Archea exam 1

transcriptional regulatory mechanisms of archael chromatin proteins -how can histones negatively affect transcription -how can they positively affect transcription -acetylation impact

- histones competively bind to promoter regions to have impact on transcription turned on or off. Histones can coat Tata bind prtoein and transcription factors and BRE which can negativley effect transcription -if you have nucleosome formation in regions where you need to recruit RNA polyermase can have positive impact on trancription (not all nucleosome formation is inhibitiory) -can have - impact on RNA polymerase during transcirption elongation becuase if it has to go through a lot of chromatin structures it can decrease rate -acetylation of Lys16 of Alba1 is shown to decrease DNA binding affinity cand can have global impact on gene regulation by permitting access of transcriptional factors to promoter site

Three domain concept of phylogeny -dude that came up with it and experiment -Wolfe discovery -Ziling discovery -Kandler discovery -Stetter discovery

-Carl Woese grew cells in P32 extracted RNA, digested with T1 ribonuclease, separated by electrophoresis and identified common patterns of 16S/18S rRNA for phylogenic classification -Wolfe: mathanogens -Zilling: RNA poly -Kandler: phospholipids and cell wall structure -stetter: hyperthermophilic bacteria and archea

gas vesicles common among haloarchaea -protein family -phyla and classes involved -what type of organisms is it found in -how is it formed

-Gas vesicle protein GpO Family -Phylum bathyarchaeota -phylum euryarchaeota: class halobacteria and methanomicrobia -found in aquatic bacteria and archaea - formed as simple protein coat composed of GsvA protein, filled with gas in equilibirum with gasses dissolved in cytoplasm, formation controlled by life, when collapsed must be made again from scratch

Origin of replication -important elements -lab analyses

-ORB: origin recognition box, specific DNA seq that binds the Origin binding protein OBP -sites located in intergenic region near genes for DNA replication )upstream of cdc6 genes in archea) -include A/t rich regions referred to as duplex unwinding elements DUE -skew analysis shows abrupt changes in strand specific GC content bias at origin of replication and termination site -pulsed field and 2D analysis used to see this in lab -clone origin into DNA and see if it can replication in organism in lab

order sulfolobales -pH and temp, environment -genera included -S layer and appendages? -located where -metabolism -UV induces.... -industrial applications

-acidic thermophiels isoalted from terrestial volcanic hot springs optimal growht at pH 2-3 and 75-80 degrees C -includes genera sulfobus, acidianus, metallosphaera -have S-layer and appendages (S-layer is protein layer over cell membrane for protection) -located almost anywhere with volacanic activity and sulfure -grow lithoautrophically by oxidizing sulfur *taking H2S to sulfate) or chemoheterotrophically using sulfur to oxidize simple reduced carbon compounds. Hetertrophic growth only in presence of O2 -Undergo UV induced celullular aggregation that is associated with high freq. exchange of genomic DNA, established host-virus systems in lab to get plaques -industrial applications of those that oxidize H2S to sulfate intracellular to treat waste water

class thermoplasmata -pH req. -cell wall? -temperature requirements -picrophilus: pH, temp req.

-acidophiles (grow optimally at pH less than 2) -many do not contain cell wall (not true for Picrophilus) -most are thermophilic -picrophilus: acid loving archaeon, minimum pH of 0.06, grows in 1M sulfuric acid (battery acid), moderate thermophile (optimum at 60 degree C)

Oder desulfurococcales -temperature requirement and environment -cofactor req? -metabolism -cell shapes -pyrodicitium forms ______

-all members are hyperthermophiles (optimal growth 85-106 deg C), often found in continental solfataric areas -thought they were sulfur dep but some are unable to grow with elemental sulfur -metaboilcally diverse (range of anerobic and aerobic), under autotrophic cond using CO2 as C source, many gain E by oxidation of H2 using elemtnal sulfure, thiosulfate, nitrate, nitrite as e- acceptor. Organotrophic growth occurs by aerobic resp. or by ferm of organic substrates -cell shapes are regular to irregular -pyrodictium forms network of cells entrapped in an extra cellular matrix of hollow tubules which is called cannulae, interconnect indiv cells with each other on level of periplasmic space (not cytoplasmic)

