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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Passalacqua, K. D. et al. Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191, 3203–3211 (2009)
Epshtein, V. & Nudler, E. Cooperation between RNA polymerase molecules in transcription elongation. Science 300, 801–805 (2003)
Vogel, U. & Jensen, K. F. The RNA chain elongation rate in Escherichia coli depends on the growth rate. J. Bacteriol. 176, 2807–2813 (1994)
Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S. & Cohen, S. N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA 99, 9697–9702 (2002)
Miller, O. L. Jr, Hamkalo, B. A. & Thomas, C. A. Jr. Visualization of bacterial genes in action. Science 169, 392–395 (1970)
Guet, C. C. et al. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Res. 36, e73 (2008)
Golding, I. & Cox, E. C. RNA dynamics in live Escherichia coli cells. Proc. Natl Acad. Sci. USA 101, 11310–11315 (2004)
Maamar, H., Raj, A. & Dubnau, D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 317, 526–529 (2007)
Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025–1036 (2005)
Valencia-Burton, M., McCullough, R. M., Cantor, C. R. & Broude, N. E. RNA visualization in live bacterial cells using fluorescent protein complementation. Nature Methods 4, 421–427 (2007)
Pilhofer, M., Pavlekovic, M., Lee, N. M., Ludwig, W. & Schleifer, K. H. Fluorescence in situ hybridization for intracellular localization of nifH mRNA. Syst. Appl. Microbiol. 32, 186–192 (2009)
Valencia-Burton, M. et al. Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells. Proc. Natl Acad. Sci. USA 106, 16399–16404 (2009)
Avedissian, M. & Lopes Gomes, S. Expression of the groESL operon is cell-cycle controlled in Caulobacter crescentus. Mol. Microbiol. 19, 79–89 (1996)
Lim, F. & Peabody, D. S. Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res. 22, 3748–3752 (1994)
Lau, I. F. et al. Spatial and temporal organization of replicating Escherichia coli chromosomes. Mol. Microbiol. 49, 731–743 (2003)
Deana, A. & Belasco, J. G. Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev. 19, 2526–2533 (2005)
Viollier, P. H. & Shapiro, L. Spatial complexity of mechanisms controlling a bacterial cell cycle. Curr. Opin. Microbiol. 7, 572–578 (2004)
Wheeler, R. T. & Shapiro, L. Differential localization of two histidine kinases controlling bacterial cell differentiation. Mol. Cell 4, 683–694 (1999)
Mangan, E. K. et al. FlbT couples flagellum assembly to gene expression in Caulobacter crescentus. J. Bacteriol. 181, 6160–6170 (1999)
Yarchuk, O., Jacques, N., Guillerez, J. & Dreyfus, M. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J. Mol. Biol. 226, 581–596 (1992)
Derman, A. I., Lim-Fong, G. & Pogliano, J. Intracellular mobility of plasmid DNA is limited by the ParA family of partitioning systems. Mol. Microbiol. 67, 935–946 (2008)
Elowitz, M. B., Surette, M. G., Wolf, P. E., Stock, J. B. & Leibler, S. Protein mobility in the cytoplasm of Escherichia coli. J. Bacteriol. 181, 197–203 (1999)
Viollier, P. H. et al. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc. Natl Acad. Sci. USA 101, 9257–9262 (2004)
Briegel, A. et al. Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography. Mol. Microbiol. 62, 5–14 (2006)
Forchhammer, J. & Lindahl, L. Growth rate of polypeptide chains as a function of the cell growth rate in a mutant of Escherichia coli 15. J. Mol. Biol. 55, 563–568 (1971)
Lewis, P. J., Thaker, S. D. & Errington, J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19, 710–718 (2000)
Mascarenhas, J., Weber, M. H. & Graumann, P. L. Specific polar localization of ribosomes in Bacillus subtilis depends on active transcription. EMBO Rep. 2, 685–689 (2001)
Carpousis, A. J., Luisi, B. F. & McDowall, K. J. Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog Mol Biol Transl Sci 85, 91–135 (2009)
Taghbalout, A. & Rothfield, L. RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proc. Natl Acad. Sci. USA 104, 1667–1672 (2007)
Khemici, V., Poljak, L., Luisi, B. F. & Carpousis, A. J. The RNase E of Escherichia coli is a membrane-binding protein. Mol. Microbiol. 70, 799–813 (2008)
Ward, D. & Newton, A. Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Mol. Microbiol. 26, 897–910 (1997)
Neidhart, F. C. & Umbarger, H. E. in Escherichia coli and Salmonella: cellular and molecular biology 2nd edition, Vol. 1 (ed. Neidhardt, F. C.) Ch. 3, 13–16 (ASM Press, 1996)
Tamames, J. Evolution of gene order conservation in prokaryotes. Genome Biol. 2, research0020.1–research0020.11 (2001)
Fang, G., Rocha, E. P. & Danchin, A. Persistence drives gene clustering in bacterial genomes. BMC Genomics 9, 4 (2008)
Ely, B. Genetics of Caulobacter crescentus. Methods Enzymol. 204, 372–384 (1991)
Evinger, M. & Agabian, N. Envelope-associated nucleoid from Caulobacter crescentus stalked and swarmer cells. J. Bacteriol. 132, 294–301 (1977)
Jensen, R. B. & Shapiro, L. The Caulobacter crescentus smc gene is required for cell cycle progression and chromosome segregation. Proc. Natl Acad. Sci. USA 96, 10661–10666 (1999)
Domian, I. J., Quon, K. C. & Shapiro, L. Cell type-specific phosphorylation and proteolysis of a transcriptional regulator controls the G1-to-S transition in a bacterial cell cycle. Cell 90, 415–424 (1997)
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.
The authors declare no competing financial interests.
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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