Imaging translation in single cells using fluorescent microscopy

Cold Spring Harbor Perspectives in Biology

Volumn 4, Issue 11, 2012, Pages

  Chao, Jeffrey A ^a   Yoon, Young J ^a   Singer, Robert H ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PUROMYCIN;

ANIMAL; ARTICLE; FLUORESCENCE MICROSCOPY; GENE EXPRESSION REGULATION; HUMAN; METHODOLOGY; NERVE CELL; PHYSIOLOGY; PROTEIN SYNTHESIS; SYNAPSE; ULTRASTRUCTURE;

ANIMALS; GENE EXPRESSION REGULATION; HUMANS; MICROSCOPY, FLUORESCENCE; NEURONS; PROTEIN BIOSYNTHESIS; PUROMYCIN; SYNAPSES;

EID: 84868591797     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a012310     Document Type: Article

References (69)

1. Aakalu G, Smith WB, Nguyen N, Jiang C, Schuman EM. 2001. Dynamic visualization of local protein synthesis in hippocampal neurons. Neuron 30: 489-502.
2. Adams SR, Campbell RE, Gross LA, Martin BR, Walkup GK, Yao Y, Llopis J, Tsien RY. 2002. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: Synthesis and biological applications. J AmChe Soc 124: 6063-6076.
3. Ando R, Hama H, Yamamoto-Hino M, Mizuno H, Miyawak A. 2002. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc Natl Acad Sci 99: 12651-12656.
4. Barhoom S, Kaur J, Cooperman BS, Smorodinsky NI, Smilansk Z, Ehrlich M, Elroy-Stein O. 2011. Quantitative single cell monitoring of protein synthesis at subcellular resolution using fluorescently labeled tRNA. Nucleic Acids Res 39: e129.
5. Bassell GJ, Zhang H, Byrd AL, Femino AM, Singer RH, Taneja KL, Lifshitz LM, Herman IM, Kosik KS. 1998. Sorting of β-actin mRNA and protein to neurites and growth cones in culture. J Neurosci 18: 251-265.
6. Beach DL, Salmon ED, Bloom K. 1999. Localization and anchoring of mRNA in budding yeast. Curr Biol 9: 569-578.
7. Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singe RH, Long RM. 1998. Localization of ASH1 mRNA particles in living yeast. Mol Cell 2: 437-445.
8. Betteridge T, Liu H, Gamper H, Kirillov S, Cooperman BS, Hou YM. 2007. Fluorescent labeling of tRNAs for dynamics experiments. RNA 13: 1594-1601.
9. Brittis PA, Lu Q, Flanagan JG. 2002. Axonal protein synthesis provides a mechanism for localized regulation at an intermediate target. Cell 110: 223-235.
10. Brodsky AS, Silver PA. 2000. Pre-mRNA processing factors are required for nuclear export. RNA 6: 1737-1749.
11. Cerutti P, Miller N. 1967. Selective reduction of yeast transfer ribonucleic acid with sodium borohydride. J Mol Biol 26: 55-66.
12. Chang L, Shav-Tal Y, Trcek T, Singer RH, Goldman RD. 2006. Assembling an intermediate filament network by dynamic cotranslation. J Cell Biol 172: 747-758.
13. Chang YF, Imam JS, Wilkinson MF. 2007. The nonsensemediated decay RNA surveillance pathway. Annu Rev Biochem 76: 51-74.
14. Chubb JR, Trcek T, Shenoy SM, Singer RH. 2006. Transcriptional pulsing of a developmental gene. Curr Biol 16: 1018-1025.
15. Corish P, Tyler-Smith C. 1999. Attenuation of green fluorescent protein half-life in mammalian cells. Protein Eng 12: 1035-1040.
16. Daigle N, Ellenberg J. 2007. λN-GFP: An RNA reporter system for live-cell imaging. Nat Methods 4: 633-636.
17. Darzacq X, Shav-Tal Y, deTurris V, Brody Y, ShenoySM, Phai RD, Singer RH. 2007. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14: 796-806.
18. De Jaco A, Lin MZ, Dubi N, Comoletti D, Miller MT, Cam S, Ellisman M, Butko MT, Tsien RY, Taylor P. 2010. Neuroligin trafficking deficiencies arising from mutations in the α/β-hydrolase fold protein family. J Biol Chem 285: 28674-28682.
19. Dieterich DC, Hodas JJ, Gouzer G, Shadrin IY, Ngo JT, Triller A, Tirrell DA, Schuman EM. 2010. In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons. Nat Neurosci 13: 897-905.
20. Donnelly CJ, Fainzilber M, Twiss JL. 2010. Subcellular communication through RNA transport and localized protein synthesis. Traffic 11: 1498-1505.
