Topic 3 - Archaea Flashcards
archaea look like eukarya/bacteria?
bacteria
are archaea and bacteria genetically similar?
NO
any known archaeal human pathogens?
NO
archaea can form ___ shapes
bizarre
Who began archaeal studies (phylogenetic trees)
Woese and Fox
what did archaea used to be called?
Archaeobacteria
what were the first “archaea” discovered?
methanogens
are archaea the only ones that can do methanogenesis?
YES
how big are archaea?
~0.5-5microns in diameter
- varies a lot! (100micron in some species)
shapes of archaeal cells
- rods, cocci, spirals (like bacteria)
- irregular shapes
- rectangular shapes
- squares (high surface area)
do archaea have chloroplasts?
NO they could be gas vacuoles but NO chloroplasts!
archaea: cytoplasm
- cytoplasm molecules similar to bacteria
- inclusion bodies (e.g., gas vacuoles) are in some species
- single circular chromosomes & no membrane-bound nucleus
- many of DNA replication enzymes of archaea “look” like eukarya’s
- development of histones may have been an early “branch point event” in evolution of archaea and eukarya (diff in archaea from eukarya)
Archaea: what is gas vacuole an example of?
inclusion bodies
difference between eukaryal and archaeal nucleosomes?
Eukaryal:
- 160-nucleotide-pair length of DNA
- octamer of histone proteins
Archaeal:
- 60-nucleotide-pair length of DNA
- tetramer of histone proteins
archaea: cytoskeleton
- cytoskeletal homologues found in both eukarya and bacteria
- i.e. kind of close to both bacteria and eukarya, but they all have cytoskeletal elements
archaea: cell envelope
- all archaea have a plasma membrane
- most have cell walls, most do NOT have outer membrane (like G+ve)
- both structures are different from equivalents in other domains
archaea vs. eukarya/bacteria bilayer plasma membrane
archaea:
- glycerol 1-phosphate (isomer of G3P)
- ether linkage (stability!)
- phytanyl (repeating isoprene units - isoprene are 5Cs)
- monolayers in some archaea (stability)
bacteria/eukarya:
- glycerol 3-phosphate
- ester linkage
- fatty acid chain
monolayers in some archaea (stability)
- phosphoglycerol molecule on both ends
- tetra ether lipids
- v stable, often in archaea living in high temp
- can include rings too
archaea: cell wall
Parts + made of?
composed of pseudomurein
- polysaccharide, similar to peptidoglycan
- N-acetylglucosamine (NAG) and N-acetyltalosaminuronic acid (NAT)
- Beta-1,3 linkages; lysozyme insensitive
- L-amino acids
(compared to peptidoglycan; Beta-1,4; NAG + NAM; D-amino acids in bacteria)
archaea: cell surface
- S layer (protection against predation/viruses, mediate adhesion)
- cannulae
– HOLLOW glycoprotein tubes
– link cells together to form a complex network “stay in touch”
flagellus vs archaellum
archaellum = archaeal flagellum
- flagellum (solid)
- grows from base, not tip
- uses ATP
Ignicoccus
- has outer membrane and periplasm like in G-ve cells
- ATP synthase enzymes are housed in outer membrane
- unusual even for archaea
4 major phyla of archaea
- Euryarchaeota
- Crenarchaeota
- Thaumarchaeota (low temp, formerly Crenarchaeota, AMMONIA-oxidizing)
- Nanoarchaetoa (small)
Crenarchaeota characteristics
- extreme temp, pressure, acidity
- many are thermophiles or hyperthermophiles
- acidophile
- barophiles (high pressure)
Crenarchaeota adaptations for survival
- tetraether lipids/lipid monolayers (pack biphytanyl into monolayer)
- modified proteins
– more-helical regions
– more salt bridges/side chain interactions
– more arginine/tyrosine
– less cysteine/serine
(there are more salt bridges in these more prevalent proteins) - strong chaperone protein complexes
- thermostable DNA-binding proteins
- reverse DNA gyrase enzyme to increase DNA supercoiling
mesophile meaning
thrives in moderate temp
Euryarchaeota characteristics
- halophiles (SALT), halobacterium (e.g., Great Salt Lake, Dead Sea, evaporation ponds)
- require NaCl conc > 1.5M
- varies: 5-34% salinity
- phototrophic (no chlorophyll, or electron transport chain (no respiration involved))
hypo/hyper/isotonic solution?
