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- EMDB-13729: Cryo-electron tomogram of a single cell of Candidatus Absconditic... -

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Basic information

Entry
Database: EMDB / ID: EMD-13729
TitleCryo-electron tomogram of a single cell of Candidatus Absconditicoccus praedator
Map data
Sample
  • Cell: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
KeywordsPatescibacteria / bacterium / UNKNOWN FUNCTION
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: 2022
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-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing 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_13729.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Voxel sizeX=Y=Z: 10.74 Å
Density
Minimum - Maximum-144.0 - 123.0
Average (Standard dev.)0.5752138 (±6.5920553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128532214
Dimensions574606222
Spacing606574222
CellA: 6508.44 Å / B: 6164.76 Å / C: 2384.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z10.7410.7410.74
M x/y/z606574222
origin x/y/z0.0000.0000.000
length x/y/z6508.4406164.7602384.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS532-128214
NC/NR/NS606574222
D min/max/mean-144.000123.0000.575

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Supplemental data

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Sample components

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Entire : Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator

EntireName: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
Components
  • Cell: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator

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Supramolecule #1: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator

SupramoleculeName: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: bacterium (bacteria)

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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: 9 / Details: The cells have been frozen in a culture medium
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: PELCO easiGlowTM (Ted Pella) 15 mA for 15 s
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV / Details: Back side blotting fir 6 s.
DetailsCell suspension
Cryo protectantno cryo-protectant
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 0.5 sec. / Average electron dose: 2.524 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.5) / Number images used: 58

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