Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi
Data files
Feb 07, 2024 version files 293.90 GB
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1a_lamellas_ehux_control_ehux.tar.bzip2
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1a_lamellas_ehux_infected_10min.tar.bzip2
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1a_lamellas_ehux_infected_30min.tar.bzip2
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1a_lamellas_ehux_infected_48h_dataset_1.tar.bzip2
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1a_lamellas_ehux_infected_48h_dataset_2.tar.bzip2
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1a_lamellas_ehux_infected_48h_dataset_3.tar.bzip2
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1a_lamellas_ehux_infected_48h_dataset_4.tar.bzip2
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1a_lamellas_ehux_infected_coccoliths.tar.bzip2
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1b_segmentations.tar.bzip2
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1c_blockFaceImaging.tar.bzip2
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2a_tomostarpy_masterBranchClone.tar.bzip2
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2b_pentamerAlignmentScript.tar.bzip2
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3_fluorescenceData.tar.bzip2
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4_msAnalysis_ehv201.tar.bzip2
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README.md
Abstract
The globally distributed marine alga Emiliania huxleyi produces reflective calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce the heat absorption in the ocean, which cools the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane decorated with numerous transmembrane proteins. The virions are prone to deformation, and parts of their capsids deviate from the icosahedral arrangement. EhV-201 virions infect E. huxleyi by using their fivefold vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. Upon the completion of genome packaging, the capsids change conformation, which enables them to acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which allows the continuous release of virions by exocytosis. Our results provide insight into how EhVs bypass the surface protective layers of E. huxleyi and exploit the organelles of an infected cell for progeny assembly.
README: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi
https://doi.org/10.5061/dryad.p5hqbzkw0
1) Emiliania huxleyi virus 201 life cycle visualization in situ:
- a) Cryo-electron tomography of lamellas of Emiliania huxleyi noncalcifying 2090 alga infected by E. huxleyi virus 201 (EhV-201) and control uninfected samples.
- b) Segmentation of two selected cryo-tomographic lamellae volumes (infected and control E. huxleyi cells).
- c) Block face imaging data of high-pressure frozen and resin-embedded samples of E. huxleyi infected by EhV-201.
2) Scripts used during the reconstruction of EhV-201 by subtomogram averaging:
- a) TomoStarPy scripts available on GitHub (22 February 2024 clone): https://github.com/fuzikt/tomostarpy
- b) Script used for alignment of EhV-201 virion pentamer vertices during generation of virion composite map
3) Super-resolution fluorescence data of EhV-201 attachment to the E. huxleyi cells.
4) Proteomic analysis of EhV-201 virion - full report
Description of the data and file structure
Note: All the data are compressed as fileName.tar.bzip2. To extract them, you can use Linux terminal (tar -xjf filename.tar.bzip2) or Windows program 7-Zip or WinRAR (extract gradually: fileName.tar.bzip2 > extract here > fileName.tar > extract here).
1.a) E. huxleyi cryo-lamellas tomography data:
- 1a_lamellas_ehux_control_ehux: xxxxxx_ehux2090_ctrl_f2medium and _100kDa_lysate (control E. huxleyi samples treated with F/2-Si medium or by 100 kDa viral lysate flow-through (more details in the article)).
- 1a_lamellas_ehux_infected_48h_dataset_1 and _2-4 (infected E. huxleyi samples at late stage of EhV-201 infection at 48 hours post-infection)
- 1a_lamellas_ehux_infected_10min and _30min (infected E. huxleyi samples at early stage of EhV-201 infection at 10 or 30 minutes post-infection)
- 1a_lamellas_ehux_infected_coccoliths (infected E. huxleyi samples which spontaneously reanimate the coccolith production at early stage of EhV-201 infection at 30 or 60 minutes post-infection)
To visualize the reconstructed tomographic volume use 3dmod from IMOD package. Available for Windows (Open file > tomoX_full_rec.mrc) and Linux (3dmod -Y tomoX_full_rec.mrc)
Intermediate reconstruction image files removed. To regenerate them use the eTomo GUI from IMOD package workflow (File > Open > tomoX.edf)
1.b) Segmentation of E. huxleyi lamellae volumes
i) Original segmentation data: "origData_dragonflySession"
- control_cell - noninfected E. huxleyi cell with a segmented thin slice of the volume.
- infected_cell - infected E. huxleyi cell by EhV-201 at a late stage of infection. Due to the PC memory issues individual materials are in separate sessions (_cellEnvelope; _innerVesicle; _membranes; _viruses).
Data contains Tomograms (tomoX_rec_noBytes_noFilter.mrc); and Segmentations (fileName.ORSSession).
To open the segmentation session files use Dragonfly ORS software (Windows, Linux).
ii) Segmentation movies generation: "movie_generation"
To visualize the segmented volumes use the ChimeraX software (Windows, Linux) command line: "open movie_segmentation_xxx_preparation.cxc"
To generate the movie, run in the same session: "open movie_segmentation_xxx_movie.cxc"
1.c) Block face imaging data
To open the stitched volumes use ImageJ (Fiji) (Windows, Linux).
2.a) TomoStarPy scripts master branch clone:
Find the installation instructions and individual scripts description in: README.md inside the "tomostarpy" folder.
Alternatively you can invoke the help for each individual script in terminal by entering (python3 scriptName.py).
2.b) Script for virion pentamer orientation:
The script requires Cyton, Cuda-python, Numpy.
Building: build_libs.bsh; Running: set parameters in run.py (help in the source code) and execute it. \
This is an single-use script without any possibility of changing the parameters too much.
3) E. huxleyi fluorescence data from super-resolution Elyra 7 microscope.
- Medium F/2-Si control (220708_F2CTRL_xxx.czi)
- Virus in F/2-Si medium control (220708_virusCTRL_xxx.czi)
- Uninfected E. huxleyi alga control (220708_algaCTRL_xxx.czi)
- Infected E. huxleyi by EhV-201 at 30 min post infection using various multiplicity of infection (220708_MOI10 and _MOI100 and _MOI1000_xxx.czi)
- Fluorescent beads used for channel alignment (220708_beads_xxx.czi).
Original 9-phase data Z-stack in a leap mode (no identifier) and SIM^2 reconstructed Z-stack data (_SIM).
To visualize the reconstructed Z-stack data (_SIM), please use ZEN (Blue or Black versions) software (Windows), or ImageJ (Fiji) (both available for Windows, Linux).
4) Proteomic data analysis
Open the file in MS Excel. Individual sheets in the Excel file are named: \
i) Gel image (image of the gel with depicted protein bands used for MS analysis).\
ii) 1 - 27 (summary of the detected proteins identified in the corresponding protein bands. Individual columns correspond to: Protein accession number; Protein description; Molecular weight (MW); Calculated isoelectric point (calc. pI); Spectral abundance factor (SAF), Normalized abundance factor (NSAF), Sequence coverage; Sum of proteins; Sum of peptides; and Sum of unique peptides. More information can be found in the notes of the column's headings, depicted by a red triangle in the cell upper right corner). \
iii) 1 - 27_peptides (contains information about all the peptides detected for each protein. Lists of peptides are in the hidden lines depicted by a plus sign on the left from the line number. Click the plus sign to expand them).
Sharing/Access information
Links to other publicly accessible locations of the data.
Code availability: