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Ovari I, Viczjan G, Erdei T, Takacs B, Tarjanyi V, Zsuga J, Szucs M, Szilvassy Z, Juhasz B, Gesztelyi R. The influence of the way of regression on the results obtained by the receptorial responsiveness method ( RRM), a procedure to estimate a change in the concentration of a pharmacological agonist near the receptor. Front Pharmacol 2024; 15:1375955. [PMID: 38756379 PMCID: PMC11096549 DOI: 10.3389/fphar.2024.1375955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
The receptorial responsiveness method (RRM) enables the estimation of a change in concentration of an (even degradable) agonist, near its receptor, via curve fitting to (at least) two concentration-effect (E/c) curves of a stable agonist. One curve should be generated before this change, and the other afterwards, in the same system. It follows that RRM yields a surrogate parameter ("cx") as the concentration of the stable agonist being equieffective with the change in concentration of the other agonist. However, regression can be conducted several ways, which can affect the accuracy, precision and ease-of-use. This study utilized data of previous ex vivo investigations. Known concentrations of stable agonists were estimated with RRM by performing individual (local) or global fitting, this latter with one or two model(s), using a logarithmic (logcx) or a nonlogarithmic (cx) parameter (the latter in a complex or in a simplified equation), with ordinary least-squares or robust regression, and with an "all-at-once" or "pairwise" fitting manner. We found that the simplified model containing logcx was superior to all alternative models. The most complicated individual regression was the most accurate, followed closely by the moderately complicated two-model global regression and then by the easy-to-perform one-model global regression. The two-model global fitting was the most precise, followed by the individual fitting (closely) and by the one-model global fitting (from afar). Pairwise fitting (two E/c curves at once) improved the estimation. Thus, the two-model global fitting, performed pairwise, and the individual fitting are recommended for RRM, using the simplified model containing logcx.
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Affiliation(s)
- Ignac Ovari
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- University of Debrecen, Doctoral School of Nutrition and Food Sciences, Debrecen, Hungary
| | - Gabor Viczjan
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamas Erdei
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Barbara Takacs
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Vera Tarjanyi
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Judit Zsuga
- Department of Psychiatry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Miklos Szucs
- Department of Urology and Andrology, Kenezy Gyula Campus, University of Debrecen, Debrecen, Hungary
| | - Zoltan Szilvassy
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bela Juhasz
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Rudolf Gesztelyi
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Liu Q, Zhang Y, Chen J, Sun C, Huang M, Che M, Li C, Lin S. An improved Deeplab V3+ network based coconut CT image segmentation method. Front Plant Sci 2023; 14:1139666. [PMID: 38148865 PMCID: PMC10749967 DOI: 10.3389/fpls.2023.1139666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023]
Abstract
Due to the unique structure of coconuts, their cultivation heavily relies on manual experience, making it difficult to accurately and timely observe their internal characteristics. This limitation severely hinders the optimization of coconut breeding. To address this issue, we propose a new model based on the improved architecture of Deeplab V3+. We replace the original ASPP(Atrous Spatial Pyramid Pooling) structure with a dense atrous spatial pyramid pooling module and introduce CBAM(Convolutional Block Attention Module). This approach resolves the issue of information loss due to sparse sampling and effectively captures global features. Additionally, we embed a RRM(residual refinement module) after the output level of the decoder to optimize boundary information between organs. Multiple model comparisons and ablation experiments are conducted, demonstrating that the improved segmentation algorithm achieves higher accuracy when dealing with diverse coconut organ CT(Computed Tomography) images. Our work provides a new solution for accurately segmenting internal coconut organs, which facilitates scientific decision-making for coconut researchers at different stages of growth.
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Affiliation(s)
- Qianfan Liu
- School of Computer Science and Technology, Hainan University, Haikou, China
| | - Yu Zhang
- School of Computer Science and Technology, Hainan University, Haikou, China
| | - Jing Chen
- Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Chengxu Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Mengxing Huang
- School of Information and Communication Engineering, Hainan University, Haikou, China
| | - Mingwei Che
- School of Information and Communication Engineering, Hainan University, Haikou, China
| | - Chun Li
- School of Information and Communication Engineering, Hainan University, Haikou, China
| | - Shenghuang Lin
- Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
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Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. Epigenomes 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
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Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
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Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
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Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
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Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn CD, Cheng X, Jiang YX, Zhou ZH, Feigon J. Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR. J Mol Biol 2023; 435:168044. [PMID: 37330293 PMCID: PMC10988774 DOI: 10.1016/j.jmb.2023.168044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains-N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65-TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65-TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65-TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.
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Affiliation(s)
- Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yao He
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yanjiao Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Mahavir Singh
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Xinyi Cheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Yi Xiao Jiang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA.
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Chowdhury MN, Chen X, Jin H. An intrinsically Disordered RNA Binding Protein Modulates mRNA Translation and Storage. bioRxiv 2023:2023.05.22.541713. [PMID: 37293096 PMCID: PMC10245857 DOI: 10.1101/2023.05.22.541713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many proteins with intrinsically disordered regions interact with cytoplasmic ribosomes. However, many of the molecular functions related to these interactions are unclear. In this study, using an abundant RNA-binding protein with a structurally well-defined RNA recognition motif and an intrinsically disordered RGG domain as a model system, we investigated how this protein modulates mRNA storage and translation. Using genomic and molecular approaches, we show that the presence of Sbp1 slows ribosome movement on cellular mRNAs and promotes polysome stalling. Sbp1-associated polysomes display a ring-shaped structure in addition to a beads-on-string morphology visualized under electron microscope. Moreover, post-translational modifications at the RGG motif play important roles in directing cellular mRNAs to either translation or storage. Finally, binding of Sbp1 to the 5'UTRs of mRNAs represses both cap-dependent and cap-independent translation initiation of proteins functionally important for general protein synthesis in the cell. Taken together, our study demonstrates an intrinsically disordered RNA binding protein regulates mRNA translation and storage via distinctive mechanisms under physiological conditions and establishes a framework with which functions of important RGG-proteins can be investigated and defined.
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Affiliation(s)
- Mashiat N. Chowdhury
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
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7
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Kumari S, Deka B, Singh KK. Serine-rich domain of RNPS1 functions in activation of alternative splicing. Genes Cells 2023. [PMID: 37204171 DOI: 10.1111/gtc.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/06/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
RNA-binding protein with serine-rich domain 1 (RNPS1) gets deposited on the mRNA during the process of splicing and concomitantly associates with the exon junction complex (EJC). RNPS1 participates in post-transcriptional gene regulation, including constitutive and alternative splicing, transcriptional regulation and nonsense-mediated mRNA decay. In this study, we found that the tethering of RNPS1 or its isolated serine-rich domain (S domain) causes exon inclusion of an HIV-1 splicing substrate. In contrast, overexpressing the RRM domain of RNPS1 acts in a dominant negative manner and leads to the exon skipping of endogenous apoptotic pre-mRNAs (Bcl-X and MCL-1). Further, tethering of core EJC proteins, eIF4A3, MAGOH, or Y14, does not lead to exon inclusion of an HIV substrate. Together, our results demonstrate how RNPS1 and its domains are differentially involved in alternative splicing activity.
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Affiliation(s)
- Sweta Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Bhagyashree Deka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Wang L, Shao TC, Wang CY, Li JJ, Jian SQ, Wang D, Cheng BF. Influence of RRM, RGG and Potential Phosphorylated Sites in Cold-Inducible Protein RBM3 on its Subcellular Localization and Neuroprotective Effects. FRONT BIOSCI-LANDMRK 2023; 28:24. [PMID: 36866549 DOI: 10.31083/j.fbl2802024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 02/12/2023]
Abstract
BACKGROUND As a potent mediator of hypothermic neuroprotection, the cold-inducible protein RBM3 is characterized with one RNA-recognition motifs (RRM) and one arginine-glycine-rich (RGG) domain. It is known that these conserved domains are required for nuclear localization in some RNA-binding proteins. However, little is known about the actual role of RRM and RGG domains in subcellular localization of RBM3. METHODS To clarify it, various mutants of human Rbm3 gene were constructed. Plasmids were transfected into cells and the localization of RBM3 protein and its varias mutants in cells and role in neuroprotection. RESULTS In human neuroblastoma SH-SY5Y cells, either a truncation of RRM domain (aa 1-86) or RGG domain (aa 87-157) led to an obvious cytoplasmic distribution, compared to a predominant nuclear localization of whole RBM3 protein (aa 1-157). In contrast, mutants in several potential phosphorylated sites of RBM3, including Ser102, Tyr129, Ser147, and Tyr155, did not alter the nuclear localization of RBM3. Similarly, mutants in two Di-RGG motif sites also did not affect the subcellular distribution of RBM3. Lastly, the role of Di-RGG motif in RGG domains was further investigated. The mutant of double arginines in either Di-RGG motif-1 (Arg87/90) or -2 (Arg99/105) exhibited a higher cytoplasmic localization, indicating that both Di-RGG motifs are required for nucleic localization of RBM3. CONCLUSIONS Our data suggest that RRM and RGG domains are both required for the nuclear localization of RBM3, with two Di-RGG domain being crucial for nucleocytoplasmic shuttling of RBM3.
