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Archaea
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Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
History:
Until 20th century: Living organisms belongs to 2 kingdoms (Plants & Animals)
In the 1950s & 1960s, previous system failed to accommodate Fungi, Protists &
Bacteria.
By the 1970s, 5 Kingdoms system: 1 prokaryotic (Bacteria) and 4 Eukaryotics
(plants, Animals, Fungi & Protists).
In the late 1970s: Discovery of entirely new group of organisms (Archaea).
It is true that most archaeans don't look that different from bacteria under the
microscope, and that the extreme conditions under which many species live
has made them difficult to culture, so their unique place among living organisms
long went unrecognized.
However, biochemically and genetically, they are as different from bacteria
as you are. Although many books and articles still refer to them as "Archaebacteria",
that term has been abandoned because they aren't bacteria -- they're Archaea.
In 1965, Linus Pauling and Emile Zuckerland proposed instead using the sequences
of the genes in different prokaryotes to work out how they are related to each other.
Archaea for Ph.D. students by
This approach, known as phylogenetics,
is the main method used today.
Dr.Farokh Rokhbakhsh-Zamin
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and Dr.Nadia KAzemiPour
Archaea: Morphology
Archaea are tiny, usually less than one micron long (one one-thousandth of a
millimeter). Even under a high-power light microscope, the largest archaeans
look like tiny dots. Fortunately, the electron microscope can magnify even
these tiny microbes enough to distinguish their physical features.
Much like bacteria, cocci and rods are common shapes, Other shapes can also
exist but no spirochetes or mycelial forms yet. They are branched/flat shapes.
Sizes vary (typically 1-2 x 1-5 m for rods, 1-5 m in diameter for cocci)
Smallest observed is 0.2 m in diameter
Largest is a multicellular form that can reach 30 mm in length!
Archaea: Morphology
Archaea are tiny, usually less than one micron long (one one-thousandth of a
millimeter). Even under a high-power light microscope, the largest archaeans
look like tiny dots. Fortunately, the electron microscope can magnify even these
tiny microbes enough to distinguish their physical features. You can see archaean
images below, made using a variety of micrographic techniques.
Some are spherical, a form known as coccus, and these may be perfectly round
or lobed and lumpy.
Some are rod-shaped, a form known as bacillus, and range from short barshaped rods to long slender hair-like forms.
Some oddball species have been discovered with a triangular shape, or even a
square shape like a postage stamp!
Structural diversity among archaeans is not limited to the overall shape of the
cell. Archaea may have one or more flagella attached to them, or may lack
flagella altogether.
The flagella are hair-like appendages used for moving around, and are attached
directly into the outer membrane of the cell.
When multiple flagella are present, they are usually attached all on one side of
the cell.
Other appendages include protein networks to which the cells may anchor
themselves in large groups.
As with other living things, archaeal cells have an outer cell membrane that
serves as a barrier between the cell and its environment. Within the membrane
is the cytoplasm, where the living functions of the archeon take place and
where the DNA is located.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
Around the outside of nearly all archaeal cells is a cell wall, a semi-rigid layer
that helps the cell maintain its shape and chemical equilibrium. All three of these
regions may be distinguished in the cells of bacteria and most other living things,
but when you take a closer look at each region, you find that the similarities are
merely structural, not chemical.
In other words, Archaea build the same structures as other organisms, but they
build them from different chemical components.
For instance, the cell walls of all bacteria contain the chemical peptidoglycan.
Archaeal cell walls do not contain this compound, though some species contain a
similar one. Likewise, archaea do not produce walls of cellulose (as do plants) or
chitin (as do fungi). The cell wall of archaeans is chemically distinct.
Like bacteria, archaeans have no internal membranes and their DNA exists as a
single loop called a plasmid.
Their tRNAs have a number of features that differ from all other living things.
The tRNA molecules (short for "transfer RNA") are important in decoding the
message of DNA and in building proteins. Certain features of tRNA structure are
the same in bacteria, plants, animals, fungi, and all known living things -- except
the Archaea. There are even features of archaeal tRNA that are more like
eukaryotic critters than bacteria, meaning that Archaea share certain features in
Archaea
for Ph.D. students by
common with you and not with
bacteria.
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
Basic Archaeal Structure : The three primary regions of an archaeal cell are
the cytoplasm, cell membrane, and cell wall. Above, these three regions are
labelled, with an enlargement at right of the cell membrane structure.
