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Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-Dimensional Superresolution Structured Illumination Microscopy

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Bacterial Chromatin

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1837))

Abstract

Superresolution imaging technology has contributed to our understanding of the subnucleoid organization in E. coli cells. Multicolor superresolution images revealing “bacterial nucleolus-like structure or organization,” “nucleolus-like compartmentalization of the transcription factories,” and “spatial segregation of the transcription and replication machineries” have enhanced our understanding of the dynamic landscape of the bacterial chromatin. This chapter provides a brief introduction into multicolor three-dimensional superresolution structured illumination microscopy (3D-SIM) used to study the spatial organization of the transcription machinery and its spatial relationship with replisomes from a microbiological research perspective. In addition to a detailed protocol, practical considerations are discussed in relation to (1) sampling and treatment of cells containing fluorescent fusion proteins, (2) imaging the transcription and replication machineries at single-cell levels, (3) performing imaging experiments to capture the spatial organization of the transcription machinery and the nucleoid, and (4) image acquisition and analysis.

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Acknowledgment

The authors would like to thank Valentin Magidson and Stephen Lockett at OMAL Facility (NCI, NIH) for their help and discussions. This research was supported by the Intramural Research Program of the National Cancer Institute (The Center for Cancer Research) NIH.

Author information

Author notes

  1. Cedric Cagliero

    Present address: Jecho Laboratories Inc., Frederick, MD, USA

  2. De Chen

    Present address: Ras Initiative, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Frederick, MD, USA

Authors and Affiliations

  1. Transcription Control Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA

    Carmen Mata Martin, Cedric Cagliero, Zhe Sun & Ding Jun Jin

Authors
  1. Carmen Mata Martin
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  2. Cedric Cagliero
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  3. Zhe Sun
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  4. De Chen
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  5. Ding Jun Jin
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Corresponding author

Correspondence to Ding Jun Jin .

Editor information

Editors and Affiliations

  1. Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands

    Remus T. Dame

1 Electronic Supplementary Material

3D model videos. 3D volume and rotation projection of a representative singe cell. (A) CC72 3D model. Nucleoid structure (red) and RNAP (green) (MP4 3176 kb)

3D model videos. 3D volume and rotation projection of a representative singe cell. (B) CC341 3D model. NusA (red), RNAP (green), Nucleoid structure (blue) (MP4 2362 kb)

3D model videos. 3D volume and rotation projection of a representative singe cell. (C) CC376 3D model. SSB (red), RNAP (green), Nucleoid structure (blue) (MP4 2352 kb)

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Martin, C.M., Cagliero, C., Sun, Z., Chen, D., Jin, D.J. (2018). Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-Dimensional Superresolution Structured Illumination Microscopy. In: Dame, R. (eds) Bacterial Chromatin. Methods in Molecular Biology, vol 1837. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8675-0_7

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  • DOI: https://doi.org/10.1007/978-1-4939-8675-0_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8674-3

  • Online ISBN: 978-1-4939-8675-0

  • eBook Packages: Springer Protocols

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