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Hayden AN, Brandel KL, Merlau PR, Vijayakumar P, Leptich EJ, Pietryk EW, Gaytan ES, Ni CW, Chao HT, Rosenfeld JA, Arey RN. Behavioral screening of conserved RNA-binding proteins reveals CEY-1/YBX RNA-binding protein dysfunction leads to impairments in memory and cognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574402. [PMID: 38260399 PMCID: PMC10802296 DOI: 10.1101/2024.01.05.574402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
RNA-binding proteins (RBPs) regulate translation and plasticity which are required for memory. RBP dysfunction has been linked to a range of neurological disorders where cognitive impairments are a key symptom. However, of the 2,000 RBPs in the human genome, many are uncharacterized with regards to neurological phenotypes. To address this, we used the model organism C. elegans to assess the role of 20 conserved RBPs in memory. We identified eight previously uncharacterized memory regulators, three of which are in the C. elegans Y-Box (CEY) RBP family. Of these, we determined that cey-1 is the closest ortholog to the mammalian Y-Box (YBX) RBPs. We found that CEY-1 is both necessary in the nervous system for memory ability and sufficient to increase memory. Leveraging human datasets, we found both copy number variation losses and single nucleotide variants in YBX1 and YBX3 in individuals with neurological symptoms. We identified one predicted deleterious YBX3 variant of unknown significance, p.Asn127Tyr, in two individuals with neurological symptoms. Introducing this variant into endogenous cey-1 locus caused memory deficits in the worm. We further generated two humanized worm lines expressing human YBX3 or YBX1 at the cey-1 locus to test evolutionary conservation of YBXs in memory and the potential functional significance of the p.Asn127Tyr variant. Both YBX1/3 can functionally replace cey-1, and introduction of p.Asn127Tyr into the humanized YBX3 locus caused memory deficits. Our study highlights the worm as a model to reveal memory regulators and identifies YBX dysfunction as a potential new source of rare neurological disease.
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Affiliation(s)
- Ashley N Hayden
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Katie L Brandel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Paul R Merlau
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | | | - Emily J Leptich
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Edward W Pietryk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
| | - Elizabeth S Gaytan
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Postbaccalaureate Research Education Program, Baylor College of Medicine, Houston, TX, 77030
| | - Connie W Ni
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Neuroscience, Rice University, Houston, TX 77005
| | - Hsiao-Tuan Chao
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Baylor Genetics Laboratories, Houston, TX 77021
| | - Rachel N Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
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2
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Khozooei S, Veerappan S, Toulany M. YB-1 activating cascades as potential targets in KRAS-mutated tumors. Strahlenther Onkol 2023; 199:1110-1127. [PMID: 37268766 DOI: 10.1007/s00066-023-02092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/23/2023] [Indexed: 06/04/2023]
Abstract
Y‑box binding protein‑1 (YB-1) is a multifunctional protein that is highly expressed in human solid tumors of various entities. Several cellular processes, e.g. cell cycle progression, cancer stemness and DNA damage signaling that are involved in the response to chemoradiotherapy (CRT) are tightly governed by YB‑1. KRAS gene with about 30% mutations in all cancers, is considered the most commonly mutated oncogene in human cancers. Accumulating evidence indicates that oncogenic KRAS mediates CRT resistance. AKT and p90 ribosomal S6 kinase are downstream of KRAS and are the major kinases that stimulate YB‑1 phosphorylation. Thus, there is a close link between the KRAS mutation status and YB‑1 activity. In this review paper, we highlight the importance of the KRAS/YB‑1 cascade in the response of KRAS-mutated solid tumors to CRT. Likewise, the opportunities to interfere with this pathway to improve CRT outcome are discussed in light of the current literature.
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Affiliation(s)
- Shayan Khozooei
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Soundaram Veerappan
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Mahmoud Toulany
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany.
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3
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Seo KW, Kleiner RE. Profiling dynamic RNA-protein interactions using small-molecule-induced RNA editing. Nat Chem Biol 2023; 19:1361-1371. [PMID: 37349582 PMCID: PMC11048738 DOI: 10.1038/s41589-023-01372-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
RNA-binding proteins (RBPs) play an important role in biology, and characterizing dynamic RNA-protein interactions is essential for understanding RBP function. In this study, we developed targets of RBPs identified by editing induced through dimerization (TRIBE-ID), a facile strategy for quantifying state-specific RNA-protein interactions upon rapamycin-mediated chemically induced dimerization and RNA editing. We performed TRIBE-ID with G3BP1 and YBX1 to study RNA-protein interactions during normal conditions and upon oxidative stress-induced biomolecular condensate formation. We quantified editing kinetics to infer interaction persistence and show that stress granule formation strengthens pre-existing RNA-protein interactions and induces new RNA-protein binding events. Furthermore, we demonstrate that G3BP1 stabilizes its targets under normal and oxidative stress conditions independent of stress granule formation. Finally, we apply our method to characterize small-molecule modulators of G3BP1-RNA binding. Taken together, our work provides a general approach to profile dynamic RNA-protein interactions in cellular contexts with temporal control.
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Affiliation(s)
- Kyung W Seo
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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4
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Lau ESW, Zhu B, Sun MA, Ngai SM, Ge W. Proteomic analysis of zebrafish folliculogenesis identifies YB-1 (Ybx1/ybx1) as a potential gatekeeping molecule controlling early ovarian folliculogenesis. Biol Reprod 2023; 109:482-497. [PMID: 37471641 DOI: 10.1093/biolre/ioad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
As in mammals, ovarian folliculogenesis in teleosts also consists of two phases: the primary growth (PG) and secondary growth (SG) phases, which are analogous to the preantral and antral phases respectively in mammals. In this study, we performed a proteomic analysis on zebrafish follicles undergoing the PG-SG transition aiming to identify factors involved in the event. Numerous proteins showed significant changes, and the most prominent one was Y-box binding protein 1 (YB-1; Ybx1/ybx1), a transcription factor and mRNA-binding protein. YB-1 belongs to the Y-box binding protein family, which also includes the gonad-specific YB-2. Interestingly, phylogenetic analysis showed no YB-2 homolog in zebrafish. Although ybx1 mRNA was expressed in various tissues, its protein Ybx1 was primarily produced in the gonads, similar to YB-2 in other species. In the ovary, Ybx1 protein started to appear in early follicles newly emerged from the germ cell cysts, reached the highest level in late PG oocytes, but decreased precipitously when the follicles entered the SG phase. In PG follicles, Ybx1 might function as a key component of the messenger ribonucleoprotein particles (mRNPs) in association with other RNA-binding proteins. Similar to mammalian YB-1, zebrafish Ybx1 also contains functional signals that determine its intracellular localization. In conclusion, Ybx1 may play dual roles of YB-1 and YB-2 in zebrafish. In the ovary, Ybx1 binds mRNAs to stabilize them while preventing their translation. At PG-SG transition, Ybx1 is removed to release the masked mRNAs for translation into functional proteins, leading to follicle activation.
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Affiliation(s)
- Esther Shuk-Wa Lau
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong 999077, China
| | - Bo Zhu
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Ming-An Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Sai Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong 999077, China
| | - Wei Ge
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
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5
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Smith MR, Costa G. RNA-binding proteins and translation control in angiogenesis. FEBS J 2022; 289:7788-7809. [PMID: 34796614 DOI: 10.1111/febs.16286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023]
Abstract
Tissue vascularization through the process of angiogenesis ensures adequate oxygen and nutrient supply during development and regeneration. The complex morphogenetic events involved in new blood vessel formation are orchestrated by a tightly regulated crosstalk between extra and intracellular factors. In this context, RNA-binding protein (RBP) activity and protein translation play fundamental roles during the cellular responses triggered by particular environmental cues. A solid body of work has demonstrated that key RBPs (such as HuR, TIS11 proteins, hnRNPs, NF90, QKIs and YB1) are implicated in both physiological and pathological angiogenesis. These RBPs are critical for the metabolism of messenger (m)RNAs encoding angiogenic modulators and, importantly, strong evidence suggests that RBP-mRNA interactions can be altered in disease. Lesser known, but not less important, the mechanistic aspects of protein synthesis can also regulate the generation of new vessels. In this review, we outline the key findings demonstrating the implications of RBP-mediated RNA regulation and translation control in angiogenesis. Furthermore, we highlight how these mechanisms of post-transcriptional control of gene expression have led to promising therapeutic strategies aimed at targeting undesired blood vessel formation.
