Global Regulation of Gene Expression and Cell Differentiation inCaulobacter crescentusin Response to Nutrient Availability

Abstract

In a developmental strategy designed to efficiently exploit and colonize sparse oligotrophic environments, Caulobacter crescentus cells divide asymmetrically, yielding a motile swarmer cell and a sessile stalked cell. After a relatively fixed time period under typical culture conditions, the swarmer cell differentiates into a replicative stalked cell. Since differentiation into the stalked cell type is irreversible, it is likely that environmental factors such as the availability of essential nutrients would influence the timing of the decision to abandon motility and adopt a sessile lifestyle. We measured two different parameters in nutrient-limited chemostat cultures, biomass concentration and the ratio of nonstalked to stalked cells, over a range of flow rates and found that nitrogen limitation significantly extended the swarmer cell life span. The transcriptional profiling experiments described here generate the first comprehensive picture of the global regulatory strategies used by an oligotroph when confronted with an environment where key macronutrients are sparse. The pattern of regulated gene expression in nitrogen-and carbon-limited cells shares some features in common with most copiotrophic organisms, but critical differences suggest that Caulobacter, and perhaps other oligotrophs, have evolved regulatory strategies to deal distinctly with their natural environments. We hypothesize that nitrogen limitation extends the swarmer cell lifetime by delaying the onset of a sequence of differentiation events, which when initiated by the correct combination of external environmental cues, sets the swarmer cell on a path to differentiate into a stalked cell within a fixed time period.Caulobacter crescentus, an aquatic oligotrophic alphaproteobacterium, undergoes an asymmetric cell division, generating two distinct daughter cells, a motile swarmer cell, possessing a single polar flagellum, and a nonmotile, stalk-bearing cell (1,12,25) (Fig. 1). The progeny swarmer and stalked cell types differ in their global programs of gene expression and their capacity to reinitiate chromosomal DNA replication. Stalked cell progeny reinitiate chromosome replication almost immediately following cell division (40,41). DNA replication in swarmer cells is repressed for a defined period of time (40, 41), during which the swarmer cells are motile and chemotactically competent. The swarmer cell phase ends with a loss of the flagellum and chemotaxis apparatus, synthesis of the hold-fast and stalk, and the initiation of DNA replication (Fig. 1).In Caulobacter, asymmetry is established through the differential polar localization of two-component signaling proteins (22,32,44). Phosphotransfer signaling events catalyzed by these proteins control core cell cycle regulators such as the global transcription factor CtrA. The phosphorylated form of this essential response regulator has a critical role in repressing the initiation of DNA replication in the swarmer cell. CtrA is degraded by a programmed proteolysis that commences upon the onset...

CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus

“…A recent study of the C. crescentus response to carbon starvation identified 154 genes that are induced (7). A total of 112 of these genes showed at least partial rpoN dependence, suggesting a significant role for 54 in Caulobacter's transcriptional response to carbon starvation (7). Many of the 42 rpoN-independent and carbon starvation-induced genes identified in that study overlap with the CrfA-regulated genes described here.…”

“…The product of the SpoT enzyme, ppGpp has been shown to play a key role in regulating the initiation of DNA replication during carbon starvation as well as enabling longterm survival in medium lacking a carbon source (16). Finally, microarray studies on carbon-deprived cells have identified a number genes encoding TonB-dependent receptors, carbon source catabolic enzymes, and transcriptional regulators whose expression is strongly upregulated during carbon starvation (7). The alternative sigma factor 54 encoded by rpoN was shown to be necessary for the complete induction of many of these genes (7).…”

“…Other CrfA-activated genes encode enzymes capable of catabolizing alternative carbon sources, such as cyclic-6-aminohexanoate dimers (CC1323), as well as enzymes that modulate intermediary metabolic pathways. A recent study of the C. crescentus response to carbon starvation identified 154 genes that are induced (7). A total of 112 of these genes showed at least partial rpoN dependence, suggesting a significant role for 54 in Caulobacter's transcriptional response to carbon starvation (7).…”

“…Finally, microarray studies on carbon-deprived cells have identified a number genes encoding TonB-dependent receptors, carbon source catabolic enzymes, and transcriptional regulators whose expression is strongly upregulated during carbon starvation (7). The alternative sigma factor 54 encoded by rpoN was shown to be necessary for the complete induction of many of these genes (7). Small noncoding RNAs (sRNAs) have been identified as a key group of regulatory molecules that enable bacteria to adapt to environmental stress (19,34).…”

Localization of the Outer Membrane Protein OmpA2 in Caulobacter crescentus Depends on the Position of the Gene in the Chromosome

“…The Gram-negative bacterium Caulobacter crescentus can be isolated from freshwater environments and is capable of growing under low-nutrient conditions (32,33). To colonize this type of environment, C. crescentus cells have different types of adaptations.…”