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Deep Learning-Based Segmentation of Cryo-Electron Tomograms

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Published on: November 11, 2022

Cryo-EM tomography and automatic segmentation delineate modular structures in the postsynaptic density.

Jae Hoon Jung¹, Xiaobing Chen¹, Thomas S Reese¹

¹Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.

Frontiers in Synaptic Neuroscience

|April 24, 2023

Summary

Postsynaptic densities (PSDs) are modular protein complexes. New cryo-EM methods reveal substructures within PSDs, suggesting a modular organization crucial for synaptic plasticity.

Keywords:

automatic segmentation cryo-EM tomography modular organization nanodomain postsynaptic density

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Area of Science:

Neuroscience
Cell Biology
Structural Biology

Background:

Postsynaptic densities (PSDs) are critical protein complexes at excitatory synapses, essential for synaptic function and plasticity.
Conventional electron microscopy (EM) visualizes PSDs as large, compact structures, but their internal organization and substructures remain unclear.
Previous studies noted irregular PSD contours and small granular structures, with recent work identifying PSD fragments.

Purpose of the Study:

To investigate the internal substructure of isolated postsynaptic densities (PSDs) using advanced cryo-electron microscopy (cryo-EM) tomography.
To develop and apply automatic segmentation for delineating and quantitatively analyzing PSD substructures.
To understand the implications of PSD substructure for synaptic function and plasticity.

Main Methods:

Isolation of postsynaptic densities (PSDs).
Cryo-electron microscopy (cryo-EM) tomography for high-resolution imaging.
Development and application of automatic segmentation algorithms for substructure analysis.

Main Results:

Identification of diverse substructures within isolated PSDs, varying in size (<30 nm to >100 nm).
A significant portion (>38%) of these substructures were comparable in size to previously observed PSD fragments.
Discovery of substructures spanning the entire PSD thickness, potentially housing both membrane-associated and cytoplasmic proteins.

Conclusions:

Isolated PSDs are composed of distinct modules of varying sizes and compositions.
This modular organization may enable PSD remodeling, facilitating synaptic plasticity and function.
The findings challenge the view of PSDs as monolithic structures, highlighting their complex internal architecture.