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Corrales-Guerrero L, Díaz-Moreno I. Deciphering the role of Zn 2+-binding histidines from TIA-1 on the assembly and dynamics of stress granules. Biofactors 2024; 50:750-755. [PMID: 38193795 DOI: 10.1002/biof.2037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
T-cell intracellular antigen-1 (TIA-1) is a key RNA-binding protein that participates in translation regulation and RNA splicing. TIA-1 undergoes liquid-liquid phase separation as a fundamental mechanism that enables the condensation of RNA and proteins into membraneless organelles called stress granules (SGs). However, this dynamic behavior can lead to aberrant fibril formation, implicated in neurodegenerative disorders, and must be tightly regulated. In this study, we investigated the role in the cell of histidine residues His94 and His96, responsible for Zn2+ binding. Using fluorescence microscopy, we found that the specific binding site formed by these residues is critical for SG assembly. Furthermore, it also plays a role maintaining the dynamic behavior of SG-assembled TIA-1. Collectively, our findings confirm the physiological relevance of TIA-1 His94 and His96 in the Zn2+-mediated regulatory mechanism for protection against fibril formation in SGs.
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Affiliation(s)
| | - Irene Díaz-Moreno
- Institute for Chemical Research, University of Seville-CSIC, Seville, Spain
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2
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Yang Y, Fritzsching KJ, He S, McDermott AE. Zinc Alters the Supramolecular Organization of Nucleic Acid Complexes with Full-Length TIA1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525508. [PMID: 36747652 PMCID: PMC9900833 DOI: 10.1101/2023.01.25.525508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
T-Cell Intracellular Antigen-1 (TIA1) is a 43 kDa multi-domain RNA-binding protein involved in stress granule formation during eukaryotic stress response, and has been implicated in neurodegenerative diseases including Welander distal myopathy and amyotrophic lateral sclerosis. TIA1 contains three RNA recognition motifs (RRMs), which are capable of binding nucleic acids and a C-terminal Q/N-rich prion-related domain (PRD) which has been variously described as intrinsically disordered or prion inducing and is believed to play a role in promoting liquid-liquid phase separation connected with the assembly of stress granule formation. Motivated by the fact that our prior work shows RRMs 2 and 3 are well-ordered in an oligomeric full-length form, while RRM1 and the PRD appear to phase separate, the present work addresses whether the oligomeric form is functional and competent for binding, and probes the consequences of nucleic acid binding for oligomerization and protein conformation change. New SSNMR data show that ssDNA binds to full-length oligomeric TIA1 primarily at the RRM2 domain, but also weakly at the RRM3 domain, and Zn 2+ binds primarily to RRM3. Binding of Zn 2+ and DNA was reversible for the full-length wild type oligomeric form, and did not lead to formation of amyloid fibrils, despite the presence of the C-terminal prion-related domain. While TIA1:DNA complexes appear as long "daisy chained" structures, the addition of Zn 2+ caused the structures to collapse. We surmise that this points to a regulatory role for Zn 2+ . By occupying various "half" binding sites on RRM3 Zn 2+ may shift the nucleic acid binding off RRM3 and onto RRM2. More importantly, the use of different half sites on different monomers may introduce a mesh of crosslinks in the supramolecular complex rendering it compact and markedly reducing the access to the nucleic acids (including transcripts) from solution.
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3
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Millar SR, Huang JQ, Schreiber KJ, Tsai YC, Won J, Zhang J, Moses AM, Youn JY. A New Phase of Networking: The Molecular Composition and Regulatory Dynamics of Mammalian Stress Granules. Chem Rev 2023. [PMID: 36662637 PMCID: PMC10375481 DOI: 10.1021/acs.chemrev.2c00608] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Stress granules (SGs) are cytosolic biomolecular condensates that form in response to cellular stress. Weak, multivalent interactions between their protein and RNA constituents drive their rapid, dynamic assembly through phase separation coupled to percolation. Though a consensus model of SG function has yet to be determined, their perceived implication in cytoprotective processes (e.g., antiviral responses and inhibition of apoptosis) and possible role in the pathogenesis of various neurodegenerative diseases (e.g., amyotrophic lateral sclerosis and frontotemporal dementia) have drawn great interest. Consequently, new studies using numerous cell biological, genetic, and proteomic methods have been performed to unravel the mechanisms underlying SG formation, organization, and function and, with them, a more clearly defined SG proteome. Here, we provide a consensus SG proteome through literature curation and an update of the user-friendly database RNAgranuleDB to version 2.0 (http://rnagranuledb.lunenfeld.ca/). With this updated SG proteome, we use next-generation phase separation prediction tools to assess the predisposition of SG proteins for phase separation and aggregation. Next, we analyze the primary sequence features of intrinsically disordered regions (IDRs) within SG-resident proteins. Finally, we review the protein- and RNA-level determinants, including post-translational modifications (PTMs), that regulate SG composition and assembly/disassembly dynamics.