Archaeal cell membranes are chemically different from all other living things,
including a "backwards" glycerol molecule and isoprene derivatives in place
of fatty acids. See text below for details.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
Archeal ribosomes are the giant processing molecules that assemble proteins for
the cell. While bacterial ribosomes are sensitive to certain chemical inhibiting
agents, archaeal and eukaryotic ribosomes are not sensitive to those agents. This
may suggest a close relationship between Archaea and eukaryotes.
The most striking chemical differences between Archaea and other living things
lie in their cell membrane. There are four fundamental differences between the
archaeal membrane and those of all other cells:
(1) chirality of glycerol, (2) ether linkage, (3) isoprenoid chains, and (4)
branching of side chains.
These may sound like complex differences, but a little explanation will make the
differences understandable. The header for each explanation is color-coded to
match the relevant portion of the diagram below.
(1) Chirality of glycerol : The basic unit from which cell membranes are built
is the phospholipid. This is a molecule of glycerol which has a phosphate
added to one end, and two side chains attached at the other end. When the cell
membrane is put together, the glycerol and phosphate end of the molecules hang
out at the surface of the membrane, with the long side chains sandwiched in the
middle (see illustration). This layering creates an effective chemical barrier
around the cell and helps maintain chemical equilibrium.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
This is the same situation as the stereoisomers of glycerol. There are two
possible forms of the molecule that are mirror images of each other. It is not
possible to turn one into the other simply by rotating it around.
While bacteria and eukaryotes have D-glycerol in their membranes, archaeans
have L-glycerol in theirs. This is more than a geometric difference. Chemical
components of the cell have to be built by enzymes, and the "handedness"
(chirality) of the molecule is determined by the shape of those enzymes. A cell
that builds one form will not be able to build the other form.
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Flexible
Rigid gives
membrane
stability to
thermophiles
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
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Gram positive
Cell wall of pseudomurein or
other complex carbohydrate
Gram negative
No outer membrane
No cell wall
Thick protein/glycoprotein coat
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Ribosomes :
bacterial/archaeal ribosome = 70S but eukaryotic (80S) S = Svedburg unit
Bacterial and archaeal ribosomal RNA:
16S small subunit & 23S and 5S in large subunit
archaea have additional 5.8S (also seen in eukaryotic large subunit)
Proteins vary (archaea more similar to eukarya than to bacteria)
1.
2.
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Cannulae:
Members of the genus Pyrodictium were isolated from hydrothermal marine
environments, with growth temperatures ranging from 80 to up to 110C.
hollow, tube like structures on the surface of these archaea
may be involved in formation of networks of multiple daughter cells 25
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Cells grow in a network of tubules termed cannulae, which connect the cells with
each other.
Cannulae are hollow tubes with an outside diameter of 25 nm, and they appear
empty when cross-fractured or thin-sectioned.
They consist of at least three different, but homologous, glycoprotein subunits
with identical N termini but with different molecular masses of 20, 22, and 24
kDa.
The structure of the cannulae is highly resistant to heat as well as denaturing
agents, as no morphological changes were observed after 60 min of incubation at
140C or 10 min at 100C and 2% sodium dodecyl sulfate.
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.
The final length of the cannulae varied between 30 and 150 micrometer with an
elongation rate of 1.0 to 1.5 micrometer/min, which is significantly higher than
the elongation rate for bacterial flagella, e.g., Salmonella (0.16 micrometer/min
in in vitro measurements)
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Hami (Hamus):
not well understood
grappling hook appearance
involvement in cell adhesion mechanisms?
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Pili:
Sulfolobus cells taken freshly from a hot spring are attached to sulfur particles
by numerous 5-nm wide pili. Pili have also been observed in many other
archaea.
There are glycosylation pathway to the assembly of both flagella and pili in
Methanococcus maripaludis. Deletion of an acetyltransferase gene involved in
the biosynthesis of the glycan that is N linked to the flagellins resulted in
nonflagellated cells. Unexpectedly, this mutant also lacked pili on the cell
surface. Pili were found in the culture supernatant, indicating that deletion of the
gene did not affect pilus formation but rather affected attachment of the pili to
the cell surface.
Even though the pilins had similarities to bacterial type IV pilins, the structure
formed by the archaeal pilins is unlike that bacterial pili.
Investigation of the biochemistry, genetics, and functions of archaeal pili has
only recently begun. Consequently, it is presently unclear if archaea possess the
vast diversity of pilus types, with assorted functions and assembly mechanisms,
presently known to occur in bacteria.
