Cellular organization of the transfer of genetic information

Current Opinion in Microbiology

Volumn 16, Issue 2, 2013, Pages 171-176

  Campos, Manuel ^a   Jacobs Wagner, Christine ^a,b  

^a YALE UNIVERSITY   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

BACTERIAL CELL; CAULOBACTER CRESCENTUS; CELL FUNCTION; CELL MOTILITY; CELL ORGANELLE; CELL TYPE; CELLULAR DISTRIBUTION; ENTROPY; GENE TRANSFER; MOLLICUTES; REVIEW; RHIZOBIUM RADIOBACTER; RIBOSOME; RNA DEGRADATION; SINORHIZOBIUM MELILOTI;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; CYTOPLASM; ORGANELLES; PROTEIN BIOSYNTHESIS; RNA STABILITY; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 84877048279     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2013.01.007     Document Type: Review

References (60)

1. Piekarski G. Zytologische Untersuchungen an Paratyphus- und Coli bacterien. Arch Mikrobiol 1937, 8:428-429.
2. 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 1971, 55:563-568.
3. Phillips L.A., Hotham-Iglewski B., Franklin R.M. Polyribosomes of Escherichia coli. II. Experiments to determine the in vivo distribution of polysomes, ribosomes and ribosomal subunits. J Mol Biol 1969, 45:23-38.
4. Azam T.A., Hiraga S., Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 2000, 5:613-626.
5. Bakshi S., Siryaporn A., Goulian M., Weisshaar J.C. Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Mol Microbiol 2012, 85:21-38.
6. Cabrera J.E., Jin D.J. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues. Mol Microbiol 2003, 50:1493-1505.
7. Klumpp S., Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci U S A 2008, 105:20245-20250.
8. Lewis P.J., Thaker S.D., Errington J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J 2000, 19:710-718.
9. Briegel A., Dias D.P., Li Z., Jensen R.B., Frangakis A.S., Jensen G.J. Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography. Mol Microbiol 2006, 62:5-14.
10. Kahng L.S., Shapiro L. Polar localization of replicon origins in the multipartite genomes of Agrobacterium tumefaciens and Sinorhizobium meliloti. J Bacteriol 2003, 185:3384-3391.
11. Montero Llopis P., Jackson A.F., Sliusarenko O., Surovtsev I., Heinritz J., Emonet T., Jacobs-Wagner C. Spatial organization of the flow of genetic information in bacteria. Nature 2010, 466:77-81.
12. Ortiz J.O., Forster F., Kurner J., Linaroudis A.A., Baumeister W. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J Struct Biol 2006, 156:334-341.
13. Seto S., Layh-Schmitt G., Kenri T., Miyata M. Visualization of the attachment organelle and cytadherence proteins of Mycoplasma pneumoniae by immunofluorescence microscopy. J Bacteriol 2001, 183:1621-1630.
14. Kuhner S., van Noort V., Betts M.J., Leo-Macias A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., et al. Proteome organization in a genome-reduced bacterium. Science 2009, 326:1235-1240.
15. Borgnia M.J., Subramaniam S., Milne J.L. Three-dimensional imaging of the highly bent architecture of Bdellovibrio bacteriovorus by using cryo-electron tomography. J Bacteriol 2008, 190:2588-2596.
16. Zimmerman S.B., Trach S.O. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 1991, 222:599-620.
17. Zimmerman S.B., Murphy L.D. Macromolecular crowding and the mandatory condensation of DNA in bacteria. FEBS Lett 1996, 390:245-248.
18. Mondal J., Bratton B.P., Li Y., Yethiraj A., Weisshaar J.C. Entropy-based mechanism of ribosome-nucleoid segregation in E. coli cells. Biophys J 2011, 100:2605-2613.
19. Hadizadeh Yazdi N., Guet C.C., Johnson R.C., Marko J.F. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Mol Microbiol 2012.
20. Wiggins P.A., Cheveralls K.C., Martin J.S., Lintner R., Kondev J. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc Natl Acad Sci U S A 2010, 107:4991-4995.
21. Dillon S.C., Dorman C.J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 2010, 8:185-195.
22. Dupaigne P., Tonthat N.K., Espeli O., Whitfill T., Boccard F., Schumacher M.A. Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome. Mol Cell 2012.
23. Wang W., Li G.W., Chen C., Xie X.S., Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011, 333:1445-1449.
24. Umbarger M.A., Toro E., Wright M.A., Porreca G.J., Bau D., Hong S.H., Fero M.J., Zhu L.J., Marti-Renom M.A., McAdams H.H., et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 2011, 44:252-264.
25. Valens M., Penaud S., Rossignol M., Cornet F., Boccard F. Macrodomain organization of the Escherichia coli chromosome. EMBO J 2004, 23:4330-4341.
26. Viollier P.H., Thanbichler M., McGrath P.T., West L., Meewan M., McAdams H.H., Shapiro L. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci U S A 2004, 101:9257-9262.
27. Stent G.S. The operon: on its third anniversary. modulation of transfer RNA species can provide a workable model of an operator-less operon. Science 1964, 144:816-820.
28. Shin D.H., Moldave K. Effect of ribosomes on the biosynthesis of ribonucleic acid in vitro. J Mol Biol 1966, 21:231-245.
