Immense diversity found in secondary metabolite gene clusters in filamentous fungi and bacteria using comparative genomics

Secondary metabolism in microorganisms is defned as non-life essential metabolism such as the production of mycotoxins and antibiotic compounds. This defnition has to some extent been obscured as it is hard to defne what is essential for the life of a microorganism in natural environments. Who is to say that the secondary metabolite penicillin produced by species of Penicillium is not essential for the life of the fungi.

The compounds produced in these reactions are possible antimicrobial, biofuels, food spoilers and other important or valuable compounds. Secondary metabolism is, therefore, the subject of great curiosity for both biological and fnancial reasons. At the Center for Microbial Secondary Metabolites (CeMiSt) we are interested in the natural role of secondary metabolites and their response to other organisms.

Here we present the analysis of four diferent sets of organsims that are of interest in the study of natural environments like soil and food products. The number of known secondary metabolite compounds far exceed the number of characterized genes involved in these pathways and the efort required to elucidate the connection between metabolites and genes require time-consuming and expensive chemical characterization.

Because of the benefts and challenges in this elucidation much efort has been given to the computational prediction of genes involved in secondary metabolism, with the most prominent software being AntiSMASH (bacteria and fungi) and SMURF (fungi). These methods provide valuable knowledge in the selection of gene targets for further analysis and can increase the speed of gene to compound association tremendously.

Although taxonomy groups living organsism into specifc groups at diferent levels, genera, species and so on, the diversity within each group can vary. We investigated the geenral conservation of protein function, using protein sequences, by an all against all BLASTp comparison. The fraction, as a function of the total number of proteins in a species, of shared proteins was then calculated and presented in a matrix in Figure 2.

The cufof for signifcant hits is defned as a reciprocal BLAST [Altschul (1990)] hit with percent identety of over 50% and alignment coverage percentage sum (query and hit coverage) over 130%. The diagonal line is a self comparison, and is therefor always 100% (purple). We see that the overall diversity between species is much larger for Bacilli (20-40%) than for Pseudomonas (50-70%).

The Penicillium are as diverse as the Bacillus while the Aspergilli are the most divers of all the sets.