BioProject

The bacterial tyrosine (BY) kinase family comprises the major group of bacterial enzymes endowed with tyrosine kinase activity. More...

The bacterial tyrosine (BY) kinase family comprises the major group of bacterial enzymes endowed with tyrosine kinase activity. We have previously shown that the BceF protein from Burkholderia cepacia IST408 belongs to this BY kinase family and is involved in the biosynthesis of the exopolysaccharide cepacian. However, little is known about the extent of regulation in the cell by this kinase protein. In order to examine this, we performed a comparative transcriptome profile between the bceF mutant and the wild-type B. cepacia IST408. As a control, the transcriptome of another exopolysaccharide-deficient mutant, which had a mutation in the bceE gene, was also determined. Overall design: For expression profiling, overnight cultures of the Burkholderia cepacia IST408 wild-type strain and the isogenic mutants bceE::Tp and bceF::Tp grown in LB medium were diluted to an initial OD640 nm of 0.1 into S medium. Triplicate samples were cultured at 30ºC with 250 r.p.m. agitation for 12 h, and RNA was extracted from the bacterial isolates. DNA-based probe-selection was performed using a CEL file derived from a hybridization of genomic DNA, and Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. The new cdf file created (Bcc1sa520656F_Xspecies.CEL80.cdf) was used in DNA-Chip Analyzer 2008 for the subsequent gene expression analyses. Less...