Samra N, Atir-Lande A, Pnueli L, Arava Y. The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner. BMC Mol Biol. 2015 Sep 24;16(1):17
Lesnik C, Golani-Armon A, Arava Y. Localized translation near the mitochondrial outer membrane: An update (Review). RNA Biol. 2015 Aug 3;12(8):801-9
Bavli-Kertselli I, Melamed D, Bar-Ziv L, Volf H, Arava Y. Overexpression of eIF5 rescues the translational defect of tpk1w in a manner that necessitates a novel phosphorylation site. FEBS J. 2015 Feb;282(3):504-20.
Lesnik C, Cohen Y, Atir-Lande A, Schuldiner M and Arava Y. OM14 is a mitochondrial receptor for cytosolic ribosomes that supports co-translational import into mitochondria. Nature Communications 2014 Dec 9;5:5711.
Lesnik C and Arava Y. Isolation of mRNAs associated with yeast mitochondria to study mechanisms of localized translation. J Vis Exp. 2014 Mar 14;(85).
Shoshani S, Piran R, Arava Y, Keinan E. Angew Chem Int Ed Engl. A molecular cryptosystem for images by DNA computing. 2012 Mar 19;51(12):2883-7.
Eliyahu E*, Lesnik C* and Arava Y. The protein chaperone Ssa1 affects mRNA localization to the mitochondria. FEBS Lett. 2012 Jan 2;586(1):64-9.
Yosefzon Y, Koh YY, Chritton JJ, Lande A, Leibovich L, Barziv L, Petzold C, Yakhini Z, Mandel-Gutfreund Y, Wickens M, Arava Y. Divergent RNA binding specificity of yeast Puf2p. RNA. 2011 Aug;17(8):1479-88.
Eliyahu E, Melamed D, Arava Y. Genome-wide analysis of RNA extracted from isolated mitochondria. Methods Mol Biol. 2011;714:287-99.
Levy S, Wilms CD, Brumer E, Kahn J, Pnueli L, Arava Y, Eilers J, Gitler D.SpRET: highly sensitive and reliable spectral measurement of absolute FRET efficiency. Microsc Microanal. 2011 Apr;17(2):176-90. Epub 2011 Feb 21.
Melamed D, Bar-Ziv L, Truzman Y, Arava Y. Asc1 supports cell-wall integrity near bud sites by a Pkc1 independent mechanism. PLoS One 2010 jun;5(6):e11389
Eliyahu E, Pnueli L, Melamed D, Scherrer T, Gerber AP, Pines O, Rapaport D, Arava Y. Tom20 mediates localization of mRNAs to mitochondria in a translation-dependent manner. Mol Cell Biol. 2009 Oct 26.
Arava Y. Compaction of polyribosomal mRNA. RNA Biol. 2009 Sep-Oct;6(4):399-401.
Melamed D. Eliyahu E, Arava Y. Exploring translation regulation by global analysis of ribosomal association. Methods. 2009 Jul;48(3):301-5.
Eldad N, Yosefzon Y, Arava Y. Identification and characterization of extensive intra-molecular associations between 3’-UTRs and their ORFs. Nucleic Acids Res. 2008 Dec;36(21):6728-38.
Melamed D, Pnueli L, Arava Y. Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels. RNA. 2008 Jul;14(7):1337-51.
Loya A, Pnueli L, Yosefzon Y, Wexler Y, Ziv-Ukelson M, Arava Y. The 3′-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein. RNA. 2008 Jul;14(7):1352-65.
Eldad N, Arava Y. A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs. Methods Mol Biol. 2008;419:231-42.
Melamed D, Arava Y. Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol. 2007;431:177-201.
Eldad N, Arava Y. Detecting ribosomal association with the 5′ leader of mRNAs by Ribosome Density Mapping (RDM). Methods Enzymol. 2007;431:163-75. Review.
Pnueli L, Arava Y. Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9. BMC Genomics. 2007 Aug 21;8:285.
Arava Y, Boas FE, Brown PO, Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res. 2005 Apr 28;33(8):2421-32. Print 2005.
Sapra AK, Arava Y, Khandelia P, Vijayraghavan U. Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Biol Chem. 2004 Dec 10;279(50):52437-46.
Arava Y. Isolation of polysomal RNA for microarray analysis. Methods Mol Biol. 2003;224:79-87 (No abstract available).
Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94.
Arava Y, Seger R, Walker MD. GRFbeta, a novel regulator of calcium signaling, is expressed in pancreatic beta cells and brain. J Biol Chem. 1999 Aug 27;274(35):24449-52.
Arava Y, Adamsky K, Ezerzer C, Ablamunits V, Walker MD. Specific gene expression in pancreatic beta-cells: cloning and characterization of differentially expressed genes. Diabetes. 1999 Mar;48(3):552-6.
Arava Y, Adamsky K, Belleli A, Shaltiel S, Walker MD. Differential expression of the protein kinase A regulatory subunit (RIalpha) in pancreatic endocrine cells. FEBS Lett. 1998 Mar 20;425(1):24-8. pdf
Argenton F, Arava Y, Aronheim A, Walker MD. An activation domain of the helix-loop-helix transcription factor E2A shows cell type preference in vivo in microinjected zebra fish embryos. Mol Cell Biol. 1996 Apr;16(4):1714-21.
The research in our lab focuses on elucidating basic mechanisms of localized translation in eukaryotes, with emphasis on translation near the ER and mitochondria. We apply various methods, including electron microscopy, biochemical purification, molecular biology, in vivo fluorescent imaging and functional genomics to understand how mRNAs approach the ER and mitochondria, what are the RNA sequences that regulate this localization and which proteins are involves.
Localized translation near the Mitochondria
Mitochondria proteins were considered for many years to be translated in the cytosol, and to be imported to the mitochondria only when fully translated. In recent years, however, an alternative model was revived, in which proteins are translated near the mitochondria and thus may be imported more efficiently. This model is based on studies of mRNA localization, that showed that many different mRNAs that encode mitochondrial proteins are in close proximity to the outer membrane of the mitochondria.We have shown that a protein receptor of the outer OM14 with mito_Maxim_2membrane (Tom20) affects mRNA localization to the mitochondria (Eliyahu E. et al 2010) and that cytosolic chaperones are also involved in this process (Eliyahu et al 2012). Most recently we identified a novel receptor (OM14) for cytosolic ribosomes on yeast mitochondria outer membrane. In vitro, this receptor is important for co-translational import of proteins, and thus provide a strong support to the idea that localizedtranslation near the mitochondria improves that efficiency of protein import (Lesnik et al 2014). Currently we are searching for partners of this receptor, and whether its role is conserved in mammalian cells.
mRNA localization to the ER
Many mRNAs are known to associated with the ER, and locally synthesize membrane or secreted proteins into this organelle. The most studied mechanism for targeting these mRNAs to the ER involves association of the SRP with the nresearch2ascent protein chain, as it emerges from the ribosome. However, work in the last few years, including from our lab (Loya A. et al 2008) revealed that mRNAs can be localized also in a manner that does not necessitate translation. We found the 3’UTR sequences are important for ER-association and we are now searching for the proteins that mediate this translation independent localization. One candidate is the Puf2 protein, that was shown to interact with ER-destined mRNAs. We found that Puf2 has a unique binding motif ( a dual UAAU sequence)(Yosefzon Y. et al 2011). The The role of Puf2 in ER targeting, as well as the importance of the UAAU motif are now under investigation in my lab.
Biochemistry, Gene regulation, Genomics, Microbiology