New Age of water
Entire biochemistry and cell biology textbooks will have to be rewritten
on how water in the cell and extracellular matrix is stage-managing the drama
of life. This continues the exclusive series started in
SiS 23.
ISIS Press Release 16/10/04
What’s the Bacterium Really Like?
Far from being a bag of macromolecules dispersed at random inside a
rather tough cell wall, the bacterium is highly and spontaneously organised
into nested functional compartments through interactions between the
macromolecules and cell water. Dr. Mae-Wan
Ho reports
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The sophisticated internal architecture of a bacterium
A bacterium is the simplest organism that exists, even though it is by
far the oldest, with a direct lineage going right back to the beginning of life
on earth some 3.8 billion years ago.
Plants and animals are referred to as eukaryotes, meaning
organisms whose cells have a ‘true’ nucleus, while the bacteria,
which have no nucleus, are referred to as prokaryotes. This is
indicative of their primitive status as "proto-cells", or forerunners to
eukaryotes. But this prejudice is unjustified, say Michael Hoppert and Frank
Mayer of Göttingen University in Germany. Frank Mayer, in particular,
spent many years studying bacteria, and can vouch for the sophisticated
internal architecture that exists in a bacterial cell.
Much of the prejudice against bacteria stems from their small size and
the tough cell wall, which make them difficult to study. The much larger plant
and animal cells show up many organelles inside such as mitochondria (where
food is oxidised to provide energy), lysosomes and peroxisomes (where
macromolecules are degraded back into building blocks), and many membrane-bound
compartments as well as a cytoskeleton of fibrous proteins that fill the
cytoplasm. But a typical electron micrograph of a bacterium on the same scale
would reveal an amorphous blob inside.
For a long time, people thought that the bacterium is little more than a
rather tough envelope filled with macromolecules scattered randomly throughout
the cytoplasm, and that its metabolism is extremely "helter-skelter and
inefficient".
In fact, bacteria are stunningly efficient, as is clear from the speed
with which they can multiply – doubling every 20 minutes or so in the
laboratory – and it makes much more sense to suppose that, even without a
membrane, the molecules required for a particular activity are grouped together
in what can be called "functional compartments".
The idea of functional compartments is not new, and has been proposed
even for eukaryotic cells since the first part of the last century (see The Rainbow and the Worm, the
Physics of Organisms). But the evidence for that has so far been
indirect.
When bacteria are sufficiently magnified - about one million times -
with a powerful enough electron microscopy, an astonishing amount of
sub-cellular organisation becomes evident; and it is possible to see several
well-defined compartments immediately.
Inside the outer cell wall layers, referred to as the
‘capsule’, an E. coli cell is further enclosed by two
membranes with a space in between – the periplasmic compartment –
where nutrients and wastes are captured and sorted, and where a cell-shape
controlling network of polysugars and peptides, the peptidoglycan, is located.
At the centre of the cell is the densely packed DNA strands of the bacterial
genome, folded into a compact body, a nucleoid, forming a loosely
defined compartment devoted to storage and use of genetic information. In
between the nucleoid and the inner membrane is the cytoplasm, filled with
ribosomes (organelles for protein synthesis) and multi-enzyme or multi-protein
complexes performing a variety of functions. The most obvious multi-protein
complex, connected to the inner membrane, is the flagellar-motor that turns a
long, helical flagellum to propel the bacterium through its aqueous
environment. Chaperonins and proteosomes are respectively responsible for
folding new proteins and disposing of used, obsolete ones. DNA polymerase
complexes attached to the DNA strands are responsible for replicating the
genetic information. The pyruvate dehydrogenase complex links three sequential
reactions together, delivering the metabolites from one reaction to another via
a flexible arm of the protein.
But where is the cytoskeleton? Using antibody-staining techniques, Frank
Mayer has found evidence of abundant fibrous proteins that form a web-like
structure just inside the inner membrane, to which the ribosomes –
organelles for synthesizing proteins – are attached.
