Detection and Expression of Biosynthetic Genes in Actinobacteria ...

BERVANAKIS, G.Chapter 3: RESULTSSection 3.1: Development of a Polymerase Chain Reaction BasedScreening Assay for the Detection of SecondaryMetabolite Biosynthetic Genes3.1.1 Primer design and PCR screening assay for actinobacterial type IIpolyketide synthases (PKS)Nucleic acid and amino acid sequence accession numbers of all available type II PKSactinobacterial genes that were retrieved from the databases and incorporated into thedesign of the primers act04f and act06r are presented in table 32.Table 32: Type II PKS genes with respective nucleic acid and amino acid sequencesincorporated into the design of the act04f and act06r PCR primers.Class/ Gene Secondary MetaboliteBiosynthetic GeneActinobacteria Amino AcidAccessionType IIPolyketides/KetosynthaseNucleotideAccessionNumberNumberPradimicin (PKS) Actinomadura verrucosospora BAA82309 AB019690Pradimicin (PKS) Actinomadura hibisca BAA23144 D87924Ardacin (ardIORF1) Kibdelosporangium aridum AAA67433 L24518Napthocyclinone (ncnA) Streptomyces arenae AAD20267 AF098965Mithramycin (mtmP) Streptomyces argillaceus CAA61989 X89899Tetracyclines (aur2A) Streptomyces aureofaciens BAA92278 AB024976Anthracycline (KS) Streptomyces bobili BAA92272 AB019690Chlorotetracyline Streptomyces aureofaciens BAB12566 AB039379Ciclacidine (KS) Streptomyces capoamus BAA92274 AB024972Actinorhodin (actIORF1) Streptomyces coelicolor A3(2) CAA45043 X63449Aclacinomycin (aknB) Streptomyces galilaeus BAA92273 AB024971Tetracenomycin (tcmK) Streptomyces glaucescens CAA33369 X15312Griseusin (gris1) Streptomyces griseus CAA54858 X77865Nogalamycin (KS) Streptomyces nogalater BAA92283 AB024981Nogalamycin (snoa1) Streptomyces nogalater CAA12017 AJ224512Daunomycin ( dpsA) Streptomyces peucetius AAA65206 L35560Platenomycin (KS) Streptomyces platensis BAA92279 AB024977Rhodomycin (KS) Streptomyces purpurascens BAA92276 AB024974Oxytetracycline (ORF1) Streptomyces rimosus CAA80985 Z25538Ravidomycin (orf1) Streptomyces rochei BAA87907 AB021222Steffimycins (KS) Streptomyces steffisburgenesis BAA92281 AB024979Frenolicin (frnL) Streptomyces roseofulvus AAA19616 L26338Panamycin (KS) Streptomyces tauricus BAA92275 AB024973Jadomycin (jadA) Streptomyces venezuelae AAB36562 AF126429Jadomycin (KS) Streptomyces venezuelae BAA92282 AB024980Anthracycline (KS) Streptomyces albus BAA92280 AB024978Monensin (KS) Streptomyces cinnamonensis CAA77596 Z11511Daunomycin (KS) Streptomyces sp. strain C5. AAA87618 L34880Aclacinomycin (KS) Streptomyces galilaeus AAF70106 AF257324Granaticin (gra-orf1) Streptomyces vioaceoruber Tü22 CAA34369 X16300The PCR assay designed for screening Type II PKS genes took advantage of theconsistent orientation of the β-ketoacyl synthase (KS α ) gene, which is one of three___________________________________________________________________________________70