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Affiliation(s)
- Lei Wang
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Tian-Ci Shao
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Chun-Ying Wang
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Jing-Jing Li
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Shao-Qin Jian
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Duo Wang
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
| | - Bin-Feng Cheng
- College of Life Science and Technology, Xinxiang Medical University, 453003 Xinxiang, Henan, China
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (Bethesda) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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Sharma N, Osman C. Yme2, a putative RNA recognition motif and AAA+ domain containing protein, genetically interacts with the mitochondrial protein export machinery. Biol Chem 2022; 403:807-817. [PMID: 35100666 PMCID: PMC9284673 DOI: 10.1515/hsz-2021-0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 02/04/2023]
Abstract
The mitochondrial respiratory chain is composed of nuclear as well as mitochondrial-encoded subunits. A variety of factors mediate co-translational integration of mtDNA-encoded proteins into the inner membrane. In Saccharomyces cerevisiae, Mdm38 and Mba1 are ribosome acceptors that recruit the mitochondrial ribosome to the inner membrane, where the insertase Oxa1, facilitates membrane integration of client proteins. The protein Yme2 has previously been shown to be localized in the inner mitochondrial membrane and has been implicated in mitochondrial protein biogenesis, but its mode of action remains unclear. Here, we show that multiple copies of Yme2 assemble into a high molecular weight complex. Using a combination of bioinformatics and mutational analyses, we find that Yme2 possesses an RNA recognition motif (RRM), which faces the mitochondrial matrix and a AAA+ domain that is located in the intermembrane space. We further show that YME2 genetically interacts with MDM38, MBA1 and OXA1, which links the function of Yme2 to the mitochondrial protein biogenesis machinery.
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Affiliation(s)
- Nupur Sharma
- Faculty of Biology, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
- Graduate School of Life Sciences, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
- Graduate School of Life Sciences, Ludwig Maximilian University Munich, D-82152Planegg-Martinsried, Germany
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Kufel-Grabowska J, Podolak A, Maliszewski D, Bartoszkiewicz M, Ramlau R, Lukaszuk K. Fertility Counseling in BRCA1/2-Mutated Women with Breast Cancer and Healthy Individuals. J Clin Med 2022; 11:jcm11143996. [PMID: 35887761 PMCID: PMC9321124 DOI: 10.3390/jcm11143996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/27/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer worldwide and the fifth leading cause of cancer death. In 2020, there were 2.3 million new cases, and 685,000 women died from it. Breast cancer among young women under 40 years of age accounts for 5% to 10% of all cases of this cancer. The greater availability of multi-gene sequence analysis by next-generation sequencing has improved diagnosis and, consequently, the possibility of using appropriate therapeutic approaches in BRCA1/2 gene mutation carriers. Treatment of young breast cancer patients affects their reproductive potential by reducing ovarian reserve. It can lead to reversible or permanent premature menopause, decreased libido, and other symptoms of sex hormone deficiency. This requires that, in addition to oncological treatment, patients are offered genetic counseling, oncofertility, psychological assistance, and sexological counseling. Given the number of BRCA1/2 gene mutation carriers among young breast cancer patients, but also thanks to growing public awareness, among their healthy family members planning offspring, the possibility of benefiting from preimplantation testing and performing cancer-risk-reduction procedures: RRM (risk-reducing mastectomy) and RRSO (risk-reducing salpingo-oophorectomy) significantly increase the chance of a genetically burdened person living a healthy life and giving birth to a child not burdened by the parent's germline mutation. The goal of this paper is to show methods and examples of fertility counselling for BRCA1/2 gene mutation carriers, including both patients already affected by cancer and healthy individuals.
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Affiliation(s)
- Joanna Kufel-Grabowska
- Department of Oncology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (J.K.-G.); (R.R.)
| | - Amira Podolak
- Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-210 Gdansk, Poland; (A.P.); (K.L.)
| | - Daniel Maliszewski
- Department of General and Oncological Surgery, Wojewódzki Szpital Specjalistyczny im. Janusza Korczaka w Słupsku Sp. z o.o., 76-200 Słupsk, Poland;
- Department of General and Oncological Surgery at Specialist Hospital in Koscierzyn, Sp.z.o.o., 83-400 Kościerzyna, Poland
- Swissmed Health Center, 80-210 Gdansk, Poland
| | - Mikołaj Bartoszkiewicz
- Department of Immunobiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence: ; Tel.: +48-61-854-76-53
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (J.K.-G.); (R.R.)
| | - Krzysztof Lukaszuk
- Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-210 Gdansk, Poland; (A.P.); (K.L.)
- Invicta Research and Development Center, 81-740 Sopot, Poland
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12
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He F, Kuwasako K, Takizawa M, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Güntert P, Shirouzu M, Yokoyama S, Muto Y. 1H, 13C and 15N resonance assignments and solution structures of the two RRM domains of Matrin-3. Biomol NMR Assign 2022; 16:41-49. [PMID: 34783967 DOI: 10.1007/s12104-021-10057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Matrin-3 is a multifunctional protein that binds to both DNA and RNA. Its DNA-binding activity is linked to the formation of the nuclear matrix and transcriptional regulation, while its RNA-binding activity is linked to mRNA metabolism including splicing, transport, stabilization, and degradation. Correspondingly, Matrin-3 has two zinc finger domains for DNA binding and two consecutive RNA recognition motif (RRM) domains for RNA binding. Matrin-3 has been reported to cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) when its disordered region contains pathogenic mutations. Simultaneously, it has been shown that the RNA-binding activity of Matrin-3 mediated by its RRM domains, affects the formation of insoluble cytoplasmic granules, which are related to the pathogenic mechanism of ALS/FTD. Thus, the effect of the RRM domains on the phase separation of condensed protein/RNA mixtures has to be clarified for a comprehensive understanding of ALS/FTD. Here, we report the 1H, 15N, and 13C resonance assignments of the two RNA binding domains and their solution structures. The resonance assignments and the solution structures obtained in this work will contribute to the elucidation of the molecular basis of Matrin-3 in the pathogenic mechanism of ALS and/or FTD.
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Affiliation(s)
- Fahu He
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kanako Kuwasako
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Masayuki Takizawa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Mari Takahashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kengo Tsuda
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takashi Nagata
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Satoru Watanabe
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
| | - Yutaka Muto
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
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13
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Szarkowska J, Cwiek P, Szymanski M, Rusetska N, Jancewicz I, Stachowiak M, Swiatek M, Luba M, Konopinski R, Kubala S, Zub R, Kucharz J, Wiechno P, Siedlecki JA, Markowicz S, Sarnowska E, Sarnowski TJ. RRM2 gene expression depends on BAF180 subunit of SWISNF chromatin remodeling complex and correlates with abundance of tumor infiltrating lymphocytes in ccRCC. Am J Cancer Res 2021; 11:5965-5978. [PMID: 35018236 PMCID: PMC8727810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023] Open
Abstract
About 40% of clear cell renal cell carcinoma (ccRCC) cases carry the pbrm1 mutation inactivating BAF180 subunit of the SWI/SNF chromatin remodeling complex (CRC). Here we show that the majority of transcriptomic changes appear at the stage I of ccRCC development. By contrast, the stage II ccRCC exhibits hyperactivation of DNA replication demonstrated by the overexpression of several genes, e.g., RRM1 and RRM2 genes encoding subunits of ribonucleotide reductase (RNR) complex. We found that the degree of RRM1 and RRM2 upregulation in ccRCC patients depends on pbrm1 mutation. We show that the BAF180 protein product of the PBRM1 gene directly binds to RRM1 and RRM2 loci. The BAF180 binding regions are targeted by regulatory proteins previously reported as SWI/SNF CRC interacting partners. BAF180 binding to RRMs loci correlates with enrichment of H3K27me3 in case of RRM1 and H3K14Ac on RRM2, indicating the existence of differential regulatory mechanism controlling expression of these genes. We found that the strong overexpression of RRM2 in ccRCC patient samples correlates with T cell infiltration. Surprisingly, the majority of tumor infiltrating lymphocytes (TILs) consisted of CD4+ T cells. Furthermore, we show that exhausted CD4+ T cells induced the expression of the RRM2 gene in the primary ccRCC cell line. Collectively, our results provide the link between PBRM1 loss, RRM2 expression and T cell infiltration, which may lead to the establishment of new treatment of this disease.
