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Enzymes in the environment
Dr Brett I Pletschke, Rhodes University
We may all be very familiar with enzymes in our bodies, specialised proteins
which aid in processes like digestion and respiration, but how much do we know
about those hard at work in nature. Researchers at Rhodes University's
Biochemistry, Microbiology and Biotechnology department are exploring novel
enzymes produced by bacteria for degrading environmental pollutants.
Enzymes perform a wide range of very important functions throughout nature.
They are highly specific and efficient, guiding the biochemistry of life with
great precision and fidelity. This fidelity is essential in the cells of living
organisms, and a multitude of mechanisms have evolved for controlling the
activity of these enzymes themselves. Enzymes play a key role in harvesting
energy from the sun via photosynthesis, perform a wide range of metabolic
functions throughout every living cell in the bodies of plants and animals, and
are in fact really the catalysts of all biological processes constituting life
on earth.
Bacteria and fungi also contain enzymes that are essential to their survival
in the environment. These organisms live in a variety of habitats, some fairly
moderate (these organisms are called mesophiles) and others in extreme
environments such as hydrothermal vents, hot springs, and sulphataric fields (extremophiles).
As extremophiles have adapted to these extreme habitats, they produce enzymes
(biocatalysts) that are able to function under conditions that their mesophilic
counterparts are not able to tolerate, and therefore are highly exploitable in
research areas such as bioremediation and biocatalysis.
Detoxifying the environment
Biodegradation is the natural degradation of matter in the natural
environment in the absence of any human intervention. Bioremediation, in
contrast, is characterised by human intervention and is the technology of
pollution treatment, using biological systems to transform and convert various
pollutant species in the environment to less toxic or non-toxic forms. An
effective bioremediation will produce harmless water and carbon dioxide as the
end products, which are then able to re-enter natural ecosystems.
Tiny microorganisms such as bacteria are often the agents of choice for
bioremediation. Scientists at Rhodes University have successfully exploited the
sulphate reducing bacteria (SRB) and methanogenic producing bacteria (MPB) for
treatment of municipal primary sewage and acid mine drainage (AMD) wastes. Both
these bacterial populations dramatically increase the rate of hydrolysis of
solid wastes under anaerobic conditions, and are also able to work together in a
very effective manner: The high levels of sulphate and metals contained in acid
mine drainage are removed using SRB, while the sulphide produced by the SRB
dramatically increases the rate at which the MPB hydrolyses primary sludge.
Biocatalysis by extremophiles
Enzymes produced by extremophiles (bacteria and fungi living in harsh
conditions) are also highly exploitable in the biocatalytic industry. For
example, thermophiles are organisms that live under conditions of extreme high
temperature. These produce thermophilic enzymes that are readily exploited in
industry, such as amylase, xylanases used in paper bleaching, proteases used in
baking, brewing and in detergents, as well as DNA polymerase enzymes used in
genetic engineering. Psychrophilic enzymes are present in psychrophiles,
organisms that have adapted to very cold climates, such as those microorganisms
living in the Artic and Antarctic regions. The psychrophiles are used in cheese
maturation and in the dairy industry (e.g. proteases) and biosensors (e.g.
dehydrogenases). Similarly, there are a host of other enzymes that are
acidophilic (tolerant to low pH), piezophilic (tolerant to high pressure) and
metalophilic (tolerant to high metal concentration). There is even a bacterium, Deinococcus
radiodurans, which is the most radiation-resistant organism known and is
recently being targeted and engineered for the bioremediation of radioactive
waste.
The sulphate reducing bacteria mentioned previously belong to the class of
acidophiles, as they are able to live in highly acidic environments in acid mine
drainage rich environments.
Monitoring the environment
These enzymes may have another important purpose - they can serve as
indicators of the "biochemical health" of the environment. Scientists
can selectively target and monitor certain molecules in nature which can help
them keep track of environmental pollution biodegradation and bioremediation
processes in a particular system such as a polluted river or in a waste
recycling plant. This is a relative new field of research, but already key
molecules have been identified in nature that may provide a lot of information
regarding the "metabolic state" of a system.
For example, monitoring enzymes responsible for sulphate activation and
reduction in anaerobic bacteria living in marine and estuarine sediments can
indicate the level of metabolic activity (sulphate activation and reduction)
that is occurring in these sediments. At the Department of Biochemistry,
Microbiology and Biotechnology at Rhodes University, we are currently
investigating enzymes and other biomolecules which can potentially provide more
information regarding the metabolic state of natural systems, thereby monitoring
the processes of bioremediation more effectively.
Novel metabolic pathways in nature
Although metabolic pathways in nature have for the most part been well
studied and characterised, there are still many pathways that exist in nature
that are poorly understood. At Rhodes, scientists are focusing efforts on the
natural biodegradative processes at work in nature that are responsible for the
cleavage of complex aromatic compounds.
There is still much to learn from enzymes, as they continuously surprise
scientists with their remarkable adaptability to extreme conditions. As a result
of increasingly more recalcitrant chemical pollutants finding their way into the
environment, microorganisms, and the enzymes they possess, have to constantly
adapt in order to deal with the presence of the pollutants. Microorganisms
either respond by implementing and optimising existing metabolic reaction
pathways in their genetic make-up to degrade harsh chemical poolutants, or they
develop new pathways, degrading these compounds into non-toxic components or
elements that can be reassimilated for their own cellular metabolism and
survival.
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