Sébastien Lemire

Bacteria are central to human health and disease, but existing tools to edit microbial consortia are limited. For example, broad-spectrum antibiotics are unable to accurately manipulate bacterial communities. Bacteriophages can provide highly specific targeting of bacteria, but assembling well-defined phage cocktails solely with natural phages can be a time-, labor-and cost-intensive process. Here, we present a synthetic-biology strategy to modulate phage host ranges by engineering phage genomes in Saccharomyces cerevisiae. We used this technology to redirect Escherichia coli phage scaffolds to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds to target E. coli by modular swapping of phage tail components. The synthetic phages achieved efficient killing of their new target bacteria and were used to selectively remove bacteria from multi-species bacterial communities with cocktails based on common viral scaffolds. We envision that this approach will accelerate phage-biology studies and enable new technologies for bacterial population editing.

RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ΔrnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.

Ubiquitous RNA-binding protein Hfq mediates the regulatory activity of many small RNAs (sRNAs) in bacteria. To identify potential targets for Hfq-mediated regulation in Salmonella, we searched for lacZ translational fusions whose activity varied in the presence or absence of Hfq. Fusions downregulated by Hfq were more common than fusions showing the opposite response. Surprisingly, in a subset of isolates from the major class, the higher activity in the absence of Hfq was due to transcriptional activation by the alternative sigma factor RpoE (sigmaE). Activation of the sigmaE regulon normally results from envelope stress conditions that elicit proteolytic cleavage of the anti-sigmaE factor RseA. Using an epitope tagged variant of RseA, we found that RseA is cleaved at an increased rate in a strain lacking Hfq. This cleavage was dependent on the DegS protease and could be completely prevented upon expressing the hfq gene from an inducible promoter. Thus, loss of Hfq function appears to affect envelope biogenesis in a way that mimics a stress condition and thereby induces the sigmaE response constitutively. In a RseA mutant, activation of the sigmaE response causes Hfq-dependent downregulation of outer membrane protein (OMP) genes including lamB, ompA, ompC and ompF. For ompA, downregulation results in part from sigmaE-dependent accumulation of MicA (SraD), a small RNA recently shown to downregulate ompA transcript levels in stationary phase. We show that the micA gene is under sigmaE control, and that DegS-mediated sigmaE release is required for the accumulation of MicA RNA upon entry into stationary phase. A similar mechanism involving additional, still unidentified, sRNAs, might underlie the growth phase-dependent regulation of other OMP mRNAs.

Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.