An Hfq-dependent post-transcriptional mechanism fine tunes RecB expression inEscherichia coli

Abstract

To preserve genome integrity, all living organisms have developed strategies to respond to chromosomal damage. One such response is the repair of DNA double-strand breaks (DSBs), one of the most toxic forms of DNA lesions. In E. coli, DSBs are repaired via the homologous recombination pathway, initiated by the RecBCD enzyme. RecBCD is essential for accurate chromosome maintenance but its over-expression can lead to reduced DNA repair ability. This apparent paradox suggests that RecBCD copy number may need to be tightly controlled within an optimal range. Using single-molecule fluorescence microscopy, we have established that RecB is present in very low abundance at mRNA and protein levels. RecB transcription shows high levels of fluctuations yet cell-to-cell protein variability remains remarkably low. We show that the post-transcriptional regulator Hfq binds to recBCD mRNAs and down-regulates RecB protein expression in vivo. Furthermore, when Hfq-mediated regulation is perturbed, we observe less effective noise reduction and reduced DNA repair capacity. Taken together, our results suggest a post-transcriptional regulatory mechanism where Hfq fine-tunes RecB expression by inhibiting RecB translation. This fine-tuning of RecB expression contributes to reducing noise in RecB protein expression and protects cells against the toxic consequences of too high RecBCD numbers.

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis

“…gene replication is not taken into account. While (i) is common, it is by no means a universal phenomenon-there are several examples where there is no such scaling in both prokaryotic [54,55] and eukaryotic cells [56][57][58][59][60]. The assumption behind (ii) is of course a means to simplify the model but clearly unrealistic.…”

Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model

“…This is due to a coordination of the mRNA synthesis rate with cell volume—we shall refer to this mechanism as balanced mRNA synthesis. However, in both prokaryotic 50 , 51 and eukaryotic cells, 52 , 53 , 54 , 55 there are examples where there is no such scaling. Since each cell has a different volume, the mechanism of volume-dependent transcription is a source of extrinsic noise, 57 potentially accounting for a significant amount of the observed cell-to-cell variation in mRNA numbers.…”

“… 22 , 45 , 46 , 47 , 48 Some of these models incorporate the scaling of transcription activity with cell volume, 22 , 48 while the rest do not. We note that the latter case is not to be seen as unphysical since while the scaling of transcription with volume is commonly observed, it is by no means a universal phenomenon (in both prokaryotic 50 , 51 and eukaryotic cells, 52 , 53 , 54 , 55 there are examples where there is no such scaling). As for the conventional one-state model shown in Equation 2 , the main limitation is the assumption of instantaneous bursts, while in reality there is a finite time for the bursts to occur.…”

Coupling gene expression dynamics to cell size dynamics and cell cycle events: exact and approximate solutions of the extended telegraph model

“…Some of these models incorporate the scaling of transcription activity with cell volume [22, 48], while the rest do not. We note that the latter case is not to be seen as unphysical since while the scaling of transcription with volume is commonly observed, it is by no means a universal phenomenon (in both prokaryotic [50, 51] and eukaryotic cells [52–55] there are examples where there is no such scaling). As for the conventional one-state model shown in Eq.…”

“…This is due to a coordination of the mRNA synthesis rate with cell volume -we shall refer to this mechanism as balanced mRNA synthesis. However, in both prokaryotic [49,50] and eukaryotic cells [51][52][53][54] there are examples where there is no such scaling. Since each cell has a different volume, the mechanism of volume-dependent transcription is a source of extrinsic noise [56], potentially accounting for a significant amount of the observed cell-to-cell variation in mRNA numbers.…”