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Affiliation(s)
- Joanna Szarkowska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Pawel Cwiek
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Michal Szymanski
- Department of Urology and Urological Oncology, Central Clinical Hospital of Ministry of the Interior and Administration in WarsawWarsaw, Poland
| | - Natalia Rusetska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Iga Jancewicz
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Malgorzata Stachowiak
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Monika Swiatek
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Maciej Luba
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Ryszard Konopinski
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Renata Zub
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Jakub Kucharz
- Department of Uro-oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Pawel Wiechno
- Department of Uro-oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Sergiusz Markowicz
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Elzbieta Sarnowska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of OncologyWarsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
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14
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Wang Z, Collier M, Benesch J. Aggregation in the spotlight. eLife 2021; 10:73586. [PMID: 34636721 PMCID: PMC8510577 DOI: 10.7554/elife.73586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022] Open
Abstract
New findings clarify apparently conflicting results about how molecular agents that preserve protein integrity prevent harmful, dense aggregates from forming.
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Affiliation(s)
- Zihao Wang
- Department of Chemistry, Oxford University, Oxford, United Kingdom
| | - Miranda Collier
- Department of Biology, Stanford University, Stanford, United States
| | - Justin Benesch
- Department of Chemistry, Oxford University, Oxford, United Kingdom
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15
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Boczek EE, Fürsch J, Niedermeier ML, Jawerth L, Jahnel M, Ruer-Gruß M, Kammer KM, Heid P, Mediani L, Wang J, Yan X, Pozniakovski A, Poser I, Mateju D, Hubatsch L, Carra S, Alberti S, Hyman AA, Stengel F. HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA-binding domain. eLife 2021; 10:69377. [PMID: 34487489 PMCID: PMC8510580 DOI: 10.7554/elife.69377] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant liquid-to-solid phase transitions of biomolecular condensates have been linked to various neurodegenerative diseases. However, the underlying molecular interactions that drive aging remain enigmatic. Here, we develop quantitative time-resolved crosslinking mass spectrometry to monitor protein interactions and dynamics inside condensates formed by the protein fused in sarcoma (FUS). We identify misfolding of the RNA recognition motif of FUS as a key driver of condensate aging. We demonstrate that the small heat shock protein HspB8 partitions into FUS condensates via its intrinsically disordered domain and prevents condensate hardening via condensate-specific interactions that are mediated by its α-crystallin domain (αCD). These αCD-mediated interactions are altered in a disease-associated mutant of HspB8, which abrogates the ability of HspB8 to prevent condensate hardening. We propose that stabilizing aggregation-prone folded RNA-binding domains inside condensates by molecular chaperones may be a general mechanism to prevent aberrant phase transitions.
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Affiliation(s)
- Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Julius Fürsch
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie Laura Niedermeier
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Louise Jawerth
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Martine Ruer-Gruß
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai-Michael Kammer
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Peter Heid
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jie Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Pozniakovski
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lars Hubatsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Florian Stengel
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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16
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Abstract
Mutations in the FUS gene cause amyotrophic lateral sclerosis (ALS-FUS). However, the exact pathogenic mechanism of mutant fused in sarcoma (FUS) protein is not completely understood. FUS is an RNA binding protein (RBP) localized predominantly in the nucleus, but ALS-linked FUS mutations can affect its nuclear localization signal impairing its import into the nucleus. This mislocalization to the cytoplasm facilitates FUS aggregation in cytoplasmic inclusions. Therapies targeting post translational modifications are rising as new treatments for ALS, in particular acetylation which could have a role in the dynamics of RBPs. Research using histone deacetylase (HDAC) inhibitors in FUS-ALS models showed that HDACs can influence cytoplasmic FUS localization. Inhibition of HDACs could promote acetylation of the FUS RNA binding domain (RRM) and altering its RNA interactions resulting in FUS maintenance in the nucleus. In addition, acetylation of FUS RRMs might also favor or disfavor its incorporation into pathological inclusions. In this review, we summarize and discuss the evidence for the potential role of HDACs in the context of FUS-ALS and we propose a new hypothesis based on this overview.
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Affiliation(s)
- Clara Tejido
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Donya Pakravan
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,Department of Neurosciences, Experimental Neurology, Leuven Brain Institute, Katholieke Universiteit Leuven (KU Leuven)-University of Leuven, Leuven, Belgium
| | - Ludo Van Den Bosch
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,Department of Neurosciences, Experimental Neurology, Leuven Brain Institute, Katholieke Universiteit Leuven (KU Leuven)-University of Leuven, Leuven, Belgium
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17
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Grandi G, Boggio Sola V, Cortesi L, Toss A, Giuliani GA, Del Savio MC, Facchinetti F. BRCA mutation carriers' perceptions on postmenopausal hormone therapy: An Italian study. Psychooncology 2021; 30:1711-1719. [PMID: 34002428 PMCID: PMC8518789 DOI: 10.1002/pon.5714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022]
Abstract
Objective To evaluate the actual perceptions of postmenopausal hormone therapy (HT) in BRCA mutation carriers (BRCAmc) in comparison with women from the general population. Methods Questionnaire‐based study of 83 BRCAmc and a control group of 89 women without a genetic mutation. Perceptions were evaluated by specific questions and Likert scales (−5–+5). Results Present and past users of HT were more frequent in the control group (p = 0.01), with a longer time of use (p = 0.03). The preferred route of administration of HT was ‘oral’ (54.6%). The most frequently reported adverse effect of HT was venous thrombosis (0.8), while a protective effect on bone health was reported. No noticeable beneficial effects of HT have been recognised for hot flushes (0.2) and vaginal dryness (0.1). The most frequently perceived beneficial and adverse effects of HT were not significantly different between BRCA mutation carriers and controls. The greatest oncological fear was breast cancer (1.0). The protective role of HT on colorectal cancer was not known (0.1). These oncological impacts were mostly overestimated in BRCAmc, however this was not significant. Few BRCAmc would think of taking HT after risk‐reducing surgeries. Conclusions Knowledge of the effects of HT on BRCAmc is relatively poor and they are likely to overstate its negative effects and underestimate its health benefits; however, this is not significant in comparison to the general population. More and better information should be given to BRCAmc to allow them to make informed decisions about the use of HT, especially before undergoing risk‐reducing surgeries.
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Affiliation(s)
- Giovanni Grandi
- Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Valentina Boggio Sola
- Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Laura Cortesi
- Department of Oncology, Haematology and Respiratory Disease, Azienda Ospedaliero-Universitaria di Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Angela Toss
- Department of Oncology, Haematology and Respiratory Disease, Azienda Ospedaliero-Universitaria di Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Andrea Giuliani
- Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Maria Chiara Del Savio
- Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Fabio Facchinetti
- Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
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18
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Abstract
La-Related Protein 1 (LARP1) is an RNA-binding protein that regulates the stability and translation of mRNAs encoding the translation machinery, including ribosomal proteins and translation factors. These mRNAs are characterized by a 5'-terminal oligopyrimidine (TOP) motif that coordinates their temporal and stoichiometric expression. While LARP1 represses TOP mRNA translation via the C-terminal DM15 region, the role of the N-terminal La-Module in the recognition and translational regulation of TOP mRNAs remains elusive. Herein we show that the LARP1 La-Module also binds TOP motifs, although in a cap-independent manner. We also demonstrate that it recognizes poly(A) RNA. Further, our data reveal that the LARP1 La-Module can simultaneously engage TOP motifs and poly(A) RNA. These results evoke an intriguing molecular mechanism whereby LARP1 could regulate translation and stabilization of TOP transcripts.