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Affiliation(s)
- Madeleine R Smith
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| | - Guilherme Costa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
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6
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DaDalt AA, Bonham CA, Lotze GP, Luiso AA, Vacratsis PO. Src-mediated phosphorylation of the ribosome biogenesis factor hYVH1 affects its localization, promoting partitioning to the 60S ribosomal subunit. J Biol Chem 2022; 298:102679. [PMID: 36370849 PMCID: PMC9731860 DOI: 10.1016/j.jbc.2022.102679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Yeast VH1-related phosphatase (YVH1) (also known as DUSP12) is a member of the atypical dual-specificity phosphatase subfamily. Although no direct substrate has been firmly established, human YVH1 (hYVH1) has been shown to protect cells from cellular stressors, regulate the cell cycle, disassemble stress granules, and act as a 60S ribosome biogenesis factor. Despite knowledge of hYVH1 function, further research is needed to uncover mechanisms of its regulation. In this study, we investigate cellular effects of a Src-mediated phosphorylation site at Tyr179 on hYVH1. We observed that this phosphorylation event attenuates localization of hYVH1 to stress granules, enhances shuttling of hYVH1 to the nucleus, and promotes hYVH1 partitioning to the 60S ribosomal subunit. Quantitative proteomics reveal that Src coexpression with hYVH1 reduces formation of ribosomal species that represent stalled intermediates through the alteration of associating factors that mediate translational repression. Collectively, these results implicate hYVH1 as a novel Src substrate and provide the first demonstrated role of tyrosine phosphorylation regulating the activity of a YVH1 ortholog. Moreover, the ribosome proteome alterations point to a collaborative function of hYVH1 and Src in maintaining translational fitness.
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7
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Naumenko KN, Sukhanova MV, Hamon L, Kurgina TA, Anarbaev RO, Mangerich A, Pastré D, Lavrik OI. The C-Terminal Domain of Y-Box Binding Protein 1 Exhibits Structure-Specific Binding to Poly(ADP-Ribose), Which Regulates PARP1 Activity. Front Cell Dev Biol 2022; 10:831741. [PMID: 35800891 PMCID: PMC9253770 DOI: 10.3389/fcell.2022.831741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Y-box-binding protein 1 (YB-1) is a multifunctional protein involved in the regulation of gene expression. Recent studies showed that in addition to its role in the RNA and DNA metabolism, YB-1 is involved in the regulation of PARP1 activity, which catalyzes poly(ADP-ribose) [PAR] synthesis under genotoxic stress through auto-poly(ADP-ribosyl)ation or protein trans-poly(ADP-ribosyl)ation. Nonetheless, the exact mechanism by which YB-1 regulates PAR synthesis remains to be determined. YB-1 contains a disordered Ala/Pro-rich N-terminal domain, a cold shock domain, and an intrinsically disordered C-terminal domain (CTD) carrying four clusters of positively charged amino acid residues. Here, we examined the functional role of the disordered CTD of YB-1 in PAR binding and in the regulation of PARP1-driven PAR synthesis in vitro. We demonstrated that the rate of PARP1-dependent synthesis of PAR is higher in the presence of YB-1 and is tightly controlled by the interaction between YB-1 CTD and PAR. Moreover, YB-1 acts as an effective cofactor in the PAR synthesis catalyzed by the PARP1 point mutants that generate various PAR polymeric structures, namely, short hypo- or hyperbranched polymers. We showed that either a decrease in chain length or an increase in branching frequency of PAR affect its binding affinity for YB-1 and YB-1–mediated stimulation of PARP1 enzymatic activity. These results provide important insight into the mechanism underlying the regulation of PARP1 activity by PAR-binding proteins containing disordered regions with clusters of positively charged amino acid residues, suggesting that YB-1 CTD-like domains may be considered PAR “readers” just as other known PAR-binding modules.
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Affiliation(s)
| | - Mariya V. Sukhanova
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Tatyana A. Kurgina
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Rashid O. Anarbaev
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Aswin Mangerich
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Olga I. Lavrik
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Olga I. Lavrik,
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8
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Gao W, Chen L, Lin L, Yang M, Li T, Wei H, Sha C, Xing J, Zhang M, Zhao S, Chen Q, Xu W, Li Y, Zhu X. SIAH1 reverses chemoresistance in epithelial ovarian cancer via ubiquitination of YBX-1. Oncogenesis 2022; 11:13. [PMID: 35273154 PMCID: PMC8913663 DOI: 10.1038/s41389-022-00387-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 01/20/2023] Open
Abstract
Chemoresistance is a severe outcome among patients with epithelial ovarian cancer (EOC) that leads to a poor prognosis. YBX-1 has been shown to cause treatment failure and cancer progression in EOC. However, strategies that directly target YBX-1 are not yet conceivable. Here, we identified that SIAH1 which was downregulated in chemoresistant EOC samples and cell lines functioned as novel E3 ligases to trigger degradation of YBX-1 at cytoplasm by RING finger domain. Mechanistic studies show that YBX-1 was ubiquitinated by SIAH1 at lys304 that lead to the instability of its target m5C-modified mRNAs, thus sensitized EOC cells to cDDP. Overexpression of SIAH1 enhanced the antitumor efficacy of cisplatin in vitro and in vivo, which were partially impaired by ectopic expression of YBX-1 or depletion of YBX-1 ubiquitination. In summary, our data identify the SIAH1/YBX-1 interaction as a therapeutic target for overcoming EOC chemoresistance.
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Affiliation(s)
- Wujiang Gao
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lu Chen
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Meiling Yang
- The first people's hospital of Nantong, Nantong, China
| | - Taoqiong Li
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hong Wei
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Chunli Sha
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jie Xing
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mengxue Zhang
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Shijie Zhao
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Qi Chen
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenlin Xu
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yuefeng Li
- Department of Radiology, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China. .,Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.
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9
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Hamon L, Budkina K, Pastré D. YB-1 Structure/Function Relationship in the Packaging of mRNPs and Consequences for Translation Regulation and Stress Granule Assembly in Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S20-S93. [PMID: 35501984 DOI: 10.1134/s0006297922140036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
From their synthesis in the nucleus to their degradation in the cytoplasm, all mRNAs have the same objective, which is to translate the DNA-stored genetic information into functional proteins at the proper time and location. To this end, many proteins are generally associated with mRNAs as soon as transcription takes place in the nucleus to organize spatiotemporal regulation of the gene expression in cells. Here we reviewed how YB-1 (YBX1 gene), one of the major mRNA-binding proteins in the cytoplasm, packaged mRNAs into either compact or extended linear nucleoprotein mRNPs. Interestingly the structural plasticity of mRNPs coordinated by YB-1 could provide means for the contextual regulation of mRNA translation. Posttranslational modification of YB-1, notably in the long unstructured YB-1 C-terminal domain (CTD), and/or the protein partners of YB-1 may play a key role in activation/inactivation of mRNPs in the cells notably in response to cellular stress.
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Affiliation(s)
- Loïc Hamon
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - David Pastré
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
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10
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Evdokimova V. Y-box Binding Protein 1: Looking Back to the Future. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S5-S145. [PMID: 35501983 DOI: 10.1134/s0006297922140024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.
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11
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Lyabin DN, Serebrova EV. In Memory of Lev Ovchinnikov. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S1-S191. [PMID: 35501982 DOI: 10.1134/s0006297922140012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Lev Ovchinnikov was a true man of Science. Until the end of his life, he retained not only loyalty to strict scientific principles, but also a benevolent attitude towards the people around him. He devoted his scientific career to the study of mRNP and regulation of protein biosynthesis. He created a unique scientific school that received international recognition.
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Affiliation(s)
- Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Eugenia V Serebrova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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12
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Budkina K, El Hage K, Clément MJ, Desforges B, Bouhss A, Joshi V, Maucuer A, Hamon L, Ovchinnikov LP, Lyabin DN, Pastré D. YB-1 unwinds mRNA secondary structures in vitro and negatively regulates stress granule assembly in HeLa cells. Nucleic Acids Res 2021; 49:10061-10081. [PMID: 34469566 PMCID: PMC8464072 DOI: 10.1093/nar/gkab748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 01/16/2023] Open
Abstract
In the absence of the scanning ribosomes that unwind mRNA coding sequences and 5'UTRs, mRNAs are likely to form secondary structures and intermolecular bridges. Intermolecular base pairing of non polysomal mRNAs is involved in stress granule (SG) assembly when the pool of mRNAs freed from ribosomes increases during cellular stress. Here, we unravel the structural mechanisms by which a major partner of dormant mRNAs, YB-1 (YBX1), unwinds mRNA secondary structures without ATP consumption by using its conserved cold-shock domain to destabilize RNA stem/loops and its unstructured C-terminal domain to secure RNA unwinding. At endogenous levels, YB-1 facilitates SG disassembly during arsenite stress recovery. In addition, overexpression of wild-type YB-1 and to a lesser extent unwinding-defective mutants inhibit SG assembly in HeLa cells. Through its mRNA-unwinding activity, YB-1 may thus inhibit SG assembly in cancer cells and package dormant mRNA in an unfolded state, thus preparing mRNAs for translation initiation.
