Lecture 4 - Archeal Cell Struture

What is methanogenesis, and which organisms carry it out?

• Methanogenesis: The biological production of methane ($CH_4$).
• Organisms: Carried out exclusively by methanogenic archaea in strictly anaerobic environments.

What are the primary environmental properties of methane gas?

• Potent greenhouse gas that contributes significantly to climate warming.
• Traps approximately $30\times$ more heat in the atmosphere than $CO_2$.

What environmental factors and human activities increase atmospheric methane?

• Ruminant agriculture: Raising livestock (such as cows) produces methane through enteric fermentation.
• Permafrost thawing: Melting frozen Arctic soil releases ancient trapped methane gas into the atmosphere.

How do plasma membrane lipids differ between Bacteria and Archaea?

• Bacteria: Possess ester-linked unbranched fatty acid phospholipids.
• Archaea: Possess ether-linked branched isoprenoid lipids (glycerol diethers and diglycerol tetraethers).

How do cell envelope components differ between Bacteria and Archaea?

• Bacteria: Possess peptidoglycan (murein) in their cell wall (with few exceptions).
• Archaea: Lack peptidoglycan entirely; cell envelopes consist of polysaccharides or proteins, most commonly arranged as an S-layer.

What are the typical cellular morphologies and dimensions of Archaea?

• Cocci (spherical): Approximately $1\text{--}3\,\mu\text{m}$ in diameter.
• Rods (bacilli): Approximately $1\text{--}2\,\mu\text{m}$ wide by $1\text{--}5\,\mu\text{m}$ long.
• Other shapes: Include spiral, pleomorphic, and flattened square morphologies.

What is the chemical composition of archaeal plasma membrane lipids?

• Major lipid: Phosphatidylglycerol archaeol.
• Polar head group: Phosphatidylglycerol.
• Hydrophobic tails: Built from repeating isoprene units (branched five-carbon chains) rather than straight fatty acids.
• Chemical linkage: Hydrocarbons are joined to glycerol via ether linkages, conferring greater chemical stability than bacterial ester linkages.

What are the two major structural arrangements of archaeal glycerol lipids?

• Glycerol diether lipids: Two $20\text{-carbon}$ ($C_{20}$) phytanyl chains attached to one glycerol; forms a conventional lipid bilayer.
• Diglycerol tetraether lipids: Two $40\text{-carbon}$ ($C_{40}$) biphytanyl chains spanning across two glycerol molecules; forms a rigid lipid monolayer.

How do internal cyclopentane rings influence archaeal membrane structure?

• Cylopentane ring structures within tetraether hydrocarbon tails pack closely together to increase membrane rigidity and thermal stability.

What additional specialized lipid classes occur in archaeal membranes?

• Phospholipids
• Sulfolipids
• Glycolipids

How many carbon atoms constitute a single isoprene unit in archaeal lipid tails?

• Each individual isoprene subunit contains $5\text{ carbons}$, which polymerize into $C_{20}$ or $C_{40}$ chains.

What are the major structural configurations of the archaeal cell envelope?

• Lack of peptidoglycan: True peptidoglycan is absent across all Archaea.
• S-layer as primary wall: A paracrystalline protein/glycoprotein S-layer is the most common and often sole wall structure.
• Slime layers: Present in certain species to mediate cell-cell contact and adhesion.
• Extracellular sheaths: Some species have additional carbohydrate or protein layers exterior to the S-layer.
• Double membrane: A rare few species possess an outer lipid membrane.

What is pseudomurein (pseudopeptidoglycan), and how is it chemically assembled?

• Definition: A peptidoglycan-like polymer found only in select methanogenic archaea.
• Carbohydrate backbone: Alternating subunits of N-acetylglucosamine (NAG) and N-acetyltalosaminuronic acid (NAT) connected by $\beta(1,3)\text{-glycosidic bonds}$.
• Cross-linking: Peptide cross-links are made exclusively of L-amino acids (unlike the D-amino acids in bacterial peptidoglycan).

Why are Archaea naturally resistant to penicillin and lysozyme?

