Lecture 20

Question 1

1. What two scientist were responsible for the discovery of Archaea?
2. What are the four major phenotypic types?
3. What five groups of organisms are united by SSU gene sequence similarity?

Answer 1

1. Ralph Wolfe & Carl Woose
2. Extreme halophiles, methanogens, extreme acidophiles (Low pH environment), and hyperthermophiles.
3. Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota.

Question 2

Archaea United by Various Cellular Traits

1. What are Archaea cell membranes composed of?
2. What do they lack in their cell wall?
3. How else do they differ from Bacteria?
4. What are their DNA replication proteins similar to?

Answer 2

1. Composed of isoprenoid-based lipids (isoprenoid chain joined by an ether linkage to glycerol).
2. Lack PTG in their cell wall. Cell walls instead are composed of S-layers (protein subunits in regular arrays), glycoprotein, methanochondroitin, or pseudomurein (sugars other than muramic acid).
3. Archaea have different kind of DNA-dependent RNA polymerase (transcription, mRNA synthesis) more similar to that of Eukarya, with many subunits, and sequence homolgy of some subunits between Archaea and Eukarya, transcription initiation also like Eukarya starting at TATA-box.
4. DNA replication proteins are more similar to Eukarya than to Bacteria.

Question 3

1. How are Archaea insensitive to many antibiotics that inhibit Bacteria and Eukarya?
   
   1. Give Examples

Answer 3

1. Examples:
   
   1. Inhibitors of Bacteria cell wall synthesis (penicillin, cycloserine, vancomycin, cephalosporin) not effective against Archaea.
   2. Not sensitive to rifampicin, which blocks Bacteria DNA-dependent RNA polymerase.
   3. Protein synthesis not blocked by chloramphenicol, cycloheximide, streptomycin, which interfere with the function of the ribosome of Bacteria.

Question 4

1. What are some kinds of places Archaea live?

Answer 4

1. Different environments:
   
   1. Salt lakes (saturated NaCl and NaCO₃).
   2. Hot springs (really hot, like 70ºC and above, that have lots of sulfur and iron compounds).
   3. Hydrothermal vents (deep and shallow seas; hot, anaerobic, lots of reduced inorganic sulfur and iron compounds).
   4. Acid mine drainage (hot and a very low pH)
   5. Anaerobic sediments.

Question 5

1. What places are Extreme Halophiles adapted to live in?
2. What are some examples of hypersaline environments?
3. What levels of salt to they generally require?
   
   1. At what levels are their optimal growth?
   2. What levels are they killed?
   3. What is an example?

Answer 5

1. Adapted to living at the high salt concentrations (1.5-4.0 M salt) and high osmotic pressures of saline and hypersaline environments.
2. Natural inland salt lakes like the Dead Sea, 340 g salt/liter.
   
   1. Great Salt Lake, 333 g salts/liter
   2. Salted food products - salted fish, animal hides treated with salt for preservation, saline soils, subterranean brines (salt deposits), sea-salt drying pans (salterns)
3. Generally require 1.5 M NaCl (about 9%, 90 g/l) or higher for growth.
   
   1. Most species require 2 to 4 M NaCl (12-23%) for optimal growth.
   2. Damaged or killed at NaCl concentrations below 1.5 M (seawater 0.6 M, 3.5% (35 g/l) NaCl)
   3. Halobacterium salinarum: aerobic, heterotrophic (uses amino acids and organic acids as carbon/energy sources). Requires high levels of Na⁺ for growth, not replaceable by K⁺ or other cations.
      
      1. Cell wall is composed of glycoprotein with an exceptionally high content of acidic amino acids (glutamate, aspertate). Na⁺ shields the negative charges on the carboxyl groups.
      2. If Na⁺ drops, the negative charges repel, and the cell lyses.

Question 6

1. Why are salt drying pans red or pink in color?
2. Under what conditions is bacteriorhodopsin (similar to vertebrate eye pigment rhodopsin) synthesized?
3. How does this light-driven ATP synthesis work?

Answer 6

1. Light-driven ATP synthesis leads to red pigments in Extreme Halophiles.
2. Under low oxygen conditions.
   
   1. A light-driven proton pump (coupled via PMF to ATPase). Bacteriorhodopsin (protein) and retinal (a carotenoid-like molecule associated with bacteriorhodopsin). Do not use chlorophyll, so this is not true photosynthesis.
3. How it works:
   
   1. Retinal absorbs light (570 nm, green) and is converted from the trans (which is protonated) to the cis configuration.
   2. That conversion causes the proton to be transferred to the protein, causing a conformational change in the protein that ejects the proton from the cell.
   3. Release of the proton allows the retinal to shift back to the trans configuration, which then picks up another proton (becomes protonated) from the cytoplasm.
   4. The formation of the proton gradient leads to ATP synthesis via the cell’s proton-translocating ATPase.
   5. This process does not use chlorophyll, so it is different from chlorophyll-based photosynthesis.

Question 7

1. What are Methanogens?
2. Where are they found?
3. What do they make as a waste product?

Answer 7

1. Strict anaerobes
2. Found in most anaerobic habitats waterlogged soils, rice paddies, lake and marine sediments, marshes, intestinal tracts of animals.
3. Methane is a waste product of metabolism of these bacteria. Methane is a flammable gas, and the process of methanogenesis allows these cells to generate ATP.