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Affiliation(s)
- Karina Budkina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France.,Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | | | - Ahmed Bouhss
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
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13
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The long non-coding RNA MIR31HG regulates the senescence associated secretory phenotype. Nat Commun 2021; 12:2459. [PMID: 33911076 PMCID: PMC8080841 DOI: 10.1038/s41467-021-22746-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Oncogene-induced senescence provides a barrier against malignant transformation. However, it can also promote cancer through the secretion of a plethora of factors released by senescent cells, called the senescence associated secretory phenotype (SASP). We have previously shown that in proliferating cells, nuclear lncRNA MIR31HG inhibits p16/CDKN2A expression through interaction with polycomb repressor complexes and that during BRAF-induced senescence, MIR31HG is overexpressed and translocates to the cytoplasm. Here, we show that MIR31HG regulates the expression and secretion of a subset of SASP components during BRAF-induced senescence. The SASP secreted from senescent cells depleted for MIR31HG fails to induce paracrine invasion without affecting the growth inhibitory effect. Mechanistically, MIR31HG interacts with YBX1 facilitating its phosphorylation at serine 102 (p-YBX1S102) by the kinase RSK. p-YBX1S102 induces IL1A translation which activates the transcription of the other SASP mRNAs. Our results suggest a dual role for MIR31HG in senescence depending on its localization and points to the lncRNA as a potential therapeutic target in the treatment of senescence-related pathologies. Senescence-associated secretory phenotype (SASP) involves secretion of factors such as pro-inflammatory cytokines. Here the authors show that MIR31HG regulates the expression and secretion of a subset of SASP components that induce paracrine invasion, through interaction with YBX1 and induction of IL1A translation.
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14
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Sangermano F, Delicato A, Calabrò V. Y box binding protein 1 (YB-1) oncoprotein at the hub of DNA proliferation, damage and cancer progression. Biochimie 2020; 179:205-216. [PMID: 33058958 DOI: 10.1016/j.biochi.2020.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022]
Abstract
The Y Box binding protein 1 (YB-1) belongs to the highly conserved Cold Shock Domain protein family and is a major component of messenger ribonucleoprotein particles (mRNPs) in various organisms and cells. Cold Shock proteins are multifunctional nucleic acids binding proteins involved in a variety of cellular functions. Biological activities of YB-1 range from the regulation of transcription, splicing and translation, to the orchestration of exosomal RNA content. The role of YB-1 in malignant cell transformation and fate transition is the subject of intensive investigation. Besides, emerging evidence indicates that YB-1 participates in several DNA damage repair pathways as a non-canonical DNA repair factor thus pointing out that the protein can allow cancer cells to evade conventional anticancer therapies and avoid cell death. Here, we will attempt to collect and summarize the current knowledge on this subject and provide the basis for further lines of inquiry.
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Affiliation(s)
- Felicia Sangermano
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy.
| | - Antonella Delicato
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Viola Calabrò
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Napoli, Italy
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15
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Kloetgen A, Duggimpudi S, Schuschel K, Hezaveh K, Picard D, Schaal H, Remke M, Klusmann JH, Borkhardt A, McHardy AC, Hoell JI. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. Int J Mol Sci 2020; 21:ijms21124453. [PMID: 32585856 PMCID: PMC7352269 DOI: 10.3390/ijms21124453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022] Open
Abstract
Medulloblastomas arise from undifferentiated precursor cells in the cerebellum and account for about 20% of all solid brain tumors during childhood; standard therapies include radiation and chemotherapy, which oftentimes come with severe impairment of the cognitive development of the young patients. Here, we show that the posttranscriptional regulator Y-box binding protein 1 (YBX1), a DNA- and RNA-binding protein, acts as an oncogene in medulloblastomas by regulating cellular survival and apoptosis. We observed different cellular responses upon YBX1 knockdown in several medulloblastoma cell lines, with significantly altered transcription and subsequent apoptosis rates. Mechanistically, PAR-CLIP for YBX1 and integration with RNA-Seq data uncovered direct posttranscriptional control of the heterochromatin-associated gene CBX5; upon YBX1 knockdown and subsequent CBX5 mRNA instability, heterochromatin-regulated genes involved in inflammatory response, apoptosis and death receptor signaling were de-repressed. Thus, YBX1 acts as an oncogene in medulloblastoma through indirect transcriptional regulation of inflammatory genes regulating apoptosis and represents a promising novel therapeutic target in this tumor entity.
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Affiliation(s)
- Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Correspondence:
| | - Sujitha Duggimpudi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Konstantin Schuschel
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Jan-Henning Klusmann
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Alice C. McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Jessica I. Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
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16
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Zeng T, Hua Y, Sun C, Zhang Y, Yang F, Yang M, Yang Y, Li J, Huang X, Wu H, Fu Z, Li W, Yin Y. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147:3007-3018. [PMID: 32427348 DOI: 10.1002/ijc.33107] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
tRNA-derived fragments, a class of small noncoding RNAs (sncRNAs), have been identified in numerous studies in recent years. tRNA-derived fragments are classified into two main groups, including tRNA halves (tiRNAs) and tRNA-derived small RNA fragments (tRFs), according to different cleavage positions of the precursor or mature tRNAs. Instead of random tRNA degradation debris, a growing body of evidence has shown that tRNA-derived fragments are precise products of specific tRNA modifications and play important roles in biological activities, such as regulating protein translation, affecting gene expression, and altering immune signaling. Recently, the relations between tRNA-derived fragments and the occurrence of human diseases, especially cancers, have generated wide interest. It has been demonstrated that tRNA-derived fragments are involved in cancer cell proliferation, metastasis, progression and survival. In this review, we will describe the biogenesis of tRNA-derived fragments, the distinct expression and function of tRNA-derived fragments in the development of cancers, and their emerging roles as diagnostic and prognostic biomarkers and precise targets of future treatments.
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Affiliation(s)
- Tianyu Zeng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijia Hua
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiqi Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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17
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Yang HW, Kim HD, Kim TS, Kim J. Senescent Cells Differentially Translate Senescence-Related mRNAs Via Ribosome Heterogeneity. J Gerontol A Biol Sci Med Sci 2020; 74:1015-1024. [PMID: 30285098 DOI: 10.1093/gerona/gly228] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
The ribosome has a lateral stalk which consists of rpLP0, rpLP1, and rpLP2. One of these proteins, rpLP2, is decreased in translating ribosome when cellular senescence is induced. Y-box binding protein-1 (YB-1) is also reduced in polysomal fraction of senescent cells. We discovered that rpLP2 depletion in the ribosome can cause the detachment of YB-1 in polysomes and that it is linked to cellular senescence. Our results also revealed that a decrement of CK2α or GRK2 in senescent cells induced an increment of unphosphorylated rpLP2, resulting in release of YB-1 from polysomes. This heterogeneous senescent ribosome has different translational efficiencies for some senescence-related genes. We also showed that the decrease of rpLP1/rpLP2 and YB-1 in senescent ribosomes was not specific to cell type or stress type and the same phenomenon was also observed in aged mouse livers regardless of gender. Taken together, our results suggest that the senescent ribosome complex appears to have low levels of rpLP1/rpLP2 and YB-1, resulting in altered translational efficiency for senescence-related genes.
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Affiliation(s)
- Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
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18
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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19
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Budkina KS, Zlobin NE, Kononova SV, Ovchinnikov LP, Babakov AV. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. BIOCHEMISTRY (MOSCOW) 2020; 85:S1-S19. [DOI: 10.1134/s0006297920140011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Lyabin DN, Eliseeva IA, Smolin EA, Doronin AN, Budkina KS, Kulakovskiy IV, Ovchinnikov LP. YB-3 substitutes YB-1 in global mRNA binding. RNA Biol 2020; 17:487-499. [PMID: 31944153 PMCID: PMC7237157 DOI: 10.1080/15476286.2019.1710050] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Y-box binding proteins are DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. The Y-box binding protein 1 (YB-1) is the most studied due to its abundance in somatic cells. YB-1 is involved in a variety of cellular processes, including proliferation, differentiation and stress response. Here, using Ribo-Seq and RIP-Seq we confirm that YB-1 binds a wide range of mRNAs and globally acts as a translation inhibitor. Surprisingly, YBX1 knockout results in only minor alterations in the expression of other genes, mostly caused by changes in RNA abundance. But YB-3 mRNA is an exception: it is better translated in the absence of YB-1, thereby producing an increased amount of YB-3 and thus suggesting that its synthesis is under YB-1 negative control. We have shown that the set of mRNAs bound to YB-3 is strikingly similar to that of YB-1, and that the mRNA-binding by YB-3 is enhanced in the absence of YB-1, resulting in a similar global reduction of translation of bound mRNAs in YB-1-null cells. Thus, YB-3 acts as a substitute for YB-1 in mRNA binding and, probably, in global translational control.
