PHYSIOLOGY
OF ARCHAEA (EX ARCHAEOBACTERIA) DOMAIN / SUPERKINGDOM
some definitions
Mendosicutes = "bacteria with defective cell wall", the old
division in which Archaea were once located.
cytoplasmic membrane or plasma membrane or plasmalemma
:
lipids are exclusively branched isoprenoid hydrocarbons linked to glycerol
by di-/tetraether bonds. Glycerol diethers cause bilayered membranes ;
glycerol tetraethers cause monolayered membranes ; mixtures of di- &
tetraethers cause mixtures of mono- & bilayered membranes. Please note
that even cyclic tetraethers maintain the 4-5 nm membrane thickness. Hyperthermophiles
use branched glycerol tetraethers to increase membrane fluidity and so
they're often cell wall-less. In psychrophiles lipids mainly contain unsaturated
fatty acids.
apart from phospholipids, it also contains sulfolipids. Only the cell wall-less
Archaea
has sterols in the plasma membrane: this is a target for polyene antibiotics
(nystatin, candicidin, ...). Please note that Archaea can be identified
on peculiar phospholipid composition if growing under standard conditions.
Glycerol is the only known substrate that undergoes facilitated diffusion
in some Archaea.
Only in anaerobs and facultative anaerobs Glc enter the cell through
group
translocation with the so-called phosphoenolpyruvate:phosphotransferase
(PEP:PTS) system. PEP =(enzyme I)=> HPr => enzyme III-P => enzyme II-P
=> Glc/GlcN/2-dGlc/Fru/Man-P. For Man transport no enzyme III is necessary.
Only enzymes II and III are substrate specific.
Although chemiosmosis occurs mainly in mesosomes, sometimes it involves
non infolded plasma membrane.
nucleoid ornuclear region = the region in which the genome
is contained (not to be confused with the nucleoid in Eukarya
peroxisome !). It usually consists of a single negatively supercoiled circular
dsDNA molecule, but in Streptomyces and Borrelia it is linear
while in Rhodobacter sphaeroides there are 2 chromosomes. It may
be mesosome bound. Only histone-like proteins are associated with
DNA ("naked" molecule). Genome size varies from 0.58 Mbp to 4.4
Mbp : G+C contents (melting point analysis) varies between 28 to 72 %.
DNA duplication (40') is slower than cell division through binary fission
(20')
and therefore new rounds of synthesis are initiated by the cell even though
the previous copy has not fully replicated. Some Archaea genes contain
introns
and the transcription systems are orthologous to Eukarya ones (TBP,
more kind of RNA polymerases...). Nanoarchaeum
equitans has the smallest genome to date, a circular chromosome
only 490 kb long, with 552 coding sequences covering 95% of the genome
and containing little noncoding or pseudogene sequence that would have
suggested reductive evolution. Function has been assigned to 66% of the
genes; 18% have homologues of unknown function, and the remainder represent
archaeal-specific sequences. Analysis of gene function, together with the
observation that overinfection of the host crenarchaeon Ignicoccus
impedes its growth, points toward the lifestyle of an obligate parasite
rather than symbiont, and it has evolved from a primitive ancestor instead
of reductively from a more complex form.
ribosomes = more than 104 per cell, sometimes membrane-attached.
70S complexes [30S (= 21 S proteins, 16S rRNA (about 1542 nucleotides))
+ 50S (= 34 L proteins, 23S rRNA (about 2900 nucleotides))]. Archaea
ribosomes are selectively sensitive to Diphteria toxin and isomycin
the initiator amino acid in protein synthesis is Met
accessory apparatuses
mesosome = a localized infold in the plasma membrane.
inclusion bodies (not surrounded by membranes, on the contrary of
Eukarya
inclusion bodies !) =
polyPi (volutin, metachromatic granules)
poly-b-hydroxybutirate (PHB) =
S
cell wall = the multilayered sheet (sacculus) that surrounds
the plasma membrane. It confers resistance to osmotic shock allowing high
intracellular osmotic pressures (15-20 atm). It is not present in Thermoplasma
genus. When present it may consist of ...
