The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3

Kadlec, Jan; Izaurralde, Elisa; Cusack, Stephen

doi:10.1038/nsmb741

Cited by 174 publications

(243 citation statements)

References 48 publications

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“…the utilization of the conserved ribonucleoprotein (RNP) motifs 1 (on ␤-strand 3) and 2 (␤-strand 1) in contact with dinucleotides. Recent structural studies have revealed that a number of RRMs recognize and bind specific proteins predominantly by using RNP motifs with slightly modified signature sequences (43)(44)(45)(46).…”

Section: Discussionmentioning

confidence: 99%

Domain Architectures and Characterization of an RNA-binding Protein, TLS

Iko

Kodama

Kasai

et al. 2004

Journal of Biological Chemistry

149

116

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Translocated in liposarcoma (TLS) is an importantprotein component of the heterogeneous nuclear ribonucleoprotein complex involved in the splicing of pre-mRNA and the export of fully processed mRNA to the cytoplasm. We examined the domain organization of human TLS by a combined approach using limited proteolysis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, circular dichroism, inductively coupled plasma atomic emission spectroscopy, and NMR spectroscopy. We found that the RNA recognition motif (RRM) and zinc finger-like domains exclusively form protease-resistant core structures within the isolated TLS protein fragments, while the remaining regions, including the Arg-Gly-Gly repeats, appear to be completely unstructured. Thus, TLS contains the unstructured N-terminal half followed by the RRM and zinc finger-like domains, which are connected to each other by a flexible linker. We also carried out NMR analyses to obtain more detailed insights into the individual RRM and zinc finger-like domains. The 113 Cd NMR analysis of the zinc finger-like domain verified that zinc is coordinated with four cysteines in the C4 type scheme. We also investigated the interaction of each domain with an oligo-RNA containing the GGUG sequence, which appears to be critical for the TLS function in splicing. The backbone amide NMR chemical shift perturbation analyses indicated that the zinc finger domain binds GGUG-containing RNA with a dissociation constant of about 1.0 ؋ 10 ؊5 M, whereas the RRM domain showed no observable interaction with this RNA. This surprising result implies that the zinc finger domain plays a more predominant role in RNA recognition than the RRM domain.The translocated in liposarcoma (TLS) 1 protein, also termed FUS, was first identified in human myxoid and round cell liposarcomas as an oncogenic fusion protein with a stressinduced DNA-binding transcription factor, CCAAT enhancerbinding homologous protein (CHOP, also known as GADD153 or DDIT3) (1, 2). The resultant fusion protein (TLS-CHOP), consisting of the N-terminal half of TLS and the full-length CHOP, appears to act as a potent transcription factor possibly by combining the TLS transactivation activity and the CHOP DNA binding activity. A different type of fusion protein, TLS-ERG (a member of the erythroblast transformation-specific (ETS) family of transcription factors), was subsequently detected in human acute myeloid leukemia (3).The normal TLS, consisting of 526 amino acids with a calculated molecular mass of 53 kDa, belongs to a family including the closely related proteins Ewing's sarcoma (EWS) (4) and TAF II 68 (TATA-binding protein-associated factor) (5). Thus, they are collectively called the TET (TLS, EWS, TAF II 68) family. EWS and TAF II 68 interact with components of the RNA polymerase II complex (5, 6). Moreover sarcoma-associated RNA-binding fly homologue (SARFH), a Drosophila homologue of TLS, is colocalized with the polymerase on active chromatin (7). The N-terminal domain of TLS is involved in transcription...

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Section: Discussionmentioning

confidence: 99%

Domain Architectures and Characterization of an RNA-binding Protein, TLS

Iko

Kodama

Kasai

et al. 2004

Journal of Biological Chemistry

149

116

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“…We also found that Upf3b/3a alone have nonspecific RNA-binding activity (data not shown). Both Upf1 and Upf2 bind RNA nonspecifically as well (35,38). Considering that splicing and EJC loading are required for NMD in mammalian cells, we propose that, after the EJC is loaded onto mRNA, this complex can interact with other mRNA-binding proteins that are already prebound, such as Upf3b/3a, resulting in remodeling of the mRNP conformation.…”

Section: Recruitment Of Ejc Core Components Onto Mrna and Ejc Assemblymentioning

confidence: 99%

“…The EJC-independent binding of Upf3b/3a onto mRNA was unexpected, because the RRM (RNA-recognition motif) of Upf3b interacts with Upf2 instead of binding RNA (35). Using a pull-down assay, we found that full-length Upf3b can bind RNA directly (data not shown), but, in light of its very basic character, we do not know whether Upf3b binds mRNA in vivo by direct RNA-protein interaction or through a more elaborate mechanism.…”

Section: Recruitment Of Ejc Core Components Onto Mrna and Ejc Assemblymentioning

confidence: 99%

Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components

Zhang

Krainer²

2007

Proc. Natl. Acad. Sci. U.S.A.

