Journal articles: 'RNA recognition motif'

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Tsai, Yihsuan S., Shawn M. Gomez, and Zefeng Wang. "Prevalent RNA recognition motif duplication in the human genome." RNA 20, no. 5 (2014): 702–12. http://dx.doi.org/10.1261/rna.044081.113.

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Kaiser, Steffen, Katharina Rimbach, Tatjana Eigenbrod, Alexander H. Dalpke, and Mark Helm. "A modified dinucleotide motif specifies tRNA recognition by TLR7." RNA 20, no. 9 (2014): 1351–55. http://dx.doi.org/10.1261/rna.044024.113.

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Lyon, Angeline M., Brad S. Reveal, Paul M. Macdonald, and David W. Hoffman. "Bruno Protein Contains an Expanded RNA Recognition Motif." Biochemistry 48, no. 51 (2009): 12202–12. http://dx.doi.org/10.1021/bi900624j.

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Rebagliati, Michael. "An RNA recognition motif in the bicoid protein." Cell 58, no. 2 (1989): 231–32. http://dx.doi.org/10.1016/0092-8674(89)90834-9.

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Xu, Lei, Ren Kong, Jingyu Zhu, Huiyong Sun, and Shan Chang. "Unraveling the conformational determinants of LARP7 and 7SK small nuclear RNA by theoretical approaches." Molecular BioSystems 12, no. 8 (2016): 2613–21. http://dx.doi.org/10.1039/c6mb00252h.

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Song, Jikui, Jered V. McGivern, Karl W. Nichols, John L. Markley, and Michael D. Sheets. "Structural basis for RNA recognition by a type II poly(A)-binding protein." Proceedings of the National Academy of Sciences 105, no. 40 (2008): 15317–22. http://dx.doi.org/10.1073/pnas.0801274105.

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We identified a functional domain (XlePABP2-TRP) of Xenopus laevis embryonic type II poly(A)-binding protein (XlePABP2). The NMR structure of XlePABP2-TRP revealed that the protein is a homodimer formed by the antiparallel association of β-strands from the single RNA recognition motif (RRM) domain of each subunit. In each subunit of the homodimer, the canonical RNA recognition site is occluded by a polyproline motif. Upon poly(A) binding, XlePABP2-TRP undergoes a dimer-monomer transition that removes the polyproline motif from the RNA recognition site and allows it to be replaced by the adenosine nucleotides of poly(A). Our results provide high-resolution structural information concerning type II PABPs and an example of a single RRM domain protein that transitions from a homodimer to a monomer upon RNA binding. These findings advance our understanding of RRM domain regulation, poly(A) recognition, and are relevant to understanding how type II PABPs function in mRNA processing and human disease.

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Horke, Sven, Kerstin Reumann, Christian Schulze, Frank Grosse, and Tilman Heise. "The La Motif and the RNA Recognition Motifs of Human La Autoantigen Contribute Individually to RNA Recognition and Subcellular Localization." Journal of Biological Chemistry 279, no. 48 (2004): 50302–9. http://dx.doi.org/10.1074/jbc.m407504200.

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Nurmohamed, Salima, Adam R. McKay, Carol V. Robinson, and Ben F. Luisi. "Molecular recognition between Escherichia coli enolase and ribonuclease E." Acta Crystallographica Section D Biological Crystallography 66, no. 9 (2010): 1036–40. http://dx.doi.org/10.1107/s0907444910030015.

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In Escherichia coli and many other bacterial species, the glycolytic enzyme enolase is a component of the multi-enzyme RNA degradosome, an assembly that is involved in RNA processing and degradation. Enolase is recruited into the degradosome through interactions with a small recognition motif located within the degradosome-scaffolding domain of RNase E. Here, the crystal structure of enolase bound to its cognate site from RNase E (residues 823–850) at 1.9 Å resolution is presented. The structure suggests that enolase may help to organize an adjacent conserved RNA-binding motif in RNase E.

