NSF Award
9974984
Lopez<br/><br/>Polyketide (PK) compounds and their biosynthetic enzymes represent diverse phenotypes in microorganisms, but the underlying causes for this diversity are not completely understood. The major hypothesis of this research is that biosynthetic polyketide synthase (PKS) sequence diversity and "programming" is driven by positive diversifying selection and accounts for the majority of polyketide metabolite diversity observed in nature. A comparative bioinformatics approach will be implemented to achieve the following objectives: a) Infer the secondary and higher order enzyme structures of published PKS loci, such as those coding for erythromycin, rapamicin, and rifamycin by comparisons with fatty acid synthases (FAS) or by using bioinformatics software such as FIREBIRD; b) Compare sequences and predicted enzyme structures of "paralogous" modules (within a single PK pathway) and correlate these with corresponding PK metabolite or PK intermediates and infer possibility of gene duplications; c) Compare orthologous (between different bacteria and different pathways) PKS enzyme module sequences and structures to obtain correlations with PK metabolite end products and also to investigate the possibility and frequency of horizontal gene transfer; d) If PKS structures appear structurally homologous, determine specific residues and codons in primary sequences which are pivotal for structural determination, while if structures are not homologous, investigate how active centers remain functional, and why they are conserved, using data on predicted structural conformations; e) Determine whether codons and residues which appear pivotal for structure determination and overall enzyme function are positively selected (to preserve analogous/homologous structures or function); f) Isolate several new or longer PKS gene sequence segments from marine microbes previously characterized from the HBOI collection. Through these analyses, a model of molecular adaptation based on the evolution of PKS enzyme sequence, structure, and function will be formulated and integrated with the biosynthesis of the ultimate phenotypic products (PK metabolites). <br/><br/><br/>Public Impact<br/><br/>Nature manifests its diversity at numerous levels, with one being the biochemical diversity of natural products. Understanding the fundamental bases of this diversity, at cellular, genetic and molecular levels, will facilitate the harnessing of natural products, such as polyketide antibiotics, for practical purposes. However a large knowledge gap exists between genetic sequence data and their phenotypes, the physical expression of genes, which this research aims to fill. Still, molecular sequence information can be used for tracking the evolutionary history, inferring molecular structures and obtaining the contemporary ecological context of certain genes coding for polyketide natural products. Moreover, despite the many natural compounds with therapeutic potential that have been discovered, the supply of those products is often less than optimal. This research can have a direct impact on polyketide supply issues since the target of study are the genes involved in the biosynthesis of polyketide compounds.
