Archaea Bacteria (Methanogens, Halophiles, Thermophiles)

MI 204 UNIT-1
Archaea bacteria
B y : D r . M o h a m m e d A z i m B a g b a n
A s s i s t a n t P r o f e s s o r
C . U . S h a h I n s t i t u t e o f S c i e n c e
A h m e d a b a d

CONTENTS
 A . I n t r o d u c t i o n a n d p h y l o g e n y
 B . G e n e r a l p r o p e r t i e s
 1 ) C e l l w a l l a n d c e l l m e m b r a n e
 2 ) C h r o m o s o m e
 3 ) R i b o s o m e
 C . S a l i e n t f e a t u r e s o f :
 1 ) M e t h a n o g e n s
 2 ) H a l o p h i l e s
 3 ) T h e r m o p h i l l i c S 0 m e t a b o l i z e r s

INTRODUCTION
Archaea constitute a domain of single-celled organisms.
These microorganisms lack cell nuclei and are therefore
prokaryotes. Archaeal cells have unique properties
separating them from the other two domains, Bacteria and
Eukaryote. Archaea are further divided into multiple
recognized phyla.

Introduction
 The archaea comprise organisms that evolved as a separate domain, often retaining highly
specialized phenotypic characteristics. A striking characteristic is the presence of ether
linkages in the lipids of their cytoplasm membranes. This distinguishes the archaea from
eukaryotes and most bacteria. Most archaea cultured to date come first unusual and
typically inhospitable environments; most grow under extreme environmental conditions.
 Archaea are extreme thermophiles and some can grow at temperatures over 100° C. Some
extremely thermophilic archaea are sulfate reducers and other metabolize elemental sulfur
and hydrogen sulfide. Yet others are extreme halophiles growing in such hostile
environments as the Dead Sea. Most archaea grow under anaerobic condition.
Methanogens, which grow only under strictly anaerobic and often thermophilic conditions
are the only organisms capable of producing methane. As studies of archaea progress
other phenotypes will undoubtedly be revealed. Already the presence of archaea have been
detected in aerobic marine waters, including Antarctic coastal environments. These newly
discovered archaea will likely extend the phenotypic characteristics of archaea from those
of thermophily, halophily sensitivity to oxygen, elemental sulfur metabolism, sulfate
reduction, and methanogenesis, which are the major specialized features of archaea that
have been cultured and studied.

Property Archaea Bacteria Eukarya
Cell membrane Ether-linked lipids Ester-linked lipids Ester-linked lipids
Cell wall
Pseudopeptidoglycan, glycoprotein,
or S-layer
Peptidoglycan, S-layer, or no cell
wall
Various structures
Gene structure
Circular chromosomes, similar
translation and transcription to
Eukarya
Circular chromosomes, unique
translation and transcription
Multiple, linear chromosomes,
but translation and transcription
similar to Archaea
Internal cell struct
ure
No membrane-
bound organelles or nucleus
No membrane-bound organelles
or nucleus
Membrane-bound organelles
and nucleus
Metabolism
Various, including diazotrophy,
with methanogenesis unique to
Archaea
Various,
including photosynthesis, aerobic
and anaerobic
respiration, fermentation,
diazotrophy, and autotrophy
Photosynthesis, cellular
respiration, and fermentation; no
diazotrophy
Reproduction
Asexual reproduction, horizontal
gene transfer
Asexual reproduction, horizontal
gene transfer
Sexual and asexual
reproduction
Protein synthesis
initiation
Methionine Formylmethionine Methionine
RNA polymerase Many One Many
EF-2/EF-G Sensitive to diphtheria toxin Resistant to diphtheria toxin Sensitive to diphtheria toxin
Comparison with other domains

Phylogeny
• Phylogeny is the study of relationships among different groups of organisms
and their evolutionary development. Phylogeny attempts to trace the
evolutionary history of all life on the planet. It is based on the phylogenetic
hypothesis that all living organisms share a common ancestry.
• The relationships among organisms are depicted in what is known as a
phylogenetic tree. Relationships are determined by shared characteristics, as
indicated through the comparison of genetic and anatomical similarities.
• A phylogeny is represented in a diagram known as a phylogenetic tree. The
branches of the tree represent ancestral and/or descendant lineages.
• Relatedness among taxa in a phylogenic tree is determined by descent from
a recent common ancestor.
• Phylogeny and taxonomy are two systems for classifying organisms in
systematic biology. While the goal of phylogeny is to reconstruct the
evolutionary tree of life, taxonomy uses a hierarchical format to classify,
name, and identify organisms.

