Sequence Diversity of Type-II Polyketide Synthase Genes in Streptomyces

Polyketides are structurally diverse secondary metabolites that include macrolides, polyethers and aromatics. They exhibit various biological activities such as antibacterial, antifungal, antiparasitic, immunosuppressive and antitumor effects, and are a rich sources of clinically useful pharmaceuticals1). In the biosynthesis of polyketides, the condensation of acyl-thioester molecules is catalyzed by polyketide synthase (PKS) with a mechanism analogous to fatty acid biosynthesis2). Three types of PKSs are known that are quite different from each other in their structures and functions. Type-I PKS is a large modular polypeptide containing multiple domains, each of which catalyze a different step in the synthesis of polyketides. On the other hand, type-II PKS consists of monofunctional polypeptides and its core part (minimal PKS) consists of two b-ketoacyl synthase (KSa and KSb) subunits and one acyl carrier protein (ACP). KSa in concert with KSb catalyzes the condensation of acyl-thioesters to form a carbon skeleton. KSb also works as a chain length-determining factor, while ACP acts as an anchor for the growing polyketide chain during the condensation and subsequent modification steps. Although type-II PKS is known to be involved in the biosynthesis of spore pigments, one of its other functions is the synthesis of aromatic antibiotics such as anthracyclines, tetracyclines and anthraquinones. The third type of PKS called type-III PKS is composed only of a single b-ketoacyl synthase, and distributed in plants3), bacteria4–6) and fungi7). Although a large number of bioactive polyketides have already been reported, the genes involved in the synthesis of most of these polyketides (pks) have not yet been investigated. In the case of type-II pks, for example, the biosynthetic genes of famous compounds such as actinorhodin, oxytetracycline and doxorubicin were cloned, sequenced and characterized, while those of other aromatic polyketides remain to be elucidated. Therefore, it is important to investigate uncharacterized pks genes for known aromatic polyketides to elucidate the structure-function relationships of PKS. Recent analysis of pks genes revealed the presence of large numbers of cryptic pks genes. For instance, the genome analyses of Streptomyces coelicolor and Streptomyces avermitilis demonstrated that they encode many pks genes whose functions have not yet been elucidated. Thus, these Streptomyces seem to produce hitherto unknown polyketides that had not been identified by traditional activity-based screenings8,9). Since the presence of novel pks genes in an organism is a good indicator of production of novel polyketide molecules in this organism, the sequencing of pks genes is often used as a screening method for the discovery of novel polyketides10–15). For example, analysis of novel pks genes in a rubromycin-producer led to the discovery of two novel angucyclines16). Since the NITE Biological Resource Center (NBRC) has a large number of Streptomyces strains along with the information on their production of antibiotics, the NBRC strains could be a good resource to explore pks genes for known polyketide antibiotics. In addition, pks gene discovery in these strains would provide information concerning their potential to produce unknown polyketides. In this study, we screened type-II pks genes in eighty three NBRC strains and determined partial sequences of detected KSa genes. Based on these results, we discuss the possible functions of these genes. Actinomycetologica (2006) 20:42–48 VOL. 20, NO. 2