hypotonic = low salt (net water gain)
hypertonic = high salt (net water loss)
isotonic = equiv salt (no net change)
Euryarchaeota adaptations
- very high intracellular [K+] offsets very high extracellular [Na+] (K+ acts as a “compatible solute”
- high intracellular K+ conc can cause protein denaturation, split dsDNA
– protein denaturation: highly acidic proteins that remain more stable in high salt env
– DNA denaturation: higher GC content (stronger, 3 Hbond)
Bacteriorhodopsin
- Euryarchaeota
- not red on its own (red pigment - retinal - that captures light)
- harnesses light energy and produces a proton motive force
- captures light = cis -> trans
Euryarchaeota
- METHANOGENS (only ones that can make methane)
– reduce CO2 with H2, produce CH4 and H2O; energy released can be used to fix C; strict anaerobes (e.g., in gut, swamp)
– makes gas in humans and combustible air in swamps
– methanogens have a lot of diversity but share a common metabolic property - halophiles
Volta experiment
- Volta performed this exp ~200 ya
- inverted funnel traps CH4 from methanogenic freshwater sediments
- fire ignites
methanogen habitats (6)
- anoxic sediments (no O2)
– marshes/swamps, lakes, rice paddies, moist landfill - animal digestive tracts (myth: ruminant animals BELCH methane, not fart)
– ruminant animal rumen (cattle, sheep, elk, etc.)
– cecal animal cecum (horses, rabbits)
– large intestine of monogastric (humans, swine, dogs) - geothermal H2/CO2 sources
– hydrothermal vents - artificial biodegradation facilities
– sewage digestors - endosymbionts of anaerobic protozoa
- termite gut symbionts
TACK superphylum
Thaumarchaeota
- now Nitrososphaerota
- separate phylum for many mesophilic crenarchaeotes
- ammonia oxidizing, fixing CO2 - important in N cycle
- mesophiles and psychrophiles
- important for biogeochemical cycling of C and N in ocean
Aigarchaeota
- none cultivated
- one genome avail - thermophile
Crenarchaeota
Korarchaeota
- distinct 16S rRNA sequence from hydrothermal env
- none cultivated
- one genome avail
mesophiles vs psychrophiles
mesophiles: 15-40 deg C
psychrophiles: <15 deg C
DPANN superphylum
Nanoarchaeota (SMALL)
- Nanoarchaeum equitans (riding on back) - sole isolated membrane so far
- distinct 16S rRNA gene sequences
Common features:
- Very small cell size (<1 μm)
- Small genomes (~1 Mb, can be less!)
- Restricted metabolisms, unable to generate basic building blocks
- Interspecies interactions (mutualistic or parasitic?)
Ignicoccus (Crenarchaeota) and Nanoarchaeum (Nanoarchaeota)
- Nanoarchaeum equitans -> obligate parasite (debatable) of crenarchaeote, Ignicoccus
– no metabolic genes, only genes for replication, transcription, translation
– a lot resources need to come from Ignicoccus (ex. ATP)
– makes an S layers but Ignococcus can NOT (mutualistic?)
Asgard superphylum
(all uncultivated)
- Lokiarchaeota
- Thorarchaeota
- Odinarchaeota
- Heimdallarchaeota
- represents the closest prokaryotic relatives of eukaryotes
Lokiarchaeota/Thorarchaeota
- thermophilic archaea - distinct from Crenarchaeota
- group w/eukaryotes on some phylogenies
(possible closest ancestor to eukaryotes) - genome shows euk-like proteins for cell compartmentalization - early stages of complex cell evol?
proposed origin of eukaryotes?
- Eukaryote-Asgard common ancestor
- Eukaryote-alphaproteobacterium common ancestor
those two combine (endosymbiosis)
