Spatial organization of the flow of genetic information in bacteria

Nature

Volumn 466, Issue 7302, 2010, Pages 77-81

  Llopis, Paula Montero ^a   Jackson, Audrey F ^a,d   Sliusarenko, Oleksii ^a   Surovtsev, Ivan ^a   Heinritz, Jennifer ^a   Emonet, Thierry ^a,b   Jacobs Wagner, Christine ^a,c  

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA; RIBONUCLEASE E;

CHROMOSOME; COLIFORM BACTERIUM; DEVELOPMENTAL BIOLOGY; GENE EXPRESSION; GENE FLOW; GENETIC ANALYSIS; HYBRIDIZATION; QUANTITATIVE ANALYSIS; SPATIAL DISTRIBUTION;

ARTICLE; BACTERIAL GENETICS; CAULOBACTER CRESCENTUS; CHROMOSOME; DIFFUSION COEFFICIENT; ESCHERICHIA COLI; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC ORGANIZATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RNA TRANSLATION;

BACTERIAL PROTEINS; CAULOBACTER CRESCENTUS; CHAPERONINS; CHROMOSOMES, BACTERIAL; DIFFUSION; DNA, BACTERIAL; ENDORIBONUCLEASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; IN SITU HYBRIDIZATION, FLUORESCENCE; LAC OPERON; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA STABILITY; RNA TRANSPORT; RNA, BACTERIAL; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); CAULOBACTER VIBRIOIDES; ESCHERICHIA COLI; EUKARYOTA;

EID: 77954242830     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09152     Document Type: Article

References (38)

1. Passalacqua, K. D. et al. Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191, 3203-3211 (2009).
2. Epshtein, V. & Nudler, E. Cooperation between RNA polymerase molecules in transcription elongation. Science 300, 801-805 (2003). (Pubitemid 36532116)
3. Vogel, U. & Jensen, K. F. The RNA chain elongation rate in Escherichia coli depends on the growth rate. J. Bacteriol. 176, 2807-2813 (1994).
4. 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).
5. Miller, O. L. Jr, Hamkalo, B. A. & Thomas, C. A. Jr. Visualization of bacterial genes in action. Science 169, 392-395 (1970).
6. Guet, C. C. et al. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Res. 36, e73 (2008).
7. Golding, I. & Cox, E. C. RNA dynamics in live Escherichia coli cells. Proc. Natl Acad. Sci. USA 101, 11310-11315 (2004).
8. Maamar, H., Raj, A. & Dubnau, D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 317, 526-529 (2007).
9. Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025-1036 (2005).
10. 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).
11. 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).
12. 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).
13. Avedissian, M. & Lopes Gomes, S. Expression of the groESL operon is cell-cycle controlled in Caulobacter crescentus. Mol. Microbiol. 19, 79-89 (1996).
14. Lim, F. & Peabody, D. S. Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res. 22, 3748-3752 (1994).
15. Lau, I. F. et al. Spatial and temporal organization of replicating Escherichia coli chromosomes. Mol. Microbiol. 49, 731-743 (2003).
16. Deana, A. & Belasco, J. G. Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev. 19, 2526-2533 (2005).
17. Viollier, P. H. & Shapiro, L. Spatial complexity of mechanisms controlling a bacterial cell cycle. Curr. Opin. Microbiol. 7, 572-578 (2004).
18. Wheeler, R. T. & Shapiro, L. Differential localization of two histidine kinases controlling bacterial cell differentiation. Mol. Cell 4, 683-694 (1999).
19. Mangan, E. K. et al. FlbT couples flagellum assembly to gene expression in Caulobacter crescentus. J. Bacteriol. 181, 6160-6170 (1999).
20. 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).
21. 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).
22. 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).
23. 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).
24. Briegel, A. et al. Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography. Mol. Microbiol. 62, 5-14 (2006).
25. 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).
26. Lewis, P. J., Thaker, S. D. & Errington, J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19, 710-718 (2000).
27. 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).
28. 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).
29. 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).
30. 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).
31. 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).
32. 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).
33. Tamames, J. Evolution of gene order conservation in prokaryotes. Genome Biol. 2, research0020.1-research0020.11 (2001).
34. Fang, G., Rocha, E. P. & Danchin, A. Persistence drives gene clustering in bacterial genomes. BMC Genomics 9, 4 (2008).
35. Ely, B. Genetics of Caulobacter crescentus. Methods Enzymol. 204, 372-384 (1991).
36. Evinger, M. & Agabian, N. Envelope-associated nucleoid from Caulobacter crescentus stalked and swarmer cells. J. Bacteriol. 132, 294-301 (1977).
37. 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).
38. 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).