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Affiliation(s)
- Hiba A. Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney M. Rubottom
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas C. Leeper
- Department of Chemistry & Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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19
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Basu R, Eichhorn CD, Cheng R, Peterson RD, Feigon J. Structure of S. pombe telomerase protein Pof8 C-terminal domain is an x RRM conserved among LARP7 proteins. RNA Biol 2020; 18:1181-1192. [PMID: 33131423 DOI: 10.1080/15476286.2020.1836891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein complex that maintains the telomeric DNA at eukaryotic chromosome ends. p65 is important for the ordered assembly of telomerase RNA (TER) with telomerase reverse transcriptase. Unexpectedly, Schizosaccharomyces pombe Pof8 was recently identified as a LARP7 protein and a core component of fission yeast telomerase essential for biogenesis. LARP7 proteins have a conserved N-terminal La motif and RRM1 (La module) and C-terminal RRM2 with specific RNA substrate recognition attributed to RRM2, first structurally characterized in p65 as an atypical RRM named xRRM. Here we present the X-ray crystal structure and NMR studies of S. pombe Pof8 RRM2. Sequence and structure comparison of Pof8 RRM2 to p65 and human Larp7 xRRMs reveals conserved features for RNA binding with the main variability in the length of the non-canonical helix α3. This study shows that Pof8 has conserved xRRM features, providing insight into TER recognition and the defining characteristics of the xRRM.
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Affiliation(s)
- Ritwika Basu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ryan Cheng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert D Peterson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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20
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Lenzen B, Rühle T, Lehniger MK, Okuzaki A, Labs M, Muino JM, Ohler U, Leister D, Schmitz-Linneweber C. The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. Int J Mol Sci 2020; 21:E5633. [PMID: 32781615 DOI: 10.3390/ijms21165633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 01/15/2023] Open
Abstract
Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.
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21
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Müntjes K, Philipp M, Hüsemann L, Heucken N, Weidtkamp-Peters S, Schipper K, Zurbriggen MD, Feldbrügge M. Establishing Polycistronic Expression in the Model Microorganism Ustilago maydis. Front Microbiol 2020; 11:1384. [PMID: 32670239 PMCID: PMC7326815 DOI: 10.3389/fmicb.2020.01384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic microorganisms use monocistronic mRNAs to encode proteins. For synthetic biological approaches like metabolic engineering, precise co-expression of several proteins in space and time is advantageous. A straightforward approach is the application of viral 2A peptides to design synthetic polycistronic mRNAs in eukaryotes. During translation of these peptides the ribosome stalls, the peptide chain is released and the ribosome resumes translation. Thus, two independent polypeptide chains can be encoded from a single mRNA when a 2A peptide sequence is placed inbetween the two open reading frames. Here, we establish such a system in the well-studied model microorganism Ustilago maydis. Using two fluorescence reporter proteins, we compared the activity of five viral 2A peptides. Their activity was evaluated in vivo using fluorescence microscopy and validated using fluorescence resonance energy transfer (FRET). Activity ranged from 20 to 100% and the best performing 2A peptide was P2A from porcine teschovirus-1. As proof of principle, we followed regulated gene expression efficiently over time and synthesised a tri-cistronic mRNA encoding biosynthetic enzymes to produce mannosylerythritol lipids (MELs). In essence, we evaluated 2A peptides in vivo and demonstrated the applicability of 2A peptide technology for U. maydis in basic and applied science.
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Affiliation(s)
- Kira Müntjes
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Magnus Philipp
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisa Hüsemann
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicole Heucken
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Kerstin Schipper
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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22
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Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
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Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
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23
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Rodoshi RT, Kim T, Choi W. Resource Management in Cloud Radio Access Network: Conventional and New Approaches. Sensors (Basel) 2020; 20:E2708. [PMID: 32397540 DOI: 10.3390/s20092708] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 11/22/2022]
Abstract
Cloud radio access network (C-RAN) is a promising mobile wireless sensor network architecture to address the challenges of ever-increasing mobile data traffic and network costs. C-RAN is a practical solution to the strict energy-constrained wireless sensor nodes, often found in Internet of Things (IoT) applications. Although this architecture can provide energy efficiency and reduce cost, it is a challenging task in C-RAN to utilize the resources efficiently, considering the dynamic real-time environment. Several research works have proposed different methodologies for effective resource management in C-RAN. This study performs a comprehensive survey on the state-of-the-art resource management techniques that have been proposed recently for this architecture. The resource management techniques are categorized into computational resource management (CRM) and radio resource management (RRM) techniques. Then both of the techniques are further classified and analyzed based on the strategies used in the studies. Remote radio head (RRH) clustering schemes used in CRM techniques are discussed extensively. In this research work, the investigated performance metrics and their validation techniques are critically analyzed. Moreover, other important challenges and open research issues for efficient resource management in C-RAN are highlighted to provide future research direction.
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24
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Takada H, Roghanian M, Murina V, Dzhygyr I, Murayama R, Akanuma G, Atkinson GC, Garcia-Pino A, Hauryliuk V. The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation of 'Long' RelA-SpoT Homolog Enzymes by Ribosomal Complexes. Front Microbiol 2020; 11:277. [PMID: 32184768 PMCID: PMC7058999 DOI: 10.3389/fmicb.2020.00277] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
The (p)ppGpp-mediated stringent response is a bacterial stress response implicated in virulence and antibiotic tolerance. Both synthesis and degradation of the (p)ppGpp alarmone nucleotide are mediated by RelA-SpoT Homolog (RSH) enzymes which can be broadly divided in two classes: single-domain 'short' and multi-domain 'long' RSH. The regulatory ACT (Aspartokinase, Chorismate mutase and TyrA)/RRM (RNA Recognition Motif) domain is a near-universal C-terminal domain of long RSHs. Deletion of RRM in both monofunctional (synthesis-only) RelA as well as bifunctional (i.e., capable of both degrading and synthesizing the alarmone) Rel renders the long RSH cytotoxic due to overproduction of (p)ppGpp. To probe the molecular mechanism underlying this effect we characterized Escherichia coli RelA and Bacillus subtilis Rel RSHs lacking RRM. We demonstrate that, first, the cytotoxicity caused by the removal of RRM is counteracted by secondary mutations that disrupt the interaction of the RSH with the starved ribosomal complex - the ultimate inducer of (p)ppGpp production by RelA and Rel - and, second, that the hydrolytic activity of Rel is not abrogated in the truncated mutant. Therefore, we conclude that the overproduction of (p)ppGpp by RSHs lacking the RRM domain is not explained by a lack of auto-inhibition in the absence of RRM or/and a defect in (p)ppGpp hydrolysis. Instead, we argue that it is driven by misregulation of the RSH activation by the ribosome.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Ievgen Dzhygyr
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO, Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
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25
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Dang M, Song J. ALS-causing D169G mutation disrupts the ATP-binding capacity of TDP-43 RRM1 domain. Biochem Biophys Res Commun 2020; 524:459-64. [PMID: 32007267 DOI: 10.1016/j.bbrc.2020.01.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
TDP-43 inclusion is a pathological hallmark for ∼97% ALS and ∼45% FTD patients. So far, >50 ALS-causing mutations have been identified, most of which are hosted by the intrinsically-disordered prion-like domain. The D169G mutation is the only one within the well-folded RRM1 domain, which, however, induces no significant change of the crystal structure and even slightly enhances the thermodynamic stability. Therefore, the mechanism for D169G to enhance the cytotoxicity remains elusive. Here by NMR, we reveal for the first time: 1) D169G does trigger significant dynamic changes for a cluster of residues. 2) Very unexpectedly, D169G disrupts the ATP-binding capacity of RRM1 although the ATP-binding pocket is on the back side of the mutation site. Taken together with our previous results, the current study provides a potential mechanism to rationalize enhancement of the TDP-43 cytotoxicity by D169G and highlights again the key roles of ATP in neurodegenerative diseases and ageing.
