JOURNAL of BIOTECHNOLOGY RESEARCH in TROPICAL REGION, Vol. 1, Oct. 2008 (Special Edition) ISSN: 1979-9756 Polymorphism Analysis of Polyketide Synthase Gene from Actinomycetes Genome DNA of Taman Nasional Gunung Halimun Soil by Using Metagenome Method 1 Polymorphism Analysis of Polyketide Synthase Gene from Actinomycetes Genome DNA of Taman Nasional Gunung Halimun Soil by Using Metagenome Method Irvan Faizal 1 *, Retno Lestari 2 , Frans Kurnia 2 , Abdul Latif 1 , Dudi Hadianto 1 , Nila Kusumawati 1 , Indra Rachmawati 1 , Bambang Marwoto 1 , Wahyu Purbowasito 1 1 Balai Pengkajian Bioteknologi–BPPT, Puspiptek Serpong 2 Department of Biology, Faculty of Mathematics and Natural Sciences, University of Indonesia, Depok Abstract Polymorphism of PolyKetide Synthase (PKS) gene from Actinomycetes using metagenome sequence based of soil sources from Taman Nasional Gunung Halimun (TNGH) was analyzed by PCR-RFLP profil- ing method. PKS gene is a gene responsible for polyketide synthesis which has role in drugs produc- tion such as antibiotics, anticancer and immunosup- pressant. Most of polyketide compounds have been used in pharmaceuticals industry based from Acti- nomycetes. Metagenome sequence based was car- ried out to screen PKS gene which the steps con- sists of DNA genome isolation, type I PKS detection, metagenome library construction, insert verification of metagenome library, PCR-RLFP profiling and grouping of clones analysis by UPGMA (unweighted pairgroup method using arithmatic mean). PCR product of PKS gene (1.4 kb in size) has been suc- cessfully detected using degenerated primer design. Twelve out of 13 PCR-RFLP profiles of verified in- serted PKS were different. UPGMA clustering me- thod revealed the existence of 2 clusters within 12 verified clones. The result suggested that there was a significant polymorphism among PKS genes of soil from TNGH. Keywords: type I polyketide synthase gene, meta- genome, degenerate primer, PCR-RFLP, UPGMA. *Correspondence to: Irvan Faizal e-mail: faizal@webmail.bppt.go.id INTRODUCTION The difficulties in cultivating microorganisms exclude the majority of the microbial soil communi- ty from a functional analysis of their genes and the subsequent use of the microbial gene products. Therefore, there is a high probability of finding novel microbial products, such as antibiotics and enzymes, in uncharacterized soil bacteria. Several studies have shown that the metagenomic approach (DNA extracted directly from varied soil/microbial habitats) permits searches for various natural prod- ucts including polyketide and biocatalysts, together with the genes responsible for them. Polyketide is one important of natural product which can be synthesized by a wide range of organ- isms, including bacteria, fungi, marine organisms (molluscs, sponges) and plants. This metabolite is also known to possess a wealth of pharmacological- ly important activities and has a great commercial interest for drug discovery and account for medicin- al sales exceeding $20 billion per year. Polyketide natural products include many clini- cally important drugs, such as erythromycin (anti- bacterial), epothilone (anti-cancer), rapamycin (im- munosuppressant), and lovastatin (antihypercholes- terolemic). They are biosynthesized from short car- boxylic acid precursors by polyketide synthases (PKSs) (Mathews et al., 2000). One of interested PKSs is type I polyketide synthases (PKS-I). PKS-I synthesizes natural products of therapeutic interest, such as erythromycin, rapamycin or epothilone, and their organization provides facility in the selection of promising clones. Properties of PKS-I make them particularly well suited for the metagenomic DNA library approach (Ginolhac et al., 2004). To date, here we describe the construction and initial screen- ing of metagenomic library of PKS-I made with DNA isolated directly taken from soil sample of Taman Nasional Gunung Halimun (TNGH), West