Subcellular localization of RNA and proteins in prokaryotes

Trends in Genetics

Volumn 28, Issue 7, 2012, Pages 314-322

  Nevo Dinur, Keren ^a   Govindarajan, Sutharsan ^a   Amster Choder, Orna ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Cell compartmentalization; Cell polarity; Localized translation; RNA targeting; Subcellular organization

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; BACTERIAL RNA; BETA GALACTOSIDASE; CARBON DIOXIDE; CARBONATE DEHYDRATASE; DINITROGENASE REDUCTASE; MESSENGER RNA; NIFH PROTEIN; RIBULOSE BISPHOSPHATE CARBOXYLASE MONOOXYGENASE; RNA POLYMERASE; UNCLASSIFIED DRUG; UNSPECIFIC MONOOXYGENASE;

AZOTOBACTER VINELANDII; BACILLUS SUBTILIS; BACTERIAL CELL; BACTERIAL MICROCOMPARTMENT; CARBON DIOXIDE TRANSPORT; CAULOBACTER CRESCENTUS; CELL MEMBRANE TRANSPORT; CELL NUCLEUS; CELL STRUCTURE; CELL VACUOLE; CELLULAR DISTRIBUTION; CYTOPLASM; DIFFUSION COEFFICIENT; DNA HELIX; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; INTRACELLULAR SPACE; INTRACELLULAR TRANSPORT; KLEBSIELLA OXYTOCA; MAGNETOSOME; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN LOCALIZATION; REVIEW; RIBOSOME; RNA BINDING; RNA LOCALIZATION; RNA PROCESSING; RNA STRUCTURE; RNA TRANSCRIPTION; RNA TRANSLATION; RNA TRANSPORT; SALMONELLA ENTERICA;

BACTERIA; BACTERIAL PROTEINS; MODELS, BIOLOGICAL; PROKARYOTIC CELLS; PROTEIN BIOSYNTHESIS; RNA, BACTERIAL;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84862490620     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2012.03.008     Document Type: Review

References (105)

