High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons

Abstract

Using 62 probe-level datasets obtained with a custom-designed Caulobacter crescentus microarray chip, we identify transcriptional start sites of 769 genes, 53 of which are transcribed from multiple start sites. Transcriptional start sites are identified by analyzing probe signal cross-correlation matrices created from probe pairs tiled every 5 bp upstream of the genes. Signals from probes binding the same message are correlated. The contribution of each promoter for genes transcribed from multiple promoters is identified. Knowing the transcription start site enables targeted searching for regulatory-protein binding motifs in the promoter regions of genes with similar expression patterns. We identified 27 motifs, 17 of which share no similarity to the characterized motifs of other C. crescentus transcriptional regulators. Using these motifs, we predict coregulated genes. We verified novel promoter motifs that regulate stress-response genes, including those responding to uranium challenge, a stress-response sigma factor and a stress-response noncoding RNA.

The dynamic interplay between a cell fate determinant and a lysozyme homolog drives the asymmetric division cycle of Caulobacter crescentus

“…First, since the accumulation of the tacA transcript slightly precedes that of spmX (Laub et al 2000;McGrath et al 2007), the temporal pattern of tacA expression is consistent with the proposed role of TacA as transcriptional regulator of spmX. Second, the abundance of the tacA message is dramatically reduced in the absence of PleC, a feature tacA shares with pilA and spmX (Chen et al 2006).…”

“…Thus, PleC is required to activate transcription of spmX as well as that of the pilA pilin gene. Incidentally, the messages of spmX and pilA exhibit nearly identical abundance patterns during the cell cycle: Both are highly abundant in swarmer cells, are down-regulated in stalked cells, and reaccumulate coincident with the compartmentalization of the predivisional cell (Laub et al 2000;McGrath et al 2007). This pattern is no surprise for the pilA message since the abundance profile of the PilA protein essentially reflects that of the message (Fig.…”

“…Third, the spmX promoter sequence suggests that an RNAP holoenzyme containing a 54 factor (E 54 ) transcribes spmX ( Fig. 6D; McGrath et al 2007). E 54 -catalyzed transcription normally requires a coactivator of a specialized clade of response regulators (Popham et al 1989), of which there are only four encoded in the Caulobacter genome and TacA is one of them (Marques et al 1997).…”

“…S7B). The staR gene that encodes a regulator of stalk elongation shares promoter sequence motifs with spmX (McGrath et al 2007) and is thought to be directly regulated by TacA (Biondi et al 2006b). Our qChIP experiments also demonstrated that TacA interacts efficiently in vivo with the promoter of staR (Fig.…”

PflI, a Protein Involved in Flagellar Positioning in Caulobacter crescentus

“…Before initiating DNA replication, swarmer cells differentiate into stalked cells by ejecting the flagellum and forming a thin extension of the cell envelope (the stalk, which is involved in nutrient uptake and surface attachment) at the pole where the flagellum once was. The sessile stalked cells then begin expressing flagellar genes in a stepwise, hierarchical manner, and a new flagellum is formed at the pole opposite the stalk (28,35,52). Division yields a flagellated swarmer progeny for dispersal and a sessile stalked progeny for local colonization.…”