archaea

horizontal gene mechanisms

• significant impact on microbial evolution

  • involve mobile genetic elements that promote their own dissemination (selfish-genes)

• generated issues associated with phenotyping of microbes

  • lactose catabolism genes can be carried on plasmids

• 16s rRNA & other chromosomal based markers with low mutation rates are needed for positive identification

molecular markers

• genes, portions of genes or other genetic sequence used to identify and taxonomically categorize organisms and viruses

  • exceptions such as prion, which are infectious proteins and require amino acid sequence instead

phylogenetic analysis

• 16s rRNA sequence is always used for those organisms that have 70s ribosomes (not viruses)

  • in addition to other markers

• 16s rRNA sequence can be compared with millions of other sequences using BLAST software

  • BLAST database generates a list of those sequences that are most similar to the sequence in question

the originals did not use 16s rRNA

• Darwin’s tree 1859: based on his observation of adaptation in the beaks of finches on the Galapagos island

• Stanier & van Niels tree 1962: based on the absence or lack of certain characteristics in prokaryotes relative to eukaryotes

archaea & evolution of the molecular tree of life

• Woese’s tree based on 16s rRNA sequence data of archaea 1990

• Loki’s tree based on 16s rRNA and conserved eukaryotic gene markers 2017

• NASA fusion tree based on Loki’s tree and chemical composition of cell membrane 2018

• archaea present a mystery to the taxonomic organization of life

• at present, the archaea are considered to be prokaryotes, but are not bacteria

archaea

• shares features with bacteria and eukaryotes

• extremely diverse

  • physiologically and morphologically

• many but not all are extremophiles

  • thermophiles: hot springs

  • hyperthermophiles: oceanic volcanic vents

  • barophiles: bottom of the ocean

  • mesophiles: human gut

archaea cell walls

• chemical composition differs from that of bacteria or eukaryotes with cell walls

  • key component: pseudomurein

  • do not have peptidoglycan

• not affected by enzymes that break down peptidoglycan or antibiotics that target the synthesis of peptidoglycan

  • lysozyme (tears, saliva, food) breaks down peptidoglycan

  • antibiotics that interfere with peptidoglycan synthesis have no effect

• gram stain means nothing → no peptidoglycan

peptidoglycan

bacteria

pseudopeptidoglycan

archaea

membrane lipids of bacteria and eukaryotes

straight chain fatty acids attached to glycerol by ester linkages

membrane lipids of archaea

• hydrocarbons attached to glycerol by ether linkages

  • ether linkages are stronger so perform well in extreme environments

  • no fatty acids instead have phytanyl chains that can cyclize and make the cell walls more resistant to harsh conditions in extreme environments

archaea membranes

• generic phospholipid found in eukaryotes & bacteria → ester bond

• have an ETHER bond between glycerol and hydrocarbon tails

• extremophiles have hydrocarbon tails with side branches that can cyclize

• ether bonding and hydrocarbon tails, and ring formation prevent leakage at high temperatures

archaeal membranes can be bilayers or monolayers

• monolayer membranes are more rigid and better able to resist harsh environments

• also prevent membranes from leaking

membrane adaptation

• when faced with environmental changes, they can modify their membranes

• membrane more open at lower temperatures or higher pressures or higher pH

• membrane less open at higher temperatures or under lower pressure or lower pH

archaea similarities with bacteria

• circular double stranded DNA genome and haploid

• polycistronic

• horizontal gene transfer, binary fission

• highly diverse metabolic pathways for energy production

archaea similarities with eukaryotes

• more than one origin of replication, similar replication proteins

• histones and nucleosome like structures

• introns

• many RNA polymerases (no sigma factors)

• many translation factors, some shared ribosome proteins

two most well described phyla in archaea

• crenarchaeota

• euryarchaeota

crenarchaeota

• extreme environments

  • thermophiles

  • psychrophiles

  • acidophiles

  • S0 oxidizers and reducers

euryarchaeota

• most diverse

• thermophiles, methanogens, acidophiles, halophiles

• extremophiles

• sulfate reducers

crenarchaeota: thermophilic or hyperthermophylic

• geothermally heated water or soils that contain elemental sulfur

• EX: yellowstone

crenarchaeota: sulfolobus and thermoproteus

• symbiotic relationship in hot acidic microbial mats

  • thermophilic and acidophilic, require sulfur

1. sulfolobus: thermoacidophiles (80-80C, pH 2-3)