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Affiliation(s)
- Sean R Millar
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jie Qi Huang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Karl J Schreiber
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yi-Cheng Tsai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jiyun Won
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jianping Zhang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5T 3A1, Canada.,The Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Ji-Young Youn
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
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4
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West DL, Loughlin FE, Rivero-Rodríguez F, Vankadari N, Velázquez-Cruz A, Corrales-Guerrero L, Díaz-Moreno I, Wilce JA. Regulation of TIA-1 Condensates: Zn2+ and RGG Motifs Promote Nucleic Acid Driven LLPS and Inhibit Irreversible Aggregation. Front Mol Biosci 2022; 9:960806. [PMID: 35911965 PMCID: PMC9329571 DOI: 10.3389/fmolb.2022.960806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Stress granules are non-membrane bound RNA-protein granules essential for survival during acute cellular stress. TIA-1 is a key protein in the formation of stress granules that undergoes liquid-liquid phase separation by association with specific RNAs and protein-protein interactions. However, the fundamental properties of the TIA-1 protein that enable phase-separation also render TIA-1 susceptible to the formation of irreversible fibrillar aggregates. Despite this, within physiological stress granules, TIA-1 is not present as fibrils, pointing to additional factors within the cell that prevent TIA-1 aggregation. Here we show that heterotypic interactions with stress granule co-factors Zn2+ and RGG-rich regions from FUS each act together with nucleic acid to induce the liquid-liquid phase separation of TIA-1. In contrast, these co-factors do not enhance nucleic acid induced fibril formation of TIA-1, but rather robustly inhibit the process. NMR titration experiments revealed specific interactions between Zn2+ and H94 and H96 in RRM2 of TIA-1. Strikingly, this interaction promotes multimerization of TIA-1 independently of the prion-like domain. Thus, through different molecular mechanisms, these stress granule co-factors promote TIA-1 liquid-liquid phase separation and suppress fibrillar aggregates, potentially contributing to the dynamic nature of stress granules and the cellular protection that they provide.
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Affiliation(s)
- Danella L. West
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Fionna E. Loughlin
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | | | - Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | | | | | - Irene Díaz-Moreno
- Institute for Chemical Research, University of Seville—CSIC, Seville, Spain
- *Correspondence: Irene Díaz-Moreno, ; Jacqueline A. Wilce,
| | - Jacqueline A. Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- *Correspondence: Irene Díaz-Moreno, ; Jacqueline A. Wilce,
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5
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Velázquez-Cruz A, Baños-Jaime B, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation. Front Mol Biosci 2021; 8:658852. [PMID: 33987205 PMCID: PMC8111222 DOI: 10.3389/fmolb.2021.658852] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.
