[Paracelsus] What's the Bacterium Really Like? (fwd)

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Subject: [Paracelsus] What's the Bacterium Really Like?

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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 <http://www.i-

sis.org.uk/isisnews/sis23.php>SiS 23.

<http://www.i-sis.org.uk/TIOCW.php>The Importance of Cell Water

<http://www.i-

sis.org.uk/WITCRL.php>What's the Cell Really Like?

<http://www.i-sis.org.uk/WITBRL.php>What's the Bacterium Really Like?

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. <mailto:m.w.ho@...>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

Hoppert and Mayer of Göttingen University

in Germany. 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

<http://www.i-

sis.org.uk/rnbwwrm.php>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, 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 " <http://www.i-

sis.org.uk/TIOCW.php>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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