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Fernandes, Humberto, Honorata Czapinska, Katarzyna Grudziaz, Janusz M. Bujnicki, and Martyna Nowacka. "Crystal structure of human Acinus RNA recognition motif domain." PeerJ 6 (July 4, 2018): e5163. http://dx.doi.org/10.7717/peerj.5163.

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Acinus is an abundant nuclear protein involved in apoptosis and splicing. It has been implicated in inducing apoptotic chromatin condensation and DNA fragmentation during programmed cell death. Acinus undergoes activation by proteolytic cleavage that produces a truncated p17 form that comprises only the RNA recognition motif (RRM) domain. We have determined the crystal structure of the human Acinus RRM domain (AcRRM) at 1.65 Å resolution. It shows a classical four-stranded antiparallel β-sheet fold with two flanking α-helices and an additional, non-classical α-helix at the C-terminus, which harbors the caspase-3 target sequence that is cleaved during Acinus activation. In the structure, the C-terminal α-helix partially occludes the potential ligand binding surface of the β-sheet and hypothetically shields it from non-sequence specific interactions with RNA. Based on the comparison with other RRM-RNA complex structures, it is likely that the C-terminal α-helix changes its conformation with respect to the RRM core in order to enable RNA binding by Acinus.

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Kang, Hyun-Seo, Carolina Sánchez-Rico, Stefanie Ebersberger, et al. "An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2." Proceedings of the National Academy of Sciences 117, no. 13 (2020): 7140–49. http://dx.doi.org/10.1073/pnas.1913483117.

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The recognition of cis-regulatory RNA motifs in human transcripts by RNA binding proteins (RBPs) is essential for gene regulation. The molecular features that determine RBP specificity are often poorly understood. Here, we combined NMR structural biology with high-throughput iCLIP approaches to identify a regulatory mechanism for U2AF2 RNA recognition. We found that the intrinsically disordered linker region connecting the two RNA recognition motif (RRM) domains of U2AF2 mediates autoinhibitory intramolecular interactions to reduce nonproductive binding to weak Py-tract RNAs. This proofreading favors binding of U2AF2 at stronger Py-tracts, as required to define 3′ splice sites at early stages of spliceosome assembly. Mutations that impair the linker autoinhibition enhance the affinity for weak Py-tracts result in promiscuous binding of U2AF2 along mRNAs and impact on splicing fidelity. Our findings highlight an important role of intrinsically disordered linkers to modulate RNA interactions of multidomain RBPs.

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Coelho, Miguel B., David B. Ascher, Clare Gooding, et al. "Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins." Biochemical Society Transactions 44, no. 4 (2016): 1058–65. http://dx.doi.org/10.1042/bst20160080.

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Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.

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Ripin, Nina, Julien Boudet, Malgorzata M. Duszczyk, et al. "Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM." Proceedings of the National Academy of Sciences 116, no. 8 (2019): 2935–44. http://dx.doi.org/10.1073/pnas.1808696116.

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Human antigen R (HuR) is a key regulator of cellular mRNAs containing adenylate/uridylate–rich elements (AU-rich elements; AREs). These are a major class of cis elements within 3′ untranslated regions, targeting these mRNAs for rapid degradation. HuR contains three RNA recognition motifs (RRMs): a tandem RRM1 and 2, followed by a flexible linker and a C-terminal RRM3. While RRM1 and 2 are structurally characterized, little is known about RRM3. Here we present a 1.9-Å-resolution crystal structure of RRM3 bound to different ARE motifs. This structure together with biophysical methods and cell-culture assays revealed the mechanism of RRM3 ARE recognition and dimerization. While multiple RNA motifs can be bound, recognition of the canonical AUUUA pentameric motif is possible by binding to two registers. Additionally, RRM3 forms homodimers to increase its RNA binding affinity. Finally, although HuR stabilizes ARE-containing RNAs, we found that RRM3 counteracts this effect, as shown in a cell-based ARE reporter assay and by qPCR with native HuR mRNA targets containing multiple AUUUA motifs, possibly by competing with RRM12.

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Chang, Shan, Hang Shi, and Ren Kong. "Molecular Dynamics Simulations of RNA-Recognition Motif Complexed with CAC-Containing RNA." Biophysical Journal 116, no. 3 (2019): 212a. http://dx.doi.org/10.1016/j.bpj.2018.11.1172.