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Affiliation(s)
- D N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - E A Smolin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A N Doronin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Department of Bioengineering, BIOCAD, Lyubuchany, Russia.,Faculty of Molecular and Cellular Biotechnology, Pushchino State Institute of Natural Science, Pushchino, Russia
| | - K S Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - I V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russia
| | - L P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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21
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Abstract
Over the past decades, tRNA was found to be a rich hub of RNA modifications such as 1-methyladenosine and 5-methycytosine modifications and others, holding more than half of all modifications occurring in RNA molecules. Moreover, tRNA was discovered to be a source of various small noncoding RNA species, such as the stress induced angiogenin cleaved tRNA halves (tiRNA) or the miRNA like tRNA derived fragments. tRNA cleavage under stress was fist discovered in bacteria and later was found to be conserved across different species, including mammals. Under cellular stress conditions, tRNA undergoes conformational changes and angiogenin cleaves it into 3' and 5' halves. 5'tiRNA halves were shown to repress protein translations. tRNA cleavage is thought of to be a cytoprotective mechanism by which cells evade apoptosis, however some data hints to the opposite; that tiRNA are cytotoxic or at least related to apoptosis initiation. tRNA cleavage also was shown to be affected by tRNA modifications via different enzymes in the cytosol and mitochondria. In this review, we will highlight the biology of tRNA cleavage, show the evidence of it being cytoprotective or a marker of cell death and shed a light on its role in disease models and human diseases as well as possible future directions in this field of RNA research.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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22
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Inhibition of Transcription Induces Phosphorylation of YB-1 at Ser102 and Its Accumulation in the Nucleus. Cells 2019; 9:cells9010104. [PMID: 31906126 PMCID: PMC7016903 DOI: 10.3390/cells9010104] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 02/04/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is an RNA/DNA-binding protein regulating gene expression in the cytoplasm and the nucleus. Although mostly cytoplasmic, YB-1 accumulates in the nucleus under stress conditions. Its nuclear localization is associated with aggressiveness and multidrug resistance of cancer cells, which makes the understanding of the regulatory mechanisms of YB-1 subcellular distribution essential. Here, we report that inhibition of RNA polymerase II (RNAPII) activity results in the nuclear accumulation of YB-1 accompanied by its phosphorylation at Ser102. The inhibition of kinase activity reduces YB-1 phosphorylation and its accumulation in the nucleus. The presence of RNA in the nucleus is shown to be required for the nuclear retention of YB-1. Thus, the subcellular localization of YB-1 depends on its post-translational modifications (PTMs) and intracellular RNA distribution.
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23
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Kim HK. Transfer RNA-Derived Small Non-Coding RNA: Dual Regulator of Protein Synthesis. Mol Cells 2019; 42:687-692. [PMID: 31656062 PMCID: PMC6821453 DOI: 10.14348/molcells.2019.0214] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/16/2023] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) play a role in various cellular processes. Accumulating evidence has revealed that tsRNAs are deeply implicated in human diseases, such as various cancers and neurological disorders, suggesting that tsRNAs should be investigated to develop novel therapeutic intervention. tsRNAs provide more complexity to the physiological role of transfer RNAs by repressing or activating protein synthesis with distinct mechanisms. Here, we highlight the detailed mechanism of tsRNA-mediated dual regulation in protein synthesis and discuss the necessity of novel sequencing technology to learn more about tsRNAs.
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Affiliation(s)
- Hak Kyun Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974,
Korea
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24
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Kretov DA, Clément MJ, Lambert G, Durand D, Lyabin DN, Bollot G, Bauvais C, Samsonova A, Budkina K, Maroun RC, Hamon L, Bouhss A, Lescop E, Toma F, Curmi PA, Maucuer A, Ovchinnikov LP, Pastré D. YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis. Nucleic Acids Res 2019; 47:3127-3141. [PMID: 30605522 PMCID: PMC6451097 DOI: 10.1093/nar/gky1303] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022] Open
Abstract
The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity. The structure of the nucleoprotein filament indicates that the CSD of YB-1 preserved its chaperone activity also in eukaryotes and shows that mRNA is channeled between consecutive CSDs. The energy benefit needed for the formation of stable nucleoprotein filament relies on an electrostatic zipper mediated by positively charged amino acid residues in the YB-1 C-terminus. Thus, YB-1 displays a structural plasticity to unfold structured mRNAs into extended linear filaments. We anticipate that our findings will shed the light on the scanning of mRNAs by ribosomes during the initiation and elongation steps of mRNA translation.
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Affiliation(s)
- Dmitry A Kretov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Marie-Jeanne Clément
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Guillaume Lambert
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | | | - Cyril Bauvais
- Synsight, a/s IncubAlliance 86 rue de Paris Orsay 91400, France
| | - Anastasiia Samsonova
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Rachid C Maroun
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Flavio Toma
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Patrick A Curmi
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Alexandre Maucuer
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | - David Pastré
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
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25
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Dimartino D, Colantoni A, Ballarino M, Martone J, Mariani D, Danner J, Bruckmann A, Meister G, Morlando M, Bozzoni I. The Long Non-coding RNA lnc-31 Interacts with Rock1 mRNA and Mediates Its YB-1-Dependent Translation. Cell Rep 2019; 23:733-740. [PMID: 29669280 PMCID: PMC5917449 DOI: 10.1016/j.celrep.2018.03.101] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 03/21/2018] [Indexed: 01/08/2023] Open
Abstract
Cytoplasmic long non-coding RNAs have been shown to act at many different levels to control post-transcriptional gene expression, although their role in translational control is poorly understood. Here, we show that lnc-31, a non-coding RNA required for myoblast proliferation, promotes ROCK1 protein synthesis by stabilizing its translational activator, YB-1. We find that lnc-31 binds to the Rock1 mRNA as well as to the YB-1 protein and that translational activation requires physical interaction between the two RNA species. These results suggest a localized effect of YB-1 stabilization on the Rock1 mRNA. ROCK1 upregulation by lnc-31, in proliferative conditions, correlates well with the differentiation-repressing activity of ROCK1. We also show that, upon induction of differentiation, the downregulation of lnc-31, in conjunction with miR-152 targeting of Rock1, establishes a regulatory loop that reinforces ROCK1 repression and promotes myogenesis. lnc-31 sustains myoblast proliferation, counteracting differentiation lnc-31 binds to Rock1 mRNA and YB-1 protein Rock-1 translation is favored through its interaction with lnc-31 and YB-1 protein lnc-31 counteracts YB-1 protein degradation, thus promoting Rock1 translation
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Affiliation(s)
- Dacia Dimartino
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Julie Martone
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Davide Mariani
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Johannes Danner
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Mariangela Morlando
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
| | - Irene Bozzoni
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y. Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. J Biol Chem 2019; 294:10998-11010. [PMID: 31160337 PMCID: PMC6635445 DOI: 10.1074/jbc.ra119.007545] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/26/2019] [Indexed: 01/07/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π-π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.
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Affiliation(s)
- Xiao-Juan Yang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Hong Zhu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Shi-Rong Mu
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Wen-Juan Wei
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Xun Yuan
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Meng Wang
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Yanchao Liu
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China
| | - Jingyi Hui
- From the CAS Center for Excellence in Molecular Cell Science, Shanghai 200031, China, ,the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and , To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-54921354; E-mail:
| | - Ying Huang
- the State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, and ,the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China, To whom correspondence may be addressed:
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. Tel.:
86-21-20778200; E-mail:
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27
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Jung YM, Yu KL, Park SH, Lee SD, Kim MJ, You JC. Investigation of function and regulation of the YB-1 cellular factor in HIV replication. BMB Rep 2018; 51:290-295. [PMID: 29429449 PMCID: PMC6033064 DOI: 10.5483/bmbrep.2018.51.6.231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Indexed: 12/21/2022] Open
Abstract
Y-box binding protein 1 (YB-1) is a member of the cold-shock domain (CSD) protein superfamily. It participates in a wide variety of cellular events, including transcription, RNA splicing, translation, DNA repair, drug resistance, and stress responses. We investigated putative functions of YB-1 in HIV-1 replication. Functional studies using overexpression or knockdown of YB-1 in conjunction with transfection of proviral DNA showed that YB-1 enhances virus production. We found YB-1 regulates HIV-1 production by stimulating viral transcription using HIV-1 LTR sequence U3RU5 with Luciferase assay. We also identified a specific region from amino acids 1 to 324 of YB-1 as necessary for the participation of the protein in the production of virions.
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Affiliation(s)
- Yu-Mi Jung
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Kyung-Lee Yu
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seong-Hyun Park
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seong-Deok Lee
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Ji-Chang You
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591; Avixgen Inc., Seoul 06649, Korea
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Światowy W, Jagodzińśki PP. Molecules derived from tRNA and snoRNA: Entering the degradome pool. Biomed Pharmacother 2018; 108:36-42. [PMID: 30216797 DOI: 10.1016/j.biopha.2018.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/03/2018] [Accepted: 09/04/2018] [Indexed: 02/02/2023] Open
Abstract
Molecules built of RNA have been the subjects of numerous studies, which have made known new functions and structures that these molecules can create. In recent years, thanks to next-generation sequencing, it is possible to observe very small RNAs and the number of newly discovered RNA molecules is rapidly increasing. Among other small oligonucleotides, structures derived from tRNA and snoRNA molecules have been observed, and these molecules were determined to not be precursors of known RNA molecules. These structures have attracted the attention of researchers because the level of accumulation of tRNA or snoRNA fragments was relatively high. Additionally, other parts of the parent molecules were absent. Derivatives of well-known RNA molecules also have functions that are different from their parent molecules. They are mainly involved in regulating the expression of genetic information in a similar way to miRNA. In addition, some of the miRNAs that have been described are derivatives of tRNA or snoRNA. Most of the research on these newly discovered molecules is based on their detection and on the study of the macro effects that they exert, in the absence of a description of the molecular mechanism by which they arise and work.
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Affiliation(s)
- Witold Światowy
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland.
| | - Paweł P Jagodzińśki
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland
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29
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Weydert C, van Heertum B, Dirix L, De Houwer S, De Wit F, Mast J, Husson SJ, Busschots K, König R, Gijsbers R, De Rijck J, Debyser Z. Y-box-binding protein 1 supports the early and late steps of HIV replication. PLoS One 2018; 13:e0200080. [PMID: 29995936 PMCID: PMC6040738 DOI: 10.1371/journal.pone.0200080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 06/19/2018] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) depends on cellular proteins, so-called cofactors, to complete its replication cycle. In search for new therapeutic targets we identified the DNA and RNA binding protein Y-box-binding Protein 1 (YB-1) as a cofactor supporting early and late steps of HIV replication. YB-1 depletion resulted in a 10-fold decrease in HIV-1 replication in different cell lines. Dissection of the replication defects revealed that knockdown of YB-1 is associated with a 2- to 5-fold decrease in virion production due to interference with the viral RNA metabolism. Using single-round virus infection experiments we demonstrated that early HIV-1 replication also depends on the cellular YB-1 levels. More precisely, using quantitative PCR and an in vivo nuclear import assay with fluorescently labeled viral particles, we showed that YB-1 knockdown leads to a block between reverse transcription and nuclear import of HIV-1. Interaction studies revealed that YB-1 associates with integrase, although a direct interaction with HIV integrase could not be unambiguously proven. In conclusion, our results indicate that YB-1 affects multiple stages of HIV replication. Future research on the interaction between YB-1 and the virus will reveal whether this protein qualifies as a new antiviral target.
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Affiliation(s)
- Caroline Weydert
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Bart van Heertum
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Lieve Dirix
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Belgium
| | - Stéphanie De Houwer
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Flore De Wit
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan Mast
- Veterinary and Agrochemical Research Centre, VAR-CODA-CERVA, Brussels, Belgium
| | - Steven J. Husson
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, 3000 Leuven, Belgium
- Systemic Physiological & Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, 2000 Antwerp, Belgium
| | - Katrien Busschots
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Rik Gijsbers
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan De Rijck
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- * E-mail:
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Matsumoto K, Kose S, Kuwahara I, Yoshimura M, Imamoto N, Yoshida M. Y-box protein-associated acidic protein (YBAP1/C1QBP) affects the localization and cytoplasmic functions of YB-1. Sci Rep 2018; 8:6198. [PMID: 29670170 PMCID: PMC5906478 DOI: 10.1038/s41598-018-24401-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
The Y-box proteins are multifunctional nucleic acid-binding proteins involved in various aspects of gene regulation. The founding member of the Y-box protein family, YB-1, functions as a transcription factor as well as a principal component of messenger ribonucleoprotein particles (mRNPs) in somatic cells. The nuclear level of YB-1 is well correlated with poor prognosis in many human cancers. Previously, we showed that a Y-box protein–associated acidic protein, YBAP1, which is identical to complement component 1, q subcomponent-binding protein (C1QBP, also called gC1qR, hyaluronan-binding protein 1 [HABP1] or ASF/SF2-associated protein p32), relieves translational repression by YB-1. Here we show that the nuclear localization of YB-1 harboring a point mutation in the cold shock domain was inhibited when co-expressed with YBAP1, whereas cytoplasmic accumulation of the wild-type YB-1 was not affected. We showed that YBAP1 inhibited the interaction between YB-1 and transportin 1. In the cytoplasm, YBAP1 affected the accumulation of YB-1 to processing bodies (P-bodies) and partially abrogated the mRNA stabilization by YB-1. Our results, indicating that YBAP1/C1QBP regulates the nucleo-cytoplasmic distribution of YB-1 and its cytoplasmic functions, are consistent with a model that YBAP1/C1QBP acts as an mRNP remodeling factor.
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Affiliation(s)
- Ken Matsumoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan. .,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan. .,Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan.
| | - Shingo Kose
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Wako, Saitama, Japan
| | - Iku Kuwahara
- Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan
| | - Mami Yoshimura
- Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Wako, Saitama, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan
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31
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El-Naggar AM, Sorensen PH. Translational control of aberrant stress responses as a hallmark of cancer. J Pathol 2018; 244:650-666. [PMID: 29293271 DOI: 10.1002/path.5030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Altered mRNA translational control is emerging as a critical factor in cancer development and progression. Targeting specific elements of the translational machinery, such as mTORC1 or eIF4E, is emerging as a new strategy for innovative cancer therapy. While translation of most mRNAs takes place through cap-dependent mechanisms, a sub-population of cellular mRNA species, particularly stress-inducible mRNAs with highly structured 5'-UTR regions, are primarily translated through cap-independent mechanisms. Intriguingly, many of these mRNAs encode proteins that are involved in tumour cell adaptation to microenvironmental stress, and thus linked to aggressive behaviour including tumour invasion and metastasis. This necessitates a rigorous search for links between microenvironmental stress and aggressive tumour phenotypes. Under stress, cells block global protein synthesis to preserve energy while maintaining selective synthesis of proteins that support cell survival. One highly conserved mechanism to regulate protein synthesis under cell stress is to sequester mRNAs into cytosolic aggregates called stress granules (SGs), where their translation is silenced. SGs confer survival advantages and chemotherapeutic resistance to tumour cells under stress. Recently, it has been shown that genetically blocking SG formation dramatically reduces tumour invasive and metastatic capacity in vivo. Therefore, targeting SG formation might represent a potential treatment strategy to block cancer metastasis. Here, we present the critical link between selective mRNA translation, stress adaptation, SGs, and tumour progression. Further, we also explain how deciphering mechanisms of selective mRNA translation occurs under cell stress holds great promise for the identification of new targets in the treatment of cancer. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Egypt
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
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32
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Suresh PS, Tsutsumi R, Venkatesh T. YBX1 at the crossroads of non-coding transcriptome, exosomal, and cytoplasmic granular signaling. Eur J Cell Biol 2018; 97:163-167. [PMID: 29478751 DOI: 10.1016/j.ejcb.2018.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/28/2018] [Accepted: 02/14/2018] [Indexed: 01/09/2023] Open
Abstract
YBX1 (Y box binding protein 1) is an RNA-/DNA-binding multifunctional protein harboring the classical cold shock protein (CSD) domain, an A/P domain, and a long C-terminal domain with alternating positively and negatively charged amino acids. It is a well-established oncogenic transcriptional factor, and regulates apoptosis, translation, cell proliferation, mRNA splicing, repair, differentiation, and stress response. The non-coding transcriptome has added yet another layer of complexity to the YBX1-mediated master regulation of cellular functions. Interestingly, YBX1 has been shown to localize to cytoplasmic granules such as P granules and stress granules. These granules regulate the non-coding transcriptome profile as well as mRNA translation and degradation. In this review, we discuss the recent findings on YBX1 signaling as mediated by various classes of non-coding RNAs, and on the functions of YBX1 at P granules, stress granules, exosomes, and mitochondria. YBX1 is a well-established target for cancer therapy and understanding its functions at organelles and ncRNA transcriptomes will shed new insights for devising organelle based anti-cancer therapies.
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Affiliation(s)
- Padmanaban S Suresh
- Department of Biosciences, Mangalore University, Mangalagangothri, 574199, India
| | - Rie Tsutsumi
- Division of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, Kerala, India.
