Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Abstract

Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter. The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.

Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter

“…Collectively, our data suggest that GapR and, by extension, the conserved domain DUF2312 encode a NAP function critical for cellular replication. While this manuscript was under revision, the Shapiro group published an article describing the identification of the same nucleoid‐associated protein in C. crescentus (Ricci et al , ). The only overlap with our study is the DNA‐binding preference of the protein to AT‐rich DNA sequences and its essential function in cell cycle progression under standard laboratory conditions (nutrient‐rich PYE medium, 30°C).…”

Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717)

“…Most of these CSPs were of unknown function at the time they were first characterized, although further studies have shown them to be highly reliable molecular markers for these groups, and biochemical studies on them are leading to discovery of novel and important functions that were hitherto unrecognized [16][17][18][19][20]. Thus, not knowing the function of a conserved protein that is uniquely shared by a given group of species should not be a cause for criticism.…”

Molecular architecture of the DNA‐binding sites of the P‐loop ATPases MipZ and ParA fromCaulobacter crescentus

“…S6). It has been shown that many nucleoid-associated proteins from C. crescentus, such as HU or GapR, are enriched in AT-rich chromosomal regions (39)(40)(41). Furthermore, AT-rich sequences are typically found at transcriptional promoters, which are heavily occupied by RNA polymerase or regulatory proteins.…”