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Pan, Junhua, Vikram N. Vakharia, and Yizhi Jane Tao. "The structure of a birnavirus polymerase reveals a distinct active site topology." Proceedings of the National Academy of Sciences 104, no. 18 (2007): 7385–90. http://dx.doi.org/10.1073/pnas.0611599104.

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Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the RNA recognition motif (RRM) found in many RNA-binding proteins. Considering that polymerases have well conserved structures, it was surprising that the RNA-dependent RNA polymerases from birnaviruses, a group of dsRNA viruses, have their catalytic motifs arranged in a permuted order in sequence. Here we report the 2.5 Å structure of a birnavirus VP1 in which the polymerase palm subdomain adopts a new active site topology that has not been previously observed in other polymerases. In addition, the polymerase motif C of VP1 has the sequence of -ADN-, a highly unusual feature for RNA-dependent polymerases. Through site-directed mutagenesis, we have shown that changing the VP1 motif C from -ADN- to -GDD- results in a mutant with an increased RNA synthesis activity. Our results indicate that the active site topology of VP1 may represent a newly developed branch in polymerase evolution, and that birnaviruses may have acquired the -ADN- mutation to control their growth rate.

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Cerdà-Costa, Núria, Jaume Bonet, M. Rosario Fernández, Francesc X. Avilés, Baldomero Oliva, and Sandra Villegas. "Prediction of a new class of RNA recognition motif." Journal of Molecular Modeling 17, no. 8 (2010): 1863–75. http://dx.doi.org/10.1007/s00894-010-0888-0.

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Ganguly, Akshay Kumar, Garima Verma, and Neel Sarovar Bhavesh. "The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition." Journal of Molecular Biology 431, no. 3 (2019): 498–510. http://dx.doi.org/10.1016/j.jmb.2018.11.020.

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Teramoto, Takamasa, Kipchumba J. Kaitany, Yoshimitsu Kakuta, Makoto Kimura, Carol A. Fierke, and Traci M. Tanaka Hall. "Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA." Nucleic Acids Research 48, no. 21 (2020): 11815–26. http://dx.doi.org/10.1093/nar/gkaa627.

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Abstract Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5′-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.

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Ferrero, Diego S., Michela Falqui, and Nuria Verdaguer. "Snapshots of a Non-Canonical RdRP in Action." Viruses 13, no. 7 (2021): 1260. http://dx.doi.org/10.3390/v13071260.

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RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

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Nakamoto, Meagan Y., Nickolaus C. Lammer, Robert T. Batey, and Deborah S. Wuttke. "hnRNPK recognition of the B motif of Xist and other biological RNAs." Nucleic Acids Research 48, no. 16 (2020): 9320–35. http://dx.doi.org/10.1093/nar/gkaa677.

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Abstract Heterogeneous nuclear ribonuclear protein K (hnRNPK) is an abundant RNA-binding protein crucial for a wide variety of biological processes. While its binding preference for multi-cytosine-patch (C-patch) containing RNA is well documented, examination of binding to known cellular targets that contain C-patches reveals an unexpected breadth of binding affinities. Analysis of in-cell crosslinking data reinforces the notion that simple C-patch preference is not fully predictive of hnRNPK localization within transcripts. The individual RNA-binding domains of hnRNPK work together to interact with RNA tightly, with the KH3 domain being neither necessary nor sufficient for binding. Rather, the RG/RGG domain is implicated in providing essential contributions to RNA-binding, but not DNA-binding, affinity. hnRNPK is essential for X chromosome inactivation, where it interacts with Xist RNA specifically through the Xist B-repeat region. We use this interaction with an RNA motif derived from this B-repeat region to determine the RNA-structure dependence of C-patch recognition. While the location preferences of hnRNPK for C-patches are conformationally restricted within the hairpin, these structural constraints are relieved in the absence of RNA secondary structure. Together, these results illustrate how this multi-domain protein's ability to accommodate and yet discriminate between diverse cellular RNAs allows for its broad cellular functions.