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33
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Roles of tRNA-derived fragments in human cancers. Cancer Lett 2018; 414:16-25. [DOI: 10.1016/j.canlet.2017.10.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022]
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Wang Y, Su J, Fu D, Wang Y, Chen Y, Chen R, Qin G, Zuo J, Yue D. The Role of YB1 in Renal Cell Carcinoma Cell Adhesion. Int J Med Sci 2018; 15:1304-1311. [PMID: 30275756 PMCID: PMC6158664 DOI: 10.7150/ijms.25580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/28/2018] [Indexed: 11/05/2022] Open
Abstract
Background: Y-box binding protein 1 (YB1) is a multifunctional protein involved in many processes related to cancer progression and metastasis. Methods: In this study, we constructed YB1 knockdown stable renal cell carcinoma (RCC) cell line 786-0. The gene expression profile of 786-0 was performed by DNA microarray analysis to identify genes that were regulated by YB1. Real-time PCR and western blotting were used to test the genes and proteins expression. Transforming growth factor-β (TGF-β) activity was detected by dual-luciferase reporter assay. Cell adhesion assay was used to determine RCC cell adhesion ability. Results: Pathway analysis revealed that YB1 knockdown influenced cell adhesion molecules (CAMs). We further verified four genes (CLDN4, NRXN3, ITGB8, and VCAN) related to CAMs by real-time PCR, and confirmed that YB1 regulated the expression of ITGB8 in RCC. Functional assays demonstrated that knockdown of YB1 significantly inhibited the cell adhesion of 786-0 cells in vitro. In addition, YB1 affected TGF-β activation. Conclusion: Our study demonstrated that YB1 modulated the adhesion ability of renal cell carcinoma cells by regulating ITGB8 and TGF-β.
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Affiliation(s)
- Yong Wang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China
| | - Jing Su
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China
| | - Donghe Fu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China.,Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, China
| | - Yiting Wang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China
| | - Yajing Chen
- Research Center of Molecular Biology, Inner Mongolia Medical University, Hohhot 010059, China
| | - Ruibing Chen
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Guoxuan Qin
- School of Microelectronics, Tianjin University, Tianjin 300072, China
| | - Jing Zuo
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China
| | - Dan Yue
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin 300070, China
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Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes (Basel) 2017; 8:genes8120366. [PMID: 29206165 PMCID: PMC5748684 DOI: 10.3390/genes8120366] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 11/16/2022] Open
Abstract
Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA. In small RNA, we discuss miRNA, transfer RNA, piwi-interacting RNA, small nucleolar RNA, small nuclear RNA, Y RNA, single recognition particle RNA, and 7SK RNA. We elaborate on the origin, detection method, and potential association with disease, putative functional mechanisms, and public resources for these non-coding RNAs. We aim to provide readers with a complete overview of non-coding RNAs and incite additional interest in non-coding RNA research.
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Affiliation(s)
- Jing Wang
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, TN 37232, USA.
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Yan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87102, USA.
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36
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Structural features of the interaction of the 3'-untranslated region of mRNA containing exosomal RNA-specific motifs with YB-1, a potential mediator of mRNA sorting. Biochimie 2017; 144:134-143. [PMID: 29133115 DOI: 10.1016/j.biochi.2017.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/08/2017] [Indexed: 12/18/2022]
Abstract
We have previously shown that YB-1 is the only protein of the HEK293 cell cytoplasmic (S100) extract that specifically interacts with RNA hairpins each containing one of the motifs ACCAGCCU (1), CAGUGAGC (2) and UAAUCCCA (3), which had been identified as often found in exosomal RNA and proposed as potential cis-acting elements targeting RNAs into exosomes. Here we explored the interactions of YB-1 with a fragment of the 3'-untranslated region (UTR) of septin 14 mRNA (SEPT14 RNA), which contains all three motifs. We demonstrated the occurrence of YB-1 among proteins pulled down from the HEK293 S100 extract using biotinylated SEPT14 RNA. With recombinant YB-1, it was found that SEPT14 RNA can bind up to 5 moles of protein per mole of RNA in a cooperative manner, which was shown to be mainly facilitated by the presence of the above motifs. RNA hairpins with motifs 1 and 2 competed with SEPT14 RNA for binding to the protein, whereas that with motif 3 was less competitive, in accordance with the affinity of YB-1 for these RNA hairpins. With YB-1-bound RNA, nucleotides protected from attack by hydroxyl radicals were revealed in all three motifs, although hairpins with motif 2 and especially with motif 1 contained many protected nucleotides outside the motifs, suggesting that the specific environments of these motifs contribute significantly to the YB-1 binding. An analysis of the environments of motifs 1-3 in the HEK293 cell mRNA 3' UTRs gained from RNA-seq data led us to conclude that the primary binding sites of YB-1 in the 3' UTRs are hairpins containing some part of the motif along with its specific surroundings; the consensus sequences of these hairpins were derived. Thus, our findings provide a new understanding of the structural basis of the interactions between YB-1 and mRNAs carrying the aforementioned motifs.
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Abrakhi S, Kretov DA, Desforges B, Dobra I, Bouhss A, Pastré D, Hamon L. Nanoscale Analysis Reveals the Maturation of Neurodegeneration-Associated Protein Aggregates: Grown in mRNA Granules then Released by Stress Granule Proteins. ACS NANO 2017; 11:7189-7200. [PMID: 28657719 DOI: 10.1021/acsnano.7b03071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
TDP-43 and FUS are two mRNA-binding proteins associated with neurodegenerative diseases that form cytoplasmic inclusions with prion-like properties in affected neurons. Documenting the early stages of the formation of TDP-43 or FUS protein aggregates and the role of mRNA stress granules that are considered as critical intermediates for protein aggregation is therefore of interest to understand disease propagation. Here, we developed a single molecule approach via atomic force microscopy (AFM), which provides structural information out of reach by fluorescence microscopy. In addition, the aggregation process can be probed in the test tube without separating the interacting partners, which would affect the thermodynamic equilibrium. The results demonstrate that isolated mRNA molecules serve as crucibles to promote TDP-43 and FUS multimerization. Their subsequent merging results in the formation of mRNA granules containing TDP-43 and FUS aggregates. Interestingly, TDP-43 or FUS protein aggregates can be released from mRNA granules by either YB-1 or G3BP1, two stress granule proteins that compete for the binding to mRNA with TDP-43 and FUS. Altogether, the results indicate that age-related successive assembly/disassembly of stress granules in neurons, regulated by mRNA-binding proteins such as YB-1 and G3BP1, could be a source of protein aggregation.
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Affiliation(s)
- Sanae Abrakhi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
| | - Dmitry A Kretov
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Moscow Region 142290, Russia
| | - Bénédicte Desforges
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
| | - Ioana Dobra
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay , 91025 Evry, France
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Kossinova OA, Gopanenko AV, Tamkovich SN, Krasheninina OA, Tupikin AE, Kiseleva E, Yanshina DD, Malygin AA, Ven'yaminova AG, Kabilov MR, Karpova GG. Cytosolic YB-1 and NSUN2 are the only proteins recognizing specific motifs present in mRNAs enriched in exosomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:664-673. [PMID: 28341602 DOI: 10.1016/j.bbapap.2017.03.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/27/2022]
Abstract
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC. RNA hairpins other than those mentioned above pull out neither YB-1 nor NSUN2. Both these proteins are found in exosomes secreted by HEK293 cells. YB-1 for all that is detected as a form having a slightly higher electrophoretic mobility than that of YB-1 associated with the above RNA hairpins, assuming changes in posttranslational modifications of the protein during its transfer from cytoplasm into exosomes. Next generation sequencing of total exosomal RNA (eRNA) reveals a large representative set of RNA species, including mRNAs containing the above-mentioned motifs. The degree of enrichment in exosomes with this kind of mRNAs strongly depends on the locations of eRNA-specific motifs within the mRNA sequences. Altogether, our findings point to YB-1 and NSUN2 as possible mediators of the process of transfer of specific mRNAs into exosomes, allowing us to speculate on an involvement of these proteins in the mRNA sorting via the recognition of the above motifs.
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Affiliation(s)
- Olga A Kossinova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana N Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Elena Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 10, Novosibirsk 630090, Russia
| | - Darya D Yanshina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alia G Ven'yaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia.
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RSK-mediated nuclear accumulation of the cold-shock Y-box protein-1 controls proliferation of T cells and T-ALL blasts. Cell Death Differ 2016; 24:371-383. [PMID: 28009354 DOI: 10.1038/cdd.2016.141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/07/2016] [Accepted: 10/27/2016] [Indexed: 12/26/2022] Open
Abstract
Deregulated proliferation is key to tumor progression. Although unrestricted proliferation of solid tumor cells correlates with the cold-shock protein Y-box (YB)-binding protein-1 accumulation in the nuclei, little is known about its expression and function in hematopoietic malignancies, such as T-cell acute lymphoblastic leukemia (T-ALL). Here we show that YB-1 protein is highly enriched in the nuclei of activated T cells and malignant human T-ALL cell lines but not in resting T cells. YB-1 S102 mutations that either mimic (S102D) or prevent phosphorylation (S102N) led to accumulation of YB-1 in the nucleus of T cells or strictly excluded it, respectively. Inactivation of ribosomal S6 kinase (RSK) was sufficient to abrogate T-cell and T-ALL cell proliferation, suggesting that RSK mediates cell-cycle progression, possibly dependent on YB-1-phosphorylation. Indeed, phosphomimetic YB-1S102D enhanced proliferation implying that S102 phosphorylation is a prerequisite for malignant T-cell proliferation. At initial diagnosis of T-ALL, YB-1 localization was significantly altered in the nuclei of tumor blasts derived from bone marrow or peripheral blood. Our data show deregulated YB-1 in the nucleus as a yet unreported characteristic of T-ALL blasts and may refine strategies to restrict progression of hematopoietic tumors.
