Module 3: Archaea (Phylogenetics) Flashcards
What are the two principle phyla of archaea?
Crenarchaeota and Euryarchaeota
What are the superphyla of archaea?
1) DPANN
2) Euryarchaeota
3) TACK
4) Asgard
What phyla make up DPANN?
1) Diapherotrites
2) Parvarchaeota
3) Aenigmarchaeota
4) Nanoarchaeota
5) Nanohaloarchaeota
6) Woesearchaeota
(DPANN + W = acronym for the phyla!)
What phyla make up TACK?
1) Thaumarchaeota
2) Aigarchaeota
3) Crenarchaeota
4) Korarchaeota
(TACK is an acronym!)
What phyla make up Asgard?
Think “HOLT”
1) Hemiarchaeota
2) Ordinarchaeota
3) Lokiarchaeota (Like marvel Loki)
4) Thorarchaeota (Like marvel Thor)
(To remember: the marvel superphyla!)
What are the two main groups within the euryarchaeota?
1) Methanogens
2) Halophiles
Euryarchaeota
A superphylum of archaea that CANNOT be defined by any single characterisitc!
Methanogens
Archaeons that produce METHANE (CH4)
What is the difference between how methanogens and halophiles are defined?
Methanogens = defined by a shared metabolic process
Halophiles = defined by a shared environmental necessity
What is the reaction that methanogens can carry out?
Reduction of CO2!
CO2 + 4H2 —-> CH4 + 2H2O + ENERGY
Methanogens use energy from CO2 reduction to _____________ which makes them _____________
Methanogens use energy from CO2 reduction to drive carbon fixation which makes them autotrophs
Methanogens are ______________ and therefore must live in ___________ environments
1) Strict anaerobes
2) ANOXIC environs.
Where are methanogens commonly found?
1) Animal digestive tract
2) Sediments of swamps, lakes, salt marshes, oceans, hot springs
What archaea are found in the human GI tract?
Methanobrevibacter smithii
What does M.smithii use to produce methane?
Uses formate and H2 (products of bacterial fermentaiton) to produce methane
How does M.smithii help fermenting bacteria within the human gut?
Utilizes and therefore removes the H2 byproduct of bacterial fermentation
==> Allows for more efficient fermentation (as high levels of hydrogen can be inhibitory to fermenting bacteria!)
Other than the GI tract, where are methanogens found in humans?
The oral cavity!
(Methanobacterium oralis)
–> Found its presence to be correlated to gingivitis and periodontitis
Optimal temperatures for methanogens
Most methanogens are one of the following:
1) Hyperthermophiles
2) Thermophiles
3) Psychrophiles
What is the morphology of methanogens?
Most commonly rod shaped or cocci
What are halophiles?
Archaeons that require high SALT concentrations for growth
(>1.5M NaCl)
In general, what salt concentration is needed for halophiles?
All of them only grow in conditions with > or = to 1.5M NaCl
Where are halophiles found?
1) Great Salt Lake
2) The Dead Sea
3) Arctic hypersaline lakes
What is the salt content of the Great Salt Lake and the Dead Sea?
Great Salt Lake = ~5-25% salinity
Dead Sea = as high as 34% salinity
–> So salty there are no macroscopic forms of life living in these areas!
(Ocean = 3.5% salinity = 0.6M)
What adaptation do halophiles possess which allow them to live in such high saline conditions?
What problems does this adaptation cause?
Maintain a high intracellular potassium concentration (provides osmotic balance to prevent cell shrinkage!)
Problems:
1) Proteins denaturation
2) DNA denaturation
How does high potassium concentration denature DNA?
Disrupts the H-bonds between nitrogenous bases of connected strands = strands separate!
What adaptations do halophiles possess to address the issues that arise due to high intracellular K+ conc?
1) Genome with high G-C content (68% of BPs = G-C)
2) Acidic proteins (AAs aspartic acid and glutamic acid are more abundant)
Why does high G-C content help prevent DNA degradation?
G-C pairs have THREE hydrogen bonds connected the nitrogenous bases
==> Much more resistant to being separated than A-T pairs (only have 2 H bonds)
What is unique about the metabolism of halobacterium genus?
They use PHOTOTROPHY to produce ATP (when O2 is low)!
Phototrophy
The acquisition of energy from sunlight
Bacteriorhodopsin
An integral protein bound to retinal that function as a light driven proton pump to generate PMF needed to power ATP synthase
What is the role of retinal in bacterirhodopsin?
Absorbs light energy (green light in particular) which then is used to power the bacteriorhodopsin pump
Bacteriorhodopsin presence causes halobacterium to take on what color?