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FIG. 6. Pili on the surface of a flaK mutant of Methanococcus maripaludis. This mutant
cannot make flagella, leaving the peritrichously located pili evident as the only surface
structure remaining on the cell surface. The sample was negatively stained with 2%
phosphotungstic acid, pH 7. Bar, 200
nm.
Archaea for Ph.D. students by
Courtesy of S.-I. Aizawa, reproducedDr.Farokh
with permission.
Rokhbakhsh-Zamin
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and Dr.Nadia KAzemiPour
Bindosome:
The bindosome in Sulfolobus solfataricus.
the actual structure has not been visualized in the membranes but rather it is
thought to be a pilus-like structure close to the cytoplasmic membrane or
integrated within the S-layer.
The main evidence in support of the presence of this hypothesized structure is
that the proposed structural components, the substrate binding proteins (SBPs),
contain class III signal peptide sequences, a feature typical of proteins which are
well known to form oligomeric structures in both archaea and bacteria.
The oligomerized complex is proposed to play a role in facilitating sugar uptake,
a function that enables Sulfolobus 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 80C.
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.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
38
Previous studies showed that S. solfataricus has a wide range of ABC transport systems
for sugar uptake. ABC transporters encompass the actual transport domain in the
membrane and cytoplasmically located ATPases, which drive the transport of the
substrate by ATP hydrolysis
At the periplasmic side of the membrane, SBPs bind the substrate and deliver it to the
transport domain. Interestingly, the signal peptides from one class of sugar binding
proteins of S. solfataricus resemble class III signal peptides found in archaeal flagellins or
bacterial pilins.
The controlled assembly/surface localization of SBPs probably enables the organism to
scavenge nutrients more readily from the environment to concentrate substrates in the
periplasmic space between the S-layer and the cytoplasmic membrane.
The bindosome may represent an affinity cascade that channels substrates to the ABC
transporters. Whether the SBPs are assembled into a pilus-like structure or are attached
in a controlled manner to the S-layer remains to be determined(Fig. 7).
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FIG. 7. (A) 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. (B) Electron micrograph
of flagellated S. solfataricus P2 cells. Flagella are
Archaea for Ph.D. students by
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present all around the cells and do notDr.Farokh
appearRokhbakhsh-Zamin
bundled. Bar, 1 m.
and Dr.Nadia KAzemiPour
Archaea
Similarities to prokaryotes
Size
Shape
Lack nucleus
Single chromosome
Genes in operons
No introns
Similarities to eukaryotes
Few plasmids
RNA polymerase/promoters
Translation machinery: ribosome and tRNA
Sequencing of Methanococcus jannaschii in 1992 showed 56% of genes not
similar to bacteria or eukaryotes!
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Proposed model for assembly of archaeal flagella using Methanococcus voltae as a model.
Sandy Y. M. Ng et al. J. Bacteriol. 2008;190:6039-6047
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
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The Nucleoid
Irregularly shaped region in bacteria and archaea
Usually not membrane bound (few exceptions)
Location of chromosome and associated proteins
Usually 1 (some evidence for polyploidy in some archaeons)
Supercoiling and nucleoid proteins (histones, Alba, condensins) aid in folding
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Bacteriorhodopsin:
The halophilic archaeon makes use of light for both energy and sensory
transduction by exploiting a family of light-sensitive proteins. The archaeal
rhodopsin, a 26.5 kDa protein, has a transmembrane domain of seven helical
protein segments which photons are captured via a retinal chromophore. The
excellent thermodynamic and photochemical stability of bacteriorhodopsin has
led to many uses in technical applications like holography, spatial light
modulators, artificial retina, neural network optical computing, and volumetric
and associative optical memories.
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Archaea systematics:
Reliable and repeatable classification of bacteria was not possible until the late 20th
century when molecular biology made it possible to sequence their DNA.
Because ribosomes are so critically important is the functioning of living things, they are
not prone to rapid evolution.
A major change in ribosome sequence can render the ribosome unable to fulfill its
duties of building new proteins for the cell. Because of this, we say that the sequence in
the ribosomes is conserved -- that it does not change much over time. This slow rate of
molecular evolution made the ribosome sequence a good choice for unlocking the
secrets of bacterial evolution. By comparing the slight differences in ribosome sequence
among a wide diversity of bacteria, groups of similar sequences could be found and
recognized as a related group.
