L3 - Archaea

Archaea were previously thought to be?

Bacteria

What happened to determine archaea as its own separate domain of life at the end of the 20th century?

Comparing ribosomal RNA sequences.

DNA - archaea vs bacteria

In most cases, archaeal DNA exists, like in bacteria, as single circular chromosomes.

Unlike in bacteria, archaeal DNA wraps around DNA-binding proteins (histones). Same in eukaryotes.

All archaea possess what in their structure?

Plasma membrane & most have a cell wall.

The chemical position of the archaeal cell envelope is significantly similar or different from other 2 domains in several ways?

Different

Archaeal lipids vs bacterial lipids (what kind of linkage?)

• Archaeal lipids have ether linkages: offer incr stability

• Bacterial lipids have ester linkages

Distinctive properties of archaea (4)

1. what do they look like?

2. where are they?

3. pathogens (yes/no)?

4. shape?

1. archaea look like bacteria: genetic analyses show them to be different

2. many live in some of the most inhospitable places on earth

3. no known archaeal human pathogens

4. bizarre shapes possible for some archaea

Phylogeny of archaea

Comparisons of rRNA gene sequences can establish phylogenetic “trees”. Woese & Fox began these studies in the 1970s.

First “archaea” discovered = ?

Methanogens

Is archaea more similar to bacteria or eukarya?

eukarya (used to be bacteria though back when we didn’t know)

Halobacterium salinarium

Notable growth requirements & natural habitat

1. 3-5 M NaCl

2. Dead Sea, salted food

Pyrococcus furiosus

Notable growth requirements & natural habitat

100 C, hydrothermal vents

Picrophilus oshimae

Notable growth requirements & natural habitat

0.7 pH

Sulfur-rich, volcanic regions

Methanogenium frigidum

Notable growth requirements & natural habitat

15 C

Ace Lake, Antarctica 

Size of archaea

Usually 0.5-5 μm in diameter. Can vary greatly (N. equitans = 0.4 μm in diameter. Thermoproteus spp. can be 100 μm long)

Shapes of archaeal cells (4)

1. rods, cocci, spirals (similar to bacteria)

2. irregular shapes (sulfolobus spp.)

3. rectangular shapes (thermoproteus spp.)

4. squares (haloquadratum walsbyi)

Cytoplasm in archaea

Cytoplasm molecules similar to bacteria.

Cytoplasm in archaea - what have been observed in some species?

Microcompartments/inclusion bodies (e.g., carbon storage, gas vacuoles) 

Cytoplasm in archaea - what kind of chromosomes and what do they lack?

single circular chromosomes, lack a membrane-bound nucleus

Cytoplasm in archaea - many of the DNA replication enzymes of archaea look like?

those of eukarya

Cytoplasm in archaea - development of histones may have been…?

An early branch point event in the evolution of archaea & eukarya

Cytoplasm in archaea - are there histones?

Yes - histones are protein structures that DNA wraps around (different in archaea & eukarya)

Cytoskeletal homologues found in which domains?

Archaea & bacteria, eukarya

Cytoskeleton: what resembles eukaryal actin?

Ta0583, actin homolog in thermoplasma acidophilum

Cytoskeleton: what resembles this closely in bacteria?

Cytoskeletal proteins from M. thermoautotrophicum and M. kandleri

cytoskeleton

All archaea do not possess a plasma membrane. T/F?

False

Do archaea have a cell wall and outer membrane?

Most do, yet most don’t have an outer membrane.

Archaea cell wall & outer membrane are ___ compared to their equivalents in other domains.

different

Plasma membrane

Unique bilayer construction

• glycerol-1-phosphate (isomer of G3P)

• phytanyl side chains (repeating isoprene units)

• ether linkages (stability)

There are monolayers in some archaea. What does this mean?

• what is found?

• stable vs unstable? where is it found?

• phosphoglycerol molecule on both ends

• very stable, often seen in archaea living in high-temp

plasma membrane - archaea vs bacteria & eukarya

Ignicoccus

• structure

• ATP?

• Is it usual or unusual?

