RNA localization: A glimpse of the machinery

RNA localization: A glimpse of the machinery

Dispatch R725 RNA localization: A glimpse of the machinery Bruce J. Schnapp Asymmetric mRNA localization within cells plays an important part in bo...

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Dispatch

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RNA localization: A glimpse of the machinery Bruce J. Schnapp

Asymmetric mRNA localization within cells plays an important part in both development and physiology. Recent studies have provided a glimpse of the conserved molecular machinery that directs the localization of specific mRNAs. Address: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA. E-mail: [email protected] Current Biology 1999, 9:R725–R727 0960-9822/99/$ – see front matter © 1999 Elsevier Science Ltd. All rights reserved.

A common feature of a number of important biological problems — from synaptic plasticity to cell fate determination — is the need to restrict where proteins are produced spatially within a cell. To this end, specific mRNAs are actively transported and localized to discrete subcellular domains, such as the dendritic spine of a neuron or one quadrant of an oocyte. As a result of a period of recent progress [1–5], capped by two new studies [6,7], we are at last beginning to identify the proteins that facilitate cytoplasmic mRNA localization. Collectively, the recent work provides compelling evidence for a conserved machinery that localizes diverse mRNAs. A developing theme is that this machinery may direct more than a transcript’s localization in the cytoplasm — some components of the machinery reside in the nucleus, where they may link a transcript’s nuclear export to its localization and translational control in the cytoplasm. A year or two ago, researchers working on the localization of entirely unrelated mRNAs — those encoding β actin at the leading edge of chick embryo fibroblasts [1] and Vg1 at the vegetal cortex of Xenopus oocytes [2,3] — isolated homologues of the same novel trans-acting factor. This protein, the Xenopus version of which was originally named Vera [2] or Vg1 RBP [3], is now generally referred to as zipcode-binding protein (ZBP) [1]. Considering that these two mRNAs are localized in distinct types of cell — one somatic the other germline — and encode different classes of proteins — Vg1 is secreted whereas β actin is cytosolic — the discovery that their localization involves the same trans-acting factor was remarkable. This convergence implied the existence of a common machinery for localizing diverse mRNAs in many different contexts. The precise function of ZBP is still unresolved, but a rather surprising clue came from its amino-acid sequence. The presence of RNA-binding motifs — one RRM and four KH domains — was no surprise, given ZBP’s high-affinity

interaction with specific mRNAs [8]. But the presence of nuclear localization and export sequences was, at the time, unexpected and puzzling. Does the machinery for cytoplasmic localization actually assemble on mRNAs while they are still in the nucleus? And are the activities of cytoplasmic localization and nuclear export linked? The idea that trans-acting factors recognize diverse transcripts and transit between nucleus and cytoplasm (Figure 1), again came to the fore when the next two candidate mRNA ‘localization factors’ were discovered. These both turned out to be heterologous nuclear ribonucleoproteins (hnRNPs): hnRNP A2 [4] and Xenopus VgRBP60 [5], a homologue of hnRNP I. Like ZBP, each of these proteins was isolated by its ability to bind cis-acting sequences in the 3′ untranslated region of a localized transcript: VgRBP60 to Vg1 mRNA, and hnRNP A2 to myelin basic protein mRNA, which is localized in oligodendrocyte processes. The analogy with ZBP is unmistakable: hnRNPs are known to interact with diverse transcripts; hnRNP A2 shuttles between nucleus and cytoplasm to facilitate nuclear export of mRNAs; and hnRNP I, while primarily nuclear, maintains a persistent interaction with Vg1 mRNA during its localization [5]. These first glimpses of the biochemistry of RNA localization have to be considered with a measure of caution. This is because ZBP, hnRNP I and hnRNP A2 were all implicated in RNA localization by their selective binding to cis-acting mRNA sequences. Although the interactions are strong and highly sequence specific, such evidence is circumstantial and not airtight; binding by these proteins in cell extracts could have obscured the detection of less abundant proteins that are the bona fide localization factors. The experimental systems used lack a way of assessing, by a functional assay or by genetics, whether the candidate trans-acting factors are required for transcript localization. Furthermore, although these proteins reside partially — some even primarily — in the nucleus, it is unclear whether their nuclear localization has any bearing on mRNA transport in the cytoplasm. These are precisely the points addressed by two new studies [6,7], both of which examined the role in mRNA localization of the Drosophila hnRNP A1 homologue known as Squid (Sqd). Schüpbach and colleagues [6] focused on the localization of gurken (grk) mRNA. In Drosophila, dorsoventral axis specification involves the sqd-dependent localization of grk mRNA to the dorsal-anterior corner of the oocyte. To dissect the function of Sqd, Norvell et al. [6] introduced sqd transgenes into sqd-deficient oocytes, so that one or

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Current Biology Vol 9 No 19

Figure 1

Sqd participate in the localization of other transcripts? And does the requirement of Sqd reflect a direct interaction with grk mRNA in the nucleus? Such questions are not readily addressed by genetic approaches. A biochemical reconstitution system is better, and herein lies the contribution of the work recently reported by Ish-Horowicz and colleagues [7].