In the 1970s, Carl Woese and his colleagues at the University of Illinois at UrbanaChampaign began investigating the sequences of bacteria with the goal of developing a
better picture of bacterial relationships. Their findings were published in 1977, and
included a big surprise. Not all tiny microbes were closely related. In addition to the
bacteria and eukaryote groups in the analysis, there was a third group of methaneproducing microbes. These methanogens were already known to be chemical oddities in
the microbial world, since they were killed by oxygen, produced unusual enzymes, and
had cell walls different from all known bacteria.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
46
These bacteria that lived at high temp. or produced methane clustered together
as a group well away from the usual bacteria and the eubacteria.
Because of this vast difference in genetic makeup, Woese proposed that life be
divided into three domains: Eukaryota, Eubacteria, and Archaebacteria.
He later decided that the term Archaebacteria was a misnomer, and shortened it
to Archaea. The three domains are shown in the next page, which illustrates
also that each group is very different from the others.
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planet.
Some live near rift vents in the deep sea at temperatures well over 100 degrees
Centigrade.
Others live in hot springs (such as the ones pictured above next page), or in
extremely alkaline or acid waters.
They have been found thriving inside the digestive tracts of cows, termites,
and marine life where they produce methane.
They live in the anoxic muds of marshes and at the bottom of the ocean, and
even thrive in petroleum deposits deep underground.
Some archaeans can survive the dessicating effects of extremely saline
waters. One salt-loving group of archaea includes Halobacterium, a wellstudied archaean. The light-sensitive pigment bacteriorhodopsin gives
Halobacterium its color and provides it with chemical energy.
Bacteriorhodopsin has a lovely purple color and it pumps protons to the
outside of the membrane. When these protons flow back, they are used in the
synthesis of ATP, which is the energy source of the cell. This protein is
chemically very similar to the light-detecting pigment rhodopsin, found in the
vertebrate retina.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
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Archaea
Bacteria
Ester-linked lipids,
peptidoglycan
Eukarya
Cell Membrane
Ether-linked lipids,
pseudopeptidoglycan
Gene Structure
Multiple, linear
chromosomes, similar
translation and
transcription to Archaea
Internal Cell
Structure
No membrane-bound
organelles or nucleus
No membrane-bound
organelles or nucleus
Membrane-bound
organelles and nucleus
Metabolism
Various, including
photosynthesis, aerobic and
Photosynthesis and
anaerobic respiration,
cellular respiration
fermentation, and autotrophy
Reproduction
Asexual reproduction,
horizontal gene transfer
Asexual reproduction,
horizontal gene transfer
Ester-linked lipids,
various structures
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Archaean Phylogeny :
The phylogeny of archaeans is based on
molecular sequences in their DNA. The
analysis of these sequences reveals three
distinct groups within the Archaea.
1. The Euryarcheota are probably the best
known, including many methaneproducers and salt-loving archaeans.
2. The Crenarcheota include those
species that live at the highest
temperatures of any known living things,
though a wide variety have recently been
discovered growing in soil and water at
more moderate temperatures.
3. The Korarcheota are only known from
their DNA sequences -- nothing more is
known about them yet since they have
only recently been discovered.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
52
In many ways, archaeal cells resemble the cells of bacteria, but in a number of important
respects, they are more like the cells of eukaryotes. The question arises whether the
Archaea are closer relatives of the bacteria or our our group, the eukaryotes.
This is a very difficult question to answer, because we are talking about the deepest
branches of the tree of life itself; we do not have any early ancestors of life around today
for comparison.
One novel approach used in addressing the question is to look at sequences of
duplicated genes. Some DNA sequences occur in more than one copy within each cell,
presumably because an extra copy was made at some point in the past. There are a very
few genes known to exist in duplicate copies in all living cells, suggesting that the
duplication happened before the separation of the three domains of life.
In comparing the two sets of sequences, scientists have found that the Archaea may
actually be more closely related to us (and the other eukaryotes) than to the bacteria.
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Methanogenic archaea
Archaeal sulfate reducers
Extremely halophilic archaea
Cell wall-less archaea
Extremely thermophilic S0-metabolizers
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Methanogens:
1.
2.
3.
4.
5.
6.
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1.
2.
3.
4.
5.
6.
7.
8.
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Halophilic Archaea:
(Eubacteria, Haloarcula, Halobacterium, Halococcus, Haloferax, Natronobacterium,
Natronococcus occultus)
1.
2.
3.
4.
5.
6.
7.
8.