Has an outer membrane and periplasm similar in arrangement to Gram-negative cells. ATP synthase enzymes are housed in outer membrane. Unusual, even for archaea. 

Archaea cell wall are composed of?

Archaea cell surface (2)

1. s-layer

2. cannulae

Archaea cell surface - s-layer

• protect against predation/viruses

• mediate adhesion

Archaea cell surface - cannulae

• hollow glycoprotein tubes

• link cells togehter to form a complex network

Do archaea have peptidoglycan cell walls?

no

What are cell walls made of for archaea?

Pseudomurein (“pseudopeptidoglycan”) —similar to peptidoglycan.

Cell walls for archaea vs bacteria - pseudomurein vs peptidoglycan

For archaea, differs in that its backbone is composed of alternating molecules of NAG & NAT, which are connected by β-1,3 glycosidic linkages instead of β-1,4 linkages in bacterial peptidoglycan.

First recognized archaeal phyla (2)

Crenarchaeota & euryarchaeota

Most cultured crenarchaeotes are? Many are also?

Thermophiles or hyperthermophiles, acidophiles

Hyperthermophiles possess what ability?

Molecular chaperones that refold denatured proteins

Thermophiles or hyperthermophiles, acidophiles special adaptations

Lipid monolayer plasma membranes & thermostable proteins, which allow them to withstand conditions of extreme heat.

2 main groups of euryarchaeotal archaea

Halophiles & methanogens

Halophiles - where do they live?

Salt-loving archaea that grow in environments with a NaCl concentration of 1.5M or higher.

Halophiles - special adaptation to osmosis (water flows to where ion concentration is highest = high salt environment is a risk to cells that lose too much water & go into osmotic shock)

Halobacterium salinarum - maintains osmotic balance by keeping a higher internal concentration of K+.

Many halophiles are?

Phototrophic

Unlike most phototrophic microbes, halophiles possess…?

No chlorophyll pigments

Can halophiles adapt to their environment? Example

Yes - they can grow on organic carbon when oxygen is high, but they can also adapt to low oxygen (and perhaps low carbon) conditions by generating a proton motive force for making ATP by using a molecule called bacteriorhodospin

Methangens

Archaea that produce methane

Where do methanogens live?

Strictly anoxic (no oxygen) conditions, like lake sediments or various gastroinestinal tracts of animals.

3 new phyla now recognized

1. thaumarchaeota

2. korarchaeota

3. nanoarchaeota

Diversity of archaea

4 major phyla

4 major phyla

1. euryarchaeota

2. crenarchaeota

3. thaumarchaeota (low temp, former crenarchaeota, many oxizide ammonia)

4. nanoarchaeota (more than 1 member now!)

Many other phyla have been proposed other than the 4 major ones. What are they? (3)

1. korarchaeota (from rRNA sequences obtained from nonculturable microbes)

2. aigarchaeota

3. and many other candidate phyla

Crenarchaeota & types (2)

Many are thermophiles or hyperthermophiles.

Acidophiles, barophiles

acidophiles

thrive in low pH (e.g., acid main drainage)

Barophiles

Thrive in high pressures (e.g., bottom of ocean)

How do crenarchaeota adapt to survive to high temps? (5)

1. Tetraether lipids/lipid monolayers

2. modified proteins

3. strong chaperone protein complexes

4. thermostable DNA-binding proteins

5. reverse DNA gyrase enzyme to increase DNA supercoiling

How do crenarchaeota adapt to survive to high temps?- Modified proteins (4)

1. more a-helical regions

2. more salt bridges/side chain interactions

3. more arginine/tyrosine

4. less cysteine/serine

know the proportions rougly

Eyrtarchaeota (halophiles) (e.g., halobacterium)

• where are they found? describe the environment & give 2 examples

• require NaCl > 1.5 M

• Live in high salt environments. E.g., Great Salt Lake in Utah & Dead Sea btwn Israel & Jordon

• Areas vary btwn 5-34% salinity

• oceans is typically 3.5% salinity (0.6M)

Halobacterium have very high what?

High intracellular [K+] offsets very high extracellular [Na+]

Halobacterium’s high intracellular K+ concentration can cause what?

Denaturing of proteins & split dsDNA. 

