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Regulation of Synaptic Pumilio Function by an Aggregation-Prone Domain

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Regulation of Synaptic Pumilio Function by an Aggregation-Prone Domain The Journal of Neuroscience, January 13, 2010 • 30(2):515–522 • 515 Development/Plasticity/Repair Regulation of Synaptic Pumilio Function by an Aggregation-Prone Domain Anna M. Salazar, Edward J. Silverman, Kaushiki P. Menon, and Kai Zinn Division of Biology, California Institute of Technology, Pasadena, California 91125 We identified Pumilio (Pum), a Drosophila translational repressor, in a computational search for metazoan proteins whose activities mightberegulatedbyassemblyintoorderedaggregates.Thesearchalgorithmwasbasedonevolutionarysequenceconservationpatterns observed for yeast prion proteins, which contain aggregation-prone glutamine/asparagine (Q/N)-rich domains attached to functional domains of normal amino acid composition. We examined aggregation of Pum and its nematode ortholog PUF-9 by expression in yeast. A domain of Pum containing the Q/N-rich sequence, denoted as NQ1, the entire Pum N terminus, and the complete PUF-9 protein localize .to macroscopic aggregates (foci) in yeast. NQ1 and PUF-9 can generate the yeast Pin؉ trait, which is transmitted by a heritable aggregate NQ1 also assembles into amyloid fibrils in vitro.InDrosophila, Pum regulates postsynaptic translation at neuromuscular junctions (NMJs). To assess whether NQ1 affects synaptic Pum activity in vivo, we expressed it in muscles. We found that it negatively regulates endogenous Pum, producing gene dosage-dependent pum loss-of-function NMJ phenotypes. NQ1 coexpression also suppresses lethality andNMJphenotypescausedbyoverexpressionofPuminmuscles.TheQ/NblockofNQ1isrequiredforthesephenotypiceffects.Negative regulation of Pum by NQ1 might be explained by formation of inactive aggregates, but we have been unable to demonstrate that NQ1 aggregates in Drosophila. NQ1 could also regulate Pum by a “dominant-negative” effect, in which it would block Q/N-mediated interac- tions of Pum with itself or with cofactors required for translational repression. Introduction Podospora anserina, aggregation of the prion protein [HET-s] Accumulation of intracellular or extracellular aggregates is a fea- controls heterokaryon incompatibility during the normal life cy- ture of many diseases. At least 40 human diseases are associated cle. In yeast (Saccharomyces), aggregation of the Q/N-rich do- with the formation of amyloid fibrils, deposits, or inclusions main of the Sup35p prion protein, which encodes a translation ϩ (Chiti and Dobson, 2006). To understand these diseases, it is termination factor, produces the [PSI ] phenotype (for review, necessary to define the normal functions of aggregation-prone see Wickner et al., 2007). regions of proteins and how these proteins are perturbed in dis- In this paper, we examine the properties of a Q/N-rich domain of ease states. the Drosophila Pumilio (Pum) protein. During early development, Ј Sequences found in normal proteins, including sequences en- Pum controls pattern formation by binding to the 3 untranslated riched in glutamine (Q) and asparagine (N), have a propensity to region (UTR) of hunchback mRNA and repressing its translation in assemble into ordered aggregates. Protein misfolding also gener- the posterior half of the embryo. It also has a variety of functions in ates aggregates. Some aggregates are toxic, whereas others might the nervous system. At the larval neuromuscular junction (NMJ), be formed as a protective response to a pathogenic event. Pum represses postsynaptic eIF-4E and GluRIIA expression and Ј The study of fungal prions has provided evidence for the idea binds directly to the 3 UTRs of both mRNAs. eIF-4E, the cap- that controlled aggregation can have regulatory functions. In binding protein, is often limiting for translation, so Pum might re- press postsynaptic translation of many mRNAs by controlling the levels of eIF-4E. NMJ bouton numbers are increased in larvae lack- Received May 31, 2009; revised Oct. 21, 2009; accepted Nov. 10, 2009. ing postsynaptic Pum, and this is at least partially attributable to an This work was supported by a McKnight Foundation Brain Disorders Award and by National Institutes of Health increase in synaptic eIF-4E levels (Menon et al., 2004, 2009). Grants RO1 NS28182, R01 NS62821, and RO1 NS43416 (K.Z.). We thank the following: Erich Schwarz (WormBase at Pum is a large (1533 aa) protein with a conserved C-terminal the California Institute of Technology, Pasadena, CA) for conducting the computational search of the fly and worm PUF RNA-binding domain (RBD) that has 80% sequence iden- proteomes for us; Dale Cameron, Lev Osherovich, and Jonathan Weissman for help with gamma integration; James Shorter,JohannesGraumann,AshleyWright,NinaSherwood,AliceSchmid,andNickiFoxforhelpfuldiscussions;the tity to human Pum2. The N-terminal 1092 aa of Pum contains Weissman(UniversityofCalifornia,SanFrancisco,SanFrancisco,CA),Lindquist(MassachusettsInstituteofTechnol- the Q/N-rich domain and is required for rescue of pum NMJ ϩ ogy, Cambridge, MA), Deshaies (California Institute of Technology), and Wharton (Duke University, Durham, NC) phenotypes (Menon et al., 2004) and repression of Na channel groups for materials; and Elena Armand, Violana Nesterova, Lisa Nesterova, and Carlos Diaz-Balzac for technical expression (Muraro et al., 2008). assistance.WethankBillTivolforassistancewithEM,whichwasperformedattheBroadCenterEMfacility.Confocal microscopy was performed at the Caltech Biological Imaging Facility. We thank Sean Brennan for assistance with Materials and Methods graphics and good music. Correspondence should be addressed to Kai Zinn, Division of Biology 114-96, California Institute of Technology, Yeast strains and methods. Plasmids and strains were obtained from Jonathan Pasadena, CA 91125. E-mail: [email protected]. Weissman’s group at University of California, San Francisco. The DOI:10.1523/JNEUROSCI.2523-09.2010 aggregation-prone domain (PrD) of New1p is fused to enhanced cyan fluo- Copyright © 2010 the authors 0270-6474/10/300515-08$15.00/0 rescent protein (CFP) under control of the CUP1 promoter within the 516 • J. Neurosci., January 13, 2010 • 30(2):515–522 Salazar et al. • Aggregation of a Translational Repressor pRS426 (URA3) plasmid. We substituted Pum and PUF-9 sequences for Table 1. Rescue of Pum overexpression lethality by coexpression of NQ1 New1p sequences in this plasmid. For focus formation and Pinϩ assays, Genotype Numbers of pupae counted yeast expressing CUP1 promoter-driven fusion proteins were induced at an optical density of 6 and grown at 30°C. For Pinϩ assays, they were plated 24B–GAL4/ϩ 324 after 48 h of growth onto ϪAde plates to select the [PSIϩ] phenotype. UAS–Pum/24B–GAL4 0 Ј [psiϪ][pinϪ], [psiϪ][PINϩ], and [PSIϩ][PINϩ] yeast strains used UAS–Pum-tub3 UTR/24B–GAL4 0 ϩ in this study bear the ade1–14(UGA) mutation and are also ura3- and UAS–GFP/ ; UAS–Pum/24B–GAL4 0 ϩ Ј leu2 (Osherovich and Weissman, 2001). We used two sets of strains for UAS–GFP/ ; UAS–Pum–tub3 UTR/24B–GAL4 0 ⌬ ϩ these experiments. The first set are isogenic [psiϪ] and [PSIϩ] deriva- UAS– NQ1–CFP/ ; UAS–Pum/24B–GAL4 0 tives of 74D-694 [MATa, his3, leu2, trp1, ura3, with the suppressible UAS–NQ1–CFP, UAS–Pum/24B–GAL4 405 Ј marker ade1–14(UGA)] (Chernoff et al., 1995). We also used strains UAS–NQ1–CFP, UAS–Pum–tub3 UTR/24B–GAL4 262 ϩ created by Osherovich and Weissman by introducing 74D markers into UAS–NQ1–CFP/ ; UAS–Pum/24B–GAL4 159 ϩ Ј the W303 background. These are as follows: YJW 508 ([PSIϩ][PINϩ] UAS–NQ1–CFP/ ; UAS–Pum–tub3 UTR/24B–GAL4 169 MATa, ade1-14, his3-11,15, leu2-3, trp1-1, ura3-1); YJW 509, a [psiϪ] [pinϪ] derivative of this strain; and YJW 564, a [psiϪ][PINϩ] deriva- tive. Data in Figure 1 were obtained using the W303-derived strains, but using a paper wick after each staining application. Grids were allowed to the 74D strains gave equivalent results. Sup35NM–yellow fluorescent air dry and then examined in a Tecnai T12 electron microscope. For protein (YFP), used for assays of Pinϩ, is in the pRS425 (LEU2) plasmid. NQ1, at this concentration of protein, the stain had a tendency to obscure ϩ We tried to generate a chimera that could produce [PSI ] directly by the fibrils. Thus, to obtain images of fibrils, a 1:5 dilution in PBS (1 ␮M substituting an NQ1–Sup35–EF chimeric gene for one copy of the Sup35 fibers) was used. gene in diploids. A chromosomally integrated gene fusion of the NQ1– Drosophila genetics and molecular biology. The UAS–NQ1–CFP and Sup35–EF chimera was generated by homologous recombination UAS–⌬NQ1–CFP plasmids are pUAST-based vectors. Injections into (gamma integration) of PCR-amplified sequences containing a His tag. embryos were performed by Rainbow Genetics. We generated Ͼ100 lines These were transformed into diploid yeast strains and grown on ϪHis for each plasmid and screened these for CFP expression after crossing to plates. Resulting colonies were PCR screened for the presence of NQ1. 24B–GAL4 and other drivers. We picked a subset of lines that had bright The diploid strains, with both NQ1–Sup35–EF and endogenous Sup35, CFP expression and mapped them to chromosomes. NQ1–CFP and could be converted to [PSIϩ] by transformation with NQ1–CFP and ⌬NQ1–CFP were expressed at approximately equivalent levels in these Sup35NM–YFP. lines. pumET9 was recombined with the 24B–GAL4 insert (both are on the To generate haploid lines with only NQ1–Sup35–EF, the diploid third chromosome), and the recombinant line was crossed to UAS– strains were sporulated using standard procedures, dissected, and grown NQ1–CFP and UAS–⌬NQ1–CFP lines with inserts on the second or third on yeast/peptone/dextrose (YPD) plates. However, we could not obtain chromosomes. For the lethality rescue experiment (Table 1), we used any viable haploid NQ1–Sup35 lines, indicating that the NQ1– second chromosome lines (from R. Wharton, Duke University, Durham, Sup35p–EF chimera is not a functional translation termination factor. It NC) bearing UAS–Pum with its own 3Ј UTR or with a tubulin 3Ј UTR, might be completely sequestered into an inactive aggregate (total loss of which increases translation efficiency. These were recombined with Sup35p is lethal) or simply have the wrong conformation.
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