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The Structure of the SOLE Element of Oskar Mrna

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The Structure of the SOLE Element of Oskar Mrna Downloaded from rnajournal.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press The structure of the SOLE element of oskar mRNA BERND SIMON,1 PAWEL MASIEWICZ,1 ANNE EPHRUSSI,2 and TERESA CARLOMAGNO1,3 1Structural and Computational Biology Unit, 2Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany 3Helmholtz Zentrum für Infektionsforschung, Braunschweig, D-38124, Germany ABSTRACT mRNA localization by active transport is a regulated process that requires association of mRNPs with protein motors for transport along either the microtubule or the actin cytoskeleton. oskar mRNA localization at the posterior pole of the Drosophila oocyte requires a specific mRNA sequence, termed the SOLE, which comprises nucleotides of both exon 1 and exon 2 and is assembled upon splicing. The SOLE folds into a stem–loop structure. Both SOLE RNA and the exon junction complex (EJC) are required for oskar mRNA transport along the microtubules by kinesin. The SOLE RNA likely constitutes a recognition element for a yet unknown protein, which either belongs to the EJC or functions as a bridge between the EJC and the mRNA. Here, we determine the solution structure of the SOLE RNA by Nuclear Magnetic Resonance spectroscopy. We show that the SOLE forms a continuous helical structure, including a few noncanonical base pairs, capped by a pentanucleotide loop. The helix displays a widened major groove, which could accommodate a protein partner. In addition, the apical helical segment undergoes complex dynamics, with potential functional significance. Keywords: NMR; RNA conformation; mRNA localization; oskar mRNA; structural biology INTRODUCTION Later work identified the formation of a stem–loop structure mRNA localization is a conserved and efficient process that upon splicing of the first intron. This structure, the SOLE el- allows confined protein expression and contributes to the ement (Fig. 1), is essential for localization (Ghosh et al. 2012). functional polarization of cells. This process is important in The SOLE RNA consists of 18 nt from exon 1 and 10 nt organismal development, cell migration, and cell fate specifi- from exon 2, ligated together at the first exon junction site. cation (St Johnston 2005; Besse and Ephrussi 2008; Medioni In vivo mutational analysis established the relevance of the et al. 2012). In Drosophila melanogaster, oskar mRNA locali- short proximal stem (PS, 6 bp) for localization, suggesting zation in the oocyte determines where the abdomen and pri- that this structural element participates in the recognition mordial germ cells will form. oskar mRNA transport to the of trans-acting factors (Fig. 1B; Ghosh et al. 2012). In con- posterior pole requires a polarized microtubule cytoskeleton trast, the nucleotide identity in the PS seemed to be unimpor- – and its associated motor kinesin (Brendza et al. 2000). It is tant. Nucleotides 524 539 were predicted to fold in the – thought that trans-acting factors recognize specific sequences medial stem loop element (MSL); mutational analysis, de- in the oskar mRNA transcript and form ribonucleoprotein signed on the assumption of the MSL structure of Figure particles that are competent for kinesin dependent transport 1A, appeared to indicate that this part of the RNA is not es- (Zimyanin et al. 2008; Ghosh et al. 2014). sential for function (Ghosh et al. 2012). However, this region The four core components of the exon junction complex, can form secondary structures alternative to that in Figure a protein complex that is deposited on the mRNA concomi- 1A, which might impinge on the design and interpretation tant with splicing 20–24 nucleotides (nt) upstream of exon– of the mutational analysis. exon junctions (Le Hir et al. 2000; Tange et al. 2004), have The SOLE RNA sequence is not sufficient for localization. been found to be required for localization of oskar mRNA When the SOLE RNA is constitutively present on an oskar at the posterior pole (Newmark and Boswell 1994; Hachet mRNA transcript, not requiring splicing for its formation, and Ephrussi 2001; Mohr et al. 2001; van Eeden et al. 2001; the mRNA is mislocalized (Ghosh et al. 2012). Conversely, Palacios et al. 2004). Consistent with the notion that the mRNA loaded with the EJC but lacking the SOLE sequence EJC requires splicing for deposition, oskar mRNA splicing is also mislocalized (Ghosh et al. 2012). These facts strongly is required for its localization (Hachet and Ephrussi 2004). indicate that the SOLE RNA and the EJC work together to en- able oskar mRNA localization. It is not known whether there Corresponding author: [email protected] Article published online ahead of print. Article and publication date are at © 2015 Simon et al. This article, published in RNA, is available under a http://www.rnajournal.org/cgi/doi/10.1261/rna.049601.115. Freely available Creative Commons License (Attribution 4.0 International), as described at online through the RNA Open Access option. http://creativecommons.org/licenses/by/4.0/. RNA 21:1–10; Published by Cold Spring Harbor Laboratory Press for the RNA Society 1 Downloaded from rnajournal.