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Lyons SM, Achorn C, Kedersha NL, Anderson PJ, Ivanov P. YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression. Nucleic Acids Res 2016; 44:6949-60. [PMID: 27174937 PMCID: PMC5001593 DOI: 10.1093/nar/gkw418] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/30/2016] [Indexed: 12/16/2022] Open
Abstract
Stress-induced angiogenin (ANG)-mediated tRNA cleavage promotes a cascade of cellular events that starts with production of tRNA-derived stress-induced RNAs (tiRNAs) and culminates with enhanced cell survival. This stress response program relies on a subset tiRNAs that inhibit translation initiation and induce the assembly of stress granules (SGs), cytoplasmic ribonucleoprotein complexes with cytoprotective and pro-survival properties. SG-promoting tiRNAs bear oligoguanine motifs at their 5'-ends, assemble G-quadruplex-like structures and interact with the translational silencer YB-1. We used CRISPR/Cas9-based genetic manipulations and biochemical approaches to examine the role of YB-1 in tiRNA-mediated translational repression and SG assembly. We found that YB-1 directly binds to tiRNAs via its cold shock domain. This interaction is required for packaging of tiRNA-repressed mRNAs into SGs but is dispensable for tiRNA-mediated translational repression. Our studies reveal the functional role of YB-1 in the ANG-mediated stress response program.
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Affiliation(s)
- Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Achorn
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nancy L Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA The Broad Institute of Harvard and M.I.T., Cambridge, MA 02142, USA
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41
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Donaubauer EM, Hunzicker-Dunn ME. Extracellular Signal-regulated Kinase (ERK)-dependent Phosphorylation of Y-Box-binding Protein 1 (YB-1) Enhances Gene Expression in Granulosa Cells in Response to Follicle-stimulating Hormone (FSH). J Biol Chem 2016; 291:12145-60. [PMID: 27080258 DOI: 10.1074/jbc.m115.705368] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/14/2022] Open
Abstract
Within the ovarian follicle, immature oocytes are surrounded and supported by granulosa cells (GCs). Stimulation of GCs by FSH leads to their proliferation and differentiation, events that are necessary for fertility. FSH activates multiple signaling pathways to regulate genes necessary for follicular maturation. Herein, we investigated the role of Y-box-binding protein-1 (YB-1) within GCs. YB-1 is a nucleic acid binding protein that regulates transcription and translation. Our results show that FSH promotes an increase in the phosphorylation of YB-1 on Ser(102) within 15 min that is maintained at significantly increased levels until ∼8 h post treatment. FSH-stimulated phosphorylation of YB-1(Ser(102)) is prevented by pretreatment of GCs with the PKA-selective inhibitor PKA inhibitor (PKI), the MEK inhibitor PD98059, or the ribosomal S6 kinase-2 (RSK-2) inhibitor BI-D1870. Thus, phosphorylation of YB-1 on Ser(102) is PKA-, ERK-, and RSK-2-dependent. However, pretreatment of GCs with the protein phosphatase 1 (PP1) inhibitor tautomycin increased phosphorylation of YB-1(Ser(102)) in the absence of FSH; FSH did not further increase YB-1(Ser(102)) phosphorylation. This result suggests that the major effect of RSK-2 is to inhibit PP1 rather than to directly phosphorylate YB-1 on Ser(102) YB-1 coimmunoprecipitated with PP1β catalytic subunit and RSK-2. Transduction of GCs with the dephospho-adenoviral-YB-1(S102A) mutant prevented the induction by FSH of Egfr, Cyp19a1, Inha, Lhcgr, Cyp11a1, Hsd17b1, and Pappa mRNAs and estradiol-17β production. Collectively, our results reveal that phosphorylation of YB-1 on Ser(102) via the ERK/RSK-2 signaling pathway is necessary for FSH-mediated expression of target genes required for maturation of follicles to a preovulatory phenotype.
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Affiliation(s)
- Elyse M Donaubauer
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164
| | - Mary E Hunzicker-Dunn
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164
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Kretov DA, Curmi PA, Hamon L, Abrakhi S, Desforges B, Ovchinnikov LP, Pastré D. mRNA and DNA selection via protein multimerization: YB-1 as a case study. Nucleic Acids Res 2015; 43:9457-73. [PMID: 26271991 PMCID: PMC4627072 DOI: 10.1093/nar/gkv822] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/29/2015] [Indexed: 12/16/2022] Open
Abstract
Translation is tightly regulated in cells for keeping adequate protein levels, this task being notably accomplished by dedicated mRNA-binding proteins recognizing a specific set of mRNAs to repress or facilitate their translation. To select specific mRNAs, mRNA-binding proteins can strongly bind to specific mRNA sequences/structures. However, many mRNA-binding proteins rather display a weak specificity to short and redundant sequences. Here we examined an alternative mechanism by which mRNA-binding proteins could inhibit the translation of specific mRNAs, using YB-1, a major translation regulator, as a case study. Based on a cooperative binding, YB-1 forms stable homo-multimers on some mRNAs while avoiding other mRNAs. Via such inhomogeneous distribution, YB-1 can selectively inhibit translation of mRNAs on which it has formed stable multimers. This novel mechanistic view on mRNA selection may be shared by other proteins considering the elevated occurrence of multimerization among mRNA-binding proteins. Interestingly, we also demonstrate how, by using the same mechanism, YB-1 can form multimers on specific DNA structures, which could provide novel insights into YB-1 nuclear functions in DNA repair and multi-drug resistance.
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Affiliation(s)
- Dmitry A Kretov
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Patrick A Curmi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Sanae Abrakhi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Bénédicte Desforges
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
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43
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Kljashtorny V, Nikonov S, Ovchinnikov L, Lyabin D, Vodovar N, Curmi P, Manivet P. The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions. PLoS One 2015; 10:e0130318. [PMID: 26147853 PMCID: PMC4493011 DOI: 10.1371/journal.pone.0130318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/19/2015] [Indexed: 11/19/2022] Open
Abstract
The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD). Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP), albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.
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Affiliation(s)
- Vladislav Kljashtorny
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 829, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Bd François Mitterrand, 91025 Evry Cedex, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France
- Assistance Publique—Hôpitaux de paris (APHP), Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Lev Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Dmitry Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nicolas Vodovar
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France
| | - Patrick Curmi
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 829, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Bd François Mitterrand, 91025 Evry Cedex, France
| | - Philippe Manivet
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France
- Assistance Publique—Hôpitaux de paris (APHP), Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
- UBCS (Unité de Biologie Clinique Structurale)-Centre de Ressources Biologiques BB-0033-00064, 2 rue Ambroise Paré, 75475 Paris cedex 10, France
- * E-mail:
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Anderson P, Ivanov P. tRNA fragments in human health and disease. FEBS Lett 2014; 588:4297-304. [PMID: 25220675 PMCID: PMC4339185 DOI: 10.1016/j.febslet.2014.09.001] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/07/2023]
Abstract
Transfer RNA (tRNA) is traditionally considered to be an adaptor molecule that helps ribosomes to decode messenger RNA (mRNA) and synthesize protein. Recent studies have demonstrated that tRNAs also serve as a major source of small non-coding RNAs that possess distinct and varied functions. These tRNA fragments are heterogeneous in size, nucleotide composition, biogenesis and function. Here we describe multiple roles that tRNA fragments play in cell physiology and discuss their relevance to human health and disease.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Transfer RNAs (tRNA) are best known for their role as adaptors during translation of the genetic code. Beyond their canonical role during protein biosynthesis, tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression. Aminoacylated tRNAs have also been implicated as substrates for non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosyntheses. Most recently tRNA fragments, or tRFs, have also been recognized to play regulatory roles. Here, we examine in more detail some of the new functions emerging for tRNA in a variety of cellular processes outside of protein synthesis.
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Affiliation(s)
- Medha Raina
- Department of Microbiology, The Ohio State Biochemistry Program, The Ohio State University Columbus, OH, USA ; Center for RNA Biology, The Ohio State University Columbus, OH, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State Biochemistry Program, The Ohio State University Columbus, OH, USA ; Center for RNA Biology, The Ohio State University Columbus, OH, USA
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46
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Roy S, Morse D. The dinoflagellate Lingulodinium has predicted casein kinase 2 sites in many RNA binding proteins. Protist 2014; 165:330-42. [PMID: 24810178 DOI: 10.1016/j.protis.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 11/18/2022]
Abstract
Many cellular processes in the dinoflagellate Lingulodinium polyedrum are controlled by a circadian (daily) clock. Since the activity of proteins involved in various metabolic pathways or in regulating gene expression can be affected by phosphorylation, we established a generalized phosphoproteome catalog using LC-MS/MS to analyze a phosphoprotein-enriched fraction. Over 11,000 peptides were identified by comparison to a Lingulodinium transcriptome, and 527 of these had at least one identified phosphosite. Gene ontology analysis revealed that RNA binding and translation were one of the major categories among these proteins identified by these peptides. Since casein kinase 2 (CK2) is known to be important in eukaryotic circadian biology substrates, we next tried to identify specific substrates for this kinase. To achieve this we first classified and catalogued the kinases in the Lingulodinium transcriptome then assigned the different phosphosites to the different kinase classes. Interestingly, potential CK2 targets include a substantial proportion of RNA binding proteins. Phosphosite identification thus provides a promising new approach to investigate the Lingulodinium circadian system.