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26
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Szabo AM, Viczjan G, Erdei T, Simon I, Kiss R, Szentmiklosi AJ, Juhasz B, Papp C, Zsuga J, Pinter A, Szilvassy Z, Gesztelyi R. Accuracy and Precision of the Receptorial Responsiveness Method ( RRM) in the Quantification of A 1 Adenosine Receptor Agonists. Int J Mol Sci 2019; 20:E6264. [PMID: 31842299 DOI: 10.3390/ijms20246264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
The receptorial responsiveness method (RRM) is a procedure that is based on a simple nonlinear regression while using a model with two variables (X, Y) and (at least) one parameter to be determined (cx). The model of RRM describes the co-action of two agonists that consume the same response capacity (due to the use of the same postreceptorial signaling in a biological system). While using RRM, uniquely, an acute increase in the concentration of an agonist (near the receptors) can be quantified (as cx), via evaluating E/c curves that were constructed with the same or another agonist in the same system. As this measurement is sensitive to the implementation of the curve fitting, the goal of the present study was to test RRM by combining different ways and setting options, namely: individual vs. global fitting, ordinary vs. robust fitting, and three weighting options (no weighting vs. weighting by 1/Y2 vs. weighting by 1/SD2). During the testing, RRM was used to estimate the known concentrations of stable synthetic A1 adenosine receptor agonists in isolated, paced guinea pig left atria. The estimates were then compared to the known agonist concentrations (to assess the accuracy of RRM); furthermore, the 95% confidence limits of the best-fit values were also considered (to evaluate the precision of RRM). It was found that, although the global fitting offered the most convenient way to perform RRM, the best estimates were provided by the individual fitting without any weighting, almost irrespective of the fact whether ordinary or robust fitting was chosen.
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27
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Dock-Bregeon AC, Lewis KA, Conte MR. The La-related proteins: structures and interactions of a versatile superfamily of RNA-binding proteins. RNA Biol 2019; 18:178-193. [PMID: 31752575 DOI: 10.1080/15476286.2019.1695712] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The La-related proteins (LaRPs) are an ancient superfamily of RNA-binding proteins orchestrating the major fates of RNA, from processing and maturation to regulation of mRNA translation. LaRPs are instrumental in modulating complex assemblies where the RNA is bound, folded, processed, escorted and presented to the functional effectors often through recruitment of protein partners. This intricate web of protein-RNA and protein-protein interactions is enabled by the modular nature of the LaRPs, comprising several structured domains connected by flexible linkers, and other sequences lacking recognizable folded motifs. Recent structures, together with biochemical and biophysical studies, have provided insights into how each LaRP family has evolved unique mechanisms of RNA recognition, not only through the conserved RNA-binding unit, the La-module, but also mediated by other family-specific motifs. Furthermore, in a series of unexpected twists and turns, they have revealed that the dynamic and conformational interplay of multi-structured domains and disordered regions operate in unison to achieve RNA substrate discrimination. This review proposes a perspective of our current knowledge of the structure-function relationship of the LaRP superfamily.
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Affiliation(s)
| | - Karen A Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
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28
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Szabo AM, Erdei T, Viczjan G, Kiss R, Zsuga J, Papp C, Pinter A, Juhasz B, Szilvassy Z, Gesztelyi R. An Advanced In Silico Modelling of the Interaction between FSCPX, an Irreversible A 1 Adenosine Receptor Antagonist, and NBTI, a Nucleoside Transport Inhibitor, in the Guinea Pig Atrium. Molecules 2019; 24:E2207. [PMID: 31212849 PMCID: PMC6630508 DOI: 10.3390/molecules24122207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/21/2022] Open
Abstract
In earlier studies, we generated concentration-response (E/c) curves with CPA (N6-cyclopentyladenosine; a selective A1 adenosine receptor agonist) or adenosine, in the presence or absence of S-(2-hydroxy-5-nitrobenzyl)-6-thioinosine (NBTI, a selective nucleoside transport inhibitor), and with or without a pretreatment with 8-cyclopentyl-N3-[3-(4-(fluorosulfonyl)-benzoyloxy)propyl]-N1-propylxanthine (FSCPX, a chemical known as a selective, irreversible A1 adenosine receptor antagonist), in isolated, paced guinea pig left atria. Meanwhile, we observed a paradoxical phenomenon, i.e. the co-treatment with FSCPX and NBTI appeared to enhance the direct negative inotropic response to adenosine. In the present in silico study, we aimed to reproduce eight of these E/c curves. Four models (and two additional variants of the last model) were constructed, each one representing a set of assumptions, in order to find the model exhibiting the best fit to the ex vivo data, and to gain insight into the paradoxical phenomenon in question. We have obtained in silico evidence for an interference between effects of FSCPX and NBTI upon our ex vivo experimental setting. Regarding the mechanism of this interference, in silico evidence has been gained for the assumption that FSCPX inhibits the effect of NBTI on the level of endogenous (but not exogenous) adenosine. As an explanation, it may be hypothesized that FSCPX inhibits an enzyme participating in the interstitial adenosine formation. In addition, our results suggest that NBTI does not stop the inward adenosine flux in the guinea pig atrium completely.
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Affiliation(s)
- Adrienn Monika Szabo
- Department of Internal Medicine, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Tamas Erdei
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Gabor Viczjan
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Rita Kiss
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Judit Zsuga
- Department of Health Systems Management and Quality Management for Health Care, Faculty of Public Health, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Csaba Papp
- Department of Health Systems Management and Quality Management for Health Care, Faculty of Public Health, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Akos Pinter
- Institute of Mathematics, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Bela Juhasz
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Zoltan Szilvassy
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Rudolf Gesztelyi
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
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29
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Schäfer IB, Yamashita M, Schuller JM, Schüssler S, Reichelt P, Strauss M, Conti E. Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase. Cell 2019; 177:1619-1631.e21. [PMID: 31104843 PMCID: PMC6547884 DOI: 10.1016/j.cell.2019.04.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/08/2019] [Accepted: 04/05/2019] [Indexed: 01/17/2023]
Abstract
The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3′ end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs’ lifetime. Oligomerization of PABP on the poly(A) tail creates a series of consecutive arches Pan2-Pan3 deadenylase recognizes the oligomerized state of poly(A)-bound PABP The dimerization interface of juxtaposed PABPs creates the Pan2-Pan3 docking site The poly(A) RNP arches are flexible and moldable by the interacting proteins
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Affiliation(s)
- Ingmar B Schäfer
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany.
| | - Masami Yamashita
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | | | - Steffen Schüssler
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Peter Reichelt
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Mike Strauss
- cryoEM Facility, MPI of Biochemistry, Munich, Germany
| | - Elena Conti
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany.
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30
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Meyer A, Golbik RP, Sänger L, Schmidt T, Behrens SE, Friedrich S. The RGG/RG motif of AUF1 isoform p45 is a key modulator of the protein's RNA chaperone and RNA annealing activities. RNA Biol 2019; 16:960-971. [PMID: 30951406 DOI: 10.1080/15476286.2019.1602438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The RNA-binding protein AUF1 regulates post-transcriptional gene expression by affecting the steady state and translation levels of numerous target RNAs. Remodeling of RNA structures by the largest isoform AUF1 p45 was recently demonstrated in the context of replicating RNA viruses, and involves two RNA remodeling activities, i.e. an RNA chaperone and an RNA annealing activity. AUF1 contains two non-identical RNA recognition motifs (RRM) and one RGG/RG motif located in the C-terminus. In order to determine the functional significance of each motif to AUF1's RNA-binding and remodeling activities we performed a comprehensive mutagenesis study and characterized the wildtype AUF1, and several variants thereof. We demonstrate that each motif contributes to efficient RNA binding and remodeling by AUF1 indicating a tight cooperation of the RRMs and the RGG/RG motif. Interestingly, the data identify two distinct roles for the arginine residues of the RGG/RG motif for each RNA remodeling activity. First, arginine-mediated stacking interactions promote AUF1's helix-destabilizing RNA chaperone activity. Second, the electropositive character of the arginine residues is the major driving force for the RNA annealing activity. Thus, we provide the first evidence that arginine residues of an RGG/RG motif contribute to the mechanism of RNA annealing and RNA chaperoning.
