Genomics & Informatics Vol. 6(4) 227-230, December 2008 *Corresponding author: E-mail kbkim@smu.ac.kr Tel +82-41-550-5377, Fax +82-41-550-5184 Accepted 28 October 2008 Computational Approach for Biosynthetic Engineering of Post-PKS Tailoring Enzymes Ki-Bong Kim 1 * and Kiejung Park 2 1 Department of Bioinformatics Engineering, Sangmyung University, Cheonan 330-720, Korea, 2 SmallSoft Co., Deajeon 305-728, Korea Abstract Compounds of polyketide origin possess a wealth of pharmacological effects, including antibacterial, anti- fungal, antiparasitic, anticancer and immunosuppressive activities. Many of these compounds and their semi- synthetic derivatives are used today in the clinic. Most of the gene clusters encoding commercially important drugs have also been cloned and sequenced and their biosynthetic mechanisms studied in great detail. The area of biosynthetic engineering of the enzymes involved in polyketide biosynthesis has recently advanced and been transferred into the industrial arena. In this work, we introduce a computational system to provide the user with a wealth of information that can be utilized for biosynthetic engineering of enzymes involved in post- PKS tailoring steps. Post-PKS tailoring steps are neces- sary to add functional groups essential for the biological activity and are therefore important in polyketide biosyn- thesis. Availability: The trial version of this system is available via WWW at http://sm.hacklib.com/. Keywords: pharmacological effects, gene clusters, bio- synthetic engineering, post-PKS tailoring step Introduction Polyketides are important natural products exhibiting an- tibacterial (rifamycin), antifungal (erythromycin), antitumor (doxorubicin), immunosuppressant (FK506) and choles- terol-lowering activities (lovastin). They are produced mainly by Streptomyces species which belong to the large group of mycelially growing, filamentous bacteria from soil known as actinomycetes. These gram-positive, fungi-like bacteria are one of the best known producers of secondary metabolites used as naturally occurring antibiotics. Each core of the polyketide is synthesized biologically under the control of an exceptionally large, multifunctional enzyme called polyketide synthase (PKS), in a manner similar to that of fatty acid synthesis, where the carbon backbones of the molecules are assembled by the successive condensation of small acyl units. There are presently three types of polyketides. Type I modular polyketides are built up by a PKS consisting of large multifunctional proteins with a different active site for each enzyme-catalyzed step in polyketide car- bon chain assembly. Type II iterative polyketides also known as aromatic polyketide are normally synthesized by a single PKS built up by discrete polypeptides which carry active sites that are used more than once in the biosynthetic pathway. Type III iterative polyketides were characterized not long ago and the type III PKS is a member of the chalcone synthase (CHS) and stilbene synthase (STS) superfamily of PKS previously only found in plants. The readily synthesized and cyclized polyketide is usually modified via hydroxylation, glycosylation, methyl- ation and acylation. These tailoring, or post PKS mod- ifications are believed to be crucial for addition of im- portant functional groups to polyketide skeletons and to the structural diversity and biological activity of this class of natural products (Rix et al., 2002; Kwan et al., 2008). The most frequently found post-PKS modifica- tions are catalyzed by oxidoreductases, a very broad group of enzymes consisting of oxygenases, oxidases, peroxidases, reductases (e.g., ketoreductases), and de- hydrogenases. In general, these enzymes introduce oxy- gen-containing functionalities, such as hydroxyl groups (‘hydroxylases’), aldehyde or keto groups, and epoxides (‘epoxidases’) or modify such functionalities by addition or removal of hydrogen atoms, e.g. transforming a ke- tone into a secondary alcohol or an aldehyde into a car- boxylic acid. Although oxidoreductases provide or mod- ify relatively small functional groups, they can have a tremendous impact on the binding properties of a mole- cule with respect to a biological ligand molecule (recep- tor protein, enzyme, DNA etc.). The term group trans- ferase refers to enzymes that possess transferase activ- ity introducing novel functional groups and altered pro- files on the product relative to the substrate. This en- zyme group contains important enzymes such as amino transferases, alkyl (usually methyl) transferases, acyl (usually acetyl) transferases, glycosyltransferases (GTs)