Unit 5

Question 1

5 phyla of Archaea

Answer 1

Euryarchaeota
Thaumarchaeota
Nanoarchaeota
Korarchaeota
Crenarchaeota

Question 2

what is the phylogenetic tree based on?

Answer 2

16S r RNA

Question 3

what is the evolution of Archaea driven by?

Answer 3

HGT between phyla

Question 4

what are the common traits shared by all Archaea?

Answer 4

• ether linked lipids
• lack of peptidoglycan in cell walls
• structurally complex RNA polymerases
• RNA polymerase resemble eukaryotic enzymes
• extreme metabolic diversity
• chemoorganotrophic or chemolithotrophic organisms
• aerobic and anaerobic organisms

Question 5

Euryarchaeota

Answer 5

halophilic (salt-loving obligate aerobes)
methanogens (strictest anaerobes)
hyperthermophilic
acidophilic
extremophilic and non-extremophilic

Question 6

what are the 2 organisms representing halophilic archaea and their characteristics?

Answer 6

halococcus
haloquadratum
- usually aerobic
- anaerobic is possible
- no fermentation

Question 7

halococcus

Answer 7

largest plasmids in nature
plasmid is 30% of total cellular DNA

Question 8

haloquadratum

Answer 8

gas vesicles for floating in hypersaline enviro

Question 9

what do organisms do in high solute enviro?

Answer 9

either accumulate or synthetize solutes intracellularly (compatible solutes)

Question 10

function of compatible solutes?

Answer 10

prevent dehydration under conditions of high osmotic strength

Question 11

what do certain Euryarchaeota do if they do not synthesize or accumulate organic compounds?

Answer 11

pump large amounts of K+ from enviro into cytoplasm
- different in K+ levels maintains pos water balance

Question 12

hyperthermophilic organisms

Answer 12

thermococcus
thermoplasma

Question 13

thermoplasma

Answer 13

• cell wall lacking
• small genome
• DNA in globular eukaryotic-like structures
• 55C
• pH 2
• sulfate respiration
• No sterols
• Lipoglyan cell wall

Question 14

methanogens

Answer 14

produce methane as integral part of energy metabolism
- major source of biogenic methane in nature

Question 15

Methanocaldococcus jannaschii

Answer 15

model methanogen
enzymes for methanogenesis
central metabolic enzymes and cell division machinery- resembles bacterial structures
transcription and translation genes resembles eurkayotic organisms

Question 16

acidophilic organisms

Answer 16

ferroplasma
picrophilus

Question 17

Ferroplasma

Answer 17

cell-wall lacking
strong acidophile
non thermophile
Fe2+ as e donor

Question 18

Picrophilus

Answer 18

phylogenetic relative Ferroplasma
more acidophilic than Ferrroplasma

Question 19

Methanopyrus

Answer 19

hyperthermophilic methanogen
unique lipids- bacterial and archaeal features
archaeal- glycerol side chain with saturated phytanyl
bacterial- glycerol side chain with fatty acids
- unusual lipids may help stabilize the cytoplasmic membrane at its high growth temps

Question 20

Thermococcus

Answer 20

organic substrates
sulfur respiration

Question 21

Nitrosopumilus maritimus

Answer 21

• Thaumarchaeota
  AOA
  CO2 fixation
• grows at NH3 concentrations that are 100x lower than those required by bacterial nitrifiers
• all isolated species are chemolithotrophic ammonia-oxidizers
• can grow at v low concentrations of NH3
• unique lipid called crenarchaeol
• major role in controlling NH3 levels in oceans

Question 22

Nanoarchaeum equitans

Answer 22

• Nanoarchaetoa
• one of the smallest
• no growth in pure culture
• growth only when attached to surface of host
• host - Ignicoccus hospitalis (hyperthermophilic species of Crenarchaeota- hospitable fireball)
• grows at high temps
• metabolically dependent on host

Question 23

ignicoccus

Answer 23

performs H2 oxidation and S^0 reduction along with CO2 fixation

Question 24

what genes did Nanoarchaeum equitans lose?

Answer 24

• amino acids biosynthesis
• nucleotides production
• coenzymes
• ATPase genes

Question 25

what genes remained in Nanoarchaeum equitans?

Answer 25

- lipids biosynthesis - glycolysis - molecular machinery - DNA repair enzymes

Question 26

Korarchaeum cryptofilum

Answer 26

- Korarchaeota - cryptic filament of youth - obligately anaerobic chemoorganotroph - hyperthermophile - inability of K. cryptofilum to synthesize molecules essential for its own growth may be explained by evolution of mutual dependence as described by Black Queen hypothesis - incapable to synthetize necessary molecules for their growth - evolution of mutual dependence

Question 27

Black Queen hypothesis

Answer 27

evolutionary strategy to lose costly functions in favor of improving growth efficiency - results in mutants becoming obligately dependent upon provider to produce necessary resource

Question 28

Crenarchaeota

Answer 28

- hyperthermophiles - species that grow optimally above boiling point of water - chemolithotrophic autotrophs - primary producers in extremes

Question 29

Eocyte tree

Answer 29

- 2D - 2 domains - ancestor of eukaryotes was thermophilic organism that did not have nucleus - organisms called eocytes - 1 branch with nucleus separated (Karyocytes) - branch 2 was prokaryotic (B and A) - unrooted

Question 30

3D tree

Answer 30

- prokaryotes branched to B and A - eukaryotes developed as separate lineage - all biochemical data, DNA and RNA polymerases that were added late onto the tree were in favor of model - unrooted

Question 31

what do Eukarya and Archaea have in common?

Answer 31

ancestral branch

Question 32

was the branch the same for eukarya, archaea and bacteria?

Answer 32

no

Question 33

are archaea distantly related to bacteria?

Answer 33

yes

Question 34

what are archaea and bacteria?

Answer 34

not monophyletic groups

Question 35

what was the last group that bridged A and E?

Answer 35

Asgard

Question 36

what group has sequence homology to core domains in eukaryotic endosomal sorting complexes proteins?

Answer 36

Cell division machinery in Crenarchaeota

Question 37

what was discovered in Asgard arachae?

Answer 37

homolog of eukaryotic ESP

Question 38

ESCRT

Answer 38

- simple, ancient origins - many archaeal have homologues of ESCRT-III and Vps4

Question 39

roles of ESCRT-III and Vps4

Answer 39

role in cytokinesis, extracellular vesicle formation and viral exit

Question 40

what is an example of homologue systems in Ascard archaea?

Answer 40

ESCRT machinery