GENERAL
PROPERTIES OF
ARCHEA
CELL WALL, CELL MEMBRANE,
CHROMOSOME, & RIBOSOME

CELL WALL
• Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.
• In most archaea the wall is assembled from surface-layer proteins, which
form an S-layer.
• An S-layer is a rigid array of protein molecules that cover the outside of the
cell (like chain mail). This layer provides both chemical and physical
protection, and can prevent macromolecules from contacting the cell
membrane.
• Unlike bacteria, archaea lack peptidoglycan in their cell walls.
• Methanobacteriales do have cell walls containing pseudopeptidoglycan,
which resembles eubacterial peptidoglycan in morphology, function, and
physical structure, but pseudopeptidoglycan is distinct in chemical structure;
it lacks D-amino acids and N-acetylmuramic acid, substituting the latter with
N-Acetyltalosaminuronic acid.

CELL WALL
• Cell walls with several distinct chemical compositions
are found among diverse archaeal species.
• Although some archaea stain Gram-negative (red-
pink) and others stain Gram-positive (blue-purple). no
archaean has a true bacterial Gram-negative or
bacterial Gram-positive cell wall structure-all archaea
lack peptidoglycan in their cell walls. Rigid cell walls,
morphologically resembling those of Gram-positive
bacteria, are found in the species of Methanopyrus,
Methanobacterium, Methanosar- cina, Halococcus,
and Natronococcus (Pseudopeptidoglycan as shown
in fig.).

CELL WALL
• However, the chemical structures of the cell
wall polymers are completely different.
Instead of peptidoglycan, the cell walls of
archaea may contain pseudopeptidoglycan,
methanochondroitin, proteins, or
glycoproteins.
• The occurrence of chemically diverse cell
walls suggests that the common archaeal
ancestor most likely lacked a cell wall and
that the diversity of archaeal cell walls
evolved independently within the various
evolutionary branches of the archaeal
domain.

CYTOPLASMIC MEMBRANE
• The cytoplasmic membranes of archaea are unique in terms of
structure and chemical composition.
• They have a high protein content and diverse lipids, including in
various Archaeal species phospholipids, sulfolipids, glycolipids,
and a nonpolar isoprenoid lipid.
• Phospholipids are never the dominant lipids in archive cytoplasmic
membranes. The lipids of the archaeal cytoplasmic membrane
have branched hydrocarbons that increase the fluidity of the
cytoplasmic membrane because they do not form a highly
crystalline structure.
• The structure of the cytoplasmic membranes of many archaea is a
lipid bilayer composed of glycerol diether lipids: this is analogous to
the lipid bilayers of bacterial and eukaryotic membranes.

• The cytoplasmic membranes of some archaea, however. are monolayers composed
of glycerol tetraether lipids. These monolayers, which are very heat stabile, have
hydrophilic portions (glycerol) at the cytoplasm and external interfaces and an
internal hydrophobic portion (hydrocarbons).
• Unlike the bacterial and eukaryotic lipids, which are usually based on ester linkages,
archaeal lipids are mainly isopranyl glycerol ethers. These molecules are synthesized
by the condensation of glycerol or other alcohols with isoprenoid hydrocarbons of 20,
25, or 40 carbon atoms.
• Ether lipids may have evolved before ester lipids found in most bacteria and all
eukaryotic cells. Only the cytoplasmic membranes of archaea and few bacteria, such
as Thermotoga and Aquifex that occur in the deepest bacterial phylogenetic
branches, have ether as well as ester linkages.

• The physiologically specialized structures and chemical compositions of the
cytoplasmic membranes of archaea are well adapted to function under the extreme
conditions where many archaea grow.
• The structures of these archaeal cytoplasmic membranes make them very resistant
to conditions that disrupt the function of a normal bilipid layer thereby enabling them
to remain as semipermeable barriers in extreme habitats.
• The cytoplasmic membrane of Sulfolobus, for example, contains long chain branched
hydrocarbons twice the length of the fatty acids in the cytoplasmic membranes of
bacteria, enabling the cytoplasmic membrane of this organism to function at pH 2
and temperatures up to 90° C.

