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Spatial organization of the flow of genetic information in bacteria

Abstract

Eukaryotic cells spatially organize mRNA processes such as translation and mRNA decay. Much less is clear in bacterial cells where the spatial distribution of mature mRNA remains ambiguous. Using a sensitive method based on quantitative fluorescence in situ hybridization, we show here that in Caulobacter crescentus and Escherichia coli, chromosomally expressed mRNAs largely display limited dispersion from their site of transcription during their lifetime. We estimate apparent diffusion coefficients at least two orders of magnitude lower than expected for freely diffusing mRNA, and provide evidence in C. crescentus that this mRNA localization restricts ribosomal mobility. Furthermore, C. crescentus RNase E appears associated with the DNA independently of its mRNA substrates. Collectively, our findings show that bacteria can spatially organize translation and, potentially, mRNA decay by using the chromosome layout as a template. This chromosome-centric organization has important implications for cellular physiology and for our understanding of gene expression in bacteria.

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Figure 1: groESL mRNAs remain confined within subcellular regions.
Figure 2: groESL and creS mRNAs largely remain at the site of birth for their entire lifespan.
Figure 3: Endogenous LacZ-encoding mRNAs display diffraction-limited dispersion from sites of transcription in E. coli.
Figure 4: Dispersion of groESL–lacO 120 mRNA.
Figure 5: mRNA limits diffusion of translating ribosomes.
Figure 6: RNase E colocalizes with the DNA in C. crescentus.

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Acknowledgements

We thank P. Angelastro, N. Ausmees, T. Cox, I. Golding, H. Lam, D. S. Peabody, D Leach, D. J. Sherratt and P. Viollier for strains and constructs, M. Cabeen for editorial help, and S. R. Kushner, J. Belasco, K. C. Huang, the Lambda lunch group at NIH, and the Jacobs-Wagner laboratory for valuable discussions. This work was funded in part by a Howard Hughes Medical Institute Predoctoral Fellowship (to A.F.J.), the National Institutes of Health (GM065835 to C.J.-W.) and the Howard Hughes Medical Institute.

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Contributions

C.J.-W., P.M.L. and A.F.J. designed experiments. P.M.L. performed the FISH, ribosome and RNaseE experiments, and analysed FISH and FRAP data. A.F.J. carried out the MS2 experiments and analysed the data. P.M.L. and J.H. performed the real-time PCR measurements. O.S. developed the tools for image and data analysis. I.S. described and implemented the mathematical model for the analysis of mRNA diffusion. T.E. provided conceptual and data analysis advice. C.J.-W., P.M.L. and A.F.J. wrote the paper.

Corresponding author

Correspondence to Christine Jacobs-Wagner.

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The authors declare no competing financial interests.

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Supplementary Information

This file contains Supplementary Figures 1-8 with legends, Supplementary Information comprising Supplementary Text, Image and data analysis, Mathematical modelling, Supplementary Tables S1-S2, Construction of plasmids and strains, FISH probes sequences and References. (PDF 1199 kb)

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Montero Llopis, P., Jackson, A., Sliusarenko, O. et al. Spatial organization of the flow of genetic information in bacteria. Nature 466, 77–81 (2010). https://doi.org/10.1038/nature09152

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