DOI: 10.5061/dryad.kkwh70s9t
title: Intracellular morphogenesis of diatom silica is guided by local variations in membrane curvature

description: Silica cell wall formation in diatoms is a showcase for the ability of
 organisms to control inorganic mineralization. The process of
 silicification by these unicellular algae is tightly regulated within a
 membrane-bound organelle, the silica deposition vesicle (SDV). Two
 opposing scenarios were proposed to explain the tight regulation of this
 intracellular process: a template-mediated process that relies on
 preformed scaffolds or a template-independent self-assembly process. The
 present work points to a third scenario, where the SDV membrane is a
 dynamic mold that shapes the forming silica. We use in-cell cryo-electron
 tomography to visualize the silicification process in situ, in its native
 state, and with a nanometer-scale resolution. Significantly, this revealed
 that the plasma membrane interacts with the SDV membrane via physical
 tethering at membrane contact sites, where the curvature of the tethered
 side of the SDV membrane mirrors the intricate silica topography. We
 propose that silica growth and morphogenesis result from
 crosstalk between membranes and their biophysical properties.
description: <em>Thalassiosira pseudonana</em> cells were
 cryo-preserved at various stages during cell wall formation and
 cryo-electron tomography data sets of cryo-FIB milled thin lamellae were
 collected.
description: # Intracellular morphogenesis of diatom silica is guided by local
 variations in membrane curvature This 240731_readme.txt file was generated
 on 2024-07-31 by Lior Aram ## GENERAL INFORMATION 1. Title of Dataset:
 Intracellular morphogenesis of diatom silica is guided by local variations
 in membrane curvature 2. Author Information A. Principal Investigator
 Contact Information Name: Assaf Gal Institution: Weizmann Institute of
 Science\ Email:
 [assaf.gal@weizmann.ac.il](mailto:assaf.gal@weizmann.ac.il) 3. Date of
 data collection 2021-2023 ## DATA & FILE OVERVIEW The folders contain
 cryo-electron tomography data related to the SDV growth stages. Folders 01
 to 36 are numbered according to their number in Fig. S3. ### Folder File
 Description * 01_Stage_I' Tp23d_TS_003.mrc A tilt series file of *T.
 psuedonana* cell lamellae. Data associated with Fig. 2 *
 Tp23d_TS_003_full_rec.mrc Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell. Data associated with Fig. 2 * 02 Tp20a_TS_011.st A tilt
 series file of *T. psuedonana* cell lamellae. * Tp20a_TS_011_full.rec
 Reconstructed cryo-electron tomogram of *T. psuedonana* cell. * 03
 Tp20a_TS_012.st A tilt series file of *T. psuedonana* cell lamellae *
 Tp20a_TS_012_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 04 Tp20a_TS_010.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp20a_TS_010_full.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 05 tp27b_008.st A tilt
 series file of *T. psuedonana* cell lamellae * tp27b_008_full.rec
 Reconstructed cryo-electron tomogram of *T. psuedonana* cell * 06
 tp27b_009.st A tilt series file of *T. psuedonana* cell lamellae *
 tp27b_009_full.rec Reconstructed cryo-electron tomogram of *T. psuedonana*
 cell * 07_Stage_I tp27b_010.st A tilt series file of *T. psuedonana* cell
 lamellae. Data associated with Fig. 2 * SIRT20_angle_tp27b_010_full.rec
 Reconstructed cryo-electron tomogram of *T. psuedonana* cell. Data
 associated with Fig. 2 * 08 Tp35d_TS_002.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp35d_TS_002_full_rec_SIRT20.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 09
 Tp35d_TS_003_new_af_orig.mrc A tilt series file of *T. psuedonana* cell
 lamellae * Tp35d_TS_003_new_af_full_rec.mrc Reconstructed cryo-electron
 tomogram of *T. psuedonana* cell * 10_Stage_II' tp28c_001.st A tilt
 series file of *T. psuedonana* cell lamellae. Data associated with Fig. 2
 * SIRT20_angle_tp28c_001_full.rec Reconstructed cryo-electron tomogram of
 *T. psuedonana* cell. Data associated with Fig. 2 * 11_Stage_II
 tp28c_002.st A tilt series file of *T. psuedonana* cell lamellae. Data
 associated with Fig. 2 * SIRT20_tp28c_002_full.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell. Data associated with Fig.
 2 * 12 Tp35a_TS_000_af.mrc A tilt series file of *T. psuedonana* cell
 lamellae * Tp35a_TS_000_af_full_rec_SIRT20.mrc Reconstructed cryo-electron
 tomogram of *T. psuedonana* cell * 13 Tp37c_TS_002_af.mrc A tilt series
 file of *T. psuedonana* cell lamellae *
 Tp37c_TS_002_af_full_rec_SIRT20.mrc Reconstructed cryo-electron tomogram
 of *T. psuedonana* cell * 14 Tp37a_TS_001.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp37a_TS_001_full_rec30SIRT.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 15_Stage_III'
 tp27b_011.st A tilt series file of *T. psuedonana* cell lamellae. Data
 associated with Fig. 2 * tp27b_011_full_SIRT20\_ noCTF.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell. Data associated with Fig.