1. Shapiro L., et al. Why and how bacteria localize proteins. Science 2009, 326:1225-1228.
2. Amster-Choder O. The compartmentalized vessel: the bacterial cell as a model for subcellular organization (a tale of two studies). Cell Logist. 2011, 1:77-81.
3. Toro E., Shapiro L. Bacterial chromosome organization and segregation. Cold Spring Harb. Perspect. Biol. 2010, 2:a000349.
4. Lewis P.J., et al. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 2000, 19:710-718.
5. Matsumoto K., et al. Lipid domains in bacterial membranes. Mol. Microbiol. 2006, 61:1110-1117.
6. Shih Y.L., Rothfield L. The bacterial cytoskeleton. Microbiol. Mol. Biol. Rev. 2006, 70:729-754.
7. Montero Llopis P., et al. Spatial organization of the flow of genetic information in bacteria. Nature 2010, 466:77-81.
8. Nevo-Dinur K., et al. Translation-independent localization of mRNA in E. coli. Science 2011, 331:1081-1084.
9. Broude N.E. Analysis of RNA localization and metabolism in single live bacterial cells: achievements and challenges. Mol. Microbiol. 2011, 80:1137-1147.
10. Donnelly C.J., et al. Subcellular communication through RNA transport and localized protein synthesis. Traffic 2010, 11:1498-1505.
11. Weil T.T., et al. Making the message clear: visualizing mRNA localization. Trends Cell Biol. 2010, 20:380-390.
12. Keiler K.C. RNA localization in bacteria. Curr. Opin. Microbiol. 2011, 14:155-159.
13. Hiraga S. Dynamic localization of bacterial and plasmid chromosomes. Annu. Rev. Genet. 2000, 34:21-59.
14. Golding I., Cox E.C. RNA dynamics in live Escherichia coli cells. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:11310-11315.
15. Briegel A., et al. Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography. Mol. Microbiol. 2006, 62:5-14.
16. Azam T.A., et al. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 2000, 5:613-626.
17. Russell B., Dix D.J. Mechanisms for intracellular distribution of mRNA: in situ hybridization studies in muscle. Am. J. Physiol. 1992, 262:C1-C8.
18. Valencia-Burton M., et al. RNA visualization in live bacterial cells using fluorescent protein complementation. Nat. Methods 2007, 4:421-427.
19. Valencia-Burton M., et al. Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:16399-16404.
20. Russell J.H., Keiler K.C. Subcellular localization of a bacterial regulatory RNA. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:16405-16409.
21. Pilhofer M., et al. Fluorescence in situ hybridization for intracellular localization of nifH mRNA. Syst. Appl. Microbiol. 2009, 32:186-192.
22. Lopian L., et al. The BglF sensor recruits the BglG transcription regulator to the membrane and releases it on stimulation. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:7099-7104.
23. Lopian L., et al. Spatial and temporal organization of the E. coli PTS components. EMBO J. 2010, 29:3630-3645.
24. Prilusky J., Bibi E. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:6662-6666.
25. Taghbalout A., Rothfield L. RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:1667-1672.
26. 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.
27. Khemici V., et al. The RNase E of Escherichia coli is a membrane-binding protein. Mol. Microbiol. 2008, 70:799-813.
28. Mitobe J., et al. RodZ regulates the post-transcriptional processing of the Shigella sonnei type III secretion system. EMBO Rep. 2011, 12:911-916.
29. Diestra E., et al. Cellular electron microscopy imaging reveals the localization of the Hfq protein close to the bacterial membrane. PLoS ONE 2009, 4:e8301.
30. Defeu Soufo H.J., Graumann P.L. Dynamic movement of actin-like proteins within bacterial cells. EMBO Rep. 2004, 5:789-794.
31. Jones L.J., et al. Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis. Cell 2001, 104:913-922.
32. Kain K.C., et al. Universal promoter for gene expression without cloning: expression-PCR. Biotechniques 1991, 10:366-374.
33. Shoji S., et al. Systematic chromosomal deletion of bacterial ribosomal protein genes. J. Mol. Biol. 2011, 413:751-761.
34. Guerout-Fleury A.M., et al. Plasmids for ectopic integration in Bacillus subtilis. Gene 1996, 180:57-61.
35. Yoo S., Twiss J.L. The road not taken: new destinations for yeast mRNAs on the move. EMBO J. 2011, 30:3564-3566.
36. Kilchert C., Spang A. Cotranslational transport of ABP140 mRNA to the distal pole of S. cerevisiae. EMBO J. 2011, 30:3567-3580.