• The lipids and proteins of the cytoplasmic membranes of halobacteria are well
adapted for the highly ionic environments in which halobacteria live.
• Halophilic archaea contain various unusual lipids in their cytoplasmic membranes.
• Polar lipids always exceed nonpolar lipids and acidic amino acids always exceed
neutral and basic amino acids in these cytoplasmic membranes. The negatively
charged residues are required for ionic Shielding to maintain protein stability. The low
proportion of nonpolar amino acids in the highly ionic environment is believed to be
necessary to induce hydrophobic bond formation within the proteins. Many
membrane-bound enzymes of extreme Halophiles show maximal activity at high salt
concentrations and are irreversibly inactivated by exposure to low salt.

ARCHAEAL CHROMOSOME
• The archaeal chromosome resembles the bacterial chromosome in that it is circular.
• However there are significant differences in the organization of the archaeal
chromosome and the proteins associated that make it more similar in some ways to
with it the chromosomes of eukaryotic cells than to the bacterial chromosome.
• Histone-like proteins are involved in maintaining the structure chromosome and also
affect the expression of the archaeal the archaeal genes, Several types of histone-
like proteins are associated with the DNA of the archaeal chromosomes.
• Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of
the proteins encoded by any one archaeal genome being unique to the domain,
although most of these unique genes have no known function.

ARCHAEAL CHROMOSOME
• Of the remainder of the unique proteins that have an identified function, most belong
to the Euryarchaeota and are involved in methanogenesis. The proteins that
archaea, bacteria and eukaryotes share form a common core of cell function, relating
mostly to transcription, translation, and nucleotide metabolism. Other characteristic
archaeal features are the organization of genes of related function – such as
enzymes that catalyze steps in the same metabolic pathway into novel operons, and
large differences in tRNA genes and their aminoacyl tRNA synthetases.

ARCHAEAL CHROMOSOME
• Archaea usually have a single circular chromosome, the size of which may be as
great as 5,751,492 base pairs in Methanosarcina acetivorans, which boasts the
largest known archaean genome. One-tenth of this size is the tiny 490,885 base-
pair genome of Nanoarchaeum equitans, which possesses the smallest
archaean genome known; it is estimated to contain only 537 protein-encoding
genes. Smaller independent pieces of DNA, called plasmids, are also found in
archaea. Plasmids may be transferred between cells by physical contact, in a
process that may be similar to bacterial conjugation.

ARCHAEAL RIBOSOME
• The 70S ribosomes of archaeal cells, which is com posed of 50S and 30S subunits,
closely resembles the 70S ribosomes of bacterial cells. Archaeal 30s ribosomal subunits
have a characteristic protrusion, referred to as a bill that does not occur in bacterial
ribosomes.
• A similar protrusion occurs in the 40S subunit of eukaryotic ribosomes. Archaeal 70S
ribosomes are less complex than the 80S ribosomes of eukaryotic cells in terms of number
of RNA and protein molecules making up the ribosomes and the number of nucleotides
within the ribosomal RNA molecules. Archaeal ribosomes, like those of bacterial cells
contain three RNA molecules-23S rRNA, 16S rRNA, and 5S rRNA and various ribosomal
proteins.

ARCHAEAL RIBOSOME
• The nucleotide sequences within the ribosomal RNA molecules are diagnostic of specific
evolutionary branches of archaea. Analysis of 16S rRNA nucleotide sequences are the
bases for establishing phylogenetic relationships among archaea and between bacteria,
archaea, and eukaryotes.
• In addition to the rRNAs incorporated into archaeal ribosomes, all archaea contain large
amounts of a stable RNA molecule designated is the 7S RNA. The function of 7S RNA is
unknown but it has been suggested that it plays a role in ribosome associated activities.
RNA The gene encoding the 7S RNA in Methanothermus fervidus and Methanobacterium
thermoautotrophicum is adjacent to the rRNA genes.

ARCHAEAL RIBOSOME
• The ribosomes of the extreme halophiles and most of the methanogens contain
approximately 54 to 56 proteins. (Bacterial ribosomes similarly contain about 55 proteins).
Additionally the ribosomes of the extreme halophiles have acidic rather than basic,
proteins, Ribosomes of the extreme Thermophiles and Methanonococcus species contain
approximately 71 ribosomal proteins. 28 in the 30S subunit and 43 in 50S subunit, In
addition many of these proteins have higher molecular weights than are found in the
ribosomal proteins of the extreme halophiles and other methanogens. Having a high
ribosomal protein content however, is not essential for translational fidelity and efficiency
and for accuracy of ribosome assembly at high temperatures.