21. Dynes JL, StewardO. 2007. Dynamics of bidirectional transport of Arc mRNA in neuronal dendrites. J Comp Neurol 500: 433-447.
22. Evdokimov AG, Pokross ME, Egorov NS, Zaraisky AG, Yampolsky IV, Merzlyak EM, Shkoporov AN, Sander I, Lukyano KA, Chudakov DM. 2006. Structural basis for the fast maturation of Arthropoda green fluorescent protein. EMBO Rep 7: 1006-1012.
23. Fusco D, Accornero N, Lavoie B, Shenoy SM, Blanchard JM, Singer RH, Bertrand E. 2003. Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. Curr Biol 13: 161-167.
24. Giepmans BN, Adams SR, Ellisman MH, Tsien RY. 2006. The fluorescent toolbox for assessing protein location and function. Science 312: 217-224.
25. Golding I, Cox EC. 2004. RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci 101: 11310-11315.
26. Golding I, Paulsson J, Zawilski SM, Cox EC. 2005. Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036.
27. Griffin BA, Adams SR, Tsien RY. 1998. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281: 269-272.
28. Grunwald D, Singer RH. 2010. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467: 604-607.
29. Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyano KA. 2006. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat Biotechnol 24: 461-465.
30. Ju W, Morishita W, Tsui J, Gaietta G, Deerinck TJ, Adams SR, Garner CC, Tsien RY, Ellisman MH, Malenka RC. 2004. Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors. Nat Neurosci 7: 244-253.
31. Kang H, Schuman EM. 1996. A requirement for local protein synthesis in neurotrophin-induced hippocampal synaptic plasticity. Science 273: 1402-1406.
32. Kislauskis EH, Zhu X, Singer RH. 1994. Sequences responsible for intracellular localization of b-actin messenger RNA also affect cell phenotype. J Cell Biol 127: 441-451.
33. Kremers GJ, Goedhart J, van Munster EB, Gadella TW Jr. 2006. Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Forster radius. Biochemistry 45: 6570-6580.
34. Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. 2011. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332: 475-478.
35. Leung KM, van Horck FP, Lin AC, Allison R, Standart N, Holt CE. 2006. Asymmetrical β-actin mRNA translation in growth cones mediates attractive turning to netrin-1. Nat Neurosci 9: 1247-1256.
36. Lim F, Peabody DS. 1994. Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res 22: 3748-3752.
37. Lin MZ, Glenn JS, Tsien RY. 2008. A drug-controllable tag for visualizing newly synthesized proteins in cells and whole animals. Proc Natl Acad Sci 105: 7744-7749.
38. Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, Chao JA, Park HY, de Turris V, Lopez-Jones M, Singe RH. 2011. A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods 8: 165-170.
39. Liu J, Xu Y, Stoleru D, Salic A. 2011. Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin. Proc Natl Acad Sci doi: 10.1073/pnas.1111561108.
40. Lowary PT, Uhlenbeck OC. 1987. An RNA mutation that increases the affinity of an RNA-protein interaction. Nuclei Acids Res 15: 10483-10493.
41. Madani F, Lind J, Damberg P, Adams SR, Tsien RY, Graslun AO. 2009. Hairpin structure of a biarsenical-tetracysteine motif determined by NMR spectroscopy. J Am Chem Soc 131: 4613-4615.
42. Maquat LE. 2004. Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 5: 89-99.
43. Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y. 2010. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol 12: 543-552.
44. Nathans D. 1964. Puromycin inhibition of protein synthesis: Incorporation of puromycin into peptide chains. Proc Natl Acad Sci 51: 585-592.
45. Ngo JT, Champion JA, Mahdavi A, Tanrikulu IC, Beatty KE, Connor RE, Yoo TH, Dieterich DC, Schuman EM, Tirrel DA. 2009. Cell-selective metabolic labeling of proteins. Nat Chem Biol 5: 715-717.