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Vasilyev, Nikita, Anna Polonskaia, Jennifer C. Darnell, Robert B. Darnell, Dinshaw J. Patel та Alexander Serganov. "Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP". Proceedings of the National Academy of Sciences 112, № 39 (2015): E5391—E5400. http://dx.doi.org/10.1073/pnas.1515737112.

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Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K+-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex–quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation–π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex–quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG–RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.

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Penumutchu, Srinivasa R. "Structural Insights into G-tract Recognition by the hnRNP H-RNA Recognition Motif." Biophysical Journal 112, no. 3 (2017): 72a. http://dx.doi.org/10.1016/j.bpj.2016.11.433.

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Shi, H., B. E. Hoffman, and J. T. Lis. "A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52." Molecular and Cellular Biology 17, no. 5 (1997): 2649–57. http://dx.doi.org/10.1128/mcb.17.5.2649.

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B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RNAs by selection and amplification from a pool of random RNA sequences by using full-length B52 protein as the target. These RNAs contained a conserved consensus motif that constitutes the core of a secondary structural element predicted by energy minimization. Deletion and substitution mutations defined the B52-binding site on these RNAs as a hairpin loop structure covering about 20 nucleotides, which was confirmed by structure-specific enzymatic probing. Finally, we demonstrated that both RNA recognition motifs of B52 are required for RNA binding, while the RS domain is not involved in this interaction.

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Colgan, Kevin J., James R. Boyne, and Adrian Whitehouse. "Identification of a response element in a herpesvirus saimiri mRNA recognized by the ORF57 protein." Journal of General Virology 90, no. 3 (2009): 596–601. http://dx.doi.org/10.1099/vir.0.007476-0.

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The herpesvirus saimiri (HVS) ORF57 protein binds viral RNA, enabling the efficient nuclear export of intronless viral mRNAs. However, it is not known how ORF57 recognizes these viral mRNAs. In this study, a systematic evolution of ligands by exponential enrichment (SELEX) approach was used to select RNA sequences that are preferentially bound by the ORF57 protein. Results identified a recurring motif, GAAGRG, within the majority of selected RNAs, which is also present in many late HVS mRNAs. RNA immunopreciptations demonstrated that disruption of this motif within a viral intronless RNA ablates ORF57 binding. These data suggest that the GAAGRG motif may be required within a HVS intronless mRNA for recognition by the ORF57 protein.

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Maucuer, Alexandre, Sylvie Ozon, Valérie Manceau, et al. "KIS Is a Protein Kinase with an RNA Recognition Motif." Journal of Biological Chemistry 272, no. 37 (1997): 23151–56. http://dx.doi.org/10.1074/jbc.272.37.23151.

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Bang, Kyeong-Mi, Na Youn Cho, Won-Je Kim, et al. "Structural Characterization of RNA Recognition Motif-2 Domain of SART3." Bulletin of the Korean Chemical Society 38, no. 4 (2017): 444–47. http://dx.doi.org/10.1002/bkcs.11106.

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Netter, C., G. Weber, H. Benecke, and M. C. Wahl. "Functional stabilization of an RNA recognition motif by a noncanonical N-terminal expansion." RNA 15, no. 7 (2009): 1305–13. http://dx.doi.org/10.1261/rna.1359909.

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Hodge, Kenneth, Chairat Tunghirun, Maliwan Kamkaew, Thawornchai Limjindaporn, Pa-thai Yenchitsomanus, and Sarin Chimnaronk. "Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication." Journal of Biological Chemistry 291, no. 33 (2016): 17437–49. http://dx.doi.org/10.1074/jbc.m116.724013.

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Dengue virus, an ∼10.7-kb positive-sense RNA virus, is the most common arthropod-communicated pathogen in the world. Despite dengue's clear epidemiological importance, mechanisms for its replication remain elusive. Here, we probed the entire dengue genome for interactions with viral RNA-dependent RNA polymerase (RdRp), and we identified the dominant interaction as a loop-forming ACAG motif in the 3′ positive-stranded terminus, complicating the prevailing model of replication. A subset of interactions coincides with known flaviviral recombination sites inside the viral protein-coding region. Specific recognition of the RNA element occurs via an arginine patch in the C-terminal thumb domain of RdRp. We also show that the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutations in the interacting region of RdRp. Disruption of the interaction resulted in loss of viral replication ability in cells. This unique RdRp-RNA interface is found throughout flaviviruses, implying possibilities for broad disease interventions.

