The Arachaea Flashcards
1
Q
How were the archaea discovered?
A
- already in 1958 Francis Crick postulated that amino acid sequences could be used to unravel the molecular phylogeny
- but only in the 1970ies the big molecular biology revolution happened
- Carl Woese compared small ribosomal subunit RNA
→ turned the prokaryal taxonomy upside down - rRNA turned out to be an ideal chronometer since it is central for the cell metabolism, is highly conserved, but also contains regions of variability
- rRNA is very abundant and can be easily isolated from biological samples
→ one can also perform cultivation-independent phylogenetic studies - 1977 Carl Woese published a study showing that a group of prokaryal organisms did neither fit to bacteria nor to eukarya
→ Domain of archaea
2
Q
What are the characteristic features of Archaea?
(General)
A
- Archaea have an atypical antibiotics sensitivity profile for prokarya (more similar to eukarya)
- What is common to many Archaea is their ability to survive and live in extreme environments
- There are extremophilic archaea, but not all Archaea are extremophilic organisms!
- Mesophilic life style is the result of horizontal gene transfer with bacteria
- Archaea are also not “exotic” life forms, but are quite abundant in certain habitats
- e.g. in sea water: archaeal cell density is about 1 x 105/ml
→ at least 20% of the microbial life in the oceans are archaea!!
- e.g. in sea water: archaeal cell density is about 1 x 105/ml
- Archaea are also not “exotic” life forms, but are quite abundant in certain habitats
- e.g. on human skin: based on 16S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome (up to 10% of cells on skin)
3
Q
What are the differences between gram-positive bacteria, gram-negative bacteria and archaea?
A
Gram-positive bacteria:
- No outer membrane
- Thicker peptidoglycan layer
- Inner membrane
Gram-negative bacteria:
- Outer membrane
- Peptidoglycan layer
- Inner membrane
Archaea:
- No outer membrane
- Pseudopeptidoglycan layer outside plasma membrane
4
Q
What are the characteristic features of Euryarchaeota?
A
- Euryarchaeota have histone proteins to pack their genomic DNA into nucleosomes
- archaeal histones dimerize (like the eukaryotic H3-H4 Dimer) and assemble into a tetramer that wraps about 60 bp of DNA
→ similar to eukarya (but they of course do NOT have a nucleus!)
5
Q
What are the characteristic features of Archaea?
(Genome, Transcription & Translation)
A
- Archaeal genomes: typically circular (like bacteria)
- Lateral gene transfer of archaea (up to 30% “foreign” DNA, mostly from bacteria)
→ archaeal genomes resemble a genetic mosaic - Replication initiation and DNA polymerase are similar to eukaryotic system
- also transcription is similar to eukaryotes (TATA-box promotors)
- Translation on 70S ribosomes, mRNAs carry Shine-Dalgarno sequences for translation initiation (like bacteria)
- Genes can be organized in operons (like bacteria)
- protein coding genes lack introns; mRNA have no 5‘-cap (like bacteria)
- Met-tRNA and not formyl-Met-tRNA is used as initiator tRNA during translation (like in eukarya)
- Initiation- and elongation factors are similar to eukaryal factors
- Genome comparisons: Metabolism is bacteria-like, while information processing functions are eukarya-like
6
Q
Name the 6 extremophilic Archaea.
A
- Methanogens: strict anaerobes producing methane
- Halophiles: need high [salt] > 3 M
- Hyper-thermophiles: live at > 70°C
- Psychrophiles: need temps. btw. 0°C – 10°C
- Acidophiles: require pH < 3
- Alkaliphiles: need pH ~ 10 for optimal growth
7
Q
What are Methanogens?
A
Extremophilic Archaea
- strict anaerobes
- producing methane by reducing CO2
- in fresh water, sea water, soil, but also as symbionts in the intestinal tracts of animals, including humans
- so far no human pathogen found among the archaea
-
Example: Methanobrevibacter smithii
- found in human intestinal tract, tooth flora
- makes up 10% of all anaerobes in the colons of healthy adults
- dominant archaeon in the human gut
- 1.85 million bp long circular genome
- 1’837 predicted genes
8
Q
What are Halophiles?
A
Extremophilic Archaea
- need high [salt] > 3 M (18%; normal sea water: 3.5%)
-
Examples:
- Haloferax volcanii:
- first isolated from the dead sea
- requires at least 1.5 M salt and 42°C (optimal growth at 3 M)
- 4.2 Mb large genome
(1 large & 3 smaller circular chromosomes; 1 plasmid) - ~ 4,300 genes
- ~ 20-40 copies of the chromosomes/cell
- Halobacterium salinarium:
- 5.2 M NaCl; dead sea
- are exposed to a high amount of UV radiation
- evolved a sophisticated DNA repair mechanism
- repairs DNA faster than other organisms
- produce bacteriorhodopsin → red color
- Haloferax volcanii:
9
Q
What are Hyper-thermophiles?