peptidoglycans (e.g. : Methanobacterium). Main sugars in glycans
are N-acetyl talosaminouronic acid (NAT or T) and GlcNAc (NAG or
G) linked to each other by a (b1->3) glycosidic
bond (lysozime insensitive !) : T units are linked to L-aminoacid
containing oligopeptides by a penicillin-insensitive transpeptidase.
only non-sulfated polysaccharides (e.g. : Methanosarcina)
only sulfated polysaccharides (e.g. : Halococcus)
only proteins (e.g. : Methanomicrobium and Methanococcus)
negatively charged aminoacid-containing peptides (e.g. : Halobacteria,
in order to counteract high [Na+], so it lyses in [Na+]
< 15% !)
adhesion accessory apparatuses => biofilms or microcolony
glycocalix = it binds cell together forming multicellular aggregates
on rocks, animal tissues, ... It varies among species and may consist of
one of the following forms :
S layer = a crystalline (i.e. : self-assembling) protein layer found
outside the cell walls of some Archaea. It presents pores with 2-3
nm diameter.
movement accessory apparatuses =>
flagella = made up of M protein (in the basal body) and flagellin
(completely different from the structure of eukaryotic flagella). ?Run
and tumble? movement controlled by the direction of the flagellar spin
(counterclockwise spin = straight run ; clockwise spin = random tumble).
cilia =
axial filaments =
gas vacuoles =
magnetosomes =
pseudopodia =
chemoreceptors =
... phototaxis ... chemotaxis : response to the concentration of chemical attractants
(lengths of the straight runs increase) or repellants (lengths of the straight
runs decrease)
... magnetotaxis
cell shapes & arrangements : they are established by cell wall but
environmental conditions can change them
coccus (plural: cocci) : cells that are spherical in shape.
streptococcus : a bacterium with spherical cells arranged in chains,
like beads on a string.
staphylococcus : a bacterium with spherical cells arranged in clusters,
like clusters of grapes.
diplococcus : a bacterium with spherical cells arranged in pairs.
tetrad : spherical bacterial cells arranged in a group of four.
A tetrad arrangement looks almost like a square under the microscope.
sarcina (plural: sarcinae) : spherical bacterial cells arranged
in a group of eight. Sarcinae look like small cubes and may be difficult
to distinguish from tetrads.
bacillus (plural: bacilli) : a bacterium with rod-shaped cells.
The picture shows bacilli arranged singly.
diplobacillus : a bacterium with rod-shaped cells arranged in pairs.
streptobacillus : a bacterium with rod-shaped cells arranged in
end-to-end chains. Streptobacilli often resemble link sausages.
coryneform bacillus : a bacterium with irregularly rod-shaped cells
arranged at angles to form V- and L-shaped arrangements.
spirillum (plural, spirilla) : a bacterium with cells that are rigid
and spiral in shape (little coil).
vibrio : a bacterium with curved or comma-shaped cells.
spirochete : a bacterium with flexible, spiral-shaped cells. Spirochetes
often appear helical or corkscrew-shaped with tapered ends.
Enhanced Microbial Genomes LIBrary (EMGLIB),
Université Claude Bernard, Lyon
Biocatalysis/Biodegradation Database
: biocatalytic reactions and biodegradation pathways primarily for xenobiotic,
chemical compounds from the University of Minnesota
The Prokaryotes: A handbook on the biology of Bacteria, Second Edition,
Vol. 1-4, 1991. Springer-Verlag, New York NY. A. Balows, H. Truper, M.
Dworkin, W. Harder & K.-H. Schleifer
Bergey's manual of systematic bacteriology, First Edition, Vol.
1-4, 1989. Williams & Williams, Baltimore MD. John Holt (editor-in-chief).
.
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