• Penicillin: Targets transpeptidase enzymes specific to bacterial peptidoglycan assembly.
• Lysozyme: Cleaves $\beta(1,4)\text{-glycosidic bonds}$ found in peptidoglycan.
• Resistance mechanism: Archaea completely lack peptidoglycan (and pseudomurein contains $\beta(1,3)$ linkages), rendering both agents ineffective.

What are the structural features and dimensions of archaeal S-layers?

• Thickness: Approximately $70\,\text{nm}$ thick.
• Anchoring: Directly tethered to the plasma membrane.
• Architecture: Appears as a geometric lattice from the surface and a protein canopy in cross-section.
• Modifications: Extensively decorated with carbohydrate chains (glycoproteins).

How do Archaea maintain cellular shape and mechanical integrity without peptidoglycan?

• Crystalline S-layer: Provides mechanical support against osmotic pressure.
• Internal cytoskeleton: Cytoskeletal filament networks maintain cell morphology.
• Alternative wall polymers: Pseudomurein and heteropolysaccharides provide structural rigidity in specific taxa.
• Osmotic adaptation: Regulation of internal solute concentrations.

How do extremely halophilic Archaea prevent osmotic collapse without peptidoglycan?

• Solute accumulation: Actively concentrate high levels of internal inorganic ions (such as potassium, $K^+$).
• Equilibrium approach: By matching internal osmolarity with hypersaline surroundings, they eliminate net turgor pressure, preventing cellular collapse.

What internal structures are shared between the bacterial and archaeal cytoplasm?

1. $70\text{S}$ Ribosomes
2. Nucleoid (containing circular chromosome)
3. Plasmids
4. Cytoskeletal protein networks

How do archaeal ribosomes compare with bacterial and eukaryotic ribosomes?

• Sedimentation coefficient: Like bacteria, they are $70\text{S}$ (composed of $50\text{S}$ and $30\text{S}$ subunits).
• Sequence composition: Nucleotide sequences are distinct from both bacteria and eukaryotes.
• Protein homology: Archaeal ribosomal proteins are more structurally homologous to eukaryotic ribosomes than bacterial ones.
• Antibiotic sensitivity: Unaffected by antibiotics that inhibit bacterial translation (e.g., streptomycin, chloramphenicol).

What molecular features indicate Archaea are more closely related to Eukarya than to Bacteria?

• Translation machinery: Shared ribosomal protein subunits and eukaryotic-like initiation/elongation factors.
• Initiator tRNA: Both Archaea and Eukarya initiate protein synthesis with methionine.
• Transcription apparatus: Archaeal RNA polymerase and transcription factors closely resemble eukaryotic RNA Polymerase II.
• Genetic packaging: Archaea utilize histone-like proteins to organize circular genomic DNA.

What are the initiator amino acids for translation across the three domains of life?

• Archaea: Methionine (Met)
• Eukarya: Methionine (Met)
• Bacteria: N-formylmethionine (fMet)

What are the major cytoskeletal and division protein homologs found in Archaea?

1. FtsZ: Tubulin homolog responsible for Z-ring assembly during cell division.
2. Crenactin: Actin homolog in Crenarchaeota that maintains rod cell shape.
3. Cdv system (CdvA, CdvB, CdvC): Cell division machinery homologous to eukaryotic ESCRT-III complexes.
4. MreB-like proteins: Actin homologs involved in cell envelope morphogenesis.
5. MinD/ParA homologs: Partitioning ATPases that govern plasmid and chromosome segregation.

What are the structural features and biological roles of archaeal cannulae and hami?

• Cannulae:
  • Hollow, heat-stable glycoprotein tubules found on marine thermophiles (e.g., Pyrodictium).
  • Interconnect daughter cells into extensive multicellular networks after division.
• Hami:
  • Filamentous appendages terminating in a three-pronged grappling-hook structure.
  • Facilitate strong cell adhesion to surfaces and mediate biofilm formation.

How does the archaeal motility organelle (archaellum) differ from the bacterial flagellum?

• Structure: Built from archaellin subunits; filaments are thinner, non-hollow, and assemble from the base.
• Energy requirement: Directly energized by ATP hydrolysis (bacterial flagella utilize proton motive force).
• Motility dynamics: Reverses direction directly (forward and backward) rather than relying on classical run-and-tumble behavior, driving high-velocity swimming.