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- EMDB-50233: Cryo-tomogram of FIB-milled meiotic yeast cell containing mitocho... -

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Basic information

Entry
Database: EMDB / ID: EMD-50233
TitleCryo-tomogram of FIB-milled meiotic yeast cell containing mitochondria with filament arrays
Map data
Sample
  • Cell: cryo FIB-milled meiotic yeast cells
Keywordsmeiosis / cell cycle / mitochondria / cryoET / protein filaments
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsWettstein R / Hugener J / Gillet L / Hernandez-Armenta Y / Henggeler A / Xu J / Van Gerwen J / Wollweber F / Arter M / Aebersold R ...Wettstein R / Hugener J / Gillet L / Hernandez-Armenta Y / Henggeler A / Xu J / Van Gerwen J / Wollweber F / Arter M / Aebersold R / Beltrao P / Pilhofer M / Matos J
Funding support Switzerland, European Union, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation176108 Switzerland
European Research Council (ERC)101002629European Union
ETH Zurich31 17-2 Switzerland
CitationJournal: Dev Cell / Year: 2024
Title: Waves of regulated protein expression and phosphorylation rewire the proteome to drive gametogenesis in budding yeast.
Authors: Rahel Wettstein / Jannik Hugener / Ludovic Gillet / Yi Hernández-Armenta / Adrian Henggeler / Jingwei Xu / Julian van Gerwen / Florian Wollweber / Meret Arter / Ruedi Aebersold / Pedro ...Authors: Rahel Wettstein / Jannik Hugener / Ludovic Gillet / Yi Hernández-Armenta / Adrian Henggeler / Jingwei Xu / Julian van Gerwen / Florian Wollweber / Meret Arter / Ruedi Aebersold / Pedro Beltrao / Martin Pilhofer / Joao Matos /
Abstract: Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a ...Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a proteomic census encompassing the entire meiotic program of budding yeast. We found that concerted waves of protein expression and phosphorylation modify nearly all cellular pathways to support meiotic entry, meiotic progression, and gamete morphogenesis. Leveraging this comprehensive resource, we pinpointed dynamic changes in mitochondrial components and showed that phosphorylation of the FF-ATP synthase complex is required for efficient gametogenesis. Furthermore, using cryoET as an orthogonal approach to visualize mitochondria, we uncovered highly ordered filament arrays of Ald4, a conserved aldehyde dehydrogenase that is highly expressed and phosphorylated during meiosis. Notably, phosphorylation-resistant mutants failed to accumulate filaments, suggesting that phosphorylation regulates context-specific Ald4 polymerization. Overall, this proteomic census constitutes a broad resource to guide the exploration of the unique sequence of events underpinning gametogenesis.
History
DepositionMay 2, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50233.png

Downloads & links

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Map

FileDownload / File: emd_50233.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.28 Å/pix.
x 330 pix.
= 6032.4 Å		18.28 Å/pix.
x 1440 pix.
= 26323.201 Å		18.28 Å/pix.
x 1024 pix.
= 18718.721 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 18.28 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-244.595460000000003 - 331.625429999999994
Average (Standard dev.)-0.000000001112365 (±25.408411000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024330
Spacing10241440330
CellA: 18718.72 Å / B: 26323.201 Å / C: 6032.4004 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cryo FIB-milled meiotic yeast cells

EntireName: cryo FIB-milled meiotic yeast cells
Components
  • Cell: cryo FIB-milled meiotic yeast cells

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Supramolecule #1: cryo FIB-milled meiotic yeast cells

SupramoleculeName: cryo FIB-milled meiotic yeast cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1500 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Crossbeam 550 FIB-1567 SEM. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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