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Project Progress

We have concentrated on evolution of proteins during this period from the point of view of distantly related families of proteins that share mechanism of reaction.

In some cases, families of proteins related transitively by sequence similarity are closely related in the actual reaction performed, such as aminotransferases, and in the organic biochemistry of the reaction mechanisms. Members of such a family are closely related to each other, differing only in specificity for the substrates.

In other cases, families of proteins related transitively have a loose structure so that all members are not related to all others. The same reaction mechanisms are employed, but are used to carry out different reactions. Another example of a family of similar sequences includes reactions with different Enzyme Commission numbers and different names such as oxidase, synthase, carboligase. Yet they are all FAD-utilizing, thiamine diphosphate-requiring decarboxylases. Protein names can fool us. Sequence similarities point out relationships.

By understanding such mechanistically similar families, we can picture an ancestral protein giving rise to each family. The diversity in evolutionary paths followed from the ancestor to the present is evident in the fact that protein families are not identical in membership in different organisms. The above-mentioned thiamine diphosphate-requiring decarboxylase families are not identical in E. coli and B. subtilis. Some members are close orthologs, but others have no instance in the other bacterium. For instance, the B. subtilis enzyme malonic semialdehyde oxidative decarboxylase is involved in utilization of myo-inositol as a carbon source. B. subtilis encounters quantities of myo-inositol in its soil environment, but E. coli does not encounter it in its various environments, thus evidently has no need for this enzyme.

Thus by examining families of proteins in different organisms, we gain an appreciation for common ancestry and for the ways that evolutionary divergence of proteins met diverse biological needs. The families in different organisms may have descended from a common ancestor but the end products of evolution that exist today in contemporary organisms have been tuned to fulfill the individual needs of that organism.