46. Pan D, Kirillov SV, Cooperman BS. 2007. Kinetically competent intermediates in the translocation step of protein synthesis. Mol Cell 25: 519-529.
47. Pan D, Qin H, Cooperman BS. 2009. Synthesis and functional activity of tRNAs labeled with fluorescent hydrazides in the D-loop. RNA 15: 346-354.
48. Raab-Graham KF, Haddick PC, Jan YN, Jan LY. 2006. Activity-and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites. Science 314: 144-148.
49. Rodriguez AJ, Shenoy SM, Singer RH, Condeelis J. 2006. Visualization of mRNA translation in living cells. J Cell Biol 175: 67-76.
50. Rogers S, Wells R, Rechsteiner M. 1986. Amino acid sequences common to rapidly degraded proteins: The PEST hypothesis. Science 234: 364-368.
51. Rostovtsev VV, Green LG, Fokin VV, Sharpless KB. 2002. A stepwise huisgen cycloaddition process: Copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew Chem Int Ed Engl 41: 2596-2599.
52. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhard J, Wolf J, Chen W, Selbach M. 2011. Global quantification of mammalian gene expression control. Nature 473: 337-342.
53. Shaner NC, Lin MZ, McKeown MR, Steinbach PA, Hazelwoo KL, Davidson MW, Tsien RY. 2008. Improving the photostability of bright monomeric orange and red fluorescent proteins. Nat Methods 5: 545-551.
54. Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH. 2004. Dynamics of single mRNPs in nuclei of living cells. Science 304: 1797-1800.
55. Smith WB, Starck SR, Roberts RW, Schuman EM. 2005. Dopaminergic stimulation of local protein synthesis enhances surface expression of GluR1 and synaptic transmission in hippocampal neurons. Neuron 45: 765-779.
56. Sonenberg N, Hinnebusch AG. 2009. Regulation of translation initiation in eukaryotes:Mechanisms and biological targets. Cell 136: 731-745.
57. Starck SR, Roberts RW. 2002. Puromycin oligonucleotides reveal steric restrictions for ribosome entry and multiple modes of translation inhibition. RNA 8: 890-903.
58. Starck SR, Green HM, Alberola-Ila J, Roberts RW. 2004. A general approach to detect protein expression in vivo using fluorescent puromycin conjugates. Chem Biol 11: 999-1008.
59. StepanenkoOV, VerkhushaVV, Kuznetsova IM, UverskyVN, Turoverov KK. 2008. Fluorescent proteins as biomarkers and biosensors: Throwing color lights on molecular and cellular processes. Curr Protein Pept Sci 9: 338-369.
60. Sutton MA, Wall NR, Aakalu GN, Schuman EM. 2004. Regulation of dendritic protein synthesis by miniature synaptic events. Science 304: 1979-1983.
61. Takizawa PA, Vale RD. 2000. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. Pro Natl Acad Sci 97: 5273-5278.
62. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
63. Terskikh A, Fradkov A, Ermakova G, Zaraisky A, Tan P, Kajava AV, Zhao X, Lukyanov S, Matz M, Kim S, et al. 2000. "Fluorescent timer": Protein that changes color with time. Science 290: 1585-1588.
64. Valegard K, Murray JB, Stockley PG, Stonehouse NJ, Liljas L. 1994. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature 371: 623-626.
65. Van Engelenburg SB, Nahreini T, Palmer AE. 2010. FACSbased selection of tandem tetracysteine peptides with improved ReAsH brightness in live cells. Chembiochem 11: 489-493.
66. Wang DO, Kim SM, Zhao Y, Hwang H, Miura SK, Sossi WS, Martin KC. 2009. Synapse-and stimulus-specific local translation during long-term neuronal plasticity. Science 324: 1536-1540.
67. Wu B, Piatkevich KD, Lionnet T, Singer RH, Verkhusha VV. 2011. Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics. Curr Opin Cell Biol 23: 310-317.
68. Yarmolinsky MB, Haba GL. 1959. Inhibition by puromycin of mino acid incorporation into protein. Proc Natl Aca Sci 45: 1721-1729.
69. Zimyanin VL, Belaya K, Pecreaux J, Gilchrist MJ, Clark A, Davis I, St Johnston D. 2008. In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization. Cell 134: 843-853.