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- EMDB-0507: cryo-electron tomography of marine bacteria T. autotrophicus, EF1... -

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Basic information

Entry
Database: EMDB / ID: EMD-0507
Titlecryo-electron tomography of marine bacteria T. autotrophicus, EF1 strain, cultured under anaerobic, repleted with sulfur source.
Map dataT. autotrophicus EF1 cell cultured under anaerobic condition, supplemented with sulfur source.
Sample
  • Cell: Thioglobus autotrophicus, EF1
    • Complex: PilQ
Biological speciesCandidatus Thioglobus (bacteria) / Thioglobus (bacteria)
Methodelectron tomography / cryo EM
AuthorsNicastro D / Zhao XW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)OCE-1232840 United States
CitationJournal: mBio / Year: 2019
Title: Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation.
Authors: Vega Shah / Xiaowei Zhao / Rachel A Lundeen / Anitra E Ingalls / Daniela Nicastro / Robert M Morris /
Abstract: Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these ...Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, " Thioglobus autotrophicus," is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype. Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in " Thioglobus autotrophicus," a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries.
History
DepositionJan 28, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseDec 18, 2019-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / 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

emd_0507.png

Downloads & links

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Map

FileDownload / File: emd_0507.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationT. autotrophicus EF1 cell cultured under anaerobic condition, supplemented with sulfur source.
Voxel sizeX=Y=Z: 5.5 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)13.034897 (±59.76259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1169-1372326
Dimensions15701330650
Spacing13301570650
CellA: 7315.0 Å / B: 8635.0 Å / C: 3575.0 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/z13301570650
origin x/y/z0.0000.0000.000
length x/y/z7315.0008635.0003575.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-1372-1169326
NC/NR/NS13301570650
D min/max/mean-128.000127.00013.035

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Supplemental data

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Sample components

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Entire : Thioglobus autotrophicus, EF1

EntireName: Thioglobus autotrophicus, EF1
Components
  • Cell: Thioglobus autotrophicus, EF1
    • Complex: PilQ

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Supramolecule #1: Thioglobus autotrophicus, EF1

SupramoleculeName: Thioglobus autotrophicus, EF1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: marine bacterium Thioglobus autotrophicus, EF1 strain
Source (natural)Organism: Candidatus Thioglobus (bacteria) / Strain: EF1

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Supramolecule #2: PilQ

SupramoleculeName: PilQ / type: complex / ID: 2 / Parent: 1 / Details: outer membrane pore complex
Source (natural)Organism: Thioglobus (bacteria) / Strain: EF1

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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: grid was washed by ethyl acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Instrument: GATAN CRYOPLUNGE 3
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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