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Simon et al. – AB C531 = 16 the intermediate time-scale regime (microseconds milli- C A U A U A seconds) affecting residues 10–25, with exchange rates and C A U U C A A A U G U A U G C G populations of the two (or more) folds being temperature de- A A U C A A G A pendent. The resonances gradually broaden upon cooling; MSL C G A 528C G 536 A G some of the base resonances move to higher fields, where G U C 527G U 537 G U 526 A G A 538 C G 539 = 24 G 525 G A C6 and C8 atoms belonging to helical structured regions G C G 539 U A C A G 524C A A U are located. Therefore, it is reasonable to assume that one U A A U A A U U A of the conformations adopted by the MSL element represents A U G A U G C A U PS U A U U A U A G C a helical structure. Here, we conducted the conformational A U C A U C G 518 = 3C G 545 = 30 analysis at 308 K, where we can observe all NMR resonances. G C C G C C G A U 518 545 C G A C G A U G C 5’ 3’ 5’ 3’ Interestingly, this temperature is close to the optimal growth temperature of D. melanogaster of 301 K. FIGURE 1. (A) Sequence of the SOLE RNA that was identified in To gain more understanding of the dynamic properties of Ghosh et al. (2012) as essential for oskar mRNA localization. The sec- the MSL region, we measured relaxation parameters. R2/R1 ondary structure is shown as predicted in Ghosh et al. (2012). The nu- ratios of the C6 and C8 atoms (Fig. 2E) are almost constant cleotides in black and blue belong to the first and second exon, – – respectively. (PS) proximal stem; (MSL) medial stem–loop. (B) for nucleotides 2 6 and 25 31 (Fig. 1A), indicating a stable Summary of the mutant analysis performed in Ghosh et al. (2012). structure in this region. Ratios of residues 8–13 and 21–23 The four mutant sequences are shown in the boxes: Three of them sup- are higher than average; in addition, if R1ρ is measured at low- port correct localization (green boxes), while one does not (dark red er B spinlock field strength for residues 10,12,19, 21, 22, and box). (C) Construct of the SOLE RNA used in this study together 1 with the experimentally derived secondary structure. Two base pairs 23, the R2/R1 ratios increase further, suggesting conforma- were added at the termini in comparison to the sequence of A. The tional exchange in the intermediate time scale (microsec- new nucleotide numbering from 1 to 32 is shown with respect to the onds–milliseconds). Conversely, the R2/R1 ratios of residues numbering of A. A continuous stacking of base pairs is seen from nucle- 14–20 and 24 are lower than average, which demonstrates otides 1–13 and from nucleotides 19–32. A24 is either bulged out or stacked between G23 and A25. fast (picoseconds) internal dynamics. All in all, the relaxation parameters are indicative of a complex internal dynamics in the MSL region. is a direct interaction between the SOLE RNA and the EJC, or Analysis of the chemical shifts of both base and ribose car- a third factor is necessary to connect the two elements. bons and protons (Fig. 3) reveals clear trends in the second- In the absence of a validated binding partner for the SOLE ary structure (Fares et al. 2007). C8 shifts of G4 and G30, as RNA, we set out to solve its solution structure, with the goal well as A5, A7, and A27 indicate that these nucleotides belong of identifying structural elements that might be essential for to regular helical structure (Fig. 3A). Conversely, the C8 res- protein recognition. We find that at 34°C no internal loop is onances of G10, G12, G19, G21, and G23 as well as A11, A14, formed after U523 and before A540; instead, the proximal A20, and A25 are shifted to low field, albeit not as much as stem is elongated by five additional base pairs, comprising expected for bulge or disordered regions (2.0 and 1.5 ppm three noncanonical ones. The long stem presents a widened for G and A, respectively). Their moderate low-field shift sug- major groove, which might be key to protein recognition. gests that they might be “partially” involved in helical struc- ture.
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