Identification of a Conserved RNA Motif Essential for She2p Recognition and mRNA Localization to the Yeast Bud

Olivier, C; Poirier, Guillaume; Gendron, Patrick; Boisgontier, Anita; Major, François; Chartrand, Pascal

doi:10.1128/mcb.25.11.4752-4766.2005

Cited by 86 publications

(122 citation statements)

References 40 publications

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“…This was confirmed in a yeast three-hybrid assay that measures the interaction between She2p and the ASH1 mRNA zip codes Olivier et al, 2005). In this assay, one of the ASH1 zip code (the domain 1 of element E2B or D1), was used as bait for the interaction with She2p.…”

Section: Nuclear Import Of She2p Is Required For Proper Localization mentioning

confidence: 87%

“…This strain also expressed the GAL4 activation domain fused with the C-terminal domain of She3p, along with a plasmid expressing a chimeric RNA containing the localization E2B-D1 fused to the MS2 stem-loop (D1). Controls: empty vector (pIIIA/MS2-2) and an inactive fragment of the localization element E2B (D2; Olivier et al, 2005). (D) Interaction between the C-terminal domain of She3p and wild-type (She2WT) or NLS-mutated (She2M5A) She2 proteins in a yeast two-hybrid assay.…”

Section: Nuclear Import Of She2p Is Essential For the Recruitment Of mentioning

confidence: 99%

“…This localization promotes the asymmetric sorting of Ash1p to the daughter cell nucleus and results in the inhibition of mating-type switching in the daughter cell (Jansen et al, 1996;Sil and Herskowitz, 1996). The RNA-binding protein She2p is responsible for the recognition of bud-localized mRNAs, via its interaction with specific localization elements in these transcripts (Olivier et al, 2005). She2p also interacts with the transport machinery, constituted of the type V myosin Myo4p, via the bridging protein She3p (Bohl et al, 2000;Long et al, 2000;Takizawa and Vale, 2000).…”

Section: Introductionmentioning

confidence: 99%

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Nuclear Shuttling of She2p Couples ASH1 mRNA Localization to its Translational Repression by Recruiting Loc1p and Puf6p

Shen

Paquin

Forget

et al. 2009

MBoC

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The transport and localization of mRNAs results in the asymmetric synthesis of specific proteins. In yeast, the nucleocytoplasmic shuttling protein She2 binds the ASH1 mRNA and targets it for localization at the bud tip by recruiting the She3p-Myo4p complex. Although the cytoplasmic role of She2p in mRNA localization is well characterized, its nuclear function is still unclear. Here, we show that She2p contains a nonclassical nuclear localization signal (NLS) that is essential for its nuclear import via the importin ␣ Srp1p. Exclusion of She2p from the nucleus by mutagenesis of its NLS leads to defective ASH1 mRNA localization and Ash1p sorting. Interestingly, these phenotypes mimic knockouts of LOC1 and PUF6, which encode for nuclear RNA-binding proteins that bind the ASH1 mRNA and control its translation. We find that She2p interacts with both Loc1p and Puf6p and that excluding She2p from the nucleus decreases this interaction. Absence of nuclear She2p disrupts the binding of Loc1p and Puf6p to the ASH1 mRNA, suggesting that nuclear import of She2p is necessary to recruit both factors to the ASH1 transcript. This study reveals that a direct coupling between localization and translation regulation factors in the nucleus is required for proper cytoplasmic localization of mRNAs.

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Section: Nuclear Import Of She2p Is Required For Proper Localization mentioning

confidence: 87%

Section: Nuclear Import Of She2p Is Essential For the Recruitment Of mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nuclear Shuttling of She2p Couples ASH1 mRNA Localization to its Translational Repression by Recruiting Loc1p and Puf6p

Shen

Paquin

Forget

et al. 2009

MBoC

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“…This has been implemented in the program MC-Search. [20,35,39]. Note that symbolic search methods depend on consistent and precise coding of all pairwise base-base interactions.…”

Section: Introductionmentioning

confidence: 99%

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

et al. 2007

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New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomicresolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and basestacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal compute...

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“…Some secondary structural motifs in UTRs involved in regulating mRNA decay rates and localization in yeast have been identified recently [32,50,51]. We grouped the 5′ UTR and 3′ UTR sequences according to cellular localization and decay rates, respectively, and predicted the structural motifs in the UTRs' RBP binding regions using RNApromo [32].…”

Section: Rbps Recognize Structural Motifs To Regulate Mrna At the Posmentioning

confidence: 99%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical non-coding RNAs (ncRNAs) and ~11% of long ncRNAs (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. . Many mRNAs are regulated by one or more RBPs as co-regulators. In Saccharomyces cerevisiae, there are approximately 600 annotated and predicted RBPs, but relatively few of them have been systematically studied to determine their regulatory targets [5]. In addition to mRNAs, numerous non-coding RNAs (ncRNAs) are targets of RBPs [6,7]. Previous studies revealed that RNAs were regulated by many RBPs post-transcriptionally [8]. It is widely accepted that altering the expression of RBPs will change cellular physiology profoundly. Studies using animal models have revealed that RBPs are involved in many human diseases, such as neurologic disorders and cancers [9]. Although the mechanisms that confer the specificity of RBP-RNA interaction are poorly understood, it is clear that this specificity is determined by both the primary sequence and secondary structure of the target RNA [10,11]. The secondary structures recognized by some RBPs are known. For example, the SAM domain of the yeast post-transcriptional regulator Vts1p recognizes the shape of the SRE of the RNA ligand [12].Currently, the most direct and powerful approach to profiling RBP-RNA interactions is UV crosslinking and immunoprecipitation (CLIP) of RNA-protein complexes,

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Identification of a Conserved RNA Motif Essential for She2p Recognition and mRNA Localization to the Yeast Bud

Cited by 86 publications

References 40 publications

Nuclear Shuttling of She2p Couples ASH1 mRNA Localization to its Translational Repression by Recruiting Loc1p and Puf6p

Nuclear Shuttling of She2p Couples ASH1 mRNA Localization to its Translational Repression by Recruiting Loc1p and Puf6p

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

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