Isolation of mRNAs associated with yeast mitochondria to study mechanisms of localized translation

Journal of Visualized Experiments

Volumn , Issue 85, 2014, Pages

  Lesnik, Chen ^a   Arava, Yoav ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

Biochemical fractionation; Biochemistry; Issue 85; Localized translation; Microarray; Mitochondria; mRNA localization; S. cerevisiae; Yeast

Indexed keywords

EID: 84897414296     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/51265     Document Type: Article

References (33)

1. Holt, C. E. & Bullock, S. L. Subcellular mRNA localization in animal cells and why it matters. Science. 326, 1212-1216, (2009). doi:10.1126/science.1176488
2. Donnelly, C. J., Fainzilber, M. & Twiss, J. L. Subcellular communication through RNA transport and localized protein synthesis. Traffic. 11, 1498-1505, (2010). doi:10.1111/j.1600-0854.2010.01118.x
3. Kellems, R. E., Allison, V. F. & Butow, R. A. Cytoplasmic type 80 S ribosomes associated with yeast mitochondria. II. Evidence for the association of cytoplasmic ribosomes with the outer mitochondrial membrane in situ. J. Biol. Chem. 249, 3297-3303 (1974).
4. Kellems, R. E. & Butow, R. A. Cytoplasmic type 80 S ribosomes associated with yeast mitochondria. 3. Changes in the amount of bound ribosomes in response to changes in metabolic state. J. Biol. Chem. 249, 3304-3310 (1974).
5. Suissa, M. & Schatz, G. Import of proteins into mitochondria. Translatable mRNAs for imported mitochondrial proteins are present in free as well as mitochondria-bound cytoplasmic polysomes. J. Biol. Chem. 257, 13048-13055 (1982).
6. Fujiki, M. & Verner, K. Coupling of cytosolic protein synthesis and mitochondrial protein import in yeast. Evidence for cotranslational import in vivo. J. Biol. Chem. 268, 1914-1920 (1993).
7. Yogev, O., Karniely, S. & Pines, O. Translation-coupled translocation of yeast fumarase into mitochondria in vivo. J. Biol. Chem. 282, 29222-29229, (2007). doi:10.1074/jbc.M704201200
8. Eliyahu, E. et al. Tom20 mediates localization of mRNAs to mitochondria in a translation-dependent manner. Mol. Cell. Biol. 30, 284-294, (2010). doi:10.1128/MCB.00651-09
9. Garcia, M. et al. Mitochondria-associated yeast mRNAs and the biogenesis of molecular complexes. Mol. Cell. Biol. 18, 362-368, (2007). doi:10.1091/mbc.E06-09-0827
10. Marc, P. et al. Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep. 3, 159-164, (2002). doi:10.1093/embo-reports/kvf025
11. Gadir, N., Haim-Vilmovsky, L., Kraut-Cohen, J. & Gerst, J. E. Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA. 17, 1551-1565, (2011). doi:10.1261/rna.2621111
12. Margeot, A. et al. In Saccharomyces cerevisiae, ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function. EMBO J. 21, 6893-6904 (2002).
13. Saint-Georges, Y. et al. Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PloS one. 3, e2293, (2008). doi:10.1371/journal.pone.0002293
14. Quenault, T., Lithgow, T. & Traven, A. PUF proteins: repression, activation and mRNA localization. Trends Cell Biol. 21, 104-112, (2011). doi:10.1016/j.tcb.2010.09.013
15. Garcia, M., Delaveau, T., Goussard, S. & Jacq, C. Mitochondrial presequence and open reading frame mediate asymmetric localization of messenger RNA. EMBO Rep. 11, 285-291, (2010). doi:10.1038/embor.2010.17
16. Eliyahu, E., Lesnik, C. & Arava, Y. The protein chaperone Ssa1 affects mRNA localization to the mitochondria. FEBS Lett. 586, 64-69, (2012). doi:10.1016/j.febslet.2011.11.025
17. Ahmed, A. U. & Fisher, P. R. Import of nuclear-encoded mitochondrial proteins: a cotranslational perspective. Int. Rev. Cell Mol. Biol. 273, 49-68, (2009). doi:10.1016/S1937-6448(08)01802-9
18. Eliyahu, E., Melamed, D. & Arava, Y. Genome-wide analysis of RNA extracted from isolated mitochondria. Methods Mol. Biol. 714, 287-299, (2011). doi:10.1007/978-1-61779-005-8_18
19. Eldad, N., Yosefzon, Y. & Arava, Y. Identification and characterization of extensive intra-molecular associations between 3'-UTRs and their ORFs. Nucleic Acids RES. 36, 6728-6738, (2008). doi:10.1093/nar/gkn754
20. Melamed, D. & Arava, Y. Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol. 431, 177-201, (2007). doi:10.1016/S0076-6879(07)31010-0
21. Margeot, A. et al. Why are many mRNAs translated to the vicinity of mitochondria: a role in protein complex assembly? Gene. 354, 64-71, (2005). doi:10.1016/j.gene.2005.04.022
22. Mathieu, L., Marsy, S., Saint-Georges, Y., Jacq, C. & Dujardin, G. A transcriptome screen in yeast identifies a novel assembly factor for the mitochondrial complex III. Mitochondrion. 11, 391-396, (2011). doi:10.1016/j.mito.2010.12.002
23. Hocine, S., Raymond, P., Zenklusen, D., Chao, J. A. & Singer, R. H. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods. 10, 119-121, (2013). doi:10.1038/nmeth.2305
24. Park, H. Y., Buxbaum, A. R. & Singer, R. H. Single mRNA tracking in live cells. Methods Enzymol. 472, 387-406, (2010). doi:10.1016/S0076-6879(10)72003-6
25. Thompson, M. A., Casolari, J. M., Badieirostami, M., Brown, P. O. & Moerner, W. E. Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function. Proc. Natl. Acad. Sci. U.S.A. 107, 17864-17871, (2010). doi:10.1073/pnas.1012868107
26. Tyagi, S. Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods. 6, 331-338, (2009). doi:10.1038/nmeth.1321
27. Garcia, M., Darzacq, X., Devaux, F., Singer, R. H. & Jacq, C. Yeast mitochondrial transcriptomics. Methods Mol. Biol. 372, 505-528, (2007). doi:10.1007/978-1-59745-365-3_35
28. Reinders, J. & Sickmann, A. Proteomics of yeast mitochondria. Methods Mol. Biol. 372, 543-557, (2007). doi:10.1007/978-1-59745-365-3_37
29. Meisinger, C., Sommer, T. & Pfanner, N. Purification of Saccharomcyes cerevisiae mitochondria devoid of microsomal and cytosolic contaminations. Anal. Biochem. 287, 339-342, (2000). doi:10.1006/abio.2000.4868
30. Glick, B. S. & Pon, L. A. Isolation of highly purified mitochondria from Saccharomyces cerevisiae. Methods Enzymol. 260, 213-223 (1995).
31. Boldogh, I. R. & Pon, L. A. Purification and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae. Methods Cell Biol. 80, 45-64, (2007). doi:10.1016/S0091-679X(06)80002-6
32. Rieder, S. E. & Emr, S. D. Isolation of subcellular fractions from the yeast Saccharomyces cerevisiae. Current protocols in cell biology/editorial board, Juan S. Bonifacino et al. Chapter 3, Unit 3, 8, (2001). doi:10.1002/0471143030.cb0308s08
33. Diekert, K., de Kroon, A. I., Kispal, G. & Lill, R. Isolation and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae. Methods Cell Biol. 65, 37-51 (2001).