Streptavidin Outperforms Antibodies in Visualizing Proteins within Phase-Separated Cellular Compartments and Enhances Imaging Sensitivity

Core Concepts

Streptavidin-based imaging of TurboID-tagged proteins provides superior detection of proteins within phase-separated cellular regions and significantly boosts signal intensity compared to antibody-based methods, enabling improved visualization in applications like expansion microscopy and correlative light-electron microscopy.

Abstract

The content describes a comparative analysis of streptavidin-based and antibody-based protein visualization methods. Key highlights and insights:

Streptavidin imaging of TurboID-tagged proteins can accurately localize target proteins, with resolution comparable to antibody-based immunofluorescence in standard light microscopy.

Streptavidin can effectively detect target proteins within phase-separated cellular regions, such as the nuclear pore channel, nucleolus, and stress granules, where antibodies often fail to bind or penetrate. This is likely due to the dense, disordered nature of these phase-separated environments.

Streptavidin imaging provides a significantly stronger signal compared to antibody-based detection, with up to a 2.9-fold increase in maximum fluorescence intensity. This advantage is particularly beneficial for imaging applications that require reduced antigen density, such as expansion microscopy and correlative light-electron microscopy (CLEM).

Streptavidin-based imaging can provide additional insights into protein interactions and dynamics. The biotinylation by TurboID can reveal historic interactions and dynamic localization changes that are not captured by steady-state antibody labeling.

The authors systematically mapped the phase-separated regions of the trypanosome nuclear pore complex by comparing streptavidin and antibody accessibility, identifying the FG-repeat nucleoporins lining the central channel as inaccessible to antibodies.

In summary, the content demonstrates the superior performance of streptavidin-based imaging of TurboID-tagged proteins, particularly in visualizing proteins within phase-separated cellular compartments and enhancing imaging sensitivity in advanced microscopy techniques.

Stats

Streptavidin signal was 2.9-fold higher in maximum fluorescence intensity compared to anti-HA antibody for NUP158-TurboID-HA in trypanosome cells.

Quotes

"Streptavidin imaging has major advantages for the detection of lowly abundant or inaccessible proteins and in addition, can provide information on protein interactions and biophysical environment."
"Importantly, proteins within phase-separated regions, such as the central channel of the nuclear pores, the nucleolus or RNA granules, were readily detected with streptavidin, while most antibodies fail to label proteins in these environments."

Key Insights Distilled From

Beyond BioID: Streptavidin outcompetes antibody fluorescence signals in protein localization and readily visualises targets evading immunofluorescence detection

by Odenwald,J.,... at www.biorxiv.org 12-02-2023

https://www.biorxiv.org/content/10.1101/2023.12.01.569576v1

Deeper Inquiries

How could the insights from this study be leveraged to develop new strategies for targeted drug delivery or protein engineering within phase-separated cellular compartments?

The insights from this study provide a valuable foundation for developing new strategies for targeted drug delivery or protein engineering within phase-separated cellular compartments. By utilizing streptavidin-based imaging to identify and visualize proteins within these compartments, researchers can gain a better understanding of the spatial organization and dynamics of these structures. This knowledge can be leveraged to design targeted drug delivery systems that specifically target proteins within phase-separated regions, allowing for more precise and effective treatment of various diseases. Additionally, the ability to visualize dynamic protein interactions using streptavidin can inform the design of engineered proteins with specific functions within these compartments, enabling the development of novel therapeutic agents or tools for cellular manipulation.

What are the potential limitations or caveats of the streptavidin-based imaging approach, and how could they be addressed in future research?

While streptavidin-based imaging offers significant advantages for visualizing proteins within phase-separated cellular compartments, there are some potential limitations and caveats to consider. One limitation is the possibility of non-specific binding of streptavidin to biotinylated proteins, leading to background noise in the imaging results. This can be addressed in future research by optimizing the staining conditions and using appropriate controls to minimize non-specific binding.
Another caveat is the potential for steric hindrance or accessibility issues that may prevent streptavidin from binding to certain proteins within phase-separated regions. Future research could explore alternative imaging techniques or probe designs to overcome these challenges and improve the specificity and accuracy of the imaging results.

Given the ability of streptavidin to reveal dynamic protein interactions, how could this technique be combined with other methods, such as live-cell imaging or single-molecule tracking, to provide a more comprehensive understanding of cellular protein networks and their spatiotemporal regulation?

Combining streptavidin-based imaging with other methods, such as live-cell imaging or single-molecule tracking, can provide a more comprehensive understanding of cellular protein networks and their spatiotemporal regulation. By incorporating live-cell imaging techniques, researchers can observe the real-time dynamics of protein interactions within phase-separated compartments, allowing for the study of dynamic processes and cellular responses in a more natural context.
Additionally, integrating single-molecule tracking with streptavidin-based imaging can enable the visualization of individual protein molecules and their movements within cellular structures. This approach can provide insights into the kinetics of protein interactions, the formation of protein complexes, and the regulation of cellular processes at the molecular level. By combining these techniques, researchers can gain a deeper understanding of the complex and dynamic nature of cellular protein networks and their spatiotemporal regulation.