Lec 5

• Archaea


  A large group of prokaryotes having unusual cell walls, membrane lipids, ribosomes, and RNA sequences, and having the ability to live in extreme environments where many microorganisms do not typically inhabit
• Archaea are quite distinct from the true bacteria and are thought to have diverged from a common ancestral line at a very early stage, before the evolution of eucaryotic organisms
• Archaean eon


  The period of geological history when life first spread across Earth
• In the Archaean, high temperatures and an atmosphere devoid of O2 and thick in toxic gases enveloped Earth
• Archaea were once thought to be remnants of this forgotten age since most isolates had been obtained from extreme environments such as volcanic systems or salt ponds
• Molecular techniques have shown that Archaea are not restricted to extreme environments; in fact, they are plentiful in our oceans and soils
• The vast majority of these Archaea belong to the phylum Thaumarchaeota, a diverse group of microbes that account for up to 20% of prokaryotic cells in the oceans and 1% of all microbes in soils
• Thaumarchaeota


  Ammonia oxidizers and critically important to the biosphere, being major players in the global nitrogen cycle
• Nitrosopumilus


  The first of the Thaumarchaeota to be isolated
• Nitrososphaera viennensis


  The first species of Thaumarchaeota to be described from soil
• Nitrososphaera viennensis


  • Cells form irregular coccoids, organism is both mesophilic and neutrophilic, mixotroph that can fix CO2 but grows best with organic matter present, conserves energy from either ammonia or urea as chemolithotrophic electron donors
• Nitrososphaera viennensis and related soil Archaea carry out nitrification in soils worldwide
• Characteristics of Archaea


  • Can survive without oxygen (anaerobic)
  • Can produce ATP using sunlight
  • Can survive enormous temperature extremes
  • Can survive under rocks and in ocean floor vents deep below the ocean's surface
  • Can tolerate huge pressure differences
  • Can live in communities of microorganisms in the gut, soil, plant tissues, etc.
• Some of the first archaeobacteria were discovered in Yellowstone National Park's hot springs, USA
• Archaeal cell surface structures

  • Entirely unique to the Domain Archaea with no equivalent in either Bacteria or Eukarya (e.g. hami and cannulae)
  • Similar to known bacterial structures but with archaeal-specific twists (e.g. pili)
  • Structures which only superficially resemble appendages found in the bacterial domain with fundamental variations (e.g. archaella, formerly known as archaeal flagella)
• Archaeal cell size and shape


  • Spherical or coccus, rod-shaped, long and thin (bacillus), variations in square and triangular shapes
• Archaeal locomotion


  • Some have flagella (archaella), can have one or many attached to the cell's outer membrane
• Archaeal cell wall


  • Semi-rigid cell wall that helps maintain shape and chemical balance, composed of pseudomurein
  • Cell membrane different from other cells based on chirality of glycerol, ether linkage, isoprenoid chains, and branching of side chains
• Thermoplasma cell membrane


  • Contains a lipopolysaccharide-like material called lipoglycan, forms a tetraether lipid monolayer membrane, can modify biphytanyl structure to include 1-4 cyclopentane rings to increase stability at high temperatures

  
• Archaeal cell wall structural types


  • S layer (most common)
  • Pseudomurein
  • Methanochondroitin
  • Glutaminylglycan
  • Sulfated heteropolysaccharides
  • Protein sheaths
• Archaeal cell wall


  • S-layer is an absolute necessity for growth and viability in the majority of archaea, forms paracrystalline 2D crystal lattices with different symmetries
• Archaeal flagella


  • Single major genetic locus involved in flagellation, more similar to bacterial type IV pili than to bacterial flagella, rotating structures with a filament
• Archaea do not possess any homologues of genes found in bacteria that are involved with bacterial flagellum structure or assembly
• Archaeal flagella are more similar to bacterial type IV pili than to bacterial flagella
• Archaeal flagella are rotating structures with a filament, as seen in bacterial flagella
• Flagellins have conserved amino acid sequences at their N termini, both in the mature proteins and in their class III signal peptides, which are similar to type IV pilins
• The flagella of two phylogenetically distant members of the Archaea, the extremely halophilic Halobacterium salinarum and thermoacidiphilic Sulfolobus shibatae, share a common subunit packing which is unlike that of bacterial flagella
• Archaeal flagella lack a central channel, a feature essential for bacterial flagellum assembly
• The assembly of archaeal flagellar proteins is different from bacteria (subunits added at base instead of pushed to the tip)
• Archaeal flagella