SALIENT FEATURES OF
Methanogens
Halophiles
Thermophillic S0 metabolizers

METHANOGENS
• Methanogens are microorganisms that produce methane
as a metabolic byproduct in hypoxic conditions. They are
prokaryotic and belong to the domain of archaea. They are
common in wetlands, where they are responsible for
marsh gas, and in the digestive tracts of animals such as
ruminants and many humans, where they are responsible
for the methane content of burping in ruminants and
flatulence in humans.
• In marine sediments, the biological production of methane,
also termed methanogenesis, is generally confined to
where sulfates are depleted, below the top layers.
Moreover, methanogenic archaea populations play an
indispensable role in anaerobic wastewater treatments.
Others are extremophiles, found in environments such as
hot springs and submarine hydrothermal vents as well as
in the "solid" rock of Earth's crust, kilometers below the
surface.

METHANOGENS
• Methanogens are coccoid (spherical shaped) or bacilli (rod shaped). There are over 50
described species of methanogens, which do not form a monophyletic group, although all
known methanogens belong to Archaea. They are mostly anaerobic organisms that cannot
function under aerobic conditions, but recently a species (Candidatus Methanothrix
paradoxum) has been identified that can function in anoxic microsites within aerobic
environments. They are very sensitive to the presence of oxygen even at trace level.
Usually, they cannot sustain oxygen stress for a prolonged time.
• However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase
(SOD) enzyme, and may survive longer than the others in the presence of O2. Some
methanogens, called hydrogenotrophic, use carbon dioxide (CO2) as a source of carbon,
and hydrogen as a reducing agent.

METHANOGENS
• The reduction of carbon dioxide into methane in the presence of hydrogen can be
expressed as follows:
CO2 + 4 H2 → CH4 + 2H2O
• Some of the CO2 reacts with the hydrogen to produce methane, which creates an
electrochemical gradient across the cell membrane, used to generate ATP through
chemiosmosis. In contrast, plants and algae use water as their reducing agent.
• Methanogens lack peptidoglycan, a polymer that is found in the cell walls of Bacteria but
not in those of Archaea. Some methanogens have a cell wall that is composed of
pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline
array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

METHANOGENS
Methane Production
• Methanogens are known to produce methane from substrates such as H2/CO2, acetate,
formate, methanol and methylamines in a process called methanogenesis. Different
methanogenic reactions are catalyzed by unique sets of enzymes and coenzymes. While
reaction mechanism and energetics vary between one reaction and another, all of these
reactions contribute to net positive energy production by creating ion concentration
gradients that are used to drive ATP synthesis.
• Approximately 65% of the methane released to the atmosphere is produced by
methanogens. Although all methanogens share the common ability to generate energy by
methanogenesis, these archaea are otherwise extremely diverse as evidenced by the
G+C contents of their DNA. which ranges from 25 to 60 mole%.

METHANOGENS
Methane Production
• Diverse methanogens have evolved several metabolic reactions for generating cellular
energy. All are based on anaerobic respiration and all produce ethane (As shown Table)

METHANOGENS
Methane Production
• Methanogenesis- Reduction Pathway. The
conversion of CO2 to CH4 (methane) is carried out
by methanogenic archaea. This is a strictly
anaerobic pathway involving the flow of electrons
from a hydrogen donor.
• Several unique electron carriers are involved in the
transfer of electrons in this pathway, including factor
420, factor 430 (F430) coenzyme M (CoM),
methanopterin (MP) and methanofuran (MF). The
oxidation of hydrogen, which occurs outside of the
cell produces hydrogen ions and supplies electrons
for the reduction of which occurs inside the cell.
Because the reduction of F420 inside the cell
consumes protons, and the oxidation of hydrogen
produces protons outside the cell, the net result is
the establishment of a proton gradient (protonmotive
force) across the membrane

METHANOGENS
Methane Production

HALOPHILES
• The halophiles, named after the Greek word for "salt-
loving", are extremophiles that thrive in high salt
concentrations. While most halophiles are classified into
the domain Archaea, there are also bacterial halophiles
and some eukaryotic species, such as the algae Dunaliella
salina and fungus Wallemia ichthyophaga.
• Some well-known species give off a red color from
carotenoid compounds, notably bacteriorhodopsin.
• Halophiles can be found in water bodies with salt
concentration more than five times greater than that of the
ocean, such as the Great Salt Lake in Utah, Owens Lake
in California, the Dead Sea, and in evaporation ponds.
They are theorized to be a possible candidate for
extremophiles living in the salty subsurface water ocean of
Jupiter's Europa and other similar moons.