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Affiliation(s)
- Alexandra Meyer
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Ralph P Golbik
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Lennart Sänger
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Tobias Schmidt
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Sven-Erik Behrens
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Susann Friedrich
- a Institute of Biochemistry and Biotechnology , Martin Luther University Halle-Wittenberg , Halle , Germany
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31
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Hsu MC, Pan MR, Chu PY, Tsai YL, Tsai CH, Shan YS, Chen LT, Hung WC. Protein Arginine Methyltransferase 3 Enhances Chemoresistance in Pancreatic Cancer by Methylating hnRNPA1 to Increase ABCG2 Expression. Cancers (Basel) 2018; 11:cancers11010008. [PMID: 30577570 PMCID: PMC6356582 DOI: 10.3390/cancers11010008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 01/27/2023] Open
Abstract
Pancreatic cancer is poorly responsive to chemotherapy due to intrinsic or acquired resistance. Our previous study showed that epigenetic modifying enzymes including protein arginine methyltransferase 3 (PRMT3) are dysregulated in gemcitabine (GEM)-resistant pancreatic cancer cells. Here, we attempt to elucidate the role of PRMT3 in chemoresistance. Overexpression of PRMT3 led to increased resistance to GEM in pancreatic cancer cells, whereas reduction of PRMT3 restored GEM sensitivity in resistant cells. We identified a novel PRMT3 target, ATP-binding cassette subfamily G member 2 (ABCG2), which is known to play a critical role in drug resistance. PRMT3 overexpression upregulated ABCG2 expression by increasing its mRNA stability. Mass spectrometric analysis identified hnRNPA1 as a PRMT3 interacting protein, and methylation of hnRNPA1 at R31 by PRMT3 in vivo and in vitro. The expression of methylation-deficient hnRNPA1-R31K mutant reduced the RNA binding activity of hnRNPA1 and the expression of ABCG2 mRNA. Taken together, this provides the first evidence that PRMT3 methylates the RNA recognition motif (RRM) of hnRNPA1 and promotes the binding between hnRNPA1 and ABCG2 to enhance drug resistance. Inhibition of PRMT3 could be a novel strategy for the treatment of GEM-resistant pancreatic cancer.
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Affiliation(s)
- Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Pei-Yi Chu
- Department of Pathology, Show Chwan Memorial Hospital, Changhua City 500, Taiwan.
| | - Ya-Li Tsai
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
| | - Chia-Hua Tsai
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
| | - Yan-Shen Shan
- Department of Surgery, National Cheng Kung University Hospital, Tainan 704, Taiwan.
- Insitute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan.
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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32
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Donenberg T, George S, Ali J, Bravo G, Hernandez K, Sookar N, Ashing KT, Narod SA, Akbari MR, Hurley J. A clinically structured and partnered approach to genetic testing in Trinidadian women with breast cancer and their families. Breast Cancer Res Treat 2019; 174:469-77. [PMID: 30515680 DOI: 10.1007/s10549-018-5045-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Breast cancer (BC) is the leading cause of cancer death in Caribbean women. Across the Caribbean islands, the prevalence of hereditary breast cancer among unselected breast cancer patients ranges from 5 to 25%. Moreover, the prevalence of BC among younger women and the high mortality in the Caribbean region are notable. This BC burden presents an opportunity for cancer prevention and control that begins with genetic testing among high-risk women. Measured response to positive genetic test results includes the number of preventive procedures and cascade testing in family members. We previously reported data on an active approach to promote cascade testing in the Bahamas and report on preventive procedures showing moderate uptake. Here, we describe a clinically structured and community-partnered approach to the dissemination and follow-up of genetic test results including family counseling for the promotion of risk mitigation strategies and cascade testing in our Trinidadian cohort of patients tested positive for BC predisposition genes. METHODS As a part of our initial study of BC genetic testing in Trinidad and Tobago, all participants received pre-test counseling including three-generation pedigree and genetic testing for BRCA1/2, PALB2, and RAD51C. The study was approved by the University of Miami IRB and the Ethics Committee of the Ministry of Health, Trinidad and Tobago. We prospectively evaluated a clinically structured approach to genetic counseling and follow-up of BC mutation carriers in Trinidad and Tobago in 2015. The intervention consisted of (1) engaging twenty-nine BC patients with a deleterious gene mutation (probands), and (2) invitation of their at-risk relatives to attend to a family counseling session. The session included information on the meaning of their results, risk of inheritance, risk of cancer, risk-reduction options, offering of cascade testing to family members, and follow-up of proband decision-making over two years. RESULTS Twenty-four of twenty-nine mutation carriers (82.8%) consented to enroll in the study. At initial pedigree review, we identified 125 at-risk relatives (ARR). Seventy-seven ARR (62%) attended the family counseling sessions; of these, 76 ARR (99%) consented to be tested for their family gene mutation. Genetic sequencing revealed that of the 76 tested, 35 (46%) ARR were carriers of their family mutation. The ARR received their results and were urged to take preventative measures at post-test counseling. At 2-year follow-up, 6 of 21 probands with intact breasts elected to pursue preventive mastectomy (28.5%) and 4 of 20 women with intact ovaries underwent RRSO (20%). CONCLUSIONS In Trinidad and Tobago, a clinically structured and partnered approach to our testing program led to a significant rate of proband response by completing the intervention counseling session, executing risk-reducing procedures as well as informing and motivating at-risk relatives, thereby demonstrating the utility and efficacy of this BC control program.
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Lixa C, Mujo A, de Magalhães MTQ, Almeida FCL, Lima LMTR, Pinheiro AS. Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution. J Biomol NMR 2018; 72:179-192. [PMID: 30535889 DOI: 10.1007/s10858-018-0217-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central β-strands, β1 and β3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the β2-β3 loop undergoes fast backbone dynamics (ps-ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI-IMS-MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding β-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer-dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.
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Affiliation(s)
- Carolina Lixa
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Amanda Mujo
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Mariana T Q de Magalhães
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fabio C L Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas, Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luis Mauricio T R Lima
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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Abstract
The IMP family of RNA binding proteins, also named as insulin-like growth factor 2 (IGF2) mRNA-binding proteins (IGF2BPs), are highly conserved RNA regulators that are involved in many RNA processing stages, including mRNA stability, localization, and translation. There are three paralogs in the IMP family, IMP1-3, in mammals that all adopt the same domain arrangement with two RNA recognition motifs (RRM) in the N terminus and four KH domains in the C terminus. Here, we report the structure and biochemical characterization of IMP3 RRM12 and its complex with two short RNAs. These structures show that both RRM domains of IMP3 adopt the canonical RRM topology with two α-helices packed on an anti-parallel four stranded β-sheet. The spatial orientation of RRM1 to RRM2 is unique compared with other known tandem RRM structures. In the IMP3 RRM12 complex with RNA, only RRM1 is involved in RNA binding and recognizes a dinucleotide sequence.
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Affiliation(s)
- Min Jia
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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Lorenzi P, Sangalli A, Fochi S, Dal Molin A, Malerba G, Zipeto D, Romanelli MG. RNA-binding proteins RBM20 and PTBP1 regulate the alternative splicing of FHOD3. Int J Biochem Cell Biol 2018; 106:74-83. [PMID: 30468920 DOI: 10.1016/j.biocel.2018.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/29/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022]
Abstract
Regulation of alternative splicing events is an essential step required for the expression of functional cytoskeleton and sarcomere proteins in cardiomyocytes. About 3% of idiopathic dilated cardiomyopathy cases present mutations in the RNA binding protein RBM20, a tissue specific regulator of alternative splicing. Transcripts expressed preferentially in skeletal and cardiac muscle, including TTN, CAMK2D, LDB3, LMO7, PDLIM3, RTN4, and RYR2, are RBM20-dependent splice variants. In the present study, we investigated the RBM20 involvement in post-transcriptional regulation of splicing variants expressed by Formin homology 2 domain containing 3 (FHOD3) gene. FHOD3 is a sarcomeric protein highly expressed in the cardiac tissue and required for the assembly of the contractile apparatus. Recently, FHOD3 mutations have been found associated with heart diseases. We identified novel FHOD3 splicing variants differentially expressed in human tissues and provided evidences that FHOD3 transcripts are specific RBM20 and PTBP1 targets. Furthermore, we demonstrated that the expression of RBM20 and PTBP1 promoted the alternative shift, from inclusion to exclusion, of selected FHOD3 exons. These results indicate that RBM20 and PTBP1 play a role in the actin filament functional organization mediated by FHOD3 isoforms and suggest their possible involvement in heart diseases.
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Affiliation(s)
- P Lorenzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - A Sangalli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - S Fochi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - A Dal Molin
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - G Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - D Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
| | - M G Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy.
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Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure 2018; 27:6-26. [PMID: 30393050 DOI: 10.1016/j.str.2018.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 11/27/2022]
Abstract
The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.
