RNA concentration and purity were determined by measuring the ratio of OD260 nm to OD280 nm. The transcript levels of spnK, spnH, and spnI were assayed by two-step quantitative real-time PCR analysis with a 7500 Real-Time PCR System (Applied Biosystems). DNase treatment and cDNA synthesis were carried out using RNase-free DNase 1 (Invitrogen) and a High-capacity cDNA Archive kit (Applied Biosystems) according to each manufacturer’s instructions. The
real time PCR amplification was performed on the 25-μL mixture [consisting of 1 μg mL−1 template cDNA, 2× Power SYBR® Green PCR Master Mix (Applied Biosystems), and 0.4 μM forward and reverse primers] under the following conditions: 2 min at 50 °C and 10 min at 95 °C, Trichostatin A cost followed by 40 cycles of 30 s at 95 °C and 1 min at 60 °C. A control (RT-minus) reaction which included all components for real time PCR except for the reverse transcriptase was always performed. Specification of PCR amplification was checked with a melting curve using an additional stage of dissociation after the final cycle, beginning at 60 °C for 30 s and then incrementally increasing the temperature until 95 °C. The data was normalized with the transcript level of principal sigma factor (sigA) (Tanaka et al., 2009) and analyzed according to 2−ΔΔCT method (Livak & Schmittgen, 2001). Results were shown as the means of three replicate experiments.
Primer pairs P17/P18, P19/P20, P21/P22, and P23/P24 were used to amplify fragments of spnH, spnK, spnI, and sigA (Table S1). As illustrated in Fig. 1, the strategy of direct cloning based on Red/ET recombination was used. The Epigenetics inhibitor minimum linear cloning vector containing enough pUC replication origin, apramycin resistance gene, and oriT of RK2 and flanked by 50-bp homology arms each to the targeting molecule was directed to clone c. 18-kb spinosyn biosynthetic genes from the purified total genomic DNA of S. spinosa CCTCC M206084 in a precise, specific and faithful manner. PvuII digestion of the final constructs (designated as
pUCAmT-spn) from five different transformants all matched well with the theoretical pattern via agarose gel electrophoresis (Fig. S1a, lanes 1–5). PCR products of spnG (c. 1188 bp), spnK (c. 1173 bp), the c. 524-bp fragment of spnF, and c. 576-bp fragment of spnS were successfully achieved using pUCAmT-spn as template (Fig. S1b). The resultant pUCAmT-spn was transferred into S. spinosa CCTCC M206084 through conjugation, yielding three exconjugants (designated S. spinosa trans1, trans2 and trans3). All the c. 18-kb spinosyn biosynthetic genes were integrated into the chromosome by a single-crossover homologous recombination because plasmid pUCAmT-spn lacked the integrase gene, attP site, and an origin of replication in S. spinosa. The integration was checked by PCR using vector-specific primers. PCR amplification for the apramycin resistance gene yielded a band of c. 0.