Project description:phyR encodes a general stress regulator protein that is conserved among several alpha-proteobacteria. This experiment is quantifying transcription in two Caulobacter strains: one strain is overexpressing phyR (gene CC3477); the other carries a phyR in-frame deletion. Both strains were cultured in M2 defined medium with xylose as the sole carbon source. The first strain (FC626) carries a plasmid integrated into the xylX locus; phyR is fused to the xylX promoter in this plasmid, generating a xylose-inducible phyR overexpression strain. The second strain (FC799) carries an in-frame deletion at the chromosomal phyR locus. Duplicate cultures of: 1) C. crescentus strain CB15 phyR in-frame deletion mutant , and 2) a xylose-inducible phyR overexpression strain, were cultured in M2 xylose defined medium and harvested at OD660=0.3
Project description:Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain render it incapable of methylating its genome on the adenine at GANTC motifs. References for strains : WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. DccrM: Gonzalez, D. and Collier, J. (2013) DNA methylation by CcrM activates the transcription of two genes required for the division of Caulobacter crescentus. Mol Microbiol, 88, 203-218. A six chip study using total RNA recovered from three separate wild-type cultures of Caulobacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.
