Topic 3 Archaea Students PDF

Topic 3 Archaea  Topic Overview Distinctive properties of archaea Archaeal cell structure Diversity of the Archaea  Distinctive properties of Archaea archaea “look” like bacteria genetic analyses show them to be very different many live in some of the most inhospitable places on Ear...

Topic 3 Archaea  Topic Overview Distinctive properties of archaea Archaeal cell structure Diversity of the Archaea  Distinctive properties of Archaea archaea “look” like bacteria genetic analyses show them to be very different many live in some of the most inhospitable places on Earth No known archaeal human pathogens Bizarre shapes possible for some archaea Figure 4.1 Phylogeny of Archaea comparisons of rRNA gene sequences can establish phylogenetic “trees” Woese and Fox began these studies in the 1970s Originally called “Archaebacteria” first “archaea” discovered were methanogens Figure 1.8  Morphology and structure size is usually 0.5–5 μm in diameter can vary greatly (N. equitans = 0.4 μm in diameter, Thermoproteus spp. can be 100 μm long!) Figure 4.3 Shapes of archaeal cells rods, cocci, spirals (similar to bacteria) irregular shapes (Sulfolobus spp.) rectangular shapes (Thermoproteus spp.) squares (Haloquadratum walsbyi) Figure 4.4 Squares Cytoplasm cytoplasm molecules similar to bacteria microcompartments/inclusion bodies (e.g., carbon storage, gas vacuoles) have been observed in some species single circular chromosomes and lack a membrane-bound nucleus many of the DNA replication enzymes of Archaea “look” like those of Eukarya development of histones may have been an early “branch point event” in the evolution of Archaea and Eukarya. histones are protein structures that DNA wraps around (different in Archaea and Eukarya) Charge? Figure 4.5  Cytoskeleton cytoskeletal homologues found in both other domains Ta0583, an actin homolog in Thermoplasma acidophilum, resembles eukaryal actin cytoskeletal proteins from M. thermoautotrophicum and M. kandleri more closely resemble those in bacteria MreB (bacteria) archaea actin (eukaryotes) Figure 4.6  Cell envelope all archaea possess a plasma membrane most have a cell wall, yet most do not have an outer membrane both structures are different from their equivalents in the other domains Plasma Membrane unique bilayer construction glycerol-1-phosphate (isomer of G3P) phytanyl side chains (repeating isoprene units) ether linkages STABILITY Figure 4.7 monolayers in some Archaea phosphoglycerol molecule on both ends STABILITY very stable, often seen in archaea living in high-temperature Figure 4.7 Ignicoccus 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 Figure 4.8  Cell wall composed of pseudomurein polysaccharide, similar to peptidoglycan N-acetylglucosamine and N-acetyltalosaminuronic acid β-1,3 linkages: lysozyme insensitive Figure 4.9 s-layer Cell surface protect against predation/viruses mediate adhesion cannulae hollow glycoprotein tubes link cells together to form a complex network Figure 4.10  Flagellum vs Archaellum grows from base rather than tip uses ATP Proton motive ATP force Figure 4.12  Diversity of Archaea Four major phyla Euryarchaeota Crenarchaeota Thaumarchaeota (low temperature, former Crenarchaeota, many oxidize ammonia) Nanoarchaeota (more than one member now!) MANY other phyla have been proposed Korarchaeota (from rRNA sequences obtained from nonculturable microbes) Aigarchaeota AND many other candidate phyla  t a e o h a rc n a re C  Crenarchaeota many are thermophiles or hyperthermophiles Figure 4.13 acidophiles barophiles thrive in low pH (e.g., thrive in high pressures acid mine drainage) (e.g., bottom of the ocean) Figure 15.32 HIGH TEMP Adaptations for survival tetraether lipids/lipid monolayers modified proteins more α-helical regions more salt bridges/side chain interactions more arginine/tyrosine less cysteine/serine strong chaperone protein complexes thermostable DNA-binding proteins reverse DNA gyrase enzyme to increase DNA supercoiling Wikipedia Wikipedia  t a e o h a s ) r c ile ya ph ur l o E ha ( halophiles (e.g., Halobacterium) require NaCl concentration > 1.5M live in high salt environments Great Salt Lake in Utah Dead Sea between Israel and Jordan areas vary between 5 to 34% salinity ocean is typically 3.5% salinity (0.6 M) Figure 4.16 Evaporating Ponds, San Francisco Figure 19.2 (Madigan 13th)  Halobacterium How do halophiles deal with the osmotic shock and loss of water? Figure 4.17  Halobacterium very high intracellular [K+] offsets very high extracellular [Na+] K+ acts as a “compatible Figure 4.18 solute”  Halobacterium high intracellular K+ concentration can cause denaturing of proteins and split dsDNA DNA denaturing à higher GC content (stronger bonds) Protein denaturing à highly acidic proteins that remain more stable in high salt environments  Halobacterium phototrophic Figure 4.20 without chlorophyll or electron transport chain bacteriorhodopsin harnesses light energy and produces a PMF gives off