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- EMDB-25419: Previously uncharacterized rectangular bacteria in the dolphin mouth -

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Basic information

Entry
Database: EMDB / ID: EMD-25419
TitlePreviously uncharacterized rectangular bacteria in the dolphin mouth
Map dataRepresentative cryoET tomogram of rectangular cell like unit from dolphin mouth.
Sample
  • Cell: Rectangular cell like unit
Biological speciesunidentified (others)
Methodelectron tomography / cryo EM
AuthorsDudek NK / Galaz-Montoya JG / Shi H / Mayer M / Danita C / Celis AI / Wu GH / Behr B / Huang KC / Chiu W / Relman DA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
Chan Zuckerberg Initiative United States
CitationJournal: Nat Commun / Year: 2023
Title: Previously uncharacterized rectangular bacterial structures in the dolphin mouth.
Authors: Natasha K Dudek / Jesus G Galaz-Montoya / Handuo Shi / Megan Mayer / Cristina Danita / Arianna I Celis / Tobias Viehboeck / Gong-Her Wu / Barry Behr / Silvia Bulgheresi / Kerwyn Casey Huang ...Authors: Natasha K Dudek / Jesus G Galaz-Montoya / Handuo Shi / Megan Mayer / Cristina Danita / Arianna I Celis / Tobias Viehboeck / Gong-Her Wu / Barry Behr / Silvia Bulgheresi / Kerwyn Casey Huang / Wah Chiu / David A Relman /
Abstract: Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA ...Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.
History
DepositionNov 11, 2021-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25419.png

Downloads & links

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Map

FileDownload / File: emd_25419.map.gz / Format: CCP4 / Size: 885.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationRepresentative cryoET tomogram of rectangular cell like unit from dolphin mouth.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.99 Å/pix.
x 521 pix.
= 7808.748 Å		14.99 Å/pix.
x 928 pix.
= 13908.864 Å		14.99 Å/pix.
x 960 pix.
= 14388.479 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.988 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-108.0 - 112.0
Average (Standard dev.)18.43095 (±12.317652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16-16-257
Dimensions928960521
Spacing960928521
CellA: 14388.4795 Å / B: 13908.864 Å / C: 7808.748 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Rectangular cell like unit

EntireName: Rectangular cell like unit
Components
  • Cell: Rectangular cell like unit

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Supramolecule #1: Rectangular cell like unit

SupramoleculeName: Rectangular cell like unit / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: unidentified (others)

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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: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Uknown / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 28

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