Recombinant proteins are used routinely in macromolecular crystallographic experiments. Efficiency in cloning thus becomes a valuable resource to a macromolecular crystallographer. The use of type IIS restriction enzymes (outside cutters) concurrent with ligation allows for rapid cloning. A vector can be modified easily to incorporate sites for outside cutters, such as BspQI or BsaI. Critical and unique to our cloning method is the upshift of reaction incubations to 50 °C where the ligase is inactivated while the restriction enzyme is still active. The result is that very low background of undesired cloning intermediates is observed. Multiple DNA molecules can be simultaneously joined with a simplicity and effectiveness that rivals overlap PCR when BsaI is used. Using type IIS enzymes thus provides great control, flexibility, and simplicity in cloning strategies.
Transcriptional regulators in the LysR or GntR families are typically encoded in the genomic neighbourhood of bacterial genes for malonate degradation. While these arrangements have been evaluated using bioinformatics methods, experimental studies demonstrating co-transcription of predicted operons were lacking. Here, transcriptional regulation was characterized for a cluster of mdc genes that enable a soil bacterium, Acinetobacter baylyi ADP1, to use malonate as a carbon source. Despite previous assumptions that the mdc-gene set forms one operon, our studies revealed distinct promoters in two different regions of a nine-gene cluster. Furthermore, a single promoter is insufficient to account for transcription of mdcR, a regulatory gene that is convergent to other mdc genes. MdcR, a LysR-type transcriptional regulator, was shown to bind specifically to a site where it can activate mdc-gene transcription. Although mdcR deletion prevented growth on malonate, a 1 nt substitution in the promoter of mdcA enabled MdcR-independent growth on this carbon source. Regulation was characterized by methods including transcriptional fusions, quantitative reverse transcription PCR, reverse transcription PCR, 5'-rapid amplification of cDNA ends and gel shift assays. Moreover, a new technique was developed for transcriptional characterization of low-copy mRNA by increasing the DNA copy number of specific chromosomal regions. MdcR was shown to respond to malonate, in the absence of its catabolism. These studies contribute to ongoing characterization of the structure and function of a set of 44 LysR-type transcriptional regulators in A. baylyi ADP1.
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