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Yan, C., and T. Mélèse. "Multiple regions of NSR1 are sufficient for accumulation of a fusion protein within the nucleolus." Journal of Cell Biology 123, no. 5 (1993): 1081–91. http://dx.doi.org/10.1083/jcb.123.5.1081.

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NSR1, a 67-kD nucleolar protein, was originally identified in our laboratory as a nuclear localization signal binding protein, and has subsequently been found to be involved in ribosome biogenesis. NSR1 has three regions: an acidic/serine-rich NH2 terminus, two RNA recognition motifs, and a glycine/arginine-rich COOH terminus. In this study we show that NSR1 itself has a bipartite nuclear localization sequence. Deletion of either basic amino acid stretch results in the mislocation of NSR1 to the cytoplasm. We further demonstrate that either of two regions, the NH2 terminus or both RNA recognition motifs, are sufficient to localize a bacterial protein, beta-galactosidase, to the nucleolus. Intensive deletion analysis has further defined a specific acidic/serine-rich region within the NH2 terminus as necessary for nucleolar accumulation rather than nucleolar targeting. In addition, deletion of either RNA recognition motif or point mutations in one of the RNP consensus octamers results in the mislocalization of a fusion protein within the nucleus. Although the glycine/arginine-rich region in the COOH terminus is not sufficient to bring beta-galactosidase to the nucleolus, our studies show that this domain is necessary for nucleolar accumulation when an RNP consensus octamer in one of the RNA recognition motifs is mutated. Our findings are consistent with the notion that nucleolar localization is a result of the binding interactions of various domains of NSR1 within the nucleolus rather than the presence of a specific nucleolar targeting signal.

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Szczypiński, Filip T., Luca Gabrielli, and Christopher A. Hunter. "Emergent supramolecular assembly properties of a recognition-encoded oligoester." Chemical Science 10, no. 20 (2019): 5397–404. http://dx.doi.org/10.1039/c9sc01669d.

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An oligoester containing an alternating sequence of hydrogen bonding donor and acceptor side-chains forms a supramolecular architecture that resembles the kissing stem-loops motif found in folded RNA.

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Levine, T. D., F. Gao, P. H. King, L. G. Andrews, and J. D. Keene. "Hel-N1: an autoimmune RNA-binding protein with specificity for 3' uridylate-rich untranslated regions of growth factor mRNAs." Molecular and Cellular Biology 13, no. 6 (1993): 3494–504. http://dx.doi.org/10.1128/mcb.13.6.3494-3504.1993.

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We have investigated the RNA binding specificity of Hel-N1, a human neuron-specific RNA-binding protein, which contains three RNA recognition motifs. Hel-N1 is a human homolog of Drosophila melanogaster elav, which plays a vital role in the development of neurons. A random RNA selection procedure revealed that Hel-N1 prefers to bind RNAs containing short stretches of uridylates similar to those found in the 3' untranslated regions (3' UTRs) of oncoprotein and cytokine mRNAs such as c-myc, c-fos, and granulocyte macrophage colony-stimulating factor. Direct binding studies demonstrated that Hel-N1 bound and formed multimers with c-myc 3' UTR mRNA and required, as a minimum, a specific 29-nucleotide stretch containing AUUUG, AUUUA, and GUUUUU. Deletion analysis demonstrated that a fragment of Hel-N1 containing 87 amino acids, encompassing the third RNA recognition motif, forms an RNA binding domain for the c-myc 3' UTR. In addition, Hel-N1 was shown to be reactive with autoantibodies from patients with paraneoplastic encephalomyelitis both before and after binding to c-myc mRNA.