  • Lack a central channel, unlike bacterial flagella
  • Assembly of flagellar proteins is different from bacteria (subunits added at base instead of pushed to the tip)
• Motility and chemotaxis


  • Essential for swarming motility on plates in Sulfolobus solfataricus
  • In Pyrococcus, flagella appear to act as cables connecting cells, perhaps as an initial prerequisite for genetic transfer, and in adhesion to abiotic surfaces
• Interactions between Pyrococcus furiosus and Methanopyrus kandleri can occur through flagella as well as cell-to-cell contact, resulting in the formation of a structured bispecies biofilm
• Pyrodictium sp.


  • Cells grow in a network of tubules termed cannulae, which connect the cells with each other
  • Hollow tubes (outside diameter of 25 nm) that appear empty when cross-fractured or thin-sectioned
  • Consist of at least three different, but homologous, glycoprotein subunits with identical N termini but with different molecular masses (20, 22, and 24 kDa)
  • Highly resistant to heat and denaturing agents
  • During cell division of Pyrodictium abyssi TAG11, two newly formed daughter cells always stay connected with the growing cannulae leading to a dense network of cells and cannulae at the end of the cultivation
  • Final length of the cannulae varied between 30 and 150 m with an elongation rate of 1.0 to 1.5 m/min, which is significantly higher than the elongation rate for bacterial flagella, e.g., Salmonella (0.16 m/min in in vitro measurements)
• Cannula might act to anchor cells to each other or as a means of communication for the exchange of either nutrients or even genetic material
• Archaeal cells (Pyrodictium sp.)

  • Coccoids approximately 0.6 m in diameter
  • Attached to each cell are ~100 filamentous hami, each hamus = 1 to 3 µm in length and 7 to 8 nm in diameter
  • Hamus filament = helical basic structure, with three prickles (each 4 nm in diameter) emanating from the filament at periodic distances (46 nm)
  • At the distal end, a tripartite, barbed grappling hook, 60 nm in diameter, was identified
  • Composed mainly of a 120-kDa protein; remain stable over broad temperature and pH ranges (0 to 70°C; pH 0.5 to 11.5)
  • Mediate strong cellular adhesion for the archaeal cells to surfaces of different chemical compositions
  • Proposed to function in surface attachment and biofilm initiation, much like flagella and pili can in bacterial biofilm formation
• Pilus-like structure in Sulfolobus solfataricus

  • Close to the cell membrane or integrated within the S-layer
  • Made up of substrate binding proteins (SBP), contain class III signal peptide sequences, a feature typical of proteins which are well known to form oligomeric structures in both archaea and bacteria
  • Oligomerized complex is proposed to play a role in facilitating sugar uptake, a function that enables S. solfataricus to grow on a broad variety of substrates
• Sulfolobus species are hyperthermophilic acidophiles typically found in volcanic springs, with optimal growth at around pH 2 to 3 in the temperature range of 75 to 80°C
• One interesting distinction that draws S. solfataricus apart from other Sulfolobus species, such as S. tokodaii and S. acidocaldarius, is the ability to grow on a wide variety of sugars as its only carbon source
• Model of the assembly of surface structures in the cell envelope of Sulfolobus solfataricus

  • Precursor proteins (SBPs, prepilins, or preflagellins) are processed by PibD and are then inserted by their specific assembly system either in the bindosome structure, the UV inducible pili or the flagellum
  • The exact nature of the bindosome structure is not known yet, and an alternate format, shown attached to the S-layer, is also indicated
  • All three assembly systems share the same core of the machinery: an integral membrane protein and a cytoplasmic ATPase
• IHO670 fibers in Ignicoccus hospitalis

  • Different from archeallins (major proteins for archaella synthesis and structure), hamus and cannula
  • Diameter of 14 nm and can be up to 20 µm in length
  • SDS-PAGE indicated the structure is composed of a single protein of 33 kDa
  • Overall helical symmetry is similar to that of the archaellar filaments of H. salinarum and S. shibatae, however the quaternary structure of Iho670 fibers is unique