Class Archaeoglobi -aerobic/anaerobic? -temperature preference (degrees C) -found where -Energy source -cousin to _____ -what do they do when stressed -industrial uses

-anaerobic -hyperthermophiles, optimal growth 80 degrees C, -found in hydrothermal vents, oil deposits, hot springs -couple the reduction of sulfate to sulfide with oxidation of oragnic C sources, make acetate, use methanogene gene to make acetete to CO2 instead of methane -close relatives to methaognes -produce biofilm when stressed -cause corrosion of iron and steel in oil and gas processing systems by producing iron sulphide -biofilms implicated in industrial applications including detoxifying metal contaminated samples and gathering metals from environmental samples

archael histones vs alba (sac10b)

-archael chromatin protein alba is reversibly acetylated at lys16 which impairs dimerization and DNA binding, when deacetylation there is dimerization of alba1 and can bind DNA and package it

origin of living cells from inorganic precursors

-archeal and bacterial cells proposed to have escaped from within naturally formed inorganic metal sulfide FeS based compartments in a hydrothermal vent during prebiotic times

arhcea and bacteria replication -how many origins of replication -recombination event number

-arhcea: some have multiple origins of replication bacteria: single origin -how many recombination events you have: uneven number of events needs sister chromosomes resolved with XerCD recombinase (single origin of replication and uneven number of recombination events) -even number of events: sister chromsomes linked noncovalently and topo IV is used to separate the chromsomes -archea with multiple origins: use XerA to resolve dimers in odd number

methanopyrus kandleri -record held -adaptation to high intracellular salinity -where was it isolated from -what feature reflects the extreme habitat and small genome

-current record holder for high temp: survive and reproduce at 122 degrees celsius -shows unusually high content of negatively charged amino acids (adaptation to high intracellular salinity?) -orginal isolate from sea floor at black smoker chimeny in Gulf of California -distinctive features is proteins invovled in signaling and reguation of gene expression and fewer genes acquired via lateral transfer from other archea, reflects the extreme habitat,s mall genome

archael preinitiation complex -what forms the pre-IC -other important proteins

-during the synthesis phaes of the cell cycle (DNA replication) the pre-RC recruits factors like Cdc45, GINS, and single stranded binding protein )SSB or RPA) to form the pre-IC -SSB/RPA coats the ssDNA behind the MCM helicase to prevent reannealing, nuclease attack, and chemical modification -euaryotic like CMG (Cdc-45-MCM-GINS) complex functions in establishing and maintaining the repication forms. GINS is scaffold that couples the MCM helicase, primase, and DNA polyerases at the replicatvie fork --> coordinated synthesis of leadinga nd lagging strand. CDC45 interacts with GINS and DNA polymerase PolD but role in replication is unclear

eukaryotic chromatin remodeling -process coupled to _____ -what controls access to chromatin and how -what else is important in remodeling -what is conserved in archaea that is foudn in eukaryotes -what archaea have and lack histones -each archaeal genome has at least ________ -chromatin uniforms vs variable

-dynamic procss with transcription -ATP dep remodeling enzymes control access and editing of chromatin, SWI/SNF family, hydrolyze ATP and drive remodeling of chromatin to enable access and editing (modifiction on tails of histones) -prefoldin also imprt in remodeling -prefolding and SWI/SNF homologs are conserved in Archaea (impt for chromatin remodeling in archaea?) -euryarchaeota mainly have histones -crenarchaeota generally lack hostones and rely on small proteins that are function homologs of bacterial NAPs -each archael genome harbors at least 2 different types of chromatin proteins with distinct architectural properties -sometimes chormatin is shown to be uniform and have MC1 that forms loops within chromatin -sometimes shown to have variable sizes kodakarensis, Alba chromatin protein bind DNA and form subdomain loop

Archaea biofilms -what kind of archaea -how does it form a biofilm -what does it associate with

