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- EMDB-13730: Cryo-electron tomography of an attached epibiotic cell of Ca. Abs... -

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Entry
Database: EMDB / ID: EMD-13730
TitleCryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator
Map data
SampleCryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator
Biological speciesbacterium (bacteria)
Methodelectron tomography / cryo EM
AuthorsGaisin V / Pilhofer M
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255European Union
European Research Council (ERC)679209European Union
CitationJournal: Environ Microbiol / Year: 2021
Title: Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'.
Authors: Michail M Yakimov / Alexander Y Merkel / Vasil A Gaisin / Martin Pilhofer / Enzo Messina / John E Hallsworth / Alexandra A Klyukina / Ekaterina N Tikhonova / Vladimir M Gorlenko /
Abstract: Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress ...Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes.
History
DepositionOct 12, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

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Map

FileDownload / File: emd_13730.map.gz / Format: CCP4 / Size: 167.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.28 Å/pix.
x 204 pix.
= 3729.12 Å
18.28 Å/pix.
x 671 pix.
= 12265.881 Å
18.28 Å/pix.
x 642 pix.
= 11735.761 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
Minimum - Maximum-371.0 - 268.0
Average (Standard dev.)0.9655066 (±7.7670774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-10725872
Dimensions671642204
Spacing642671204
CellA: 11735.761 Å / B: 12265.881 Å / C: 3729.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z18.28000155763218.28000149031318.28
M x/y/z642671204
origin x/y/z0.0000.0000.000
length x/y/z11735.76112265.8813729.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS258-10772
NC/NR/NS642671204
D min/max/mean-371.000268.0000.966

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Supplemental data

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Sample components

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Entire Cryo-electron tomography of an attached epibiotic cell of Ca. Abs...

EntireName: Cryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator
Number of Components: 1

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Component #1: cellular-component, Cryo-electron tomography of an attached epibi...

Cellular-componentName: Cryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator
Recombinant expression: No
SourceSpecies: bacterium (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Cell / Method: cryo EM
Sample solutionpH: 9
Support filmPELCO easiGlowTM Ted Pella 15 mA for 15 s
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: OTHER / Temperature: 295.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.524 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: electron tomography / Number of Sections: 61
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD

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