| The dimorphic, freshwater, oligotrophic bacterium Caulobacter crescentus alters its transcriptome in response to its environment and its cell cycle stage. This thesis uses genome-wide microarray expression data as well as data from traditional molecular biology experiments to investigate the mechanisms Caulobacter uses to coordinate transcription with other cellular processes.; We introduce an abstraction for time-varying biological signals that represents each signal as regions where the signal is low, regions where the signal is high, and regions of transition between the low and high states. Using this low/high/transition abstraction and microarray data of gene expression during the cell cycle, we show that Caulobacter changes its transcriptome three main times during the cell cycle. Periods of transcriptional change are separated by intervals where the transcriptome is maintained relatively constant.; We show that in addition to its previously known function as a DNA replication initiation factor, Caulobacter DnaA also acts as a transcription factor, which helps Caulobacter coordinate DNA replication with cell cycle progression. We identify genes in the DnaA regulon and show that transcription of gcrA, which encodes a global cell cycle regulator, requires DnaA. This indicates that DnaA is an essential element in the top-level circuit controlling the Caulobacter cell cycle.; Using whole-genome microarrays, we examine how Caulobacter alters its transcriptome during growth on three standard laboratory media, including peptone-yeast extract medium (PYE), and minimal salts media with glucose or xylose as the sole carbon source. Amino acid degradation pathways constitute the largest class of genes induced in PYE. In contrast, many of the genes up-regulated in minimal media encode enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induces expression of genes encoding enzymes of the Entner-Doudoroff pathway, which we demonstrate to be essential in Caulobacter for growth on glucose. A conserved DNA motif upstream of many xylose-induced genes is identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggests that Caulobacter may interpret this pentose as a signal to produce enzymes associated with plant polymer degradation. |