Question 8

1. What are the three classes and reactions of compounds that methanogens can use as a substrate for methanogenesis?

Answer 8

1. CO₂ type substrates (CO₂, formate, CO)
   
   1. CO₂ + 4H₂ → CH₄ + 2H₂O
2. methyl substates (methanol, methylamine, etc.)
   
   1. CH₃OH + H₂ → CH₄ + H₂O
3. acetotrophic substrates (acetate, pyruvate)
   
   1. CH₃COO^- + H₂O → CH₄ + HCO₃-

Question 9

1. What is an example of a Methanogen?
2. How big is their genome?
3. How many genes does it have?
4. How does it survive with such a small genome?
5. What Hot Springs to the pictures show?

Answer 9

1. Methanocaldococcus jannaschi
   
   1. Thermophilic, from submarine hydrothermal vent.
   2. Uses only CO₂ + 4H₂ → CH₄ + 2H₂O
2. 1.66 Mb, circular genome
3. 1700 genes
   
   1. central metabolic pathway genes similar to Bacteria.
   2. core molecular process genes (e.g., tanscription, translation similar to Eukarya)
   3. 40% of genes (including genes for methanogenesis) no counterpart in Bacteria or Eukarya; novel cellular functions not present in Bacteria or Eukarya
4. Exist in environments that are abundant in nutrients, lack competition and the environment is stable.
5. Pictures:
   
   1. sulfur-rich, acidic hot spring - H₂S and S⁰ oxidized to H₂SO₄
   2. sulfur-rich, acidic hot spring - H₂S and S⁰ oxidized to H₂SO₄
   3. boiling hot spring - neutral pH
   4. iron-rich, acidic hot spring

Question 10

1. What is the growth temperature optimum for Hyperthermophiles?
2. What is an example?
   
   1. What is their cell shape?
   2. What is their pH optimum?
   3. What is their cardinal temperature?
   4. What do they oxidize?
   5. Where are they found?
   6. What are its chemical conditions?

Answer 10

1. 75-80°C or higher
2. Sulfolobus acidocaldarius (Crenarchaeota)
   
   1. irregular lobed cell
   2. 2-3, survives from pH 1-5
   3. 55°C (min), 75°C (opt), 87°C (max)
   4. aerobe, oxidizes H₂S and S⁰ to H₂SO₄, fixes CO₂ (autotrophy) or can use organic carbon compounds (heterotrophy).
   5. Found in sulfotaras: a kind of terrestrial hot spring with hot gases like H₂S and steam.
   6. lots of sulfur and hydrogen. Steam rich in H₂S, often acidic (pH 2) due to oxidation of H₂S and S⁰ to H₂SO₄. Temperatures up to 100°C.

Question 11

1. Hyperthermophile Example 2
   
   1. Cell shape?
   2. What is their pH optimum?
   3. What is their cardinal temperature?
   4. What are they resistant to?
   5. What do they oxidize?
   6. Where are they found?
   7. What are the chemical conditions?
   8. What is black material?

Answer 11

1. Pyrolobus Fumarii
   
   1. Lobed coccus
   2. pH optimum 5.5
   3. temp. 90, 106, 113°C
   4. resistant to (no growth, but not killed by) 121°C for 1 hour survives autoclaving.
   5. anaerobe, oxidizes H₂ with the reduction of NO₃- to NH₄+ or S₂O₃^2- to H₂S
   6. found in hydrothermal vents, areas of new sea floor generation.
   7. vent water loaded with H₂S and other reduced minerals (no oxygen). When vent water hits seawater, cools (350°C down to 5°C lower), various metalic sulfides precipitate out (sulfides of iron, copper, zinc), and Ca²⁺ precipitates with SO_4​^2- of seawater.
   8. metal sulfides and calcium sulfate.

Question 12

1. Example 3 of Hyperthermophiles:
   
   1. What are their host?
   2. What are Nanoarchaeum dependent on their host for?
   3. What is their genome size?
   4. Where are they found?

Answer 12

1. Nanoarchaeum equitans, an obligately symbiotic Archaea (Nanoarchaeota).
   
   1. Ignicoccus hospitalis (Crenarchaeota), which obtains energy by using H₂ to reduce S⁰
   2. Unable to reproduce independently, dependent on Ignicoccus for: amino acids, nucleotides, coenzymes, lipids, and catabolic enzymes (glycolosis).
   3. Genome size: 490,885 nucleotides (0.5 Mb). One of the smallest cellular genomes. An example of reductive evolution. 552 proteins encoded: DNA replication enzymes, transcription proteins, translation proteins, and DNA repair enzymes.
   4. Isolated from a submarine hydrothermal vent near Iceland.

Question 13

Thermal Limits of the Biosphere

1. At what temp. does Pyrolobus live at?
   
   1. Strain 121?
   2. Methanopyrus kandleri?
2. What is thought to be the limit?

Answer 13

1. 113°C
   
   1. 121°C
   2. 122°C
2. 150°C is the limit for life because ATP is instantly degraded at this temperature.