A collection of yeast cellular electron cryotomography data

Area of Science:

• Cell Biology
• Structural Biology
• Microscopy

Background:

• Cellular macromolecular complexes function in a crowded environment, but their in situ mechanisms remain unclear due to unknown 3D organization.
• Traditional electron microscopy methods involve fixation and dehydration, which can alter cellular structures.
• Electron cryotomography (cryo-ET) offers a life-like view of cellular ultrastructure at ~4-nm resolution without fixation.

Purpose of the Study:

• To provide a large, accessible dataset of cryo-electron tomograms for studying yeast cell organization.
• To enable researchers to investigate the in situ distribution, organization, and interactions of macromolecular complexes.
• To facilitate advancements in structural cell biology and high-throughput image analysis.

Main Methods:

• Collected over 1,000 cryo-electron tomography (cryo-ET) raw datasets from cryosectioned budding yeast (Saccharomyces cerevisiae).
• Utilized genetic and chemical perturbations to study chromatin and mitotic machinery.
• Deposited unpublished tilt series and cryotomograms in the EMPIAR resource for public access.

Main Results:

• Shared >1,000 cryo-ET datasets of cryosectioned yeast cells, including unpublished tilt series.
• Made data freely available through the EMPIAR resource, enhancing discoverability via metadata in Google Sheets, EMPIAR, and GigaDB.
• Demonstrated the potential for mining cryo-ET data for novel in situ cell-biological and structural insights.

Conclusions:

• Cryo-ET datasets provide valuable resources for understanding nanoscale organization in yeast and eukaryotic cells.
• These data support template matching and subtomogram averaging to reveal 3D distributions and structures of macromolecular complexes.
• The datasets serve as crucial testbeds for image analysis pipelines, software training, and educational purposes in structural cell biology.