Protocol for single-molecule labeling and tracking of bacterial cell division proteins

Fluorogenic Probes for Real-Time Tracking of Bacterial Cell Wall Dynamics with Nanoscopy

The bacterial cell wall, an essential structure for maintaining cell morphology and protecting against environmental hazards, is predominantly composed of peptidoglycan (PG). This intricate macromolecule undergoes dynamic synthesis and remodeling throughout the cell cycle. Despite its importance, monitoring PG dynamics in live cells, particularly with detailed spatial distribution, poses significant challenges. To this end, we present a series of rhodamine-based fluorogenic probes specifically optimized for real-time and super-resolution imaging of PG synthesis. By fine-tuning the self-aggregation of the probes through the incorporation of hydrophobic linkers, we achieved a substantial reduction in background fluorescence and significant fluorogenicity after labeling. These advancements have enabled us to attain wash-free labeling across a diverse array of bacterial species. Our approach facilitates the direct visualization of PG synthesis patterns, enabling the quantification of septal PG (sPG) synthesis rates in living bacterial cells. Furthermore, it allows for simultaneous imaging of cell division machinery in living cells via both two-dimensional (2D) and three-dimensional (3D) STED microscopy. This study provides a powerful toolkit for investigating the architecture and dynamics of the bacterial cell wall, paving new paths for research on PG-related cellular processes.

Single-molecule tracking in living microbial cells

Some microbes are referred to as model organisms because they are easy to study in the laboratory and hold the ability to retain their characteristics during DNA replication, DNA transcription, and other fundamental processes. Studying these microbes in living cells via single-molecule imaging allows us to better understand these processes at highly improved spatiotemporal resolution. Single particle tracking photoactivated localization microscopy (sptPALM) is a robust tool for detecting the positions and motions of individual molecules with tens of nanometers of spatial and millisecond temporal resolution in vivo, providing insights into intricate intracellular environments that traditional ensemble methods cannot. With this approach, the fluorophores are photoactivated stochastically, a series of images are recorded, and the positions of fluorophores are identified in these images, and ultimately the locations are linked together to yield trajectories of individual molecules. Quantitative kinetic and spatial information, such as reaction rates, diffusion coefficients, and localization maps, can be obtained by further analysis. Here, we present a single-molecule tracking protocol that includes sample preparation, data acquisition and brief data processing. This protocol will enable researchers to directly unveil molecular and cellular mechanisms underlying the essential biological processes.

Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance

Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.

The divisome is a self-enhancing machine in Escherichia coli and Caulobacter crescentus

During bacterial cytokinesis, polymers of the bacterial tubulin FtsZ coalesce into the Z ring to orchestrate divisome assembly and septal cell wall synthesis. Previous studies have found that Z ring condensation and stability is critical for successful cell division. However, how FtsZ filaments condense into a Z ring remains enigmatic and whether septal cell wall synthesis can feedback to the Z ring has not been investigated. Here, we show that FtsZ-associated proteins (Zaps) play important roles in Z ring condensation and stability, and discover septal cell wall synthesis as a novel player for Z ring condensation and stabilization in Escherichia coli and Caulobacter crescentus. Moreover, we find that the interaction between the Z ring membrane anchor, FtsA, and components of the septal cell wall synthetic complex are critical for septal cell wall synthesis-mediated Z ring condensation. Altogether, these findings suggest that the divisome is a self-enhancing machine in these two gram-negative bacteria, where the Z ring and the septal cell wall synthetic complex communicate with and reinforce each other to ensure robustness of cell division.

Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein

The small ultrared fluorescent protein (smURFP) is a bright near-infrared (NIR) fluorescent protein (FP) that forms a dimer and binds its fluorescence chromophore, biliverdin, at its dimer interface. To engineer a monomeric NIR FP based on smURFP potentially more suitable for bioimaging, we employed protein design to extend the protein backbone with a new segment of two helices that shield the original dimer interface while covering the biliverdin binding pocket in place of the second chain in the original dimer. We experimentally characterized 13 designs and obtained a monomeric protein with a weak fluorescence. We enhanced the fluorescence of this designed protein through two rounds of directed evolution and obtained designed monomeric smURFP (DMsmURFP), a bright, stable, and monomeric NIR FP with a molecular weight of 19.6 kDa. We determined the crystal structures of DMsmURFP both in the apo state and in complex with biliverdin, which confirmed the designed structure. The use of DMsmURFP in in vivo imaging of mammalian systems was demonstrated. The backbone design-based strategy used here can also be applied to monomerize other naturally multimeric proteins with intersubunit functional sites.