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PMID: 15277674 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

RNA dynamics in live Escherichia coli cells.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 101 ·No. 31 ·2004-08-03 ·Pages 11310-5

Golding I, Cox EC

Abstract

We describe a method for tracking RNA molecules in Escherichia coli that is sensitive to single copies of mRNA, and, using the method, we find that individual molecules can be followed for many hours in living cells. We observe distinct characteristic dynamics of RNA molecules, all consistent with the known life history of RNA in prokaryotes: localized motion consistent with the Brownian motion of an RNA polymer tethered to its template DNA, free diffusion, and a few examples of polymer chain dynamics that appear to be a combination of chain fluctuation and chain elongation attributable to RNA transcription. We also quantify some of the dynamics, such as width of the displacement distribution, diffusion coefficient, chain elongation rate, and distribution of molecule numbers, and compare them with known biophysical parameters of the E. coli system.

MeSH Terms
Diffusion Escherichia coli/genetics,metabolism Gene Expression Regulation, Bacterial/physiology Green Fluorescent Proteins Indicators and Reagents/metabolism Luminescent Proteins/genetics,metabolism Microscopy, Fluorescence Polymers/metabolism RNA, Bacterial/metabolism RNA, Messenger/metabolism Recombinant Fusion Proteins/genetics,metabolism
Chemicals
Indicators and Reagents Luminescent Proteins Polymers RNA, Bacterial RNA, Messenger Recombinant Fusion Proteins Green Fluorescent Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Golding Ido
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Cox Edward C
References (47)
47 references, click to expand
  1. Dynamic spatial regulation in the bacterial cell.
    Cell. 2000 Jan 7;100(1):89-98 PMID: 10647934
  2. Optical methods for exploring dynamics of single copies of green fluorescent protein.
    Cytometry. 1999 Jul 1;36(3):232-8 PMID: 10404973
  3. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase.
    Science. 2000 Mar 31;287(5462):2497-500 PMID: 10741971
  4. Reversible unfolding of single RNA molecules by mechanical force.
    Science. 2001 Apr 27;292(5517):733-7 PMID: 11326101
  5. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms.
    Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8319-25 PMID: 11459970
  6. Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator.
    Nucleic Acids Res. 2001 Sep 15;29(18):3873-81 PMID: 11557820
  7. Making contacts on a nucleic acid polymer.
    Trends Biochem Sci. 2001 Dec;26(12):733-40 PMID: 11738597
  8. Stochastic gene expression in a single cell.
    Science. 2002 Aug 16;297(5584):1183-6 PMID: 12183631
  9. The dynamic microbe: green fluorescent protein brings bacteria to light.
    Mol Microbiol. 2002 Sep;45(5):1191-6 PMID: 12207688
  10. Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase.
    Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11682-7 PMID: 12193647
  11. Dynamic cellular location of bacterial plasmids.
    Curr Opin Microbiol. 2002 Dec;5(6):586-90 PMID: 12457702
  12. Single mRNA molecules demonstrate probabilistic movement in living mammalian cells.
    Curr Biol. 2003 Jan 21;13(2):161-7 PMID: 12546792
  13. Dynamic proteins and a cytoskeleton in bacteria.
    Nat Cell Biol. 2003 Mar;5(3):175-8 PMID: 12646867
  14. Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles.
    Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7865-70 PMID: 12766229
  15. Spatial and temporal organization of replicating Escherichia coli chromosomes.
    Mol Microbiol. 2003 Aug;49(3):731-43 PMID: 12864855
  16. Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila.
    Curr Biol. 2003 Jul 15;13(14):1159-68 PMID: 12867026
  17. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.
    Nature. 2003 Dec 11;426(6967):684-7 PMID: 14634670
  18. Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle.
    J Biol Chem. 2004 Jan 30;279(5):3239-44 PMID: 14597619
  19. Summing up the noise in gene networks.
    Nature. 2004 Jan 29;427(6973):415-8 PMID: 14749823
  20. Kinetics of plasmid segregation in Escherichia coli.
    Mol Microbiol. 2004 Jan;51(2):461-9 PMID: 14756786
  21. Electronmicroscopy of genetic activity.
    Annu Rev Biochem. 1973;42:379-96 PMID: 4581229
  22. Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro.
    Proc Natl Acad Sci U S A. 1981 Jul;78(7):4180-4 PMID: 7027254
  23. Temperature dependence of RNA synthesis parameters in Escherichia coli.
    J Bacteriol. 1982 Aug;151(2):879-87 PMID: 6178724
  24. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions.
    Cell. 1982 Jun;29(2):319-28 PMID: 6288254
  25. RNA binding site of R17 coat protein.
    Biochemistry. 1987 Mar 24;26(6):1563-8 PMID: 3297131
  26. Translational repression by bacteriophage MS2 coat protein expressed from a plasmid. A system for genetic analysis of a protein-RNA interaction.
    J Biol Chem. 1990 Apr 5;265(10):5684-9 PMID: 2108146
  27. Use of synthetic oligoribonucleotides to probe RNA-protein interactions in the MS2 translational operator complex.
    Nucleic Acids Res. 1990 Jun 25;18(12):3521-8 PMID: 1694577
  28. Control of translational repression by protein-protein interactions.
    Nucleic Acids Res. 1992 Apr 11;20(7):1649-55 PMID: 1579455
  29. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.
    Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8794-7 PMID: 1528894
  30. Crystal structure of an RNA bacteriophage coat protein-operator complex.
    Nature. 1994 Oct 13;371(6498):623-6 PMID: 7523953
  31. Complementation of RNA binding site mutations in MS2 coat protein heterodimers.
    Nucleic Acids Res. 1996 Jun 15;24(12):2352-9 PMID: 8710507
  32. FACS-optimized mutants of the green fluorescent protein (GFP).
    Gene. 1996;173(1 Spec No):33-8 PMID: 8707053
  33. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition.
    J Cell Biol. 1996 Dec;135(6 Pt 2):1685-700 PMID: 8991083
  34. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements.
    Nucleic Acids Res. 1997 Mar 15;25(6):1203-10 PMID: 9092630
  35. Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations.
    Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8168-72 PMID: 9223333
  36. On/off blinking and switching behaviour of single molecules of green fluorescent protein.
    Nature. 1997 Jul 24;388(6640):355-8 PMID: 9237752
  37. Chromosome and low copy plasmid segregation in E. coli: visual evidence for distinct mechanisms.
    Cell. 1997 Sep 19;90(6):1113-21 PMID: 9323139
  38. Subunit fusion confers tolerance to peptide insertions in a virus coat protein.
    Arch Biochem Biophys. 1997 Nov 1;347(1):85-92 PMID: 9344468
  39. Non-genetic population heterogeneity studied by in situ polymerase chain reaction.
    Mol Microbiol. 1998 Mar;27(6):1099-105 PMID: 9570396
  40. Accurate insertional inactivation of lacZalpha: construction of pTrueBlue and M13TrueBlue cloning vectors.
    Gene. 1998 Jun 15;213(1-2):83-91 PMID: 9630534
  41. A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein.
    Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9244-9 PMID: 9689065
  42. In vivo visualization of chromosomes using lac operator-repressor binding.
    Trends Cell Biol. 1998 Mar;8(3):121-4 PMID: 9695822
  43. Localization of ASH1 mRNA particles in living yeast.
    Mol Cell. 1998 Oct;2(4):437-45 PMID: 9809065
  44. Protein mobility in the cytoplasm of Escherichia coli.
    J Bacteriol. 1999 Jan;181(1):197-203 PMID: 9864330
  45. Single-molecule imaging of RNA polymerase-DNA interactions in real time.
    Biophys J. 1999 Feb;76(2):709-15 PMID: 9929475
  46. Quantitative study of polymer conformation and dynamics by single-particle tracking.
    Biophys J. 1999 Mar;76(3):1598-605 PMID: 10049340
  47. Compartmentalization of transcription and translation in Bacillus subtilis.
    EMBO J. 2000 Feb 15;19(4):710-8 PMID: 10675340
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0404443101
Published
2004-08-03
Epub
2004-00-26
Pages
11310-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC509199
Subset
IM
Grants
NHGRI NIH HHS · R01 HG001506 · United States
NHGRI NIH HHS · HG 001506 · United States
External Links
PubMed source DOI: 10.1073/pnas.0404443101 PMC Full Text View journal details
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