Journal: 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.
Download / File: emd_13729.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Voxel size
X=Y=Z: 10.74 Å
Density
Minimum - Maximum
-144.0 - 123.0
Average (Standard dev.)
0.5752138 (±6.5920553)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-128
532
214
Dimensions
574
606
222
Spacing
606
574
222
Cell
A: 6508.44 Å / B: 6164.76 Å / C: 2384.28 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Integer*27
Å/pix. X/Y/Z
10.74
10.74
10.74
M x/y/z
606
574
222
origin x/y/z
0.000
0.000
0.000
length x/y/z
6508.440
6164.760
2384.280
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
360
360
360
MAP C/R/S
1
2
3
start NC/NR/NS
532
-128
214
NC/NR/NS
606
574
222
D min/max/mean
-144.000
123.000
0.575
-
Supplemental data
-
Sample components
-
Entire : Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
Entire
Name: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
Components
Cell: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
-
Supramolecule #1: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator
Supramolecule
Name: Cryo-electron tomogram of a cell of Ca. Absconditicoccus praedator type: cell / ID: 1 / Parent: 0
Source (natural)
Organism: bacterium (bacteria)
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
electron tomography
Aggregation state
cell
-
Sample preparation
Buffer
pH: 9 / Details: The cells have been frozen in a culture medium
Grid
Model: 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
Vitrification
Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV / Details: Back side blotting fir 6 s.
Details
Cell suspension
Cryo protectant
no cryo-protectant
Sectioning
Other: NO SECTIONING
Fiducial marker
Manufacturer: Cytodiagnostics / Diameter: 10 nm
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi