Drummond, Sheona P., Hildyard, John, Firczuk, Helena, Reamtong, Onrapak, Li, Ning, Kannambath, Shichina, Claydon, Amy J., Beynon, R. J. (Robert J.), Eyers, Claire E. and McCarthy, John E. G.. (2011) Diauxic shift-dependent relocalization of decapping activators Dhh1 and Pat1 to polysomal complexes. Nucleic Acids Research, Vol.39 (No.17). pp. 7764-7774. ISSN 1362-4962

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Abstract

Dhh1 and Pat1 in yeast are mRNA decapping activators/ translational repressors thought to play key roles in the transition of mRNAs from translation to degradation. However, little is known about the physical and functional relationships between these proteins and the translation machinery. We describe a previously unknown type of diauxic shiftdependent modulation of the intracellular locations of Dhh1 and Pat1. Like the formation of P bodies, this phenomenon changes the spatial relationship between components involved in translation and mRNA degradation. We report significant spatial separation of Dhh1 and Pat1 from ribosomes in exponentially growing cells. Moreover, biochemical analyses reveal that these proteins are excluded from polysomal complexes in exponentially growing cells, indicating that they may not be associated with active states of the translation machinery. In contrast, under diauxic growth shift conditions, Dhh1 and Pat1 are found to co-localize with polysomal complexes. This work suggests that Dhh1 and Pat1 functions are modulated by a relocalization mechanism that involves eIF4A. Pulldown experiments reveal that the intracellular binding partners of Dhh1 and Pat1 change as cells undergo the diauxic growth shift. This reveals a new dimension to the relationship between translation activity and interactions between mRNA, the translation machinery and decapping activator proteins.

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Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Gene expression, Genetic translation, Messenger RNA, Yeast -- Physiology
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
ISSN:	1362-4962
Date:	28 June 2011
Volume:	Vol.39
Number:	No.17
Page Range:	pp. 7764-7774
Identification Number:	10.1371/journal.pone.0023630
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access
Funder:	Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Royal Society (Great Britain)
Grant number:	BB/E015778 (BBSRC), BBF019963/1 (BBSRC)
References:	1. Schwartz,D.C. and Parker,R. (1999) Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol. Cell. Biol., 19, 5247–5256. 2. Schwartz,D.C. and Parker,R. (2000) mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Mol. Cell. Biol., 20, 7933–7942. 3. Parker,R. and Sheth,U. (2007) P bodies and the control of mRNA translation and degradation. Mol. Cell, 25, 635–646. 4. Coller,J. and Parker,R. (2005) General translational repression by activators of mRNA decapping. Cell, 122, 875–886. 5. Wyers,F., Minet,M., Dufour,M.E., Vo,L.T. and Lacroute,F. (2000) Deletion of the PAT1 gene affects translation initiation and suppresses a PAB1 gene deletion in yeast. Mol. Cell. Biol., 20, 3538–3549. 6. Minshall,N. and Standart,N. (2004) The active form of Xp54 RNA helicase in translational repression is an RNA-mediated oligomer. Nucleic Acids Res., 32, 1325–1334. 7. Nakamura,A., Amikura,R., Hanyu,K. and Kobayashi,S. (2001) Me31B silences translation of oocyte-localizing RNAs through the formation of cytoplasmic RNP complex during Drosophila oogenesis. Development, 128, 3233–3242. 8. Linz,B., Koloteva,N., Vasilescu,S. and McCarthy,J.E.G. (1997) Disruption of ribosomal scanning on the 5’-untranslated region, and not restriction of translational initiation per se, modulates the stability of nonaberrant mRNAs in the yeast Saccharomyces cerevisiae. J. Biol. Chem., 272, 9131–9140. 9. McCarthy,J.E. (1998) Posttranscriptional control of gene expression in yeast. Microbiol. Mol. Biol. Rev., 62, 1492–1553. 10. Vilela,C., Velasco,C., Ptushkina,M. and McCarthy,J.E. (2000) The eukaryotic mRNA decapping protein Dcp1 interacts physically and functionally with the eIF4F translation initiation complex. EMBO J., 19, 4372–4382. 11. Carmen,A.A., Brinkle,P.K., Park,C.S. and Holland,M.J. (1995) Transcriptional regulation by an upstream repression sequence from the yeast enolase gene ENO1. Yeast, 15, 1031–1043. 12. Montero Llopis,P., Jackson,A.F., Sliusarenko,O., Surovtsev,I., Heinritz,J., Emonet,T. and Jacobs-Wagner,C. (2010) Spatial organization of the flow of genetic information in bacteria. Nature, 466, 77–81. 13. Daou-Chabo,R., Mathy,N., Benard,L. and Condon,C. (2009) Ribosomes initiating translation of the hbs mRNA protect it from 50-to-30 exoribonucleolytic degradation by RNase J1. Mol. Microbiol., 71, 1538–1550. 14. Hu,W., Sweet,T.J., Chamnongpol,S., Baker,K.E. and Coller,J. (2009) Co-translational mRNA decay in Saccharomyces cerevisiae. Nature, 461, 225–229. 15. Sheth,U. and Parker,R. (2003) Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science, 300, 805–808. 16. Bergkessel,M. and Reese,J.C. (2004) An essential role for the Saccharomyces cerevisiae DEAD-box helicase DHH1 in G1/S DNA-damage checkpoint recovery. Genetics, 167, 21–33. 17. Piccininni,S., Varaklioti,A., Nardelli,M., Dave,B., Raney,K.D. and McCarthy,J.E. (2002) Modulation of the hepatitis C virus RNA-dependent RNA polymerase activity by the non-structural (NS) 3 helicase and the NS4B membrane protein. J. Biol. Chem., 277, 45670–45679. 18. Koloteva,N., Mu¨ ller,P.P. and McCarthy,J.E.G. (1997) The position dependence of translational regulation via RNA-RNA and RNA-protein interactions in the 50-untranslated regions of eukaryotic mRNA is a function of the thermodynamic competence of 40S ribosomes in translational initiation. J. Biol. Chem., 272, 16531–16539. 19. Vilela,C., Linz,B., Velasco Ramirez,C., Rodrigues-Pousada,C. and McCarthy,J.E.G. (1999) Posttermination ribosome interactions with the 50 UTR modulate yeast mRNA stability. EMBO J., 18, 3139–3152. 20. Rigaut,G., Shevchenko,A., Rutz,B., Wilm,M., Mann,M. and Se´raphin,B. (1999) A generic protein purification method for protein complex purification and proteome purification. Nat. Biotechnol., 17, 1030–1032. 21. Perkins,D.N., Pappin,D.J.C., Creasy,D.M. and Cottrell,J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551–3567. 22. Adams,S.R., Campbell,R.E., Gross,L.A., Martin,B.R., Walkup,G.K., Yao,Y., Llopis,J. and Tsien,R.Y. (2002) New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc., 124, 6063–6076. 23. Adams,S.R. and Tsien,R.Y. (2008) Preparation of the membrane-permeant biarsenicals FlAsH-EDT2 and ReAsH-EDT2 for fluorescent labeling of tetracysteine-tagged proteins. Nat. Protocols, 3, 1527–1534. 24. Brengues,M. and Parker,R. (2007) Accumulation of polyadenylated RNA, Pab1, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae. Mol. Biol. Cell., 18, 2592–2602. 25. Hoyle,N.P., Castelli,L.M., Campbell,S.G., Holmes,L.E. and Ashe,M.P. (2007) Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. J. Cell Biol., 179, 65–74. 26. Ishihama,Y., Oda,Y., Tabata,T., Sato,T., Nagasu,T., Rappsilber,J. and Mann,M. (2005) Exponentially modified proteı´n abundance index (emPAI) for estimation of absolute proteı´n amount in proteomics by the number of sequenced peptides per proteı´n. Mol. Cell. Proteomics, 4, 1265–1272. 27. Shinoda,K., Tomita,M. and Ishihama,Y. (2010) emPAI Calc – for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics, 26, 576–577. 28. Webster,D.L. and Watson,K. (1993) Ultrastructural changes in yeast following heat shock and recovery. Yeast, 11, 1165–1175. 29. Anderson,P. and Kedersha,N. (2006) RNA granules. J. Cell. Biol., 172, 803–808. 30. Yang,Z., Jakymiw,A., Wood,M.R., Eystathioy,T., Rubin,R.L., Fritzler,M.J. and Chan,E.K.L. (2004) GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation. J. Cell Sci., 117, 5567–5578. 31. Kedersha,N. and Anderson,P. (2002) Stress granules: sites of mRNA triage that regulate mRNA stability and translatability. Biochem. Soc. Trans., 30, 963–969. 32. Teixeira,D., Sheth,U., Valencia-Sanchez,M.A., Brengues,M. and Parker,R. (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA, 11, 371–382. 33. Berthelot,K., Muldoon,M., Rajkowitsch,L., Hughes,J.M.X. and McCarthy,J.E.G. (2004) Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Mol. Microbiol., 51, 987–1001. 34. Marsden,S., Nardelli,M., Linder,P. and McCarthy,J.E.G. (2006) Unwinding single RNA molecules using helicases involved in eukaryotic translation initiation. J. Mol. Biol., 361, 327–335. 35. Linder,P. (2006) Dead-box proteins: a family affair–active and passive players in RNP-remodelling. Nucleic Acids Res., 34, 4168–4180. 36. Mas,A., Alves-Rodrigues,I., Noueiry,A., Ahlquist,P. and Diez,J. (2006) Host deadenylation-dependent mRNA decapping factors are required for a key step in brome mosaic virus RNA replication. J. Virol., 80, 246–251. 37. Ahlquist,P. (2006) Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nature Rev. Microbiol., 4, 371–382. 38. Kwong,A.D., Rao,B.G. and Jeang,K.-T. (2005) Viral and cellular RNA helicases as antiviral targets. Nature Rev. Drug Discov., 4, 845–853. 39. Hurt,E., Hannus,S., Schmelzl,B., Lau,D., Tollervey,D. and Simos,G. (1999) A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants. J. Cell Biol., 144, 389–401. 40. Kraft,C., Deplazes,A., Sohrmann,M. and Peter,M. (2008) Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat. Cell Biol., 10, 602–610. 41. Pilkington,G. and Parker,R. (2008) Pat1 contains distinct functional domains that promote assembly and activation of decapping. Mol. Cell Biol., 28, 1298–1312. 42. Coller,J.M., Tucker,M., Sheth,U., Valencia-Sanchez,M.A. and Parker,R. (2001) The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA, 7, 1717–1727.
URI:	http://wrap.warwick.ac.uk/id/eprint/38330

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