HALOPHILES
• These archaea are extreme halophiles requiring 12% to 15% salt for growth.
• Halobacterium and Halococcus (archaeal species assigned names before the recognition
of the archaea) have been isolated from various highly saline environments, including
natural salinas (highly saline environments) and solar salt ponds of marine origin, rock salt,
hypersaline soils, inland salt lakes and salted fish, bacon, and sausages.
• Halophilic archaea have several physiological adaptations that permit their growth in
habitats with salt concentrations that cause cellular water loss and protein denaturation in
other organisms These archaea have high internal concentrations of potassium chloride,
and their enzymes must have a greater tolerance of salt than the enzymes of non
halophilic organisms.

HALOPHILES
• In many cases, high concentrations of salt are
required by halophiles to maintain their enzymatic
activities. Halophilic archaea. such is
Halobacterium, have unique chloride which are
based on halorhodopsin, that transport chloride into
the cell so as to maintain osmotic balance and
make up for the loss of chloride ions that leave the
cell when protons are expelled. The maintenance
of appropriate chloride concentrations is critical for
the survival of Halobacterium. The cell wall of
Halobacterium appears to be stabilized by sodium
ions. The ribosomes of Halobacterium require high
concentrations of potassium for stability. These
adaptive features permit Halobacterium species to
live in the saturated brine environments of salt
lakes.

THERMOPHILIC METABOLIZERS
• The adaptation to thermophilic growth is
one of the most striking features of the
archaea (As shown in Fig.). One
evolutionary line of archaea, the
crenarchaeota, are extreme
thermophiles.
• Organisms with optimal growth
temperatures above 80°C are almost
always archaea and to date only
archaea have been shown to have
growth temperatures above 100° C.

• Pyrodictium brockii has an optimal growth temperature of 105°C which clearly
approaches the upper temperature limits for life. The highest temperature at which
archaeal growth can occur is not known. As long as liquid water exists, even very high
temperatures apparently do not preclude the existence of life as demonstrated by the
hyperthermophilic archaea. Clearly the ability to grow at very high temperatures requires
specialized physiological adaptations.
• The proteins of extremely thermophilic ar chaea must resist thermal denaturation.
Comparisons of proteins from extremely thermophilic archaea and non thermophiles,
however, does not reveal any major differences in patterns of amino acid sequences. Any
motifs of amino acid arrangements that provide the basis of protein stability in extreme
thermophiles are indirect and not universal.

• From a biophysical viewpoint, protein folding must be critical in protecting amino groups against
thermal conversion to ammonia. Stabilization by relatively high levels of hydrophobic amino
acids most likely is necessary to help maintain the integrity of proteins in hyperthermophilic
archaea.
• Besides proteins the genome and cytoplasmic membranes must remain functional at high
temperatures. The double helical DNA of the genome must not melt that is, it must not be
converted to single-stranded DNA at elevated temperatures. DNA of thermophilic archaea
tends to have relatively high G+C contents, which helps maintain the integrity of their hereditary
molecules. The cytoplasmic membranes of archaea that can live at extremely high
temperatures are very stable due to isoprenoid phytanylglycerol diethers and biphy
tanyldiglycerol tetraethers constituents. The thermal stability of the archaeal membranes
permits them to grow in locations at temperatures well above those where bacteria can grow.

• .Thermophilic and extremely thermophilic
archaea occur in various habitats, such as
geothermal vents, solfataras (volcanic vents
that give off steam and sulfur-containing
gaseous compounds), and anaerobic
bioreactors (As shown in Fig.).
• These include the thermal deep sea vents
where volcanic raise water temperature too well
over 100°C Archaea isolated from vents in the
erupding thermal areas surrounding deep
oceans can grow under very high pressure at
110°C.

• Extremely thermophilic archaea have also been found in the pools surrounding terrestrial
thermal vents. Thermococcus and Pyrococcus Species are extremely thermophilic
archaea live near such geothermal vents. They utilize organic carbon from peptides or
amino acids and Sometimes carbohydrates.
• Many thermophilic archaea also grow surrounding habitats rich in elemental sulfur.
Elemental sulfur serves as an electron acceptor, which form H2S as a result of their
metabolism. These thermophilic sulfur-metabolizing archaea in pieces of Pyrodictium,
Pyrobaculum, De- pyrococcus, Thermococcus, and Thermomicrobium. The optimal
temperatures for these archaea generally are 80°C to 100°C. Additionally thermophilic
methanogens have been isolated from Various habitats, including the sludges from
anaerobic bioreacters.

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