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Levine, T. D., F. Gao, P. H. King, L. G. Andrews, and J. D. Keene. "Hel-N1: an autoimmune RNA-binding protein with specificity for 3' uridylate-rich untranslated regions of growth factor mRNAs." Molecular and Cellular Biology 13, no. 6 (1993): 3494–504. http://dx.doi.org/10.1128/mcb.13.6.3494.

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We have investigated the RNA binding specificity of Hel-N1, a human neuron-specific RNA-binding protein, which contains three RNA recognition motifs. Hel-N1 is a human homolog of Drosophila melanogaster elav, which plays a vital role in the development of neurons. A random RNA selection procedure revealed that Hel-N1 prefers to bind RNAs containing short stretches of uridylates similar to those found in the 3' untranslated regions (3' UTRs) of oncoprotein and cytokine mRNAs such as c-myc, c-fos, and granulocyte macrophage colony-stimulating factor. Direct binding studies demonstrated that Hel-N1 bound and formed multimers with c-myc 3' UTR mRNA and required, as a minimum, a specific 29-nucleotide stretch containing AUUUG, AUUUA, and GUUUUU. Deletion analysis demonstrated that a fragment of Hel-N1 containing 87 amino acids, encompassing the third RNA recognition motif, forms an RNA binding domain for the c-myc 3' UTR. In addition, Hel-N1 was shown to be reactive with autoantibodies from patients with paraneoplastic encephalomyelitis both before and after binding to c-myc mRNA.

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Patel, Nikesh, Emma Wroblewski, German Leonov, et al. "Rewriting nature’s assembly manual for a ssRNA virus." Proceedings of the National Academy of Sciences 114, no. 46 (2017): 12255–60. http://dx.doi.org/10.1073/pnas.1706951114.

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Satellite tobacco necrosis virus (STNV) is one of the smallest viruses known. Its genome encodes only its coat protein (CP) subunit, relying on the polymerase of its helper virus TNV for replication. The genome has been shown to contain a cryptic set of dispersed assembly signals in the form of stem-loops that each present a minimal CP-binding motif AXXA in the loops. The genomic fragment encompassing nucleotides 1–127 is predicted to contain five such packaging signals (PSs). We have used mutagenesis to determine the critical assembly features in this region. These include the CP-binding motif, the relative placement of PS stem-loops, their number, and their folding propensity. CP binding has an electrostatic contribution, but assembly nucleation is dominated by the recognition of the folded PSs in the RNA fragment. Mutation to remove all AXXA motifs in PSs throughout the genome yields an RNA that is unable to assemble efficiently. In contrast, when a synthetic 127-nt fragment encompassing improved PSs is swapped onto the RNA otherwise lacking CP recognition motifs, assembly is partially restored, although the virus-like particles created are incomplete, implying that PSs outside this region are required for correct assembly. Swapping this improved region into the wild-type STNV1 sequence results in a better assembly substrate than the viral RNA, producing complete capsids and outcompeting the wild-type genome in head-to-head competition. These data confirm details of the PS-mediated assembly mechanism for STNV and identify an efficient approach for production of stable virus-like particles encapsidating nonnative RNAs or other cargoes.

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Romac, J. M., D. H. Graff, and J. D. Keene. "The U1 small nuclear ribonucleoprotein (snRNP) 70K protein is transported independently of U1 snRNP particles via a nuclear localization signal in the RNA-binding domain." Molecular and Cellular Biology 14, no. 7 (1994): 4662–70. http://dx.doi.org/10.1128/mcb.14.7.4662-4670.1994.

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Expression of the recombinant human U1-70K protein in COS cells resulted in its rapid transport to the nucleus, even when binding to U1 RNA was debilitated. Deletion analysis of the U1-70K protein revealed the existence of two segments of the protein which were independently capable of nuclear localization. One nuclear localization signal (NLS) was mapped within the U1 RNA-binding domain and consists of two typically separated but interdependent elements. The major element of this NLS resides in structural loop 5 between the beta 4 strand and the alpha 2 helix of the folded RNA recognition motif. The C-terminal half of the U1-70K protein which was capable of nuclear entry contains two arginine-rich regions, which suggests the existence of a second NLS. Site-directed mutagenesis of the RNA recognition motif NLS demonstrated that the U1-70K protein can be transported independently of U1 RNA and that its association with the U1 small nuclear ribonucleoprotein particle can occur in the nucleus.