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Pre-mRNA splicing not only removes introns and joins exons to generate spliced mRNA but also results in remodeling of the spliced messenger ribonucleoprotein, influencing various downstream events. This remodeling includes the loading of an exon-exon junction complex (EJC). It is unclear how the spliceosome recruits the EJC onto the mRNA and whether EJC formation or EJC components are required for pre-mRNA splicing. Here we immunodepleted the EJC core component eIF4A3 from HeLa cell nuclear extract and found that eIF4A3 is dispensable for pre-mRNA splicing in vitro. However, eIF4A3 is required for the splicing-dependent loading of the Y14/Magoh heterodimer onto mRNA, and this activity of human eIF4A3 is also present in the Drosophila ortholog. Surprisingly, the loading of six other EJC components was not affected by eIF4A3 depletion, suggesting that their binding to mRNA involves different or redundant pathways. Finally, we found that the assembly of the EJC onto mRNA occurs at the late stages of the splicing reaction and requires the second-step splicing and mRNA-release factor HRH1/hPrp22. The EJC-dependent and -independent recruitment of RNA-binding proteins onto mRNA suggests a role for the EJC in messenger ribonucleoprotein remodeling involving interactions with other proteins already bound to the pre-mRNA, which has implications for nonsense-mediated mRNA decay and other mRNA transactions.messenger ribonucleoprotein remodeling ͉ nonsense-mediated mRNA decay ͉ pre-mRNA splicing E ukaryotic gene expression requires elaborate posttranscriptional control mechanisms to ensure that the genetic information is precisely transferred from DNA to its final products. The quality control of mRNA synthesis plays a central role in this process (1). During pre-mRNA splicing, introns are removed by the spliceosome, and the exons are ligated to form the mature mRNA. Splicing also affects many other aspects of downstream events, including mRNA export, surveillance, localization, and translation (2). These effects have been linked to the recruitment of specific proteins onto the mRNA during splicing, with the consequent remodeling of the messenger ribonucleoprotein (mRNP) composition and structure.The exon-exon junction complex (EJC) is loaded onto the newly spliced mRNA Ϸ20-24 nt upstream of exon-exon junctions in a sequence nonspecific manner (3, 4). Several EJC factors are essential for mRNA localization in oocytes (5), nonsense-mediated mRNA decay (NMD) (5-7), and translational enhancement (8). The crystal structure of an EJC core complex, assembled from individual recombinant proteins and an RNA fragment, provided important details about how the complex is organized and stably binds to its RNA target (9, 10). However, the EJC is normally loaded onto mRNA during the course of pre-mRNA splicing (3), and the molecular mechanisms responsible for splicing-coupled loading of the EJC remain unknown.Among the EJC components, the ATP-dependent DEAD-box RNA helicase eIF4A3 was proposed to be the key factor in formation of the comp...

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“…The RNP motifs at such protein-interfaces remain similar to those of classical, RNAbinding RRMs and as such, can be challenging to distinguish based on primary sequences alone. Examples include Y14-Mago nashi in the exon-junction complex (Fribourg et al 2003;Lau et al 2003;Shi and Xu 2003;Bono et al 2006), the nonsense-mediated decay factors Upf2-Upf3 (Kadlec et al 2004), and inter-RRM packing of Prp24 in the U2 snRNP (Bae et al 2007;Montemayor et al 2014). In other cases, the "RRM" has acquired distinct sequence features for binding proteins, whereas the RNP motifs have diverged and lost the ability to bind RNA.…”

Section: Introductionmentioning

confidence: 99%

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Loerch

Kielkopf

2016

RNA

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U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.

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The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3

Cited by 174 publications

References 48 publications

Domain Architectures and Characterization of an RNA-binding Protein, TLS

Domain Architectures and Characterization of an RNA-binding Protein, TLS

Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

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