engleski

The evolution of modular polyketide synthases

Natural products derived from bacteria have traditionally been an important source of new leads for the pharmaceutical industry. The clustering of genes encoding enzymes that biosynthesise these compounds are very interesting evolutionary systems, as they are subject to strong selective pressure and can undergo horizontal gene transfer. Gene clusters that encode modular polyketide synthases (PKSs) can undergo recombination events including duplication and deletion that contribute to their evolution. Modular PKSs are large multifunctional proteins composed of individual catalytic domains that can be grouped into modules, whose properties determine the extender unit that is built into the polyketide at each step. Most evolutionary studies have concentrated on the evolution of single domains within modules, which does not identify whether sequences are orthologues or paralogues. We identified orthologous clusters so that it was possible to examine the evolution of sets of orthologous domains within modules. This analysis was greatly assisted by using the ClustScan computer package (Starcevic et al., Nucleic Acids Res. 36: 6882-6892, 2008) for the efficient annotation of clusters in a hierarchical fashion. Gene conversion was detected by examining phylogenetic trees constructed from the sequences of single domains: ketosynthase (KS), acyl transferase (AT), acyl carrier protein (ACP), ketoreductase (KR), dehydratase (DH) and enoyl reductase (ER). In most cases, phylogenetic trees based on DNA and protein sequences gave essentially the same results. However, for the KS domain, DNA analysis showed over 50% more gene conversion events than the protein analysis ; this was interpreted as being due to strong selection pressure to preserve activity of this highly conserved domain. It was found that gene conversion was common and could affect any of the domains in a module. However, the frequencies of gene conversion varied between domains ranging from 27% for KS and 5% for ACP. To our surprise, this seemed to follow the biosynthetic order of the domains in a module (KS≈AT>DH>ER>KR>ACP). KS seems to be a generic domain with no contribution to specificity of the product and gene conversion between the KS domains of a cluster would explain the previous observation that all KS domains of a cluster group together in phylogenetic trees. AT determines substrate choice and AT domains with the same specificities from different clusters group together. In this case, constraints of function would explain why the gene conversion events do not result in grouping of all AT domains of a cluster. We suggest that a module could in fact be considered an evolutionary unit that drives selection in modular PKSs. Strategies for deducing evolutionary relationships of clusters in the presence of large amount of gene conversion will also be discussed.

Modular evolution; biological molecules; systems

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