37. Yuan J., et al. Protein transport across and into cell membranes in bacteria and archaea. Cell Mol. Life Sci. 2010, 67:179-199.
38. Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. Biochim. Biophys. Acta 2011, 1808:841-850.
39. Ramamurthi K.S. Protein localization by recognition of membrane curvature. Curr. Opin. Microbiol. 2010, 13:753-757.
40. Romantsov T., et al. Cardiolipin promotes polar localization of osmosensory transporter ProP in Escherichia coli. Mol. Microbiol. 2007, 64:1455-1465.
41. Huitema E., et al. Bacterial birth scar proteins mark future flagellum assembly site. Cell 2006, 124:1025-1037.
42. Ramamurthi K.S., Losick R. Negative membrane curvature as a cue for subcellular localization of a bacterial protein. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:13541-13545.
43. Lenarcic R., et al. Localisation of DivIVA by targeting to negatively curved membranes. EMBO J. 2009, 28:2272-2282.
44. Eswaramoorthy P., et al. Cellular architecture mediates DivIVA ultrastructure and regulates min activity in Bacillus subtilis. mBio 2011, 2. e00257-11.
45. Kirkpatrick C.L., Viollier P.H. Poles apart: prokaryotic polar organelles and their spatial regulation. Cold Spring Harb. Perspect. Biol. 2011, 3:a006809.
46. Alley M.R., et al. Polar localization of a bacterial chemoreceptor. Genes Dev. 1992, 6:825-836.
47. Kentner D., et al. Determinants of chemoreceptor cluster formation in Escherichia coli. Mol. Microbiol. 2006, 61:407-417.
48. Porter S.L., et al. Signal processing in complex chemotaxis pathways. Nat. Rev. Microbiol. 2011, 9:153-165.
49. Tsokos C.G., et al. A dynamic complex of signaling proteins uses polar localization to regulate cell-fate asymmetry in Caulobacter crescentus. Dev. Cell 2011, 20:329-341.
50. Scheu P., et al. Polar accumulation of the metabolic sensory histidine kinases DcuS and CitA in Escherichia coli. Microbiology 2008, 154:2463-2472.
51. Vats P., et al. The dynamic nature of the bacterial cytoskeleton. Cell Mol. Life Sci. 2009, 66:3353-3362.
52. Grotjohann T., et al. Diffraction-unlimited all-optical imaging and writing with a photochromic GFP. Nature 2011, 478:204-208.
53. Ingerson-Mahar M., Gitai Z. A growing family: the expanding universe of the bacterial cytoskeleton. FEMS Microbiol. Rev. 2012, 36:256-267.
54. Garner E.C., et al. Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis. Science 2011, 333:222-225.
55. Dominguez-Escobar J., et al. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 2011, 333:225-228.
56. van Teeffelen S., et al. The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:15822-15827.
57. Jockusch B.M., Graumann P.L. The long journey: actin on the road to pro- and eukaryotic cells. Rev. Physiol. Biochem. Pharmacol. 2012, 161:67-85.
58. Vats P., et al. Assembly of the MreB-associated cytoskeletal ring of Escherichia coli. Mol. Microbiol. 2009, 72:170-182.
59. van den Ent F., et al. Bacterial actin MreB assembles in complex with cell shape protein RodZ. EMBO J. 2010, 29:1081-1090.
60. White C.L., et al. Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD. Mol. Microbiol. 2010, 76:616-633.
61. Shaevitz J.W., Gitai Z. The structure and function of bacterial actin homologs. Cold Spring Harb. Perspect. Biol. 2010, 2:a000364.
62. Kim S.Y., et al. Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:10929-10934.
63. Wang S., et al. Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:E595-E604.
64. Erickson H.P., et al. FtsZ in bacterial cytokinesis: cytoskeleton and force generator all in one. Microbiol. Mol. Biol. Rev. 2010, 74:504-528.
65. Thanedar S., Margolin W. FtsZ exhibits rapid movement and oscillation waves in helix-like patterns in Escherichia coli. Curr. Biol. 2004, 14:1167-1173.
66. Campo N., et al. Subcellular sites for bacterial protein export. Mol. Microbiol. 2004, 53:1583-1599.
67. Shiomi D., et al. Helical distribution of the bacterial chemoreceptor via colocalization with the Sec protein translocation machinery. Mol. Microbiol. 2006, 60:894-906.
68. Formstone A., et al. Localization and interactions of teichoic acid synthetic enzymes in Bacillus subtilis. J. Bacteriol. 2008, 190:1812-1821.
69. Gerdes K. RodZ, a new player in bacterial cell morphogenesis. EMBO J. 2009, 28:171-172.
