Dynamic translation regulation in Caulobacter cell cycle control

Abstract

Progression of the Caulobacter cell cycle requires temporal and spatial control of gene expression, culminating in an asymmetric cell division yielding distinct daughter cells. To explore the contribution of translational control, RNA-seq and ribosome profiling were used to assay global transcription and translation levels of individual genes at six times over the cell cycle. Translational efficiency (TE) was used as a metric for the relative rate of protein production from each mRNA. TE profiles with similar cell cycle patterns were found across multiple clusters of genes, including those in operons or in subsets of operons. Collections of genes associated with central cell cycle functional modules (e.g., biosynthesis of stalk, flagellum, or chemotaxis machinery) have consistent but different TE temporal patterns, independent of their operon organization. Differential translation of operon-encoded genes facilitates precise cell cycle-timing for the dynamic assembly of multiprotein complexes, such as the flagellum and the stalk and the correct positioning of regulatory proteins to specific cell poles. The cell cycleregulatory pathways that produce specific temporal TE patterns are separate from-but highly coordinated with-the transcriptional cell cycle circuitry, suggesting that the scheduling of translational regulation is organized by the same cyclical regulatory circuit that directs the transcriptional control of the Caulobacter cell cycle.T he Caulobacter crescentus cell cycle produces two daughter cell types at each cell division: a nonreplicative motile swarmer cell, and a replication-competent sessile stalked cell. At the time of the asymmetric cell division, each daughter cell activates a different genetic program. Caulobacter has a cyclical genetic circuit that controls the varying temporal and spatial expression of multiple functional modules (Fig. 1) that implement biogenesis of polar organelles, replication and segregation of the chromosome, and cytokinesis (1-4). The circular 4-Mb genome has 3,885 ORFs and 199 noncoding RNAs (5, 6). mRNA profiling by microarrays or RNA-seq (7-10) and global promoter activity profiles from 5′ Global RACE experiments (11) have shown that several hundred Caulobacter mRNAs have significant temporal transcriptional variation over the cell cycle. The expression of cell cycle-controlled mRNAs largely correlates with the times they are required for the functional modules that implement progression of the cell cycle (8). The transcriptional activity of most of the Caulobacter cell cycle-regulated promoters is controlled by a genetic circuit comprised of four transcriptional master regulators, a DNA methyltransferase (2), and a dynamic set of polar-localized phospho-signaling proteins that control asymmetric cell division (12-15). Because regulation of translation has an immediate impact on protein production, a major cellular energy drain, tight regulation of translation is essential for rapid cell adaptation to changing circumstances. In eukaryotic cells translational contr...

Spatial organization and dynamics of RNase E and ribosomes inCaulobacter crescentus

“…To confirm that these correlations are valid, we also imaged a lowly-transcribed gene, CCNA01879, that is in the bottom 0.5% of RNA-seq analysis 32 ( Fig. 5a).…”

“…The increase in the number of clusters in the cell during the swarmer to stalked transition is consistent with biochemical data showing increased overall RNA abundance during this time in the cell cycle. 32 This increase in clusters may also be attributed to the initiation of DNA replication that occurs during this time period leading to an increase in overall transcription.…”

“…Ribosome profiling 32 and Western blot analysis 2 have shown that RNase E levels in Caulobacter vary as a function of the cell cycle, with maximum levels at the swarmer to stalked transition and just prior to cell division. To determine if RNase E clusters fluctuate as a function of the cell cycle, we performed two-color 3D imaging of RNase E-eYFP and PAmCherry-PopZ (to mark the cell poles).…”

Allosteric control of a bacterial stress response system by an anti‐σ factor

“…PhyR, NepR and σ EcfG are abundant proteins in the cell. Calculated concentrations inside C. crescentus approach 41, 90 and 12 μM respectively, in the absence of stress based on published intracellular protein levels and ribosome profiling data (and assuming a cell volume of 0.3 femtoliters) (Li et al ., ; Schrader et al ., ). Interactions detected in our NMR experiments may thus reflect interactions present in the cell.…”

Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus

“…In synchronized C. crescentus cultures, CtrA‐dependent expression of EipA (CC_1035/CCNA_1087) begins in the middle of the cell cycle S phase and terminates in G2 (Laub et al ., ; ; Hottes et al ., ; McGrath et al ., ; Fang et al ., ; Zhou et al ., ; Schrader et al ., ); see CauloBrowser (Lasker et al ., ) for a compilation of cell cycle expression data (http://www.caulobrowser.org). C. crescentus cells become predivisional at this developmental stage and begin to invaginate and divide.…”