pm (JEIO Tech Co SI-900R) aerobically Flask cultures were ca

p.m. (JEIO Tech. Co. SI-900R) aerobically. Flask cultures were carried out in a 500-mL Erlenmeyer flask containing 100 mL medium. The MR medium contains (L−1): (NH4)2HPO4, 4 g; KH2PO4, 6.67 g; citric acid, 0.8 g; Protein Tyrosine Kinase inhibitor MgSO43H2O, 0.8 g; and trace metal solution (Lee & Lee, 1996), 5 mL. For N-source-limited cultivation, (NH4)2HPO4 was replaced with 4 g L−1 Na2HPO4 and 1.8 g L−1 NH4Cl was added. For the selection of R. eutropha harboring the intron donor plasmid after conjugation, kanamycin

was added at 300 μg mL−1 in MR medium and 500 μg mL−1 in LB medium (Slater et al., 1998; Burgdorf et al., 2001; Ewering et al., 2006). Kanamycin was added at 500 μg mL−1 in LB broth and an agar plate Sorafenib during the IPTG induction experiments for the expression of the Ll.LtrB intron cassette. Escherichia coli TOP10 was used as a general cloning host strain and E. coli S17-1 was used as a donor strain for conjugation (Table 1). For the cultivation of recombinant E. coli, kanamycin and chloramphenicol were used at 50 and 30 μg mL−1 in LB medium, respectively. The intron donor plasmid pBBR1Int (Fig. 1) contains a mobile II group cassette of pCACYS3-tac (4-kb XmaI fragment) cloned downstream of the tac promoter (Ptac) between the XbaI and the HindIII sites of pTac99A. The retargeted intron segment was prepared by overlapping PCR using the primers

3-mercaptopyruvate sulfurtransferase including prIBS, prUniv, prEBS2, and prEBS1 (350-bp BsrGI/HindIII fragment). As detailed below, the final intron donor plasmid pBBR1RInt was constructed by cloning the PCR product into pBBR1Int (Fig. 1). All the primers used in this study are listed in Table 2. The optimally matched target sites in the chromosomal DNA were identified

and the PCR primers to amplify the retargeted intron were designed using a computer algorithm (http://www.sigma-genosys.com/targetron; Perutka et al., 2004). As an example gene to be knocked out in R. eutropha, the phaC1 gene (NC_008313, region: 1557353–1559122) encoding polyhydroxyalkanoate synthase was chosen. The best target site in the R. eutropha phaC1 gene, phaC1reh743s, where the terminal ‘s’ indicates the sense strand for the intron orientation, was identified as the site between positions +743 and +744 from the start codon of the phaC1 gene (5′-CCCGCTGCTGATGGTGCCGCCGTGCATCAA– intron–CAAGTACTACATCCT-3′) by the algorithm. The intron donor plasmid pBBR1RInt was constructed by cloning the phaC1-targeted intron into the pBBR1Int to modify the sequences of EBS1 and EBS2 in the intron RNA complementary to the sequences of IBS1 and IBS2 in the target DNA site (Fig. 1 and Table 1). The 350-bp retargeted intron was amplified by overlapping PCR with prIBS and prEBS1 from two fragments amplified with two pairs of primers: prIBS-prUniv and prEBS2-prEBS1 (Fig. 1 and Table 2).

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