Thus, there is no doubt that the bacterial cell is just as highly
organised as cells of ‘higher’ organisms.
Spontaneous order out of chaos due to interactions with cell water
But how are these functional compartments formed? Studies in the
laboratory of Hoppert and Mayer suggest that they form spontaneously as the
result of the intrinsic properties of the biological molecules themselves and
the way they interact with water in the cytoplasm. Also, the specific structure
of water itself could influence the level of enzyme activity in particular
microenvironments.
For example, there are compartments called inclusion bodies in certain
bacteria, which appear to be storage granules consisting of starch or fats that
are not soluble in water. Among the fats often found in inclusion bodies are
long chains of fatty acids called polyhydroxyalkanoates (PHAs). Like most fats,
they are hydrophobic (water-hating). However, the enzymes that synthesize PHAs
are soluble in water. So, while they are synthesized, PHAs are linked to the
enzymes and form a complex, part of which is water-soluble and part of which is
not. Eventually, the complex rounds up into a spherical compartment in which
the water-soluble enzymes form the outer shell, shielding the water insoluble
PHAs inside. Water is expelled from the interior, creating an inner compartment
separate from the cytoplasm by the water-soluble enzyme molecules. As the PHA
inclusion bodies mature, amphiphilic molecules (molecules that love
water at one end and hate it at the other) - specific proteins and
phospholipids - are added to the growing circumference of the boundary layer,
while more PHAs are added to the interior.
Reversed micelles offer clue to spontaneous organisation
Hoppert and Mayer studied enzyme activity in artificial ‘reversed
micelles’. A conventional micelle is formed when water surrounds
amphiphilic molecules that tend to form a sphere, with their water-hating ends
inside the sphere and their water-loving ends outside in the water. A reversed
micelle is just the opposite. The water-loving ends are inside the sphere
interacting with water, while the water-hating ends are outside in touch with a
sea of organic solvent.
Depending on the size of the reversed micelle and the location of the
water molecules within, the water can adopt two different structures. Water
close to the periphery of the micelle in direct contact with the barrier
molecules differs from that in the centre, and both are different from bulk
water (see Fig. 1). The low-density water forms a lot more intermolecular
hydrogen bonds than bulk water, and tends to resemble ice. It also has less
charge, is less reactive and more viscous than bulk water. High-density water
molecules, by contrast, are less likely to form hydrogen bonds with their
neighbours than in bulk water, and are also less free to move about.
Figure 1. A reversed micelle with enzyme trapped
inside.
In the living cell, all compartments and macromolecular assemblies
affect water structure, according to Hoppert and Mayer, so there is a
non-random variation in high and low density water throughout the cell (see "The importance of cell water",
this series), and in turn this would affect the function of the proteins.
It is possible to measure the vibrational frequency of proteins
dissolved in low-density water using the reverse micelle system. This revealed
that low-density water decreases the vibrational frequency compared with
proteins dissolved in bulk water. The vibrational frequency affects enzyme
activity. For example, lowering the vibrational frequency of an enzyme may
increase the temperature at which the enzyme achieves optimum rate of reaction.
Enzymes seem to like low-density water best, where they are presumably more
free to move around.
Hoppert and Mayer found that the enzyme activity also depends on the
size of the reverse micelles, and remarkably, all enzymes reach optimum
activity at a particular size that is approximately the spacing of the
periplasmic space in the living cell, about 2 to 10 nanometres wide. Hoppert
and Mayer introduced the term ´nanospaces´ to describe them. An
organisation into nanospaces is not only found in bacteria; it is also common
in any other living cell. This suggests that enzymes may be sitting in a
microenvironment of structured water that promotes optimum activity inside the
cell. Thus, the layered structure of dense and light water within the cell is
part and parcel of the subcellular organisation that enables the cell to
function most efficiently.
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