DNA denaturing → ?

Higher GC content (stronger bonds) (guanine cytosine)

Protein denaturing → ?

Highly acidic proteins that remain more stable in high salt environments.

Halobacterium are ____.

Phototrophic

Phototrophic

W/o chlorophyll or electron transport chain

Bacteriorhodospin

Harnesses light energy & produces a PMF (gives off reddish blue b/c retinol)

Euryarchaeota (Methanogens)

• what do they reduce & produce?

• energy released can be used to…?

• strict ___?

• found where?

• reduce CO2 w/ H2, produce CH4 & H2O

• fix C

• anaerobes

• human gut & swamp sediments

Methane produced forms what in humans & swamps?

Gas, combustible air

Methanogens possess a great deal of? But share?

Diversity, common metabolic property

Volta experiment

Volta performed this experiment ~200 yrs ago. Inverted funnel traps CH4 from methanogenic freshwater sediments. Flame ignites.

Methanogen habitats (6)

• describe habitats

1. Anoxic sediment

   1. Marshes, swamps, lakes, rice paddies, moist landfills

2. Animal digestive tracts

   1. ruminant animal rumen (cattle, sheep, elk, deer, camels)

   2. cecal animal *cecum (horses, rabbits)

   3. large intestine of monogastrals (humans, swine, dogs)

3. Geothermal H2/CO2 sources

   1. Hydrothermal vents

4. Artificial biodegradation facilities

   1. sewage sludge digestors

5. endosymbionts of anerobic protozoa

6. termite gut symbionts

Archaea classification

TACK superphylum (4)

Thaum, aig, cren, kor archaeota

Thaumarchaeota

Now nitrososphaerota. Separates phylum for many mesophilic crenarchaeotes. Ammonium oxidizing - important in N cycle.

Mesophiles temp vs psychrophiles

Mesophiles & psychrophiles are important for?

Biogeochem cycling of C and N in ocean.

Possible some members belong in new phylum - mesophiles and psychrophiles

• cenarachaeum symbiosum resides in marine sponge

• shares some genes with crenarchaeotes but also some w/ euryarchaeotes

• belongs to the thaumarchaeota

Emerging phyla (2)

kor, aigarchaeota

Korarchaeota

• # of rRNA sequences?

• cultivation?

• genome?

• Distinct 165 rRNA sequences obtained from hydrothermal environments

• no species have been cultivated yet

• 1 genome available

Aigarchaeota

• cultivation?

• genome?

• no species have been cultivated yet

• 1 genome available - thermophile

DPANN superphylum

ultrasmall archaea

Nanoarchaeota

• isolation?

• genomes?

• size?

• rRNA?

• nanoarchaeum equitans sole isolated member (so far)

• 2 other genomes available

• POSSIBLY ONE OF THE Smallest living organisms on earth

• distinct 165 sRNA gene sequences - classification method

Ignicoccus

Crenarchaeota

Nanoarchaeum equitans discovered where? Obligate…?

Hydrothermal vent north of Iceland. Obligate parasite of the crearchaeote, ignicoccus.

Mbp - nanoarchaeum

• do they have metabolic genes?

• what do they carry?

• 0.49 Mbp

• no

• genes for replication, transcription, translation

DPANN superphylum common features

• cell size?

• genomes

• metabolism

• interactions>

• mutualistic or parasitic?

• very small cell size (< 1μm)

• small genomes (~1 Mb, can be less!)

• restricted metabolisms, unable to generate basic building blocks

• interspecies interactions

• mutualistic

Asgard superphyluym

Consisting of a group of uncultivated archaea that includes lokiarchaeota, thorarchaeota, odinarchaeota, heimdallarchaeota. Asgard superphylum represents the closest prokaryotic relatives of eukaryotes.

Lokiarchaeota/thorarchaeota - hermophilic archaea are distinct from?

Crenarchaeota

Lokiarchaeota/thorarchaeota - group with the____ on some phylogenies. What does this suggest?

Eukaryotes. Possible closest ancestor to eukaryotes.

Genomes show eukaryote-like proteins for ___ - early stages of complex cell evolution?

Cell compartmentalization