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Affiliation(s)
- Philippe Youkharibache
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Stella Veretnik
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| | - Qingliang Li
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
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Erdei T, Szabo AM, Lampe N, Szabo K, Kiss R, Zsuga J, Papp C, Pinter A, Szentmiklosi AJ, Szilvassy Z, Juhasz B, Gesztelyi R. FSCPX, a Chemical Widely Used as an Irreversible A₁ Adenosine Receptor Antagonist, Modifies the Effect of NBTI, a Nucleoside Transport Inhibitor, by Reducing the Interstitial Adenosine Level in the Guinea Pig Atrium. Molecules 2018; 23:E2186. [PMID: 30200192 DOI: 10.3390/molecules23092186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 11/23/2022] Open
Abstract
Based on in silico results, recently we have assumed that FSCPX, an irreversible A1 adenosine receptor antagonist, inhibits the action of NBTI that is apparent on E/c curves of adenosine receptor agonists. As a mechanism for this unexpected effect, we hypothesized that FSCPX might modify the equilibrative and NBTI-sensitive nucleoside transporter (ENT1) in a way that allows ENT1 to transport adenosine but impedes NBTI to inhibit this transport. This assumption implies that our method developed to estimate receptor reserve for agonists with short half-life such as adenosine, in its original form, overestimates the receptor reserve. In this study, therefore, our goals were to experimentally test our assumption on this effect of FSCPX, to improve our receptor reserve-estimating method and then to compare the original and improved forms of this method. Thus, we improved our method and assessed the receptor reserve for the direct negative inotropic effect of adenosine with both forms of this method in guinea pig atria. We have found that FSCPX inhibits the effects of NBTI that are mediated by increasing the interstitial concentration of adenosine of endogenous (but not exogenous) origin. As a mechanism for this action of FSCPX, inhibition of enzymes participating in the interstitial adenosine production can be hypothesized, while modification of ENT1 can be excluded. Furthermore, we have shown that, in comparison with the improved form, the original version of our method overestimates receptor reserve but only to a small extent. Nevertheless, use of the improved form is recommended in the future.
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38
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Boyle PC, de Groot T, Andralojc KM, Parnell TA. Healthy Singleton Pregnancies From Restorative Reproductive Medicine ( RRM) After Failed IVF. Front Med (Lausanne) 2018; 5:210. [PMID: 30109231 PMCID: PMC6079215 DOI: 10.3389/fmed.2018.00210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives: To determine the live birth rate for patients who chose to undergo treatment with Restorative Reproductive Medicine (RRM) after previous IVF (includes ICSI). To look at birth outcomes with RRM after IVF, particularly rates of twin and higher order pregnancies, premature birth, low birth weight, and potential cost savings achieved with RRM. Setting: Two outpatient clinics in Ireland providing advanced RRM treatment of infertility. Materials and methods: All patients presenting between January 2004 and January 2010, with a history of infertility and previous IVF treatment were included if they proceeded beyond the initial consultation and began treatment. Main outcome is live birth per couple calculated using life table analysis. Results: 403 patients met the study criteria, among which 74 had a subsequent live birth. These women had significant negative predictive characteristics for healthy live birth including: advanced reproductive age (average 37.2 years), an average of 5.8 years of infertility with 2.1 (range 1–9) previous IVF attempts, with only 5% having previously had a live birth from IVF. Despite these undesirable prognostic indicators, the overall RRM live birth rate was 32.1% (crude 18.4%). Women aged 35–38 had a live birth rate of 37.5% (crude 23.6%) and older women over 40 had a live birth rate of 27.4% (crude 16.0%). The average birth weight was 3374g (7lb 7oz) with 92% being born at 37+ weeks and no very low birth weight babies. There was only one twin pregnancy in the study population; the potential health care savings for avoidable multiple pregnancies in these patients was estimated at £205 672 (USD$284 915). Conclusions: Patients who have already tried IVF can achieve comparable live birth outcomes with RRM compared to another cycle of IVF. RRM has a low risk of twin or multiple births, and very good neonatal outcomes with a potential cost savings to the health care system.
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Affiliation(s)
- Phil C Boyle
- International Institute for Restorative Reproductive Medicine, London, United Kingdom.,NeoFertility Clinic, Dublin, Ireland
| | - Theun de Groot
- International Institute for Restorative Reproductive Medicine, London, United Kingdom
| | - Karolina M Andralojc
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Tracey A Parnell
- International Institute for Restorative Reproductive Medicine, London, United Kingdom.,Department of Family Medicine, University of British Columbia, Vancouver, BC, Canada
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Kobayashi A, Kanaba T, Satoh R, Ito Y, Sugiura R, Mishima M. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein. Biomol NMR Assign 2017; 11:123-126. [PMID: 28284018 DOI: 10.1007/s12104-017-9731-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1H, 13C, and 15N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.
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Affiliation(s)
- Ayaho Kobayashi
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
| | - Teppei Kanaba
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
- Bruker BioSpin K. K., 3-9, Moriya-cho, Kanagawa, Yokohama, 221-0022, Japan
| | - Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, 3-4-1 Kowake, Higashi-Osaka, 577-8502, Japan
| | - Yutaka Ito
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, 3-4-1 Kowake, Higashi-Osaka, 577-8502, Japan
| | - Masaki Mishima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan.
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40
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Iwaoka R, Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, Katahira M. Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA. Biomol NMR Assign 2017; 11:265-268. [PMID: 28808919 DOI: 10.1007/s12104-017-9760-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
Musashi1 (Msi1) is an RNA-binding protein that is involved in cell fate determination. Here, we report the 1H, 15N, and 13C resonance assignments of Msi1 second RNA-binding domain in free form and in complex with RNA. The assignments can be utilized for NMR structure and dynamics analyses of the Msi1:RNA complex, and moreover, for chemical shift perturbation analyses to evaluate the binding of potential small molecule inhibitors against Msi1:RNA interaction.
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Affiliation(s)
- Ryo Iwaoka
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Kengo Tsuda
- RIKEN Center for Life Science Technologies, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takao Imai
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Abstract
HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic. DOI:http://dx.doi.org/10.7554/eLife.25736.001
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Affiliation(s)
- Irene Beusch
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire d'expression génétique microbienne, UMR 8261, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de biologie physico-chimique, Paris, France
| | - Ahmed Moursy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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van Roon AMM, Oubridge C, Obayashi E, Sposito B, Newman AJ, Séraphin B, Nagai K. Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. RNA 2017; 23:968-981. [PMID: 28348170 PMCID: PMC5435868 DOI: 10.1261/rna.059378.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/17/2017] [Indexed: 05/02/2023]
Abstract
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5' end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the Bact spliceosome, corroborating the biological relevance of our crystal structure.
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Affiliation(s)
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eiji Obayashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Benedetta Sposito
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM), U964/Université de Strasbourg, 67404 Illkirch, France
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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Zsuga J, Erdei T, Szabó K, Lampe N, Papp C, Pinter A, Szentmiklosi A, Juhasz B, Szilvássy Z, Gesztelyi R. Methodical Challenges and a Possible Resolution in the Assessment of Receptor Reserve for Adenosine, an Agonist with Short Half-Life. Molecules 2017; 22:839. [PMID: 28534854 PMCID: PMC6154002 DOI: 10.3390/molecules22050839] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 02/03/2023] Open
Abstract
The term receptor reserve, first introduced and used in the traditional receptor theory, is an integrative measure of response-inducing ability of the interaction between an agonist and a receptor system (consisting of a receptor and its downstream signaling). The underlying phenomenon, i.e., stimulation of a submaximal fraction of receptors can apparently elicit the maximal effect (in certain cases), provides an opportunity to assess the receptor reserve. However, determining receptor reserve is challenging for agonists with short half-lives, such as adenosine. Although adenosine metabolism can be inhibited several ways (in order to prevent the rapid elimination of adenosine administered to construct concentration–effect (E/c) curves for the determination), the consequent accumulation of endogenous adenosine biases the results. To address this problem, we previously proposed a method, by means of which this bias can be mathematically corrected (utilizing a traditional receptor theory-independent approach). In the present investigation, we have offered in silico validation of this method by simulating E/c curves with the use of the operational model of agonism and then by evaluating them using our method. We have found that our method is suitable to reliably assess the receptor reserve for adenosine in our recently published experimental setting, suggesting that it may be capable for a qualitative determination of receptor reserve for rapidly eliminating agonists in general. In addition, we have disclosed a possible interference between FSCPX (8-cyclopentyl-N3-[3-(4-(fluorosulfonyl)benzoyloxy)propyl]-N1-propylxanthine), an irreversible A1 adenosine receptor antagonist, and NBTI (S-(2-hydroxy-5-nitrobenzyl)-6-thioinosine), a nucleoside transport inhibitor, i.e., FSCPX may blunt the effect of NBTI.