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40

Romac, J. M., D. H. Graff, and J. D. Keene. "The U1 small nuclear ribonucleoprotein (snRNP) 70K protein is transported independently of U1 snRNP particles via a nuclear localization signal in the RNA-binding domain." Molecular and Cellular Biology 14, no. 7 (1994): 4662–70. http://dx.doi.org/10.1128/mcb.14.7.4662.

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Abstract:

Expression of the recombinant human U1-70K protein in COS cells resulted in its rapid transport to the nucleus, even when binding to U1 RNA was debilitated. Deletion analysis of the U1-70K protein revealed the existence of two segments of the protein which were independently capable of nuclear localization. One nuclear localization signal (NLS) was mapped within the U1 RNA-binding domain and consists of two typically separated but interdependent elements. The major element of this NLS resides in structural loop 5 between the beta 4 strand and the alpha 2 helix of the folded RNA recognition motif. The C-terminal half of the U1-70K protein which was capable of nuclear entry contains two arginine-rich regions, which suggests the existence of a second NLS. Site-directed mutagenesis of the RNA recognition motif NLS demonstrated that the U1-70K protein can be transported independently of U1 RNA and that its association with the U1 small nuclear ribonucleoprotein particle can occur in the nucleus.

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Coburn, Katherine, Zephan Melville, Ehson Aligholizadeh, et al. "Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif." Acta Crystallographica Section F Structural Biology Communications 73, no. 4 (2017): 209–14. http://dx.doi.org/10.1107/s2053230x17003454.

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The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growthviathe coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e.hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein–nucleic acid interactions. This structure helps to serve as a foundation for biophysical studies of this RNA-binding protein and structure-based drug-design efforts for targeting hnRNP A18 in cancer, such as malignant melanoma, where hnRNP A18 levels are elevated and contribute to disease progression.

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de Beauchene, Isaure Chauvot, Sjoerd J. de Vries, and Martin Zacharias. "Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins." Nucleic Acids Research 44, no. 10 (2016): 4565–80. http://dx.doi.org/10.1093/nar/gkw328.

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Cassola, Alejandro, and Alberto C. Frasch. "An RNA Recognition Motif Mediates the Nucleocytoplasmic Transport of a Trypanosome RNA-binding Protein." Journal of Biological Chemistry 284, no. 50 (2009): 35015–28. http://dx.doi.org/10.1074/jbc.m109.031633.

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Manival, X. "RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins." Nucleic Acids Research 29, no. 11 (2001): 2223–33. http://dx.doi.org/10.1093/nar/29.11.2223.

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Fushimi, Kazuo, Shizuka Uchida, Ryousuke Matsushita, and Toshifumi Tsukahara. "Prediction of tertiary structure of NSSRs’ RNA recognition motif and the RNA binding activity." Science and Technology of Advanced Materials 6, no. 5 (2005): 475–83. http://dx.doi.org/10.1016/j.stam.2005.02.023.

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Qin, Xiaojian, Qi Huang, Linlin Zhu, et al. "Interaction with Cu2+ disrupts the RNA binding affinities of RNA recognition motif containing protein." Biochemical and Biophysical Research Communications 444, no. 2 (2014): 116–20. http://dx.doi.org/10.1016/j.bbrc.2014.01.006.

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Naeeni, Amir R., Maria R. Conte, and Mark A. Bayfield. "RNA Chaperone Activity of Human La Protein Is Mediated by Variant RNA Recognition Motif." Journal of Biological Chemistry 287, no. 8 (2011): 5472–82. http://dx.doi.org/10.1074/jbc.m111.276071.

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Hendrix, Donna K., Steven E. Brenner, and Stephen R. Holbrook. "RNA structural motifs: building blocks of a modular biomolecule." Quarterly Reviews of Biophysics 38, no. 3 (2005): 221–43. http://dx.doi.org/10.1017/s0033583506004215.

