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- EMDB-0616: Cryo-electron tomography of marine bacterium Candidatus Thioglobu... -

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Basic information

Entry
Database: EMDB / ID: EMD-0616
TitleCryo-electron tomography of marine bacterium Candidatus Thioglobus singularis strain PS1
Map datamarine bacterium Candidatus Thioglobus singularis strain PS1
Sample
  • Cell: Marine bacteria Candidatus Thioglobus singularis strain PS1
    • Complex: PilQ
Biological speciesCandidatus Thioglobus singularis PS1 (bacteria)
Methodelectron tomography / cryo EM
AuthorsNicastro D / Zhao X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)OCE-1232840 United States
CitationJournal: 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
Header (metadata) releaseFeb 20, 2019-
DepositionFeb 24, 2019-
Map releaseApr 17, 2019-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

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  • 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

emd_0616.png

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Map

FileDownload / File: emd_0616.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS SIGNED BYTE
Annotationmarine bacterium Candidatus Thioglobus singularis strain PS1
Voxel sizeX=Y=Z: 5.5 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)33.395523 (±58.3291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-666-467172
Dimensions27012101381
Spacing21012701381
CellA: 11555.5 Å / B: 14855.5 Å / C: 2095.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z5.55.55.5
M x/y/z21012701381
origin x/y/z0.0000.0000.000
length x/y/z11555.50014855.5002095.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-467-666172
NC/NR/NS21012701381
D min/max/mean-128.000127.00033.396

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Supplemental data

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Sample components

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Entire : Marine bacteria Candidatus Thioglobus singularis strain PS1

EntireName: Marine bacteria Candidatus Thioglobus singularis strain PS1
Components
  • Cell: Marine bacteria Candidatus Thioglobus singularis strain PS1
    • Complex: PilQ

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Supramolecule #1: Marine bacteria Candidatus Thioglobus singularis strain PS1

SupramoleculeName: Marine bacteria Candidatus Thioglobus singularis strain PS1
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1

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Supramolecule #2: PilQ

SupramoleculeName: PilQ / type: complex / ID: 2 / Parent: 1 / Details: outer membrane pore complex
Source (natural)Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1

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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: 7 / Details: artificial sea water
GridModel: 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Instrument: GATAN CRYOPLUNGE 3
DetailsCells were harvested by centrifugation at 39,000xg at 4 degrees Celsius for 1 hour.
Cryo protectantNo
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61

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