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Yorodumi- EMDB-0617: Cryo-electron tomography of marine bacterium Candidatus Thioglobu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0617 | |||||||||
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Title | Cryo-electron tomography of marine bacterium Candidatus Thioglobus singularis strain PS, showing the S layer on outer membrane | |||||||||
Map data | marine bacterium Candidatus Thioglobus singularis strain PS1 | |||||||||
Sample |
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Biological species | Candidatus Thioglobus singularis PS1 (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Nicastro D / Zhao X | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Environ Microbiol / Year: 2019 Title: Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. Authors: Rachel L Spietz / Rachel A Lundeen / Xiaowei Zhao / Daniela Nicastro / Anitra E Ingalls / Robert M Morris / Abstract: A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some ...A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0617.map.gz | 604.5 MB | EMDB map data format | |
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Header (meta data) | emd-0617-v30.xml emd-0617.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_0617.png | 171.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0617 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0617 | HTTPS FTP |
-Validation report
Summary document | emd_0617_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_0617_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_0617_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0617 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0617 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0617.map.gz / Format: CCP4 / Size: 841.9 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | marine bacterium Candidatus Thioglobus singularis strain PS1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Marine bacteria Candidatus Thioglobus singularis strain PS1
Entire | Name: Marine bacteria Candidatus Thioglobus singularis strain PS1 |
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Components |
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-Supramolecule #1: Marine bacteria Candidatus Thioglobus singularis strain PS1
Supramolecule | Name: Marine bacteria Candidatus Thioglobus singularis strain PS1 type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1 |
-Supramolecule #2: PilQ
Supramolecule | Name: PilQ / type: complex / ID: 2 / Parent: 1 / Details: outer membrane pore complex |
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Source (natural) | Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: artificial sea water |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa Details: The grid was washed with ethyl acetate prior to glow discharge. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Instrument: GATAN CRYOPLUNGE 3 |
Details | Cells were harvested by centrifugation at 39,000xg at 4 degrees Celsius for 1 hour. |
Cryo protectant | No |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: aldrich / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average exposure time: 5.6 sec. / Average electron dose: 1.52 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 0.5 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 26000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61 |
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