29. Das H.K., Goldstein A., Lowney L.I. Attachment of ribosomes to nascent messenger RNA in Escherichia coli. J Mol Biol 1967, 24:231-245.
30. Mehdi Q., Yudkin M.D. Coupling of transcription to translation in the induced synthesis of beta-galactosidase. Biochim Biophys Acta 1967, 149:288-290.
31. Burmann B.M., Schweimer K., Luo X., Wahl M.C., Stitt B.L., Gottesman M.E., Rosch P. A NusE:NusG complex links transcription and translation. Science 2010, 328:501-504.
32. Proshkin S., Rahmouni A.R., Mironov A., Nudler E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 2010, 328:504-508.
33. Libby E.A., Roggiani M., Goulian M. Membrane protein expression triggers chromosomal locus repositioning in bacteria. Proc Natl Acad Sci U S A 2012, 109:7445-7450.
34. Espeli O., Mercier R., Boccard F. DNA dynamics vary according to macrodomain topography in the E. coli chromosome. Mol Microbiol 2008, 68:1418-1427.
35. Fiebig A., Keren K., Theriot J.A. Fine-scale time-lapse analysis of the biphasic, dynamic behaviour of the two Vibrio cholerae chromosomes. Mol Microbiol 2006, 60:1164-1178.
36. Passalacqua K.D., Varadarajan A., Ondov B.D., Okou D.T., Zwick M.E., Bergman N.H. Structure and complexity of a bacterial transcriptome. J Bacteriol 2009, 191:3203-3211.
37. Taniguchi Y., Choi P.J., Li G.W., Chen H., Babu M., Hearn J., Emili A., Xie X.S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538.
38. Golding I., Cox E.C. RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci U S A 2004, 101:11310-11315.
39. Maamar H., Raj A., Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 2007, 317:526-529.
40. 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 2009, 32:186-192.
41. So L.H., Ghosh A., Zong C., Sepulveda L.A., Segev R., Golding I. General properties of transcriptional time series in Escherichia coli. Nat Genet 2011, 43:554-560.
42. Kuhlman T.E., Cox E.C. Gene location and DNA density determine transcription factor distributions in Escherichia coli. Mol Syst Biol 2012, 8:610.
43. dos Santos V.T., Bisson-Filho A.W., Gueiros-Filho F.J. DivIVA-mediated polar localization of ComN, a posttranscriptional regulator of Bacillus subtilis. J Bacteriol 2012, 194:3661-3669.
44. Nevo-Dinur K., Nussbaum-Shochat A., Ben-Yehuda S., Amster-Choder O. Translation-independent localization of mRNA in E. coli. Science 2011, 331:1081-1084.
45. Lowary P.T., Uhlenbeck O.C. An RNA mutation that increases the affinity of an RNA-protein interaction. Nucleic Acids Res 1987, 15:10483-10493.
46. Golding I., Paulsson J., Zawilski S.M., Cox E.C. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123:1025-1036.
47. Winkler J., Seybert A., Konig L., Pruggnaller S., Haselmann U., Sourjik V., Weiss M., Frangakis A.S., Mogk A., Bukau B. Quantitative and spatio-temporal features of protein aggregation in Escherichia coli and consequences on protein quality control and cellular ageing. EMBO J 2010, 29:910-923.
48. Borogovac A., Broude N.E. Visualization of induced RNA in single bacterial cells. Methods Mol Biol 2011, 714:189-199.
49. Valencia-Burton M., McCullough R.M., Cantor C.R., Broude N.E. RNA visualization in live bacterial cells using fluorescent protein complementation. Nat Methods 2007, 4:421-427.
50. Magliery T.J., Wilson C.G., Pan W., Mishler D., Ghosh I., Hamilton A.D., Regan L. Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J Am Chem Soc 2005, 127:146-157.
51. English B.P., Hauryliuk V., Sanamrad A., Tankov S., Dekker N.H., Elf J. Single-molecule investigations of the stringent response machinery in living bacterial cells. Proc Natl Acad Sci U S A 2011, 108:E365-E373.
52. Sanamrad A., Persson F., Elf J. Isotropic diffusion of the small ribosomal subunit in Escherichia coli. Quantitative Biol 2012, arXiv:1205.5857 [q-bio.QM].
53. Montero Llopis P., Sliusarenko O., Heinritz J., Jacobs-Wagner C. In vivo biochemistry in bacterial cells using FRAP: insight into the translation cycle. Biophys J 2012, 103:1848-1859.
54. 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 U S A 2002, 99:9697-9702.
55. Bremer H., Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella 1996, ASM Press, Washington, DC, pp. 1553-1569. edn 2.
56. Khemici V., Poljak L., Luisi B.F., Carpousis A.J. The RNase E of Escherichia coli is a membrane-binding protein. Mol Microbiol 2008, 70:799-813.
57. Liou G.G., Jane W.N., Cohen S.N., Lin N.S., Lin-Chao S. RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E. Proc Natl Acad Sci U S A 2001, 98:63-68.
58. Taghbalout A., Rothfield L. RNaseE and RNA helicase B play central roles in the cytoskeletal organization of the RNA degradosome. J Biol Chem 2008, 283:13850-13855.
59. Lehnik-Habrink M., Schaffer M., Mader U., Diethmaier C., Herzberg C., Stulke J. RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol 2011, 81:1459-1473.
60. Hunt A., Rawlins J.P., Thomaides H.B., Errington J. Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 2006, 152:2895-2907.