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- EMDB-27747: Electron cryotomogram of Geobacter sulfurreducens cell. -

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Basic information

Entry
Database: EMDB / ID: EMD-27747
TitleElectron cryotomogram of Geobacter sulfurreducens cell.
Map dataTomograph of a Geobacter sulfurreducens cell grown directly on a grid poised at -0.07 V vs. SHE.
Sample
  • Cell: Geobacter sulfurreducens cell
Biological speciesGeobacter sulfurreducens PCA (bacteria)
Methodelectron tomography / cryo EM
AuthorsHowley ET / Williams DR / Torres CI
Funding support United States, 1 items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N0014-20-1-2269 United States
CitationJournal: NPJ Biofilms Microbiomes / Year: 2023
Title: Intracytoplasmic membranes develop in Geobacter sulfurreducens under thermodynamically limiting conditions.
Authors: Ethan Howley / Anna Mangus / Dewight Williams / César I Torres /
Abstract: Geobacter sulfurreducens is an electroactive bacterium capable of reducing metal oxides in the environment and electrodes in engineered systems. Geobacter sp. are the keystone organisms in ...Geobacter sulfurreducens is an electroactive bacterium capable of reducing metal oxides in the environment and electrodes in engineered systems. Geobacter sp. are the keystone organisms in electrogenic biofilms, as their respiration consumes fermentation products produced by other organisms and reduces a terminal electron acceptor e.g. iron oxide or an electrode. To respire extracellular electron acceptors with a wide range of redox potentials, G. sulfurreducens has a complex network of respiratory proteins, many of which are membrane-bound. We have identified intracytoplasmic membrane (ICM) structures in G. sulfurreducens. This ICM is an invagination of the inner membrane that has folded and organized by an unknown mechanism, often but not always located near the tip of a cell. Using confocal microscopy, we can identify that at least half of the cells contain an ICM when grown on low potential anode surfaces, whereas cells grown at higher potential anode surfaces or using fumarate as electron acceptor had significantly lower ICM frequency. 3D models developed from cryo-electron tomograms show the ICM to be a continuous extension of the inner membrane in contact with the cytoplasmic and periplasmic space. The differential abundance of ICM in cells grown under different thermodynamic conditions supports the hypothesis that it is an adaptation to limited energy availability, as an increase in membrane-bound respiratory proteins could increase electron flux. Thus, the ICM provides extra inner-membrane surface to increase the abundance of these proteins. G. sulfurreducens is the first Thermodesulfobacterium or metal-oxide reducer found to produce ICMs.
History
DepositionJul 30, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27747.png

Downloads & links

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Map

FileDownload / File: emd_27747.map.gz / Format: CCP4 / Size: 901.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomograph of a Geobacter sulfurreducens cell grown directly on a grid poised at -0.07 V vs. SHE.
Voxel sizeX=Y=Z: 7.408 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)47.676456 (±5.5215745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-169-118215
Dimensions15041530411
Spacing15301504411
CellA: 11334.24 Å / B: 11141.632 Å / C: 3044.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Geobacter sulfurreducens cell

EntireName: Geobacter sulfurreducens cell
Components
  • Cell: Geobacter sulfurreducens cell

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Supramolecule #1: Geobacter sulfurreducens cell

SupramoleculeName: Geobacter sulfurreducens cell / type: cell / ID: 1 / Parent: 0
Details: Cell was grown directly on the grid, with the grid poised at a potential of -0.07 V vs. SHE to serve as an electron acceptor for the cell.
Source (natural)Organism: Geobacter sulfurreducens PCA (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: 7
GridModel: C-flat-2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 6 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.5 µm / Nominal defocus min: 6.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: eTomo / Number images used: 65

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