-euryarchaeon SM1 -forms extracellular hami appendanges in association with bacterium Thiothrix in sulfurous salt marshes. The microbes jointly form a macroscopic string of pearls, using grappling hooks (cannelon) to tether itself in equal distribution

revolution in classification of archaea

-euryarcheaota and Dpan related but distinct -TACK superphylum starting to rencompass other groups -those in red were in existence before recently, black are new expanded groups

distribution of FtsZ and dynamin among 3 domains -FtsZ and MreB related to what in eukaryotes -_____ and most bacteria have _______ -TACK and some bacteria lack ______ -plastids and primitive mitochondira have ______ -most mictochondira deficient in _______ -______ is related to tubulin and _____is related to actin in eukarytoes -FtsZ forms _____ during cell division -unlike bacteria most euryatchaeota have _________

-euryarhaea and most bacteria have FtsZ -TACK superphylum and some bacteria and lokiarchaeota lack FTSZ -plastids and primitive mitochondria have FTSZZ but also have dynamic and dividing rings -most mitochondria deficient in FTSZ -FtsZ related to tubulin and MreB related to actin of eukaryotes -FtsZ forms Z ring during cell division in euryarchaeota analogous to bacteria (splits sister cells form each other) -unlike bacteria most euryarchaeota have multiple FtsZ homologs that are related but distinct from FtsZ (renamed as CetZ - missing C terminal extension of FtsZ)

long branch attraction artifact -definition -how is this relevant to archaea

-false rooting at the base of a tree that can occur when comparing fast evolving organsims that appear to be of similar sequence but are actually distant lineages -archea and eukarya are clustering closer together and bacteira is more removed but long branch attraction artifact caused these to look more similar

methanogens -found where -temperature preferred -anaerobic/aerobic? -source of E and C -industrial uses

-found in almost every anaerobic environemnt with low sulfate (freshwater, extreme temperatures like hydrothermal vents) -hyperthermophiles to mesophiles -strict anaerobes: produce methane gas as product of central metabolism -use Co2 + H2 acetate, and methylated compounds as source of energy and carbon -target of control in cattle industry and greenhouse gas emissions (give antibiotics to reduce methogens in the rumen of the cattle and it will bulk it up) -useful in produce biogas and minimizing volatile odors of dairy waste

CetZ1 -what does it do -experiment used to prove it

-found to control cell shape in Haloarchaea Approach 1. detected cetZ1 genes from haloarchaeon and found no difference in growth rate or cell size 2. expressed arhcael ftsz and cetz1 analogous to FtsZ mutations that generate hyperstable filaments in bacteria 3. found FtsZ were heterogenous in cell size 4. swimming defect in CetZ1 overexpression mutants 5. ovserved in motitliy assay sthat cells on leading edge are rod shaped and irregular disc shaped in center (rods not observed in the mutants) 6. overexpressed CetZ1 and cells form rods 7. fused ftsz1 and cetz1 to flourescent proteins and saww that ftz1 localized to cell division plane and cetz1 localized in patches near envelope of disc shaped cell and in the pole in motile rods suggesting protein involved in motility and forming rod shape *cells got huge and shape and motility affected in mutants

Phylum thaumarchaeota -name origin -metabolism -important for ? -where are they foun d -5 important groups

-greek 'thaumas' = wonder -all organisms are chemolithoauthrophic ammonia-oxidizers (many not all) -important for nitrogen and carbon cycles -found abundant in open ocean waters and soil ecosytems such as the everglades 1-Cenarchaeum symbiosum: first discovered member, symbiont of marine sponge 2-Nitrosopumilus maritimus isolated from sediment in tropical tank at the Seattle Aquarium dominates open ocean waters based on metanogenomics 3-Nitrososphaera viennensis isoalted from garden soil in Vienna Austria, soil ammonia oxidizing archaeon, irregular shape, large intracellular compartment, have electron dense inclusions, tubular like strucutres intracellularly 4-Nitrosopheaera gargensis isoalted from Garga hot spring in Siberia (optimal growth at 46 degrees C) 5-Giant Tharumarchaeota: from salt marsh, high sulfide content in India, many archea line inside filament to form Giant (over 1 inch long)

