Transfer-messenger RNA and SmpB mediate bacteriostasis in Escherichia coli cells against tRNA cleavage

Abstract

RNAs, such as mRNA, rRNA and tRNA, are essential macromolecules for cell survival and maintenance. Any perturbation of these molecules, such as by degradation or mutation, can be toxic to cells and may occasionally induce cell death. Therefore, cells have mechanisms known as quality control systems to eliminate abnormal RNAs. Although tRNA is a stable molecule, the anticodon loop is quite susceptible to tRNA-targeting RNases such as colicin E5 and colicin D. However, the mechanism underlying cellular reaction to tRNA cleavage remains unclear. It had long been believed that tRNA cleavage by colicins E5 and D promptly induces cell death because colony formation of the sensitive cells is severely reduced; this indicates that cells do not resist the tRNA cleavage. Here, we show that Escherichia coli cells enter a bacteriostatic state against the tRNA cleavage of colicins D and E5. The bacteriostasis requires small protein B (SmpB) and transfer-messenger RNA (tmRNA), which are known to mediate trans-translation. Furthermore, another type of colicin, colicin E3 cleaving rRNA, immediately reduces the viability of sensitive cells. Moreover, nascent peptide degradation has an additive effect on bacteriostasis. Considering the recent observation that tRNA cleavage may be used as a means of cell-to-cell communication, tRNA cleavage could be used by bacteria not only to dominate other bacteria living in the same niche, but also to regulate growth of their own or other cells.

Contact‐dependent growth inhibition induces high levels of antibiotic‐tolerant persister cells in clonal bacterial populations

“…Even so, new classes of CDI toxins like those encoded by the maf‐ genes in Neisseria gonorrhea (Jamet et al , ) are still being discovered, suggesting CDI systems to be even more widespread than we know. Finally, other classes of bacteriostatic toxins, like some colicins (Sakai et al , ) and Type VI secretion effectors (Whitney et al , ), could also in principal contribute to inter‐bacterial induction of persister formation at high cell densities. Thus, cell‐to‐cell contact‐mediated delivery of bacterial toxins could be a common bet‐hedging mechanism used for creating population density‐dependent heterogeneity.…”

“…Even so, new classes of CDI toxins like those encoded by the maf-genes in Neisseria gonorrhea (Jamet et al, 2015) are still being discovered, suggesting CDI systems to be even more widespread than we know. Finally, other classes of bacteriostatic toxins, like some colicins (Sakai et al, 2015) and Type VI secretion effectors (Whitney et al,…”

tRNA-targeting ribonucleases: molecular mechanisms and insights into their physiological roles

“…Further incubation, however, results in the loss of colony-forming activity, indicating that the bacteriostasis is transiently maintained for several hours. 66) This resembles the "point of no return" observed in the programmed cell death mediated by the mazEF module, one of the most studied TA systems. 67) Alternatively, the challenged cells then enter a specific phase, such as a viable but nonculturable (VBNC) state, 68) where the cells are alive but exhibit impaired colony-forming activity.…”

“…We found that sensitive cells were not immediately killed, but were driven into a bacteriostatic state for several hours with susceptible tRNAs almost completely cleaved. 66) This phenomenon is not limited to ts colicin D; cells challenged by wild-type colicins E5 or D maintained high viability for as long as five hours, based on LIVE/DEAD staining results. Further incubation, however, results in the loss of colony-forming activity, indicating that the bacteriostasis is transiently maintained for several hours.…”

“…We speculated that tRNA cleavage possibly induces a transient bacteriostasis, despite the drop in CFUs of cells challenged by colicins E5 or D. We constructed a temperature-sensitive (ts) colicin D mutant to control its tRNA cleavage activity. 66) After tRNAs were subjected to cleavage by ts colicin D at a permissive temperature for several hours, cell viability was determined by plating and incubating the cells at a nonpermissive temperature. We found that sensitive cells were not immediately killed, but were driven into a bacteriostatic state for several hours with susceptible tRNAs almost completely cleaved.…”