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.