Single-Molecule and Superresolution Imaging in Live Bacteria Cells

Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions. Here, single-molecule and superresolution imaging are applied to the study of proteins in live Caulobacter crescentus cells to illustrate the power of these methods in bacterial imaging. Based on these techniques, the diffusion coefficient and dynamics of the histidine protein kinase PleC, the localization behavior of the polar protein PopZ, and the treadmilling behavior and protein superstructure of the structural protein MreB are investigated with sub-40-nm spatial resolution, all in live cells.Since its advent 20 years ago, single-molecule fluorescence imaging has given rise to a host of exciting experiments (Ambrose and Moerner 1991). Beyond enabling fundamental investigations of the physics of emissive molecules, one main advantage of this technique is its use in biologically relevant, live-cell experiments. Optical fluorescence microscopy is an important instrument for cell biology, as light can be used to noninvasively probe a sample with relatively small perturbation of the specimen, enabling dynamical observation of the motions of internal structures in living cells. Single-molecule epifluorescence microscopy extends these capabilities by achieving nanometer-scale resolution, taking advantage of the fact that one can precisely characterize the point spread function (PSF) of a microscope, allowing the center of a distribution, and thus the exact position of an emitter, to be localized with accuracy much better than the diffraction limit itself. This localization accuracy improves beyond the diffraction limit roughly as one over the square root of the number of detected photons (Thompson et al. 2002). Detecting 100 photons from a single, isolated molecule can therefore improve the resolution of an optical measurement from the ∼250-nm diffraction limit down to 25 nm.Single-molecule imaging has been used in the investigation of a number of live-cell samples. In 2000, the lateral heterogeneity of the plasma membrane was investigated by tracing the motion of single dye-labeled lipids in native human airway smooth muscle (HASM) cells (Schütz et al. 2000), and epidermal growth factor (EGF) receptor signaling was explored with a fluorescent protein fusion and a labeled ligand (Sako et al. 2000). Single fluorophore-labeled molecules have subsequently been used in many ways (Moerner 2003), for instance to investigate the effect of varying cholesterol concentration on the mobility of proteins in the plasma membrane of Chinese hamster ovary (CHO) cells (Vrljic et al. 2002; Vrljic et al. 2005) and to explore the real-time dynamic behavior of cell-penetrating-peptide (CPP) molecular transporters on the plasma membrane of CHO cells (Lee et al. 2008). Furthermore, in 2001, Harms et al. characterized the emission of fluorescent proteins in biocompatible environments and noted that the yellow fluorescent protein EYFP was well-suited to single-molecule imaging in cells (Harms et al. 2001). Such fluorescent proteins can be genetically encoded as tags for native proteins in cells; these fusions have been used in many live-cell single-molecule experiments.More recently, single-molecule epifluorescence microscopy has been used to probe the inner workings of live bacteria. The small size of prokaryotic cells makes the optical diffraction limit particularly noticeable, which has stimulated the push toward superlocalization and superresolution to overcome this obstacle. As a result, the nascent field of bacterial structural biology has benefited greatly from single-molecule investigations of proteins in live cells. The overall shapes of such cells can be seen in a standard light microscope, but those interested in probing subcellular details, such as protein structure and localization, have typically had to resort to in vitro characterization combined with extrapolation to the cellular environment, as well as to indirect methods such as biochemical assays. Although cryo-electron microscopy can provide extremely high spatial resolution, fixation or plunge-freezing is essential, and methods for identifying specific proteins out of many are still lacking. As a consequence, bacterial cell biology is an area of study ripe for investigation with direct, noninvasive optical methods of probing position, coupling and structure, with resolution below the standard diffraction limit.Several groups have extended single-molecule imaging techniques to live bacterial samples. In 2004, single PleC proteins were visualized in Caulobacter crescentus cells (Deich et al. 2004), and the behavior of this system is described in more detail later. More recently, Xie and coauthors have used single-molecule fluorescence techniques to study DNA-binding proteins, mRNA, and membrane proteins to provide much insight into the mechanisms of bacterial gene expression; these efforts have been documented in a recent review (Xie et al. 2008). As well, Conley et al. used covalently linked Cy3-Cy5-thiol switchable fluorophores to illuminate the stalks of C. crescentus cells with high resolution (Conley et al. 2008). In this article, we focus on the application of single-molecule imaging and single-molecule-based superresolution imaging to investigate the localization, movement, and structure of three important proteins, PleC, PopZ, and MreB, in live C. crescentus cells.