70. Barak I., et al. Lipid spirals in Bacillus subtilis and their role in cell division. Mol. Microbiol. 2008, 68:1315-1327.
71. van Noort J., et al. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:6969-6974.
72. Dame R.T. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 2005, 56:858-870.
73. Murat D., et al. Cell biology of prokaryotic organelles. Cold Spring Harb. Perspect. Biol. 2010, 2:a000422.
74. Schuler D. Genetics and cell biology of magnetosome formation in magnetotactic bacteria. FEMS Microbiol. Rev. 2008, 32:654-672.
75. Hsin J., et al. Self-assembly of photosynthetic membranes. Chemphyschem 2010, 11:1154-1159.
76. Bobik T.A. Polyhedral organelles compartmenting bacterial metabolic processes. Appl. Microbiol. Biotechnol. 2006, 70:517-525.
77. Parsons J.B., et al. Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Mol. Cell 2010, 38:305-315.
78. Drews G., Niklowitz W. [Cytology of Cyanophycea. II. Centroplasm and granular inclusions of Phormidium uncinatum]. Arch. Mikrobiol. 1956, 24:147-162.
79. Yeates T.O., et al. The protein shells of bacterial microcompartment organelles. Curr. Opin. Struct. Biol. 2011, 21:223-231.
80. Cheng S., et al. Bacterial microcompartments: their properties and paradoxes. Bioessays 2008, 30:1084-1095.
81. Yeates T.O., et al. Bacterial microcompartment organelles: protein shell structure and evolution. Annu. Rev. Biophys. 2010, 39:185-205.
82. Savage D.F., et al. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science 2010, 327:1258-1261.
83. Kerfeld C.A., et al. Protein structures forming the shell of primitive bacterial organelles. Science 2005, 309:936-938.
84. Lenz P., Sogaard-Andersen L. Temporal and spatial oscillations in bacteria. Nat. Rev. Microbiol. 2011, 9:565-577.
85. Loose M., et al. Protein self-organization: lessons from the min system. Annu. Rev. Biophys. 2011, 40:315-336.
86. Gerdes K., et al. Pushing and pulling in prokaryotic DNA segregation. Cell 2010, 141:927-942.
87. Nan B., Zusman D.R. Uncovering the mystery of gliding motility in the myxobacteria. Annu. Rev. Genet. 2011, 45:21-39.
88. Mauriello E.M., et al. Gliding motility revisited: how do the myxobacteria move without flagella?. Microbiol. Mol. Biol. Rev. 2010, 74:229-249.
89. Leonardy S., et al. Regulation of dynamic polarity switching in bacteria by a Ras-like G-protein and its cognate GAP. EMBO J. 2010, 29:2276-2289.
90. Miertzschke M., et al. Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity. EMBO J. 2011, 30:4185-4197.
91. Mauriello E.M., et al. Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA. EMBO J. 2010, 29:315-326.
92. Etienne-Manneville S. Cdc42 - the centre of polarity. J. Cell Sci. 2004, 117:1291-1300.
93. Charest P.G., Firtel R.A. Big roles for small GTPases in the control of directed cell movement. Biochem. J. 2007, 401:377-390.
94. Wu B., et al. Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics. Curr. Opin. Cell Biol. 2011, 23:310-317.
95. Paige J.S., et al. RNA mimics of green fluorescent protein. Science 2011, 333:642-646.
96. Bertrand E., et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 1998, 2:437-445.
97. Beach D.L., et al. Localization and anchoring of mRNA in budding yeast. Curr. Biol. 1999, 9:569-578.
98. Brodsky A.S., Silver P.A. Pre-mRNA processing factors are required for nuclear export. RNA 2000, 6:1737-1749.
99. Takizawa P.A., Vale R.D. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:5273-5278.
100. Daigle N., Ellenberg J. LambdaN-GFP: an RNA reporter system for live-cell imaging. Nat. Methods 2007, 4:633-636.
101. Hu C.D., et al. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell 2002, 9:789-798.
102. Michnick S.W. Protein fragment complementation strategies for biochemical network mapping. Curr. Opin. Biotechnol. 2003, 14:610-617.
103. Rackham O., Brown C.M. Visualization of RNA-protein interactions in living cells: FMRP and IMP1 interact on mRNAs. EMBO J. 2004, 23:3346-3355.
104. Ozawa T., et al. Imaging dynamics of endogenous mitochondrial RNA in single living cells. Nat. Methods 2007, 4:413-419.
105. Yiu H.-W., et al. RNA detection in live bacterial cells using fluorescent protein complementation triggered by interaction of two RNA aptamers with two RNA-binding peptides. Pharmaceuticals 2011, 4:494-508.