what is effect of reverse gyrase

-have beta hairpin fold related to beta hairpin fold in DNA helicase of bacteria that is important for nucelotide exision repair (reverse gyrase function not just in positive supercoiling but also in recognise DNA damage with beta hairpin and coating DNA and protecting it from DNA damage) -reverse gyrase: mediates positive supercoiling on chromatin structure and dynamics -reverse gyrase is only protein that is specifcic and common to all hyperthermophiles -unusla type I A topoisomerase fused to helicase domain, introduces positive supercoiling into DNA by ATP-DEP reaction -mutant of thermoccoccus shows reduced growth but still grows at 90 degress C -in absence of ATP minor nonspecific effect on rate of depurination and major speicfic effect on rate of ds breakage of DNA recognizes nicekd DNA and coats the site of damage through cooperative binding prevents inappropriate aggregation of denatured DNA regions and promotes correct annealing -suggested to detect damaged DNA and act as splint to prevent DNA damage in vicitniy of lesion (main damaged DNA in conformation that is amenable to repair)

arhcael chromatin proteins properties

-high cell abundance -small size 7-10 kDA -positive charge -bind dsDNA with little or no seq. specificty (coat dsDNA kind of like ssbp)

order thermoproteales -temperature and oxygen? -Tenax: oxygen req., metabolism, electron acceptor -pendens: temperature, pH, metabolism, structure, growth

-hyperthermophilic anaerobes from acidic hot springs an dwater holes. Optimal growth at 85 but can grow in 95 degrees C -Thermoproteus tenax: strictly anaerrobic and sulfur-dep., able to grow chemolithoautotrophically (CO2/H2) and chemoorganoheterotrophically in presence of organic substrates, universal electron acceptor is elemental sulfur (but polysulfides and thiosulfate also used) -Thermofilum pendens: thermophile and moderate acidophile. Respires with sulfur and uses peptides as E source, unusual long filamentous structure, golf club shaped cells are found with spherical enlargement at one end that likely detaches to form new cell almost always found associated with T. tenax. growth of T. pendens in the absence of T. tenax req. unknown lipid growth factor from T. tenax to be present

sulfolobus homolgous -what does it lack -use what for cell division -in eukaryotes vsp4 and ESCRT used for _____ -ESCRTIII and VPS4 gene homologs of ________ are convserved and expressed ________ -what do they do during cell cycle

-lack ftsZ and MreB homologs -proposed to use ESCRT system homologs for cell division -in eukaryotes Vsp4 and ESCRT used for endosomal sorting complex for transport, trafficking, etc. -ESCRT III and Vps4 gene homologs of Crenarchaea are conseved expressed with cell cycle -interact and locaize mid cell during division cause accumulation of enlarged cell when Vsp4 overexpressed (impt for cell division)

two domain tree of life -what group changed the vision -mito late scenario -garden variety archaeon

-lokiarcheoata have suggested only 2 domains of life, very eukaryotic like and clusters close with eukryaotes -mitochondria late scenario: complex amtiochondriate eukaryote complex organism engluphs alphaproteobacterium = fusion partner, -garden variety archaeon = fusion partner archea fairly evolved engluphed alphaprotebacterum and the fusion partner ultimately came the eukaryote that we know today

bacterirhodopsin -what is it -how is it formed -what happens with photons -dark state -where are protons pumped -is it photosynthetic -what group is it common in

-membrane associated proton pump -light driven H+ pumps in membrane that is formed by retinal chromophore derived from vitamin A that is covalently attached to a lysin rediues on rodopsin. -adsorption of photon cuases the all-trans-retinal to become 13-cis retinal resulting in pumping of H+ and generation of deltap. -Enzyme cycles back to all trans retinal in the dark state -protons pumped to outside of cell and increases PMF (more H+ outside than inside) -not photosynthetic but uses light -common among haloarchaea

phylum lokiarchaeota -relative to what -meatbolism

-metagenome seq. has identified it as closest relative of eukaryotes known to date -comparative genomic evidence suggests that it is hydrogen dependent

DPANN superphylum (clade) -easy to find? -where do you find them -important in ?

-microbial dark matter: hard to find -common in surface water of oligotrophic high altitude lakes -found among fermenting organisms corenrich with dentrifiers from sendiments: -impt in nitrogen cycling?

genome organization -do bacteria have chromatin -why does DNA need organized

-most bacteria have no membrane bound nucleus but do have chromatin proteins that compact genomes to fit in cell (length 1000X shorter) -DNA must be packaged but available for transcription, replication, and repair

Archea distinguishing features -membrane like/unlike bacteria? -backbone like/unlike bacteria? -metabolism and experiment

-no membrane bound nucleus like bacteria -differ from bacteria in cell membrane becuase bacteria have D-glycerol phosphate backbone ester linked to fatty acid chains, archea have glycerol phosphate backbones in L conformination and ether linked to isoprene chains -unique metabolism like methanogenesis: volta experiment

order acidilobales and fervidicoccales -oxygen req -metabolism

-not well studied -strict anaerobes isolated from terrestial hot springs -Acidilobus saccharovorans: an organotrophic, thermoacidophile, ETC is branched with two sites of H+ translocation and is linked to reduction of elemtnal sulfur and thiosulfate

interply between transcription factors and histones

-proposed to modulate transcriptional regulation in archaea -methanocaldococcus jannaschii upstream activation site (UAS) located directly upstream of rubredoxin rb2 promoter. Both histones and the Lrp-type regulator Ptr2 have been shown to bind this region -in absence of Ptr2 the histone tetramers bind to the UAS and upstream and downstream regions --> transcriptional repression (no rb2 expression) -TATA binding prtoein and transcription facotr B binding can overcome transcirptional repression mediated by histones (low rb2 expression) -At high Ptr2 conc, the transcritpion factor binds to the UAS and activates transcription by trecurtig TBP to the promoter which leads to high expression levels (high rb2 expression)

crenactin -who has this -what is related to in eukaryotes -what is it correlated to -what does it form that is important for _____

-some archaea of crenarchaeoata have this -close homolog of eukaryotic actin (structure and seq) -corrlated with rod shape and filamentous cell morphologies -forms helical structures with arcade proteins which are thoguht to be important for cell divsion in crenarchaeota

Class thermococci -oxygen, temp, and pressure requirements (degrees C and pH) -energy -mobile? -where are they found and give species -plays major role in ______

-strict anaerobic hyperthermophiles, grows 60-100 ddegrees C, 5-9 pH, and often barophile (living in depths of 200-1000 ft) -heterotrophic: grow on organic substrates primarily w/ elemental sulfur which is reduced to hydrogen sulfide -some are immobile but others use flagella -thermococcus kodakarensis was isolate from solfatara (shallow volcanic center in Japan). other such as T. peptonophilus from vents -play major role in ecology and metabolic activity of microbial consortia in hot water ecosystems

Haloarchaea -where are they found -easy or hard to culture -environment -age -square boxes: species -what do they produce to float and why

-thrive in high salt habitats: salt ponds in San Fransicso, dead sea, salt crystals -usually easy to culture -some are dual extremophiles (alkaliphilic andhalophilic): Natrialba magadii from Kenya lake magadsi at 3.5 M NaCl, pH 9.5, and 40 C -analysis of DNA supports long term survival. Suggested to be 195-200 million years old (oldest cultivated organisms to date) -haloquadratum walsbyi: salt square boxes, very difficult to cultivate -often produce gas vessicles as flotation devices (get to the light to use bacteriorhodopsin)

phylum bathyarchaeota -easy or hard to culture -found where and important for what -terminology then vs now -lineages -metabolism

-uncultivated but found in diverse habits -one of predominant archael groups in anoxic environments and may have signficiant roles in global biogeochemical cycles -originally termed MCG *miscellaneous crenarchaeota group) but now recognized as distinct phylum -two distinct lineages BA1 and BA2 are proposed to mediate methylotrohpic methanogenesis based on metagenomcis -thus methane metabolism may not be restricted to euryarchaeota phylum -genomic and enzymatic evidence for acetogenesis (make acetate), take organic matter and hydrolyze, fermeting hydrolytic products to acetate -debate if they can produce methane or not

minichromosome maintenance helicases (MCMs) -what stimulates binding -structure -what do they do -how does DNA enter -2 models for DNA unwinding