Cytoplasm Translated protein

Nucleus

AA

Unknown factors (such as motor proteins, translational regulators)

Nuclear targeting RNA binding

Protein binding?

Trans-acting localization factor

5′

AA AA A

Transport A AA

AAAAA

Coding region

Localization element

Localized mRNA Current Biology

Localized mRNAs have in their 3′ untranslated regions localization elements — cis-acting sequences that specify localization of the mRNAs to a discrete subregion of the cell. These localization elements interact with trans-acting factors in the nucleus; some of these are hnRNPs already known to have a role in the nuclear export of RNAs. Each identified trans-acting factor has multiple domains that bind RNA (only one is depicted), as well as domains for nuclear import and export. It is likely that nuclear export and cytoplasmic localization are linked, and that additional components of the localization–translational control machinery reside in the cytoplasm, where they recognize transcripts in the context of the bound nuclear partner proteins.

other of two Sqd splice variants were produced. These Sqd isoforms, A and S, have distinct subcellular distributions — Sqd S is primarily nuclear and Sqd A primarily cytoplasmic — and were found to have complementary effects on grk function. In oocytes where Sqd S was the sole isoform present, grk mRNA was localized normally — in the dorsal-anterior corner of the oocyte — but abnormally low levels of Grk protein were produced. But in oocytes where Sqd A was the sole isoform present, grk mRNA was mislocalized, yet the Grk protein was properly localized — as in wild-type oocytes, grk mRNA translation was specifically activated only in the dorsal-anterior corner of the oocyte. These findings have a number of important implications. First, that only the nuclear isoform, Sqd S, can support proper grk mRNA localization strengthens the case that assembly of the localization machinery on cis-acting RNA elements begins in the nucleus. Second, that Sqd A spatially regulates grk translation underscores a link, evident already in the literature, between the localization of mRNA transcripts and the regulation of their translation. The results leave little doubt that Sqd is required for grk mRNA localization, but important questions remain. Does

This work involved transcripts of Drosophila pair-rule genes — those genes of the hierarchy that controls segmentation in the fruitfly that are expressed in a striped pattern with a two-segment periodicity. The pair-rule transcripts are synthesized in blastoderm embryos, within the monolayer of nuclei that subdivides the cortical cytoplasm into apical and basal regions. The pair-rule transcripts become localized specifically to the apical region. On the basis of a number of circumstantial observations, Ish-Horowicz and colleagues had put forth the hypothesis that the localization of pair-rule transcripts occurs by vectorial nuclear export. It was in the process of testing this hypothesis with a new microinjection assay that an important discovery was made. Lall et al. [7] injected blastoderm embryos with transcripts of the pair-rule gene fushi tarazu (ftz), tagged with a fluorescent group. While the fluorescent transcripts had biological activity in the embryo by a number of criteria, they failed to become apically localized, implying that cytoplasmic factors are not sufficient to promote transcript localization. Of course, the authors recognized that this negative finding, while consistent with the vectorial export model, was hardly conclusive. So, as an additional test of their model, they injected into the embryo, not naked ftz mRNA, but ftz mRNA that had been preincubated with a nuclear extract. If, as expected, the RNA failed to localize after being exposed to this surrogate ‘nuclear environment’, the vectorial export model would be favored, albeit by default. As we all know, an unexpected outcome — one that does not jive with a dearly held hypothesis — is an all too common occurrence in the laboratory. In most cases, results of this kind fail to enlighten. On occasion, however, an unexpected outcome can change our thinking about a problem. Such was the case here. The tagged ftz transcripts that were injected into the embryo after incubation in nuclear extract were seen to localize rapidly to the apical cytoplasm. This surprising result was all the more striking because the nuclear extract was not from Drosophila, but from human cells. Knowing that hnRNPs are among the most highly conserved nuclear proteins, and in light of the earlier work from Schüpbach’s group [6], Lall et al. [7] naturally tested whether the requirement for incubation with a nuclear extract could be fulfilled by purified hnRNPs. Again the outcome was clear: injected ftz transcripts localized correctly when they had