• aerobic heterotroph: grows in hot acidic sulfurous springs

  • oxidized sulfur: S0 to H2SO4

2. thermoproteus: thermoacidophiles

• anaerobic autotroph: grows in hot acidic sulfurous springs

  • reduce sulfur: S0 to H2S and fix carbon

sulfolobus and thermoproteus

• sulfolobus aerobic heterotoph

• thermoproteus anaerobic autotroph

euryarchaeota

• five major groups: more diverse than crenarchaeota

  • methanogens

  • halobacteria

  • thermoplasms

  • hyperthermophiles

methanogens

• strict (obligate) anaerobes

• cellulolytic (can break down cellulose)

• widespread in nature

• habitat: environments rich in organic matter

  • animal remains

  • human intestines

  • anaerobic sludge digesters

  • freshwater and marine sediments

  • swamps, marshes, hot springs

  • anaerobic protozoa

ecological importance of methanogens

• important in wastewater treatment

• dangerous in landfills

• produce significant amounts of methane

  • protons pumped during generation of methane

  • potential fuel and energy source

  • a greenhouse gas, may contribute to global warming

• human health aspect

  • higher amounts of methanogens in the intestines correlates with the inability to lose weight

    • intestinal methane production is associated with a higher body mass index

methane venting

• below:

  • PVC pipes are used to vent methane

  • methane venting from ocean floor

  • methane venting during processing of petroleum

  • marsh gas on fire

harvesting methane (natural gas)

• hydrogen production by steam-methane reforming

• methanogens: animals like cows

• anthropogenic: produced by human activity

halobacteria

• no cell walls, cell membrane is covered with tough S-layers

• extreme halophiles: require salt or will die by lysis

  • the cytoplasm of H. salinarum contains > 4M potassium chloride (KCl)

• aerobic respiration

• pigments and high salt provide radiation protection

• > 20 genome copies per cell allows for robust DNA recombinational repair from UV damage

halobacteria and rhodopsins

• rhodopsins: functions

  • humans: eyes

  • archaea: use this molecule for “other” functions

• bacteriorhodopsin: visual purple

  • generates ATP from light energy

  • purple membrane: aggregation of bacteriorhodopsin

• halorhodopsin: maintains intracellular connections of salts

• sensory rhodopsins: photoreceptors

  • control flagella → phototaxis

thermoplasma

• no cell walls

  • extremely tough plasma membranes

  • tough external S-layers

• hot acidic springs

  • sulfur: 55-60 C, pH 1-2

  • picophilus has an optima of pH 0.7

hyperthermophiles: thermococcus kodakarensis

• hyperthermophilic anaerobe from deep sea volcanic vents

  • S0 to H2S

• growth temp 88C to 102C → can grow above boiling

• has a reverse gyrase, which induces positive supercoiling in DNA and makes DNA more resistance to thermal denaturing

• high transformation ability

hyperthermophiles: pyrococcus furiosus

• rushing fireball

• hyperthermophilic anaerobe from deep sea volcanic vents

  • like many volcanic vent microbes reduce sulfur

• optimum growth temperature 88 C to 110 C

• has a reverse gyrase which makes DNA more resistant to thermal denaturing

• high transformation ability

hyperthermophile: archaeoglobus fulgidus

• ancient sphere → it shines under UV fluorescent light at 420nm

• deep sea volcanic vents, high temp oil deposits and hot springs

• optimum growth at 83 C

• reverse gyrase responsible for positive supercoiling of DNA making it more resistant to thermal denaturization

• no cell wall, instead have a crystalline S-layer arranged in an hexagonal array (like a tight mesh)

lokiarchaeota: prokaryote to eukaryote

• new genetic analysis of many molecular markers places the deep sea benthic group lokiarchaeota with eukarya

  • discovered at “loki’s castle” in volcanic vents in the north sea off of norway

  • named lokiarchaeota after “loki” the norse mythology shape shifiting diety

evolution of the eukaryotic cell

• theory proposes that different prototypes of primitive cells arose about 4 billion years ago

  • these cells would later split in two groups with one group leading to the bacteria and the other to the archaea and eukaryotes

• later a fusion of bacteria and archaea began the evolution of the eukaryotic cell

  • eukaryotic cells and bacteria cells have bilayer membranes

    • have fatty acids with ester linkages

  • archaea and eukaryotes have similar molecular mechanisms

• then two other fusions would take place at a later date generating ancient eukaryotic cells with:

  • mitochondria: created by 1st fusion

  • chloroplasts: created by 2nd fusion