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Abstract
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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Affiliation(s)
- Sarah Loerch
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department for Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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Strange RM, Russelburg LP, Delaney KJ. Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes. Genetica 2016; 144:487-96. [PMID: 27450547 DOI: 10.1007/s10709-016-9918-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022]
Abstract
Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.
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Abstract
The majority of human genes undergo alternative splicing to produce multiple isoforms with distinct functions. The dysregulations of alternative splicing have been found to be closely associated with various human diseases; thus new approaches to modulate disease-associated splicing events will provide great therapeutic potentials. Here we report protocols for constructing novel artificial splicing factors that can be designed to specifically modulate alternative splicing of target genes. By following the method outlined in this protocol, it is possible to design and generate artificial splicing factors with diverse activities in regulating different types of alternative splicing. The artificial splicing factors can be used to change splicing of either minigenes or endogenous genes in cultured human cells, providing a new strategy to study the regulation of alternative splicing and function of alternatively spliced products.
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Affiliation(s)
- Yang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Zefeng Wang
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, CB # 7365, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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Cieniková Z, Jayne S, Damberger FF, Allain FHT, Maris C. Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing. RNA 2015; 21:1931-42. [PMID: 26370582 PMCID: PMC4604433 DOI: 10.1261/rna.052373.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/21/2015] [Indexed: 05/20/2023]
Abstract
The human hnRNP C is a ubiquitous cellular protein involved in mRNA maturation. Recently, we have shown that this protein specifically recognizes uridine (U) pentamers through its single RNA recognition motif (RRM). However, a large fraction of natural RNA targets of hnRNP C consists of much longer contiguous uridine stretches. To understand how these extended sites are recognized, we studied the binding of the RRM to U-tracts of 8-11 bases. In vivo investigation of internal translation activation of unr (upstream of N-ras) mRNA indicates that the conservation of the entire hnRNP C binding site, UC(U)8, is required for hnRNP C-dependent IRES activation. The assays further suggest a synergistic interplay between hnRNP C monomers, dependent on the protein's ability to oligomerize. In vitro spectroscopic and thermodynamic analyses show that isolated RRMs bind to (U)11 oligomers as dimers. Structural modeling of a ternary double-RRM/RNA complex indicates additionally that two RRM copies can be accommodated on the canonical sequence UC(U)8. The proposed tandem RRM binding is in very good agreement with the transcriptome-wide recognition of extended U-tracts by full-length hnRNP C, which displays a cross-linking pattern consistent with a positively cooperative RRM dimer binding model.
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Affiliation(s)
- Zuzana Cieniková
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Sandrine Jayne
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Fred Franz Damberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Christophe Maris
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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Miyazaki S, Sato Y, Asano T, Nagamura Y, Nonomura KI. Rice MEL2, the RNA recognition motif ( RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR. Plant Mol Biol 2015; 89:293-307. [PMID: 26319516 DOI: 10.1007/s11103-015-0369-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 08/22/2015] [Indexed: 06/04/2023]
Abstract
Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.
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Affiliation(s)
- Saori Miyazaki
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
- Office for the Promotion of Global Education Programs, Shizuoka University, Jyouhoku, Nakaku, Hamamatsu, Shizuoka, 432-8561, Japan.
| | - Yutaka Sato
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Tomoya Asano
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Takaramachi, Kanazawa, 920-0934, Japan.
- Wakasa Seikatsu Co. Ltd, 22 Naginataboko-cho, Shijo-Karasuma, Shimogyo-ku, Kyoto, 600-8008, Japan.
| | - Yoshiaki Nagamura
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
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Tejedor JR, Tilgner H, Iannone C, Guigó R, Valcárcel J. Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing. RNA 2015; 21:1187-1202. [PMID: 25904137 PMCID: PMC4436670 DOI: 10.1261/rna.049890.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
The OLR1 gene encodes the oxidized low-density lipoprotein receptor (LOX-1), which is responsible for the cellular uptake of oxidized LDL (Ox-LDL), foam cell formation in atheroma plaques and atherosclerotic plaque rupture. Alternative splicing (AS) of OLR1 exon 5 generates two protein isoforms with antagonistic functions in Ox-LDL uptake. Previous work identified six single nucleotide polymorphisms (SNPs) in linkage disequilibrium that influence the inclusion levels of OLR1 exon 5 and correlate with the risk of cardiovascular disease. Here we use minigenes to recapitulate the effects of two allelic series (Low- and High-Risk) on OLR1 AS and identify one SNP in intron 4 (rs3736234) as the main contributor to the differences in exon 5 inclusion, while the other SNPs in the allelic series attenuate the drastic effects of this key SNP. Bioinformatic, proteomic, mutational and functional high-throughput analyses allowed us to define regulatory sequence motifs and identify SR protein family members (SRSF1, SRSF2) and HMGA1 as factors involved in the regulation of OLR1 AS. Our results suggest that antagonism between SRSF1 and SRSF2/HMGA1, and differential recognition of their regulatory motifs depending on the identity of the rs3736234 polymorphism, influence OLR1 exon 5 inclusion and the efficiency of Ox-LDL uptake, with potential implications for atherosclerosis and coronary disease.
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Affiliation(s)
- J Ramón Tejedor
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Hagen Tilgner
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Camilla Iannone
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Roderic Guigó
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08020 Barcelona, Spain
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Pohlmann T, Baumann S, Haag C, Albrecht M, Feldbrügge M. A FYVE zinc finger domain protein specifically links mRNA transport to endosome trafficking. eLife 2015; 4. [PMID: 25985087 PMCID: PMC4466420 DOI: 10.7554/elife.06041] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/15/2015] [Indexed: 12/20/2022] Open
Abstract
An emerging theme in cellular logistics is the close connection between mRNA and membrane trafficking. A prominent example is the microtubule-dependent transport of mRNAs and associated ribosomes on endosomes. This coordinated process is crucial for correct septin filamentation and efficient growth of polarised cells, such as fungal hyphae. Despite detailed knowledge on the key RNA-binding protein and the molecular motors involved, it is unclear how mRNAs are connected to membranes during transport. Here, we identify a novel factor containing a FYVE zinc finger domain for interaction with endosomal lipids and a new PAM2-like domain required for interaction with the MLLE domain of the key RNA-binding protein. Consistently, loss of this FYVE domain protein leads to specific defects in mRNA, ribosome, and septin transport without affecting general functions of endosomes or their movement. Hence, this is the first endosomal component specific for mRNP trafficking uncovering a new mechanism to couple mRNPs to endosomes. DOI:http://dx.doi.org/10.7554/eLife.06041.001 DNA contains the instructions to build proteins. These instructions are first copied to make a molecule of messenger RNA (or mRNA for short). A large machine called the ribosome then reads the mRNA molecule and translates it to build a protein. Many proteins must get to particular locations in a cell to carry out their roles. For some proteins, this is achieved by transporting the mRNAs to the right location before they get translated, via a process called ‘mRNA trafficking’. However, mRNAs do not move by themselves; instead they bind to a host of mRNA-binding proteins, and the ribosomes that are required for translation to take place. Cells also move proteins between different locations using small bubble-like structures called vesicles. These vesicles are surrounded by a membrane, and so this process is known as ‘membrane trafficking’. Previous work has shown that these two processes are often linked, as vesicles can also carry mRNA molecules. But it is not fully understood how mRNA molecules are connected to vesicles. Now, Pohlmann et al. have used a fungus called Ustilago maydis as a model system to investigate how mRNAs and vesicles can move together in cells that grow to form filament-like structures called hyphae. This fungus uses these filaments to penetrate into plant tissues and causes a disease called corn smut. The experiments revealed a vesicle protein called Upa1 that contains a new type of binding site that allows Upa1 to bring an important RNA-binding protein to the surface of vesicles. Since the RNA-binding protein binds mRNA and the translating ribosomes, this can explain how mRNAs can associate with membranes to move together along hyphae. When Pohlmann et al. engineered fungi that lacked the gene for Upa1, these mutants had problems transporting their mRNAs and associated ribosomes. These findings reveal a direct connection between mRNA trafficking and membrane trafficking. Future studies could now investigate whether similar processes take place in other cells that grow as long filaments, such as plant pollen tubes or nerve cells. These studies might provide new insights into plant reproduction or brain activity. DOI:http://dx.doi.org/10.7554/eLife.06041.002
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Affiliation(s)
- Thomas Pohlmann
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Baumann
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Carl Haag
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mario Albrecht
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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