-when cdc6 binds ORB, MCMs come in and bind to this region -have N terminal domain and ATPase domain, C terminal helix turn helix domain -MCMs are replicative helicases that separate dsDNA in front of replication fork. Use ATP hydrolysis to translocate across strand of DNA to displace the other strand -DNAs enter the central role of the hexameric ring. During unwinding MCM can displace proteins and RNA from the DNA. MCM C terminal domain may fold into HTH but function appears to be repressive/regulatory -N terminal domain forms hexamers on it's own -Beta hairpin in hexamer important for interaction with DNA (DNA enters this hexamer) 2 models for unwinding by MCM helicase 1. double starnded DNA only 1 strand enters the hexamer and the other strand is displaced, ATPase domain leads this function (c terminal domain) 2. double stranded DNA enteres into the pore and 1 strand exits through side of complex and other exits through central domain

phylum candidatus korarchaeota -culture history -where are they found: temp and pH req. -genome seq revealed_______

-yet to be isoalted in pure culture but are found in low abundance in hydrothermal environments (less than 55 deg C in springs at pH 4.7-8.5) -analysis of genome seq form mixed culture revealed features supporting the hypothesis of deep branching ancestry of Korarchaeota

7 industrial uses of archaea

1-alkaline hydrolases: improving cleaning efficiency 2-alkali treated wood pulp bleached by alkaline stable xylanases 3-use heat from light to trigger specific biochmiecal reactions remotely with material from thermophiles 4-high salt/solvent stable light biosensors from bacteriorhodopsin 5-bioleaching of metals from mines by acidophilic microbes 6-cold active hydrolases used in food/textile industy like lactose free milk 7-thermostable enzymes like DNA polymerase for PCR

DNA replication and 5 biotechnological applications

1-thermostable and thermal labile enzymes useful for nucelic acid manipulation like PCR, gene silencing, cloning, site directedn mutagenesis, and sequencing 2-DNA polymerase classified into 7 families A, B, C, D, X, Y and RT (B, D, Y in archea) 3-archeal B type (polB)- used for high fiedlity PCR, DNA sequencing, and site directed mutagenesis 4-Archael family Y tupe (pol Y) - have potenail for error prone PCR and random mutageneiss bc low fidelity and strong thermostability 5-taq DNA pol: from thermophili cTHermus aquaticus, usually from family A which lack 3' to 5' exonuclease and are thus low fidelity

DNA replication 5 basic steps

1. origin 2. origin binding protein initiates the event 3. helicase recruitment and DNA melting 4. prime leading strand 5. extend leading strand and prime lagging strand (polymerase goes 5' to 3' direction)

what is the origin binding proteins that binds ORBS in archea

Cdc6 or Orc1/cdc6

skew analysis

DNA plotters available, gives tracks from outside to inside, you can see skew of GC content from one side of the genome to the other and you can see where origin of replication might be

cytoskeleton and cell divsion -eukarya cytoskeleton and dynamin -archea important element -lokiarchaeota and euryarchaeota presence of these elements

EUKARYA -cytoskeletoin: network of cytoplasmic protein filaments like actin, filaments, resp for cell shape, movement, endocytosis, etc. -dynamin: key role in things like division of organelles, cytokenesis, and endocytosis ARCHAEA -FtsZ/Tubulin: form rings req. for cell divsion in some archea (common in bacteria) -MreB/ParM/ actin-like proteins: segregation origins of replication in some archea( common in bacteria) -crenactin: close homolog of eukaryotic actin, appears needed for rod shaped and filamentous morphologoy of some archea -ESCRT system homologs: linked to cell divison in Sulfolobus -Lokiarchaeota have lots of ESPs like those in cell divsion and cytoskeleton formation -euryarchaeota have absense of ESPs in these things

archaeal elongation complex -how many replication forks -important components

after replication bubbble is formed other componenets of replisome are recruited toestablish the two replication forks -primse: DNA dep RNA polymerase that makes RNA primers on template DNA, catalytic and regualatory subunit, very similar to eukaryotic primase -replication factor C (RF-C): clamp loader, recognizes the primer and binds, enables PCNA the sliding clamp to come in which is hexamer and loops around 2 strand of DNA, loop serves as scaffold for DNA Polyermase to come in, then clamp-polymerase interaction -pcna SLIDING clamp: ring shaped that encircles DNA and tethers polymerase for DNA synthesis. after compleeting an okazaki fragemnt the DNA poly dissociates form the clamp. left on the DNA to interact with proteins needs for fragment maturation, chromatin remodeling, etc.

