Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells

Maltose-Derivatized Fluorescence Turn-On Imaging Probe for Bacteria Detection

We report a maltose-derivatized fluorescence turn-on imaging probe, Mal-Cz, to detect E. coli and Staphylococci. The fluorescence turn-on is achieved through an intramolecular C-H insertion reaction of the perfluoroaryl azide-functionalized carbazole to give a fluorescent product. Confocal fluorescence microscopy confirmed the successful uptake of Mal-Cz by E. coli and Staphylococci upon photoactivation. The Mal-Cz probe could selectively detect E. coli and S. epidermidis in the presence of P. aeruginosa and M. smegmatis without interference from these bacteria. Both the photoactivation and bacteria detection can be accomplished using a hand-held UV lamp at 365 nm, with the limit of detection of 103 CFU/mL by the naked eye. Mal-Cz could also be used to detect E. coli and S. epidermidis spiked in milk by the naked eye under a hand-held UV lamp. The uptake of Mal-Cz requires metabolically active bacteria: the uptake was reduced in stationary phase bacteria and was diminished in bacteria that were killed by heating or treating with antibiotics or sodium azide. The uptake decreased with increasing concentration of added free maltose, indicating that Mal-Cz hijacked the maltose uptake pathways. In E. coli, the maltose transport systems, including maltoporin LamB, maltose binding protein MBP, and the maltose ATP binding cassette (ABC) transporter MalFGK2, are all critical for the transport of Mal-Cz. The uptake was diminished in the deletion mutants ΔLamB, ΔMalE, ΔMalF, and ΔMalK.

Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.

Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells

RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face.

Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets.

Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes.

The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs.

Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.

Mechanical expansion microscopy

This chapter describes two mechanical expansion microscopy methods with accompanying step-by-step protocols. The first method, mechanically resolved expansion microscopy, uses non-uniform expansion of partially digested samples to provide the imaging contrast that resolves local mechanical properties. Examining bacterial cell wall with this method, we are able to distinguish bacterial species in mixed populations based on their distinct cell wall rigidity and detect cell wall damage caused by various physiological and chemical perturbations. The second method is mechanically locked expansion microscopy, in which we use a mechanically stable gel network to prevent the original polyacrylate network from shrinking in ionic buffers. This method allows us to use anti-photobleaching buffers in expansion microscopy, enabling detection of novel ultra-structures under the optical diffraction limit through super-resolution single molecule localization microscopy on bacterial cells and whole-mount immunofluorescence imaging in thick animal tissues. We also discuss potential applications and assess future directions.