DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus

Supporting data for Hottes et al., "DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus" The microarray component of this work monitors mRNA expression during the cell cycle of synchronized populations of Caulobacter crescentus cells. Transcription during the normal cell cycle is compared with transcription during a cell cycle where expression of dnaA, which encodes a key DNA replication initiation factor, is delayed. Keywords: time course, cell cycle, metabolism 1. Using a synchronized population of CB15N cells, we monitored expression during the cell cycle in cells grown in M2G media. Samples were taken throughout the cell cycle and each sample was compared to a common reference. (22 arrays; 11 time points each of which has a technical replicate) 2. Using a synchronized population of CB15N cells, we monitored expression during the cell cycle in cells grown in PYE media. Samples were taken throughout the cell cycle and each sample was compared to a common reference. (14 arrays; 11 time points of which 3 have a technical replicate) 3. We monitered mRNA expression during a cell cycle where expression of dnaA, which encodes a replication initiation factor, was delayed. We used a strain where the only copy of dnaA was on the chromosome under the control of an inducible promoter. First, we isolated swarmer-stage cells from a culture grown in conditions where dnaA was expressed. Then, the swarmer cells were released into conditions where dnaA was not expressed. The cells blocked in the G1-stage. Later, expression of dnaA was turned on, causing the cells to initiate DNA replication and finish the cell cycle. Samples were taken throughout the cell cycle and each sample was compared to a common reference. (21 arrays; 15 time points of which 6 have a technical replicate) 4. We repeated the experiment described in 3 with a different culture of cells (22 arrays, 14 timepoints of which 8 have technical replicate) 5. In 3 and 4 (above) we controlled dnaA expression using a xylose-inducible promoter. To identify genes whose expression is sensitive to xylose, we compared expression of asynchronous populations of CB15N grown on M2G (minimal media with glucose as the sole carbon source) to asynchronous populations of CB15N grown on M2GX (minimal media with glucose and xylose as carbon sources). (4 arrays, all biological replicates)