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Affiliation(s)
- Sougata Roy
- Institut de Recherche en BiologieVégétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, Québec, Canada H1X 2B2
| | - David Morse
- Institut de Recherche en BiologieVégétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, Québec, Canada H1X 2B2.
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47
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Willis WL, Hariharan S, David JJ, Strauch AR. Transglutaminase-2 mediates calcium-regulated crosslinking of the Y-box 1 (YB-1) translation-regulatory protein in TGFβ1-activated myofibroblasts. J Cell Biochem 2014; 114:2753-69. [PMID: 23804301 DOI: 10.1002/jcb.24624] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/25/2013] [Indexed: 01/23/2023]
Abstract
Myofibroblast differentiation is required for wound healing and accompanied by activation of smooth muscle α-actin (SMαA) gene expression. The stress-response protein, Y-box binding protein-1 (YB-1) binds SMαA mRNA and regulates its translational activity. Activation of SMαA gene expression in human pulmonary myofibroblasts by TGFβ1 was associated with formation of denaturation-resistant YB-1 oligomers with selective affinity for a known translation-silencer sequence in SMαA mRNA. We have determined that YB-1 is a substrate for the protein-crosslinking enzyme transglutaminase 2 (TG2) that catalyzes calcium-dependent formation of covalent γ-glutamyl-isopeptide linkages in response to reactive oxygen signaling. TG2 transamidation reactions using intact cells, cell lysates, and recombinant YB-1 revealed covalent crosslinking of the 50 kDa YB-1 polypeptide into protein oligomers that were distributed during SDS-PAGE over a 75-250 kDa size range. In vitro YB-1 transamidation required nanomolar levels of calcium and was enhanced by the presence of SMαA mRNA. In human pulmonary fibroblasts, YB-1 crosslinking was inhibited by (a) anti-oxidant cystamine, (b) the reactive-oxygen antagonist, diphenyleneiodonium, (c) competitive inhibition of TG2 transamidation using the aminyl-surrogate substrate, monodansylcadaverine, and (d) transfection with small-interfering RNA specific for human TG2 mRNA. YB-1 crosslinking was partially reversible as a function of oligomer-substrate availability and TG2 enzyme concentration. Intracellular calcium accumulation and peroxidative stress in injury-activated myofibroblasts may govern SMαA mRNA translational activity during wound healing via TG2-mediated crosslinking of the YB-1 mRNA-binding protein.
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Affiliation(s)
- William L Willis
- Department of Physiology and Cell Biology, The Integrated Biomedical Sciences Graduate Program, and the Ohio State Biochemistry Program, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, Ohio, 43210
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Lyabin DN, Nigmatullina LF, Doronin AN, Eliseeva IA, Ovchinnikov LP. Identification of proteins specifically interacting with YB-1 mRNA 3' UTR and the effect of hnRNP Q on YB-1 mRNA translation. BIOCHEMISTRY (MOSCOW) 2014; 78:651-9. [PMID: 23980891 DOI: 10.1134/s0006297913060102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, proteins specifically interacting with the 3' untranslated region (UTR) of mRNA of the multifunctional Y-box-binding protein 1 (YB-1) were identified. One of these, hnRNP Q, was shown to specifically interact with the regulatory element (RE) in YB-1 mRNA 3' UTR and to inhibit translation of this mRNA. Its binding to the RE was accompanied by displacement from this element of the poly(A)-binding protein (PABP), a positive regulator of YB-1 mRNA translation, and by enhanced binding of the negative YB-1 mRNA translation regulator - YB-1 itself.
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Affiliation(s)
- D N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 protein: functions and regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:95-110. [PMID: 24217978 DOI: 10.1002/wrna.1200] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/23/2013] [Accepted: 09/27/2013] [Indexed: 12/15/2022]
Abstract
The Y-box binding protein 1 (YB-1, YBX1) is a member of the family of DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. It falls into a group of intrinsically disordered proteins that do not follow the classical rule 'one protein-one function' but introduce a novel principle stating that a disordered structure suggests many functions. YB-1 participates in a wide variety of DNA/RNA-dependent events, including DNA reparation, pre-mRNA transcription and splicing, mRNA packaging, and regulation of mRNA stability and translation. At the cell level, the multiple activities of YB-1 are manifested as its involvement in cell proliferation and differentiation, stress response, and malignant cell transformation. WIREs RNA 2014, 5:95-110. doi: 10.1002/wrna.1200 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Kumari P, Gilligan PC, Lim S, Tran LD, Winkler S, Philp R, Sampath K. An essential role for maternal control of Nodal signaling. eLife 2013; 2:e00683. [PMID: 24040511 PMCID: PMC3771576 DOI: 10.7554/elife.00683] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/06/2013] [Indexed: 12/26/2022] Open
Abstract
Growth factor signaling is essential for pattern formation, growth, differentiation, and maintenance of stem cell pluripotency. Nodal-related signaling factors are required for axis formation and germ layer specification from sea urchins to mammals. Maternal transcripts of the zebrafish Nodal factor, Squint (Sqt), are localized to future embryonic dorsal. The mechanisms by which maternal sqt/nodal RNA is localized and regulated have been unclear. Here, we show that maternal control of Nodal signaling via the conserved Y box-binding protein 1 (Ybx1) is essential. We identified Ybx1 via a proteomic screen. Ybx1 recognizes the 3’ untranslated region (UTR) of sqt RNA and prevents premature translation and Sqt/Nodal signaling. Maternal-effect mutations in zebrafish ybx1 lead to deregulated Nodal signaling, gastrulation failure, and embryonic lethality. Implanted Nodal-coated beads phenocopy ybx1 mutant defects. Thus, Ybx1 prevents ectopic Nodal activity, revealing a new paradigm in the regulation of Nodal signaling, which is likely to be conserved. DOI:http://dx.doi.org/10.7554/eLife.00683.001 In many organisms, embryonic development is controlled in part by RNAs that are deposited into the egg as it forms inside the mother. These ‘maternal RNAs’ may localize to particular regions of the egg or embryo, where they are then exclusively translated into protein and carry out their specific function. This helps to establish asymmetry in the developing organism—that is, to produce tissues that will eventually become the top or bottom, front or back, and left or right of the organism. One such maternal RNA encodes Nodal, a key signaling molecule that is conserved across vertebrate and some invertebrate organisms. In zebrafish, the equivalent RNA is called squint, and plays an important role in embryonic development. The squint RNA deposited by the mother localizes to the dorsal region—the embryo’s back—and signals that region to make dorsal tissues, but how squint is regulated is not well understood. Now, Kumari et al. identify a protein that controls the positioning of squint RNA, and find that it can also prevent this RNA from being translated into protein. The squint RNA contains a ‘dorsal localization element’ that recruits it to the dorsal cells of the embryo by the 4-cell stage (i.e., within two cell divisions after the egg is fertilized). Kumari et al. identified a protein called Ybx1 that could bind to this element: this protein may help to correctly position RNAs in many other organisms, including fruit flies and mammals. Strikingly, embryos formed abnormally when their maternally derived Ybx1 protein was mutant, and these mutations also prevented the squint RNA from localizing properly. This suggests that maternally derived Ybx1 protein directly regulates the squint RNA. As well as positioning the squint RNA correctly, the embryo must translate this RNA into protein at the right time. In embryos with mutant maternal Ybx1 protein, the Squint protein could be detected at the 16-cell stage, whereas in wild-type embryos this protein is not translated until the 256-cell stage; this indicates that Ybx1 protein might normally repress the translation of the squint RNA. Indeed, Kumari et al. found that Ybx1 binds to another protein—eIF4E—that recruits mRNAs to the ribosome (the cell’s translational machinery). Ybx1 might therefore prevent eIF4E from associating with other components of the ribosomal complex, and initiating the translation of the squint RNA, until additional signals have been received. It will be interesting to determine how widespread this regulatory mechanism is in other organisms. DOI:http://dx.doi.org/10.7554/eLife.00683.002
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Affiliation(s)
- Pooja Kumari
- Temasek Life Sciences Laboratory , National University of Singapore , Singapore , Singapore ; Department of Biological Sciences , National University of Singapore , Singapore , Singapore
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