Notes on Archaea | I love my lavie <3

Archaea

Prepared by: Andrea Nichelle C. Moreno

Structural and Functional Diversity

Discovery of Domain Archaea

• The study titled Phylogenetic structure of the prokaryotic domain: The primary kingdoms
  • First published in PNAS Vol 71 no. 11 on November 1977
  • Written by Carl R. Woese and George E. Fox
• It was headlined in the front page of the New York Times for November 3, 1977
  • Headline: Scientists Discover a Way of Life That Predates Higher Organisms
• According to the abstract, they conducted a phylogenetic analysis based on rRNA sequence characterization.
• Through this living systems were expected to represent 3 aboriginal lines of descent:
  • eubacteria — all typical bacteria
  • archaebacteria — contains methanogenic bacteria
  • urkaryotes (spelling copied from the abstract) — represented in the cytoplasmic content of eukaryotic cells

Phylogenetic Diversity of Archaea

• Archaea are prokaryotes
• Phylogenetically closer to Eukarya
• Archaea possess similar characteristics to bacteria and eukarya
• It is less popular in the 3 domains as it does not thrive or dominate in the same ecological niches as Bacteria and Eukarya.

Commemorating the Archaea

• There is a plaque that commemorates Carl Woese’s use of molecular sequencing and oligonucleotide cataloging of 16S rRNA
• Found in Burrill Hall, University of Illinois, Urbana-Champaign

Unique Characteristics of Archaeal Cells

• Archaea has simple cellular organization with a single bounding membrane
• Its membranes are made of lipids comprised of isoprenoid chains ether-linked to a glycerol backbone
• Archaea do not have peptidoglycan in cell walls.
• Varied shapes and sizes

Cell Organization, Shape, and Size

• Its shapes are like of bacteria with several unique geometric shapes like flat square and triangle
• Their typical size is from 0.7 um to 4um
  • Filaments can be up to 100 um
  • Others can be only 300 nm

Cell Wall

• Pseudomurein — fake peptidoglycan
• Methanochondroitin
  • represents chondroitin present in vertebrates
• S-layer
  • a paracrystalline surface layer that is resistant to osmotic lysis, high temperature, and low pH
• Protein sheath
  • this gives resistance to detergents
• The difference between methanogen pseudomurein and bacterial murein
  • Pseudomurein incorporates L-amino acids, B (1-3) bonds, and N-acetyltalosaminuronic acid, along with unique isopeptide bonds. Substitutions like glutamic acid to aspartic acid and alanine to threonine or serine are possible.
  • Bacterial murein consists of D- and L-amino acids, B (1-4) bonds, and N-acetylmuramic acid in the glycan chain.

Membranes of Archaea: Modifications for Thermophilic Archaea

• Ether-linkage allows stability in extreme heat
• The structure of the lipid units of extreme archaea contains an ether bond between the glycerol head and the hydrophobic tail. There will be a substitution from the ester linkage to the ether bond which results in the thermotolerant quality of lipids
• Phospholipid monolayer is able to resist heat denaturation

Genome Organization

• Archaea are likely to have small circular genomes.
• Its genes are often grouped by function so that its transcriptions are coordinated.
• Some have many copies of the nucleoid per cell while others inherit DNA as a single copy genome. Hence, archaea replicate and organize their genomes in distinct and diverse ways.

Cytoskeleton

• In some cases, the same class of cytoskeletal filaments are found in bacteria and eukaryote.
• The cytoskeletal machinery in eukaryotes was a product from Archaea as a result of eukaryogenesis.
  • Eukaryogenesis - evolutionary process that gave rise to eukaryotic cells
  • The actin amino acid levels of Asgard archaea and eukaryotes are similar.
• Archaea also has homologies with bacterial-type cytoskeletal families.
• There is a correlation between the presence of actin-family cytoskeletal proteins in the genomes of archaea and its elongated cell shape.

Cell Division

• Cell division of archaea is similar to bacteria; however, there are key differences.
• A similarity to bacteria is archaea’s formation of a constriction ring to separate cells.
• The precise mechanisms used by archaea to separate the cells are not yet fully understood.
• Different constriction ring mechanisms:

Archaea species have several varied make up for its cell envelope, cytoskeleton, membrane remodeling, and structure surface.

Structural and Functional Characteristics of Archaea

Comparison between archaea and bacteria:

PM - plasma membrane; O. - origin; AB - antibiotic.

Comparison of archaea, bacteria, and eukarya:

Classification of Archaea

Phylogenetic Diversity of Archaea

• The first two major groups of archaea are:
  • crenarchaeota - hyperthermophiles
  • euryarchaeota - contains extreme halophiles and extreme acidophiles

Phylogeny of Archaea

• Archaea are diverse and are present in all environments
• Extremophiles are a popular archaea
• The supergroups of archaea are: TACK, DPANN, and Asgard
• Euryarchaeota - an archaean phylum that does not fall within a superphylum
• TACK group contains: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota
• DPANN group contains: Diapherotrites, Parvachaeota, Aenigmarchaeota, Nanoarchaeota, and Nanoarchaeota
• Asgard
  • It is the closest prokaryotic relative of eukaryotes.
  • In 2010, members of phylum Lokiarchaeota were discovered.

