This study reports the essential Caulobacter genome at 8 bp resolution determined by saturated transposon mutagenesis and high-throughput sequencing. This strategy is applicable to full genome essentiality studies in a broad class of bacterial species.

Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) and a DNA methyltransferase. Using a modified global 5′ RACE protocol, we globally mapped transcription start sites (TSSs) at base-pair resolution, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Out of 2726 TSSs, 586 were shown to be cell cycle-regulated and we identified 529 binding sites for the cell cycle master regulators. Twenty-three percent of the cell cycle-regulated promoters were found to be under the combinatorial control of two or more of the global regulators. Previously unknown features of the core cell cycle circuit were identified, including 107 antisense TSSs which exhibit cell cycle-control, and 241 genes with multiple TSSs whose transcription levels often exhibited different cell cycle timing. Cumulatively, this study uncovered novel new layers of transcriptional regulation mediating the bacterial cell cycle.

No abstract

Significance DnaA is an essential and conserved bacterial protein that enables the initiation of DNA replication. Although it is commonly held that the onset of bacterial chromosome segregation depends on the initiation of DNA replication, we have found that in Caulobacter crescentus , chromosome segregation can be induced in a DnaA-dependent, yet replication-independent manner. The chromosome replication origin, containing essential DnaA binding motifs, resides 8 kb from the centromere parS region that also contains DnaA binding motifs. The centromere parS region bound to the ParB partition protein initiates movement across the cell followed by the origin region. Mutations in a centromere DnaA motif that alter DnaA–centromere interaction exhibit aberrant patterns of ParB/ parS translocation, implicating DnaA in the process of chromosome segregation.