chromosome segregation in bacteria vs archaea

bacteria: parA and parB important for chromsome segregation, parB binds parS sites (close to origin of replication), parB interacts with membrane at pole of old cell pole (most recent cell division event occured at opposite pole), other siter chromosome also bound by parA protein which starts to depolymerize --> genome is pulled to opposite pole of cell (helps separate 2 chromosomes) archea: seg A and seg B (segA homolog of parA, seg B is atypical parB), function in pulling sister chromosomes apart but require additional AspA protein that seems to spread across DNA in non specific way near origin recognition box and serves as linker to bind segB and segA binds on top of that (dont know if there is a depolymerization or polymerization of segA to push genomes to the poles)

Phylum Euryarchaeota

has methanogens and haloarchaea

Asgardian superphylum -includes what -why are they important

includes lokiarchaeota -complex archaea that bridge gap between prokarytoes and eukarytoes

LUCA -definition -where did it originate -metabolism -environment -pros to the theory -cons to the theory -root of archaeal trees in the ______

last universal common ancestor -hypothesized to have orginated in alkaline hydrothermal vents (Natural PMF to drive biologcial processes) -metabolism is hypothesized to have been related to methanogen/acetogen -hypothized to be hyperthermophiles that life originated in hot environemnt PROS: -hyperthermophiles represent the extremely short and deeply branching off lineages in trees -many hyperthermophiles grow chemolithoautotrophically with inorganic energy sources using CO2 as the sole carbon source CONS -G+C content of 16S rRNA from msot hyperthermophiles is high and leads to long branch attraction artifcats in the trees (organisms cluster together and branch deeply in trees, short genomes causes similar probs) -protein phylogeneis do not always support 16S rRNA trees -hyperthermophiles have develpoed additioanl mod to help protect against thermal denaturation (tRNA mod, membrane lipid cyclization), goes against hyperthermal first model -short half life of important biomolecules -high temp may cause reactions to proceed less controlled than at lower temp *root of archea tree is within methanogens

Phylum candidatus aigarchaeota -part of what group -easy or hard to culture -temperature and environment

part of TACK -uncultivated of archaea detected by metagenomics -includes hyperthermophiles and moderate thermophiels in variety of environments

Phylum Candidatus Geoarchaeota -part of what group -easy or hard to culture -where are they found

part of TACK -uncultivated: detected by metagenomics -found in high temp acidic iron mats in Yellowstone National Park

Nanoarchaeota -what do they require for growth -where are they found: temp and pH req. -where do they branch on archaeal tree -nanoarchaeum equitans: found where, replicates when, metabolism, genes

phylum within DPANN -obligate symbionts with reduced genomes, cells are very small (0.4 uM), coccoids, cannot culture without partner -found in marine thermal vents and terrestial acidic hot springs (90 degrees C pH 2.5-3.0 in Yellowstone park) -branch close to the root of the archael phylogenic tree: may be artifact due to small genome size -Nanoarchaeum equitans best characterized from hydrothermal vent replicates only when attached to host Ignicoccus a hyperthermophile at 90 degrees C metabolism unknown but host is autotroph that grows with H2 as e- donor and elemental sulfur as e- acceptor lacks identifiable genes for most metabolic functions including syn of building blocks and coenzymes like amino acids and nucleotides smallest genome known at 490 kbp

archeal family B polymerase (Pol B) -what does it bind -what is it's function -adaptation to environment -what motif is important

uniquely bind uracil -proposed to scan DNA templates for Damaged bases like uracil produced by the deamination of cytosine adenine -if damaged encountered the enzymes stop replication -DNA bases deaminated at all temps but increased in high temp where hyperthemophilic live -ability of pol B to uniquely bind uracil is adaptation to environment -NPL motif is important for fidelity and can be modified

bacterial vs archeal genomes

usually circualr but some bacteria liner -single origin of replication in bacteria -single or muiltple origins in archea (haloarchea can replicate by homologous recombination without origins) many archea and bacteria -have more than 1 indep replicating genetic element (chromosomes) -are oligoploid (up to 10 copies) or polyploid (more than 10 genome copies). genome copy number is regulated inr esp to growth phase/rate. (used to store phosphate?)