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1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2 RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition motifs 2242.5 Tools for identifying and classifying elements and motifs 2263. Types of RNA structural motifs 2283.1 Helices 2283.2 Hairpin loops 2283.3 Internal loops 2303.4 Junction loops/multiloops 2303.5 Binding motifs 2323.5.1 Metal binding 2323.5.2 Natural and selected aptamers 2343.6 Tertiary interactions 2344. Future directions 2365. Acknowledgments 2396. References 239RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common ‘structural elements’. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.

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Takagaki, Y., and J. L. Manley. "RNA recognition by the human polyadenylation factor CstF." Molecular and Cellular Biology 17, no. 7 (1997): 3907–14. http://dx.doi.org/10.1128/mcb.17.7.3907.

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Polyadenylation of mammalian mRNA precursors requires at least two signal sequences in the RNA: the nearly invariant AAUAAA, situated 5' to the site of polyadenylation, and a much more variable GU- or U-rich downstream element. At least some downstream sequences are recognized by the heterotrimeric polyadenylation factor CstF, although how, and indeed if, all variations of this diffuse element are bound by a single factor is unknown. Here we show that the RNP-type RNA binding domain of the 64-kDa subunit of CstF (CstF-64) (64K RBD) is sufficient to define a functional downstream element. Selection-amplification (SELEX) experiments employing a glutathione S-transferase (GST)-64K RBD fusion protein selected GU-rich sequences that defined consensus recognition motifs closely matching those present in natural poly(A) sites. Selected sequences were bound specifically, and with surprisingly high affinities, by intact CstF and were functional in reconstituted, CstF-dependent cleavage assays. Our results also indicate that GU- and U-rich sequences are variants of a single CstF recognition motif. For comparison, SELEX was performed with a GST fusion containing the RBD from the apparent yeast homolog of CstF-64, RNA15. Strikingly, although the two RBDs are almost 50% identical and yeast poly(A) signals are at least as degenerate as the mammalian downstream element, a nearly invariant 12-base U-rich sequence distinct from the CstF-64 consensus was identified. We discuss these results in terms of the function and evolution of mRNA 3'-end signals.

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Kim, Henry S., Yuki Kuwano, Ming Zhan, et al. "Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR." Molecular and Cellular Biology 27, no. 19 (2007): 6806–17. http://dx.doi.org/10.1128/mcb.01036-07.

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ABSTRACT The RNA-binding protein TIAR (related to TIA-1 [T-cell-restricted intracellular antigen 1]) was shown to associate with subsets of mRNAs bearing U-rich sequences in their 3′ untranslated regions. TIAR can function as a translational repressor, particularly in response to cytotoxic agents. Using unstressed colon cancer cells, collections of mRNAs associated with TIAR were isolated by immunoprecipitation (IP) of (TIAR-RNA) ribonucleoprotein (RNP) complexes, identified by microarray analysis, and used to elucidate a common signature motif present among TIAR target transcripts. The predicted TIAR motif was an unexpectedly cytosine-rich, 28- to 32-nucleotide-long element forming a stem and a loop of variable size with an additional side loop. The ability of TIAR to bind an RNA oligonucleotide with a representative C-rich TIAR motif sequence was verified in vitro using surface plasmon resonance. By this analysis, TIAR containing two or three RNA recognition domains (TIAR12 and TIAR123) showed low but significant binding to the C-rich sequence. In vivo, insertion of the C-rich motif into a heterologous reporter strongly suppressed its translation in cultured cells. Using this signature motif, an additional ∼2,209 UniGene targets were identified (2.0% of the total UniGene database). A subset of specific mRNAs were validated by RNP IP analysis. Interestingly, in response to treatment with short-wavelength UV light (UVC), a stress agent causing DNA damage, each of these target mRNAs bearing C-rich motifs dissociated from TIAR. In turn, expression of the encoded proteins was elevated in a TIAR-dependent manner. In sum, we report the identification of a C-rich signature motif present in TIAR target mRNAs whose association with TIAR decreases following exposure to a stress-causing agent.

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Journal articles on the topic 'RNA recognition motif'

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