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been preincubated with either Drosophila Sqd, or human hnRNP A1, hnRNP A2 or hnRNP B. These remarkable experiments constitute the first direct demonstration, using a functional assay, that a specific protein implements intracellular localization via direct binding to the mRNA. Moreover, they lead to a credible proposal: that additional components of the localization machinery — in the cytoplasm — recognize transcripts only in the context of the bound nuclear partner [7]. The identification of these putative additional components is obviously a key goal. There is also an apparent discrepancy with previous findings that will need to be resolved: in some systems, such as oligodendrocytes and Xenopus oocytes, the mRNAs for myelin basic protein [9] or Vg1 [10] were found to become properly localized after injection into the cytoplasm in the absence of nuclear factors. In summary, independent lines of research on distinctly different localized mRNAs have thus converged on a subset of trans-acting localization factors with similar characteristics, and in some cases, on exactly the same protein. This provides some reassurance that the field as a whole is on the right track. Still, what we have at this point are mere hints about the machinery, nothing that defines a mechanism. The most pressing questions seem quite clear. Are the different proteins — ZBP, hnRNP I, hnRNP A1 and hnRNP A2 — components of a single RNA localization machine? How do we reconcile the fact that different mRNAs interact with the same trans-acting localization factors with the expectation that the localization of each mRNA must at some level be specifically determined? Perhaps what has been uncovered so far are components of a core machinery. Proper localization of mRNAs may involve a layer of less abundant factors that impose specificity. But the most intriguing conundrum is how to reconcile the classical description of hnRNPs, as proteins that bind transiently to virtually all nascent transcripts, with the idea that at least some bind selectively and persistently to a minor subset of transcripts which are then localized in the cytoplasm. Acknowledgements Many thanks to David Ish-Horowicz (ICRF, London) for an interesting discussion. I want to extend my gratitude to Kim Mowry (Brown University, Providence R.I.) for providing me with a preprint of her recent work and for comments on an earlier version of this manuscript. As always, I am indebted to the members of my laboratory, particularly Sunjong Kwon, for frequent stimulating discussions. Sunjong Kwon, Virgil Muresan, and Farah Esfandiari provided comments on the manuscript. Work on RNA localization in my laboratory is supported by the NIH.

References 1. Ross AF, Oleynikov Y, Kislauskis EH, Taneja KL, Singer RH: Characterization of a beta-actin mRNA zipcode-binding protein. Mol Cell Biol 1997, 17:2158-2165. 2. Deshler JO, Highett MI, Abramson T, Schnapp BJ: A highly conserved RNA-binding protein for cytoplasmic mRNA localization in vertebrates. Curr Biol 1998, 8:489-496.

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3. Havin L, Git A, Elisha Z, Oberman F, Yaniv K, Schwartz SP, Standart N, Yisraeli JK: RNA-binding protein conserved in both microtubuleand microfilament-based RNA localization. Genes Dev 1998, 12:1593-1598. 4. Hoek KS, Kidd GJ, Carson JH, Smith R: Hnrnp A2 selectively binds the cytoplasmic transport sequence of myelin basic protein mRNA. Biochemistry 1998, 37:7021-7029. 5. Cote CA, Gautreau D, Denegre JM, Kress T, Terry NA, Mowry KL: A Xenopus protein related to hnRNPI has a role in cytoplasmic RNA localization. Mol Cell 1999, in press. 6. Norvell A, Kelley RL, Wehr K, Schüpbach T: Specific isoforms of Squid, a Drosophila hnRNP, perform distinct roles in Gurken localization during oogenesis. Genes Dev 1999, 13:864-876. 7. Lall S, Francis-Lang H, Flament A, Norvell A, Schüpbach T, IshHorowicz D: Squid hnRNP protein promotes apical cytoplasmic transport and localization of Drosophila pair-rule transcripts. Cell 1999, 98:171-180. 8. Deshler JO, Highett MI, Schnapp BJ: Localization of Xenopus Vg1 mRNA by vera protein and the endoplasmic reticulum. Science 1997, 276:1128-1131. 9. Ainger K, Avossa D, Morgan F, Hill SJ, Barry C, Barbarese E, Carson JH: Transport and localization of exogenous myelin basic protein mRNA microinjected into oligodendrocytes. J Cell Biol 1993, 123:431-441. 10. Yisraeli JK, Melton DA: The maternal mRNA Vg1 is correctly localized following injection into Xenopus oocytes. Nature 1988, 336:592-595.