Makes them have a red hue (because they absorb green light but reflect more red)
Picrophilus genus
A Euryarchaeote
–> Thermophile (optimal growth at 60C)
–> AND acidophile (optimal growth at 0.7pH)
–> Found in volcanic areas
–> Their PM has been found to actually destabilize at more basic pH conditions!
Crenarchaeota
A very diverse phylum of archaea that cannot be described by one characteristic
But ALL crenarchaeota are either :
1) thermophiles
2) hyperthermophiles
And SOME are also:
1) acidophiles
2) barophiles
Thermophile vs Hyperthermophile
Thermophile = Optimal growth at >55C
Hyperthermophile = Optimal growth at >80C
Acidophiles
Archaea that grow optimally in environs with pH<5.5
Barophiles
Archaea that grow optimally under high pressure
(Ex: archaea found in deep sea vents)
What is the best characterized acidophile?
Sulfolobus solfactaricus
–> Isolated from volcanic crater
–> Optimal conditions: 80C, pH = 3.0
Adaptations to Extreme Conditions in Crenarchaeota:
PM
Monolayer (AKA tetralipid) plasma membrane
–> Provides greater stability at higher temperatures (good for thermophiles + hyperthermophiles)
Adaptations to Extreme Conditions in Crenarchaeota:
Proteins (5)
1) Greater percentage of a-helical regions in proteins
2) Greater proportion of arginine and tyrosine AAs
==> These two cause strengthened interactions between AAs
3) Greater # salt bridges + side chain interactions
4) Decreased proportion of cysteine and serine
5) Molecular chaperones
Why does decreased cysteine and serine proportion in proteins increase stability at high temps?
Because cysteine in particular is very sensitive to high temps; easily degraded at high temps
Molecular Chaperones
Proteins that help other proteins fold/refold properly
Archaeal chaperonins more closely resemble ____________
Eukaryal chaperonins than bacterial chaperonins
Thermosome
Protein complex that functions as a molecular chaperone to refold partially denatured proteins in HYPERTHERMOPHILES
Adaptations to Extreme Conditions in Crenarchaeota:
DNA
1) Thermostable DNA binding proteins (to increase DNA melting point!)
2) Reverse DNA Gyrase (increase supercoiling of DNA which increases temp at which DNA unwinds)
What does reverse DNA gyrase do?
Increases the supercoiling of DNA
Thaumarchaeota
Phylum of archaea characterized by consisting of MESOPHILES and PSYCHROPHILES
Mesophile
“Intermediate Loving”
==> Optimal: 15-40C
Psychrophile
“Cold loving”
==> Optimal: <15C
Thaumarchaeota may be major contributors to _________________ via _______________
1) Oceanic Biogeochemical Cycles
2) Carbon and Nitrogen cycling
Where have thaumarchaeota mostly been found?
What is the issue with studying them?
1) Mainly found in marine environs.
2) Most of them haven’t been successfully cultivated! (detected by presence of rRNA gene sequence)
What is special about Nitrosopumilus maritimus?
An ammonia oxidizer as a method of obtaining energy!
What was the first identified psychrophile?
Cenarchaeum symbiosum
–> Resides WITHIN marine sponge
–> Optimal = 8-18C
–> Has NOT yet been successfully cultivated!
Korarchaeota
A phylum in which NO members have been successfully cultivated
–> Detected in environs by rRNA sequences
Nanoarchaeota
A new phylum of archaea with only ONE cultivated member (N. equitans)
What is unique about N. equitans?
CANNOT grow independently!
Requires I. hospitalis to grow (potentially parasitic to I. hospitalis!)
N. Equitans genome
1) Very small genome <500,000 BPs
2) Missing critical genes for synthesis of AAs, nucleotides, lipids, cofactors
Nanoarchaeota (+ larger DPANN) are characterized by:
1) Small size
2) Small genome
3) Metabolic dependence on another organism
Taq Polymerase
The first thermostable DNA polymerase isolated for use in PCR
Where is Taq polymerase from?
Bacterium Thermus aquaticus
(found in hot springs)
What is a better alternative to Taq polymerase?
Pfu
–> A DNA polymerase isolated from hyperthermophilic archaea
Where is Pfu isolated from?
Pyrococcus furiosus
Why is Pfu preferred over taq?
1) Higher thermostability than taq
2) 3’–>5’ exonuclease ability (DNA proofreading capability)
==> Produces PCR fragments with lower rate of error
Half life differences of Taq and Pfu
95C 1/2 life time:
Taq = 40 mins
Pfu = 120 mins
