Optimizing Enzyme Processes

Enzymes are frequently used in biotechnology to carry out specific biological reactions, either as chemical replacements for industrial processes or for the production of commercial bioproducts, foods and/or drugs. A large proportion of research goes into finding or creating enzymes with specific properties but sometimes the enzyme isn't 100% suited to the conditions under which it is needed. Enhancing the characteristics of the enzyme to make it more suitable, characteristics like thermostability, pH optima, or substrate specificity, can be done using a number of approaches. Each approach differs in terms of the amount of control and specificity it offers in terms of changing the protein or gene on a molecular level.
1) Natural Selection
Technically, this is not an example of how biotechnology is used to change a gene or enzyme, but it is an example of how researchers might obtain enzymes with desired traits, in the simplest, most obvious way possible. The simplest choice is to do nothing on the molecular level, but seek out naturally-occurring proteins with the characteristics that suit our intended needs.
Although this is one of the most traditional of applied early biotechnological practices, utilized long before we had the scientific “know-how” to control genetic and protein sequences, it is still in use today. For example, in the hunt for truly thermostable enzymes, capable of metabolic catalysis at temperatures as high as 80-100°C, scientists actively search deep-sea hydrothermal vents worldwide, for new species of bacteria expressing new genes. 2) Selective Pressure
If a naturally-occurring enzyme with the desired traits is not readily available, the next simplest option to obtaining one is to create an environment of accelerated natural selection. That is, take a microorganism expressing an enzyme with properties as close to the desired traits as you can find, and expose it to conditions of gradually-increased intensity. If the thermostable enzyme you have has an optimum temperature of 60°C, you might try growing the microorganism at 65, then 70, then 75°C and gradually work up to the temperature you desire, in the presence of the substrate of interest. If the substrate is a carbon source, providing it as the only carbon source in the media forces the microbe to utilize that source as food, and gradually raising the temperature might result in adaptations to more effective enzyme activity at the higher temperatures.
A similar approach can be used to change substrate specificity for an enzyme for which multiple carbon sources can be used, some more preferentially than others. The key is to have a means of selecting for the strains that have adapted and show some advantage, whether it be out and out survival, or faster growth on certain substrates, at certain temperatures, or at a certain pH. Examples of this are a bioindicator that is detectable through some kind of analytical method, once the dersired enzyme reaction takes place, or a pH indicator, if the reaction changes the pH of the culture growth media.