role of external pH on the magnitude of the proton motive
force generated by Sulfolobus spp. (Figure 20.11).
5. Define halophiles. How do halophiles cope with osmotic stress? What are
the functions of archaerhodopsins and sensory rhodopsins of
Halobacterium salinarum?
6. How do thermoplasmas, a group of archaea lacking cell walls, cope with
high temperatures and acidic pH?
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