Extremophiles Archaea

• extreme temperatures - extreme psychrophiles (cold) and extreme thermophiles (hot)
• extreme pH - extreme acidophiles and extreme alkalophiles
• extreme amount of solutes - extreme halophiles and methanogens

Adaptations to Life at High Temperature

• Protein folding and thermostability
  • has hydrophobic cores
  • increased ionic interactions on protein surfaces
  • chaperonins - refold partially denatured proteins
• DNA Stability
  • contains high intracellular solute resulting in a stabilized DNA
  • has reverse DNA gyrase which introduces positive supercoils into DNA to make it more stable
  • has higher guanine and cytosine content
• Lipid stability
  • has dibiphytanyl tetraether type lipids that form a lipid monolayer membrane structure

Adaptations of Halophilic Archaea

• Water balance in Extreme Halophiles
  • accumulates or synthesizes compatible solutes
  • Species like the Halobacterium pump large amounts of K⁺ into the cell as the intracellular K⁺ concentration exceeds the Na⁺ concentration; hence, the positive water balance is maintained.
• Proteins of Halophiles
  • highly acidic
  • contains fewer hydrophobic amino acids and lysine residues

Adaptation of Methanogens

• Pseudomurein
• Methanochondroitin
• Protein or glycoprotein
• S-layers

Role of Archaea in Eukaryotic Evolution

How did eukaryotes evolve from prokaryotes?

• Current data proposes that the first eukaryote came from an archaeon engulfing a bacterium and merging into a single bioentity.
• The specific archaeon is hypothesized to be part of the Asgard supergroup of Archaea.
• The appearance, way of life, and evolutionary story is unknown since there are no living cells that can be studied in the lab.

Endosymbiotic Theory

1. Endomembrane components including nucleus and endoplasmic reticulum came from the plasma membrane infoldings of an ancestral prokaryote.
2. The first endosymbiotic event marks the evolution of the mitochondria from the consumption of aerobic bacteria by the ancestral eukaryote. (Modern heterotrophic eukaryote)
3. The second endosymbiotic event is the consumption of photosynthetic bacteria by the early eukaryote resulting in chloroplasts. (Modern photosynthetic eukaryote)

Article: Isolation of an Archaeon at the Prokaryote- Eukaryote Interface (January, 2020)

1. Deep-sea methane seep sediment was collected using deep submergence research vehicle “Shinkai 6500” (2006).
2. Pre-cultivation of microorganisms using DHS reactor to emulate methane seep sediment environment (2006-2012).
3. Isolation and characterization of reactor-enriched organisms. Strain MK-D1 obtained (2018).

• The paper is an isolation project of an Asgard archaeon related to Lokiarchaeota from deep marine sediment.
• Candidatus Prometheoarchaeum syntrophicum
  • anaerobic
  • extremely slow-growing
  • small coccus (~550 nm in diameter)
  • no visible organelle-like structure
  • creates protrusions that are long and typically branching
• Hypothetical eukaryogenesis model:
  • entangle - engulf - endogenize (E³)

Etiology of Prometheoarchaeum syntrophicum

• Prometheoarchaeum
  • Prometheus (Greek): a god who shaped man from mud and gave them ability to make fire
  • archaeum from archaea (Greek): an ancient life
• syntrophicum, syn (Greek)
  • Syntrophy - cooperative interaction of at least two microbial species to degrade a single substrate

New Insights into Eukaryogenesis: Evolution Towards the Facultatively Aerobic LECA

• transition from anaerobiosis to aerobiosis
  • aerotolerance might be caused by a symbiotic interaction with facultative O₂-respiring organisms
• gaining an O₂-respiring and ATP-providing endosymbiont (the mitochondrion)
• development of intracellular structures
• Theory: The host archaeon engulfed a metabolic partner through extracellular structures resulting in a primitive chromosome- surrounding structure.
  • The structure is similar to the nuclear membrane.

Proposed theory:

Future researches

• Isolation of other Asgard archaea strains which are able to grow faster is better for laboratory manipulation and analysis.
• Lokiarchaeota is not the closest sister lineage to the eukaryotes. It is suggested that the archaeon shares a RCA with the Heimdallarchaeota and its relatives.
• Whether MK-D1 cellular protrusions are shared across all Asgard archaea or not are unknown.

Importance of Archaea

Ecological Roles

• 20% of microbial cells in the ocean are archaea
• Archaea are able to recycle elements like carbon, nitrogen, and sulfur through different habitats.
• Organism interaction
  • archaea may have a mutualistic and commensalistic relationship exemplified by methane oxidizers in ruminant gut
  • no reports on parasitism and pathogenicity

Archaea in Health and Medicine

• Archaea as pathogens are not yet well studied; however, there are some identified species to be disease prone:
  • Methanobrevibacter smithii - found in stools of people with diverticulosis and causes obesity in mice with gut problems.
  • Methanobrevibacter oralis - found in gums of people with periodontal disease and 40% of human brain abscesses.
• Extremozymes and archaeocins produce medically important products discussed by a study titled:
  • Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts
  • authored by: Kira S. Makarova, Yuri I. Wolf, Svetlana Karamycheva, Dapeng Zhang, L. Aravind, Eugene V. Koonin Christa M. Schleper, Editor

Archaea in Food and Industry

• Although roles are not established, archaea can grow and survive in olive brines, salted anchovies, kimchi etc.
• In the industry, extremozymes can withstand different extreme conditions and higher reaction rates such as in:
  • radioactive waste treatment
  • bioremediation
  • mineral extraction
  • creation of microbial fuel cells

Archaea research

• The video discussed the importance of the glycine to thioglycine substitution on the methane production of methanogens.
• It was revealed that although the shift to thioglycine will not affect methane production, the thioglycine will help make the Methanosarcina enzyme stable in increasing temperatures; hence, stabilizing growth and methane production.