A
Extremophilic Archaea
- live at >70°C
-
Example: Geogemma barossii (aka Strain 121)
- lives at 121°C
- doubling time 24 h
- habitats are the “black smokers” (hydrothermal springs on the ocean floor)
10
Q
What are Psychrophiles?
A
Extremophilic Archaea
- need temps. btw. 0°C – 10°C
-
Example: Polaromonas vacuolata
- found in subglacial lakes in the Antarctic
- isolated ecosystem underneath 800 m ice
- 0.49°C and pH 8.1
- cell density 1.3 x 105 / ml
11
Q
What are acidophiles?
A
Extremophilic Archaea
- require pH < 3
- Example: Picrophilus torridus
- lives at pH 0 and 65°C
- found in sulfur fields
- intracellular pH very low (pH 4.6)
- acid stable cell wall (S-layer, ether lipids, low proton permeability)
- 1.5 Mb circular genome
- high coding density of 92%
12
Q
What are alkaliphiles?
A
Extremophilic Archaea
- need pH ~ 10 for optimal growth
- Soda deserts and soda lakes (pH 10.5 – 12)
- most are halo-alkaliphiles
-
Example: Natronococcus occultus
- pH 8.5 - 11
- NaCl up to 30%
- temp: up to 50°C
- GC content: 64%
13
Q
What are some molecular adaptations to extreme habitats?
A
- Archaea have typically an elevated GC content (> 50%)
- modified RNA nucleosides are overrepresented (e.g. in tRNAs)
- Proteins have high proportion of charged amino acids (Lys, Arg, His, Asp, Glu)
- genomes encode multiple chaperones
- use thermostable low molecular weight compounds
(e. g. NADPH is instable at 95°C → replaced by iron sulfide in hyperthermophiles) - encode special proteins:
- e.g. Reverse gyrase
- Type I Topoisomerase (catalyzes DNA single-strand breaks)
- gene fusion of a helicase with a type I Topoisomerase
- unusual, since it introduces positive supercoils
- only found in thermophilic archaea and thermophilic bacteria
- assumption: reverse gyrase stabilizes DNA at high temps
- e.g. Reverse gyrase
→ It is still unclear at the molecular level, what makes an organisms extremophilic
14
Q
What are the characteristic features of Archaea?
(Strucure)
A
- cell wall often consists of S-layer:
- S-layer proteins build two-dimensional crystalline surface on some bacteria and almost all archaea
- Do this spontaneously on solid surfaces
- S-layers consist of a single protein or glyco-protein (Mw 40 – 200 kDa) and form a layer with identical pores
- Produce a quasi periplasmic space in archaeal cell wall
- typical archaeal cell membrane consists of phospholipids carrying branched isoprene
- side chains that are linked to the glycerol via ether bridges
- bacteria and eukarya use D-glycerol, while archaea have L-glycerol
–> Tetraether membrane or transmembrane phospholipid
15
Q
What are Thaumarchaeota?
A
- most abundant archaea on earth
- Initially classified as ‘mesophilic Crenarchaeota’
- This novel phylum comprises all known archaeal ammonia oxidizers
- Most of the gene signatures analyzed belonged to the phylum Thaumarchaeota
- also found in hospitals and clean room facilities
- all man-made environments studied by the authors have revealed the presence of archaeal 16S rRNA genes
- metabolic potential for ammonia oxidation was supported by the successful detection of thaumarchaeal amoA genes in human skin samples.
- chemolithotrophic ammonia turnover could influence the pH regulation of the human skin and therefore the natural protective layer
17
Q
What are the Mechanisms of gene flow in archaea?
A
- Transformation, transduction & conjugation also found in archaea
-
In addition: new types of archaeal DNA transfer mechanisms
- Example: Chromosomal DNA exchange via the Ups and Ced system
18
Q
What is the Ups and Ced system?
A
Mechanism of gene flow in archaea
- upon UV damage Sulfolobus spp aggregate species-specifically (a)
- Chromosomal DNA exchanged
- likely needed to repair damaged DNA via homolgous recombination
- ups operon: encodes pilus (b,c)
- ced genes: encode membrane proteins (channels) that facilitate DNA transfer (d)
20
Q
How does the archaeal phylogenetic tree look like?
A
