High-resolution imaging of bacterial spatial organization with vertical cell imaging by nanostructured immobilization (VerCINI)

Kevin D. Whitley, Stuart Middlemiss, Calum Jukes, Cees Dekker, Séamus Holden

Published: 2022-01-30 DOI: 10.1038/s41596-021-00668-1

Supplementary information

Supplementary Information

Supplementary Fig. 1 and Supplementary Methods.

Suboptimal cell trapping visualized by bright-field microscopy . B. subtilis PY79 cells improperly trapped in microhole arrays where microhole width (>1.1 µm) is too large to immobilize most cells. Lateral diffusive motion in the holes (wobbling) can be observed in ~50% of trapped cells. The video shows acceptable but not excellent cell loading efficiency. A few cells can be seen sitting on top of rather than within microholes, likely those that did not wash off during sample preparation. Video was recorded at 100 Hz and plays in real time. Scale bar, 10 µm.

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References

Supplementary information

Huang, B., Babcock, H. & Zhuang, X. Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143, 1047–1058 (2010).
Pasquina-Lemonche, L. et al. The architecture of the Gram-positive bacterial cell wall. Nature 582, 294–297 (2020).
Garner, E. C. et al. Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis. Science 333, 222–225 (2011).
Domínguez-Escobar, J. et al. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 333, 225–228 (2011).
Bisson-Filho, A. W. et al. Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division. Science 355, 739–743 (2017).
Yang, X. et al. GTPase activity–coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. Science 355, 744–747 (2017).
Kirkpatrick, C. L. & Viollier, P. H. Poles apart: prokaryotic polar organelles and their spatial regulation. Cold Spring Harb. Perspect. Biol. 3, a006809–a006809 (2011).
Kuwada, N. J., Traxler, B. & Wiggins, P. A. Genome‐scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle. Mol. Microbiol. 95, 64–79 (2015).
Laloux, G. & Jacobs-Wagner, C. How do bacteria localize proteins to the cell pole? J. Cell Sci. https://doi.org/10.1242/jcs.138628 (2014).
Surovtsev, I. V. & Jacobs-Wagner, C. Subcellular organization: a critical feature of bacterial cell replication. Cell 172, 1271–1293 (2018).
Bowman, G. R., Lyuksyutova, A. I. & Shapiro, L. Bacterial polarity. Curr. Opin. Cell Biol. 23, 71–77 (2011).
Whitley, K. D. et al. FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division. Nat. Commun. 12, 2448 (2021).
Perez, A. J. et al. Movement dynamics of divisome proteins and PBP2x:FtsW in cells of Streptococcus pneumoniae. Proc. Natl Acad. Sci. USA 116, 3211–3220 (2019).
Chai, Y., Norman, T., Kolter, R. & Losick, R. An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes Dev. 24, 754–765 (2010).
Söderström, B., Chan, H., Shilling, P. J., Skoglund, U. & Daley, D. O. Spatial separation of FtsZ and FtsN during cell division. Mol. Microbiol. 107, 387–401 (2018).
McCausland, J. W. et al. Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism. Nat. Commun. 12, 609 (2021).
Trouve, J. et al. Nanoscale dynamics of peptidoglycan assembly during the cell cycle of Streptococcus pneumoniae. Curr. Biol. https://doi.org/10.1016/j.cub.2021.04.041 (2021).
Bakshi, S., Choi, H. & Weisshaar, J. C. The spatial biology of transcription and translation in rapidly growing Escherichia coli. Front. Microbiol. 6, 636 (2015).
Zhou, Z. et al. The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis. Mol. Biol. Cell 26, 78–90 (2015).
Thiyagarajan, S., Munteanu, E. L., Arasada, R., Pollard, T. D. & O’Shaughnessy, B. The fission yeast cytokinetic contractile ring regulates septum shape and closure. J. Cell Sci. https://doi.org/10.1242/jcs.166926 (2015).
Wollrab, V., Thiagarajan, R., Wald, A., Kruse, K. & Riveline, D. Still and rotating myosin clusters determine cytokinetic ring constriction. Nat. Commun. 7, 11860 (2016).
Strahl, H. et al. Transmembrane protein sorting driven by membrane curvature. Nat. Commun. 6, (2015).
Briegel, A. et al. New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography. Biochemistry 53, 1575–1585 (2014).
Deshpande, S. & Dekker, C. On-chip microfluidic production of cell-sized liposomes. Nat. Protoc. 13, 856–874 (2018).
Whitley, K. VerCINI_nanofab. Zenodo https://doi.org/10.5281/ZENODO.5548030 (2021).
de Jong, I. G., Beilharz, K., Kuipers, O. P. & Veening, J.-W. Live cell imaging of Bacillus subtilis and Streptococcus pneumoniae using automated time-lapse microscopy. J. Vis. Exp. 53, e3145 (2011).
Ellefsen, K. L., Dynes, J. L. & Parker, I. Spinning-spot shadowless TIRF microscopy. PLoS ONE 10, e0136055 (2015).
McGorty, R., Kamiyama, D. & Huang, B. Active microscope stabilization in three dimensions using image correlation. Opt. Nanoscopy 2, 3 (2013).
Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Holden, S. & Whitley, K. HoldenLab/ring-fitting2: v1.1.2.1. Zenodo https://doi.org/10.5281/ZENODO.4570259 (2021).
Luisier, F., Vonesch, C., Blu, T. & Unser, M. Fast interscale wavelet denoising of Poisson-corrupted images. Signal Process 90, 415–427 (2010).
Thevenaz, P., Ruttimann, U. E. & Unser, M. A pyramid approach to subpixel registration based on intensity. IEEE Trans. Image Process 7, 27–41 (1998).
Jakobs, M. A., Dimitracopoulos, A. & Franze, K. KymoButler, a deep learning software for automated kymograph analysis. eLife 8, e42288 (2019).
Wang, P. et al. Robust growth of Escherichia coli. Curr. Biol. 20, 1099–1103 (2010).
Tam, J. et al. A microfluidic platform for correlative live-cell and super-resolution microscopy. PloS ONE 9, e115512 (2014).
Almada, P. et al. Automating multimodal microscopy with NanoJ-Fluidics. Nat. Commun. 10, 1223 (2019).
Whitley, K. D. et al. DeepAutoFocus. Zenodo https://doi.org/10.5281/ZENODO.4573121 (2021).
Holden, S. HoldenLab/VerciniAnalysisJ: v1.1.1. Zenodo https://doi.org/10.5281/ZENODO.4617277 (2021).
Erratum for the Report: "Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division" by A. W. Bisson-Filho, Y.-P. Hsu, G. R. Squyres, E. Kuru, F. Wu, C. Jukes, Y. Sun, C. Dekker, S. Holden, M. S. VanNieuwenhze, Y. V. Brun, E. C. GarnerErratum for the Report: “Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division”. Science 367, eaba6311 (2020).
Tinevez, J.-Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).

High-resolution imaging of bacterial spatial organization with vertical cell imaging by nanostructured immobilization (VerCINI)

Supplementary information

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