 2 * 16 tp27b_012.st A tilt series file of *T. psuedonana* cell lamellae *
 tp27b_012_full.rec Reconstructed cryo-electron tomogram of *T. psuedonana*
 cell * 17 tp27b_013.st A tilt series file of *T. psuedonana* cell lamellae
 * tp27b_013_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 18 Tp20d_TS_000.st A tilt series file of *T.
 psuedonana* cell lamellae * Tp20d_TS_000_full.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 19 Tp19b_TS_003_new.st A
 tilt series file of *T. psuedonana* cell lamellae *
 Tp19b_TS_003_new_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 20_Stage_III Tp19b_TS_004_new.st A tilt series file of
 *T. psuedonana* cell lamellae. Data associated with Fig. 2 *
 220504_Tp19b_TS_004_new_full_rec.mrc Reconstructed cryo-electron tomogram
 of *T. psuedonana* cell. Data associated with Fig. 2 * 21 Tp20a_TS_001.st
 A tilt series file of *T. psuedonana* cell lamellae *
 Tp20a_TS_001_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 22 Tp20a_TS_002.st A tilt series file of *T.
 psuedonana* cell lamellae * Tp20a_TS_002_full.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 23 Tp23d_TS_007.mrc A
 tilt series file of *T. psuedonana* cell lamellae *
 Tp23d_TS_007_full_rec.mrc Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 24 Tp23d_TS_008.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp23d_TS_008_full_rec_SIRT20.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 25 Tp23d_TS_006.mrc A
 tilt series file of *T. psuedonana* cell lamellae *
 Tp23d_TS_006_full_rec.mrc Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 26 Tp36d_TS_002.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp36d_TS_002_full_rec_SIRT20.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 27 Tp36d_TS_004.mrc A
 tilt series file of *T. psuedonana* cell lamellae *
 Tp36d_TS_004_full_rec.mrc Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 28 Tp36d_TS_001.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp36d_TS_001_full_rec_SIRT20_new.mrc
 Reconstructed cryo-electron tomogram of *T. psuedonana* cell * 29
 Tp34a_TS_001.mrc A tilt series file of *T. psuedonana* cell lamellae *
 Tp34a_TS_001_full_rec.mrc Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 30 Tp34a_TS_002.mrc A tilt series file of *T.
 psuedonana* cell lamellae * Tp34a_TS_002_full_rec_SIRT20.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell * 31_Stage_IV'
 Tp20d_TS_003.mrc A tilt series file of *T. psuedonana* cell lamellae. Data
 associated with Fig. 2 * Tp20d_TS_003_full_rec.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell. Data associated with Fig.
 2 * 32_Stage_IV Tp20d_TS_002_orig.st A tilt series file of *T. psuedonana*
 cell lamellae. Data associated with Fig. 2 *
 Tp20d_TS_002_orig_full_rec_CTFcorrected_SIRT20.mrc Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell. Data associated with Fig.
 2 * 33 Tp24c_tomo5.st A tilt series file of *T. psuedonana* cell lamellae
 * Tp24c_tomo5_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * 34 Tp24c_tomo7.st A tilt series file of *T. psuedonana*
 cell lamellae * Tp24c_tomo7_full.rec Reconstructed cryo-electron tomogram
 of *T. psuedonana* cell * 35_Stage_V' Tp23d_TS_009.mrc A tilt series
 file of *T. psuedonana* cell lamellae. Data associated with Fig. 2 *
 SIRT20_CTF_corrected_Tp23d_TS_009_full_rec.mrc Reconstructed cryo-electron
 tomogram of *T. psuedonana* cell. Data associated with Fig. 2 * 36_Stage_V
 tp28c_025.st A tilt series file of *T. psuedonana* cell lamellae. Data
 associated with Fig. 2 * tp28c_025_full.rec Reconstructed cryo-electron
 tomogram of *T. psuedonana* cell. Data associated with Fig. 2 * Fig. S7
 lam37_tomo1.st A tilt series file of *T. psuedonana* cell lamellae *
 Tp11c_lam37_tomo1_full.rec Reconstructed cryo-electron tomogram of *T.
 psuedonana* cell * Fig. S11 Tp19b_TS_009.st A tilt series file of *T.
 psuedonana* cell lamellae * Tp19b_TS_009_full.rec Reconstructed
 cryo-electron tomogram of *T. psuedonana* cell