reddish hue Figure 4.19  cis trans  t a e o ) ha n s r c g e ya n o u r a E eth ( m  Euryarchaeota methanogens reduce CO2 with H2, produce CH4 and H2O energy released can be used to fix C strict anaerobes found in human gut and swamp sediments Figure 4.14 methane produced forms gas in humans and combustible air in swamps methanogens possess a great deal of diversity but share a common metabolic property Figure 4.15  Volta experiment Volta performed this experiment ~200 years ago inverted funnel traps CH4 from methanogenic freshwater sediments flame ignites  Methanogen habitats Anoxic sediments marshes/swamps, lakes, rice paddies, moist landfill Animal digestive tracts ruminant animal rumen (cattle, sheep, elk, deer, camels) cecal animal *cecum* (horses, rabbits) large intestine of monogastrals (humans, swine, dogs)  Methanogen habitats Geothermal H2/CO2 sources hydrothermal vents Artificial biodegradation facilities sewage sludge digestors Endosymbionts of anaerobic protozoa Termite gut symbionts  Figure 25.26 Studying methanogens Figure 24.40 12th edition  e a ha y ) r c lo g r A ec o he ttl e t O a l i n d (a  Diversity of Archaea Four major phyla Euryarchaeota Crenarchaeota Thaumarchaeota (low temperature, former Crenarchaeota, many oxidize ammonia) Nanoarchaeota (more than one member now!) MANY other phyla have been proposed Korarchaeota (from rRNA sequences obtained from nonculturable microbes) Aigarchaeota AND many other candidate phyla TEXTBOOK VIEW (2nd) Figure 4.21 TEXTBOOK VIEW (3rd) Figure 4.21 Current, still evolving, picture 2024  C K m A l u T phy e r up s The TACK super phylum contains Thaum-, Aig-, Cren-, and Kor- archaeota  Crenarcheaota Korarcheaota “TACK” Superphylum (Guy L. et al., 2011) Aigarcheaota Thaumarcheaota Euryarcheaota A. V. Mardanov and N. V. Ravin, 2012  t a e o ) ha AC K r c fT a r o um be h a m em T ey (k  New phyla Thaumarchaeota (now Nitrososphaerota) separate phylum for many mesophilic crenarchaeotes Ammonium oxidizing – important in N cycle Nitrosopumilus maritimus  Mesophiles and Psychrophiles Mesophiles 15‒40°C Psychrophiles < 15°C Important for biogeochemical cycling of C and N in ocean possible some members belong in new phylum Cenarchaeum symbiosum resides in a marine sponge shares some genes with crenarchaeotes but also some with euryarchaeotes Belongs to the Thaumarchaeota  Mesophiles and Psychrophiles North Pacific Ocean Karner et al. 2000. Nature Figure 15.13  Emerging phyla Korarchaeota distinct 16S rRNA sequences obtained from hydrothermal environments no species have been cultivated yet One genome available Aigarchaeota no species have been cultivated yet One genome available – thermophile – Candidatus Caldiarchaeum subterraneum  Crenarcheaota Korarcheaota “TACK” Superphylum (Guy L. et al., 2011) Aigarcheaota Thaumarcheaota Euryarcheaota A. V. Mardanov and N. V. Ravin, 2012  N N m PA yl u D rph p e s u Ultrasmall Archaea Nanoarchaeum equitans obligate symbiont Ignicoccus hospitalis N. equitans Burghardt et al., 2009 Hydrothermal environment Ultrasmall Archaea: ARMAN (Association with Euryarchaeota) ARMAN Thermoplasmatales B. J. Baker, L. R. Comolli et al., 2010 Acidic environment A. V. Mardanov and N. V. Ravin, 2012  ta e o h a o f rc er o a em b ) an y m AN N N k P e ( D Nanoarchaeota Nanoarchaeum equitans sole isolated member (so far) Two other genomes available possibly one of the smallest living organisms on Earth! distinct 16S rRNA gene sequences – classification method  Ignicoccus and Nanoarchaeum Crenarchaeota *NANOARCHAEOTA* Nanoarchaeum equitans discovered in hydrothermal vent north of Iceland Obligate parasite of the crenarchaeote, Ignicoccus 0.4 μm (1% of the volume of E. coli) 0.49 Mbp genome! no metabolic genes only carries genes for replication, transcription and translation  Ignicoccus and Nanoarchaeum Crenarchaeota *NANOARCHAEOTA* Pe rip las m Figure 19.20 Figure 19.14 Cytoplasm  DPANN superphylum (very small Archaea) 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? Burghardt et al., 2009 2017: Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of uncultivated archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota. The Asgard superphylum represents the eukaryotes. r d closest prokaryotic relatives of m g a l u s A ph y e r up s 2017: Asgard or Asgardarchaeota is a proposed superphylum consisting of a a group of uncultivated archaea that t includes Lokiarchaeota, Thorarchaeota, o Odinarchaeota, Heimdallarchaeota. The Asgard superphylum represents the closest prokaryotic relatives of e a) a t eukaryotes. h e o r c ha c k ia o ra r L o Th n d (a Lokiarchaeota/Thorarchaeota Thermophilic Archaea – distinct from the Crenarchaeota Group with the Eukaryotes on some phylogenies Possible closest ancestor to the Eukaryotes? Genome shows Eukaryote-like proteins for cell compartmentalization – early stages of complex cell evolution? Still a lot of work to be done to understand these organisms and their impact on our view of early evolution 2019