Gram negative or Gram positive, Rods and regular to highly irregular cells.
chemooorganotrophs
aerobic or facultatively anaerobic
Neutrophilic or alkalophilic.
Mesophilic or slightly thermophilic (up to 55 C).
requirement for high concentrations of sodium chloride (1.5 Molar or above).
Carotenoids give reddish color
Bacteriorhodopsin capture light for energy in anaerobic respiration
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Methanogenes:
Subgroup 1:
Methanobacterium, Methanobrevibacter, Methanosphaera, Metthanothermus
Subgroup 2 :
Methanococcus, Methanocorpusculum, Methanoculleus, Methanogenium
Methanolacinia paynteri, Methanomicrobium mobile, Methanoplanus,
Methanospirillum hungatei
Subgroup 3:
Methanococcoides methylutens, Methanohalobium evstigatus, Methanohalophilus,
Methanolobus, Methanosarcina, Methanothrix
1. Gram-negative or Gram-positive
2. A wide range of morphological types Cells are coccoid bodies, pseudosarcina or
rods
3. nonmotile or motile
4. Very strictly anaerobic
5. Produces methane
6. Cells do not contain muramic acid. Lipids are predominantly isoprenoid
hydrocarbons ether-linked to glycerol.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
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7.
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Biotechnological Applications:
The extremophilic nature of many Archaea: to probe the potential
biotechnological applications of their stable cellular components.
This is particularly true of their enzymes (called extremozymes), which are
able to remain catalytically active under extremes of temperature, salinity, pH
and pressure.
Many interesting enzymes have been isolated from extremophilic microbes.
Specific archaeal metabolites have also been purified and characterized and
some of them have potential industrial uses.
Genes encoding several enzymes from extremophiles have been cloned in
mesophilic hosts, with the objective of overproducing the enzyme and altering
its properties to suit commercial applications.
Escherichia coli, Bacillus subtilis and yeasts have been used successfully as
mesophilic hosts for several archaeal genes. Genetic engineering techniques are
valuable tools for creating novel biocatalysts that can improve bioprocesses and
facilitate the realization of innovative or novel biotransformations.
Molecular biology has the potential both to overcome the limitations on
enzyme availability and to design new biocatalysts specific to a particular
industrial purposes.
Archaea for Ph.D. students by
Dr.Farokh Rokhbakhsh-Zamin
and Dr.Nadia KAzemiPour
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Condition
Thermophile
Psychrophile
Product
Application
Glucose, fructose for sweeteners
Xylanases
Paper bleaching
proteases
DNA polymerase
Genetic engineering
Proteases
Dehydrogenases
Biosensors
Amylases
Acidophile
Low pH (0-4)
Sulfor oxidation
Desulfurization of coal
Alkalophile
High pH (8-11)
Cellulase
Halophile
Whole M.O.
Biopolymer
Piezophile
High pressure
Whole M.O.
Whole M.O.
Bioremediation, biomineralization
Radiophile
Whole M.O.
Bioremediation of radionuclide
contaminated sites
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The continuous production of halophilic -amylase can be performed via wholecell immobilization of Halobacterium salinarum in alginate beads and a
polyvinyl alcohol film. The cells were osmotically stable and showed
continuous enzyme production for 45 days. The stabilized cells could be
permeabilized by chloroform treatment without leakage of the intracellular
components. Using this procedure, cells can be reused under improved
stabilized conditions for biotechnological applications
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Archaeosomes:
Liposomes are lipid-bilayer bounded vesicles that can be used as a delivery vehicle
for certain vaccines, enzymes and drugs. The term Archaeosome was
introduced by Sprott and co-workers to describe liposomes made with ether lipids
that are unique to the Archaea domain confering considerable stability on liposomal
vesicles. Extensive mouse model studies involving intravenous, oral and
subcutaneous administration of archaeosomes demonstrated that archaeosomes are
safety molecules and they are not toxic.
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In addition to the serine proteases, other types of enzymes have been identified
in extremophiles. Good examples are a thiol protease (propylpeptidase) from
Pyrococcus sp. and a new type of protease from P. furiosus.
Psychrophilic enzymes have potential applications in a broad range of
industrial, agricultural and medical processes. The recent interest in this field is
due to the challenge of finding stable proteases that function in cold water.
In addition, peptidyl synthesis studies with mesophilic enzymes have shown
that low temperature favors high yields because of reduced hydrolysis of the
acyl-enzyme intermediate.
In most other processes, reduced energy consumption due to low temperature
operation will be a significant advantage.
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