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Affiliation(s)
- Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
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6
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Loughlin FE, West DL, Gunzburg MJ, Waris S, Crawford SA, Wilce MCJ, Wilce JA. Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1. Nucleic Acids Res 2021; 49:2403-2417. [PMID: 33621982 PMCID: PMC7969032 DOI: 10.1093/nar/gkab080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022] Open
Abstract
TIA-1 is an RNA-binding protein that sequesters target RNA into stress granules under conditions of cellular stress. Promotion of stress granule formation by TIA-1 depends upon self-association of its prion-like domain that facilitates liquid-liquid phase separation and is thought to be enhanced via RNA binding. However, the mechanisms underlying the influence of RNA on TIA-1 self-association have not been previously demonstrated. Here we have investigated the self-associating properties of full-length TIA-1 in the presence of designed and native TIA-1 nucleic acid binding sites in vitro, monitoring phase separation, fibril formation and shape. We show that single stranded RNA and DNA induce liquid-liquid phase separation of TIA-1 in a multisite, sequence-specific manner and also efficiently promote formation of amyloid-like fibrils. Although RNA binding to a single site induces a small conformational change in TIA-1, this alone does not enhance phase separation of TIA-1. Tandem binding sites are required to enhance phase separation of TIA-1 and this is finely tuned by the protein:binding site stoichiometry rather than nucleic acid length. Native tandem TIA-1 binding sites within the 3′ UTR of p53 mRNA also efficiently enhance phase separation of TIA-1 and thus may potentially act as potent nucleation sites for stress granule assembly.
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Affiliation(s)
- Fionna E Loughlin
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Danella L West
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Menachem J Gunzburg
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria 3052, Australia
| | - Saboora Waris
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simon A Crawford
- Ramaciotti Centre For Cryo Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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7
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Ostareck DH, Ostareck-Lederer A. RNA-Binding Proteins in the Control of LPS-Induced Macrophage Response. Front Genet 2019; 10:31. [PMID: 30778370 PMCID: PMC6369361 DOI: 10.3389/fgene.2019.00031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
Innate immune response is triggered by pathogen components, like lipopolysaccharides (LPS) of gram-negative bacteria. LPS initiates Toll-like receptor 4 (TLR4) signaling, which involves mitogen activated protein kinases (MAPK) and nuclear factor kappa B (NFκB) in different pathway branches and ultimately induces inflammatory cytokine and chemokine expression, macrophage migration and phagocytosis. Timely gene transcription and post-transcriptional control of gene expression confer the adequate synthesis of signaling molecules. As trans-acting factors RNA binding proteins (RBPs) contribute significantly to the surveillance of gene expression. RBPs are involved in the regulation of mRNA processing, localization, stability and translation. Thereby they enable rapid cellular responses to inflammatory mediators and facilitate a coordinated systemic immune response. Specific RBP binding to conserved sequence motifs in their target mRNAs is mediated by RNA binding domains, like Zink-finger domains, RNA recognition motifs (RRM), and hnRNP K homology domains (KH), often arranged in modular arrays. In this review, we focus on RBPs Tristetraprolin (TTP), human antigen R (HUR), T-cell intracellular antigen 1 related protein (TIAR), and heterogeneous ribonuclear protein K (hnRNP K) in LPS induced macrophages as primary responding immune cells. We discuss recent experiments employing RNA immunoprecipitation and microarray analysis (RIP-Chip) and newly developed individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP), photoactivatable ribonucleoside-enhanced crosslinking (PAR-iCLIP) and RNA sequencing techniques (RNA-Seq). The global mRNA interaction profile analysis of TTP, HUR, TIAR, and hnRNP K exhibited valuable information about the post-transcriptional control of inflammation related gene expression with a broad impact on intracellular signaling and temporal cytokine expression.
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Affiliation(s)
- Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
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8
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García-Mauriño SM, Díaz-Quintana A, Rivero-Rodríguez F, Cruz-Gallardo I, Grüttner C, Hernández-Vellisca M, Díaz-Moreno I. A putative RNA binding protein from Plasmodium vivax apicoplast. FEBS Open Bio 2017; 8:177-188. [PMID: 29435408 PMCID: PMC5794462 DOI: 10.1002/2211-5463.12351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/03/2017] [Accepted: 11/14/2017] [Indexed: 01/30/2023] Open
Abstract
Malaria is caused by Apicomplexa protozoans from the Plasmodium genus entering the bloodstream of humans and animals through the bite of the female mosquitoes. The annotation of the Plasmodium vivax genome revealed a putative RNA binding protein (apiRBP) that was predicted to be trafficked into the apicoplast, a plastid organelle unique to Apicomplexa protozoans. Although a 3D structural model of the apiRBP corresponds to a noncanonical RNA recognition motif with an additional C‐terminal α‐helix (α3), preliminary protein production trials were nevertheless unsuccessful. Theoretical solvation analysis of the apiRBP model highlighted an exposed hydrophobic region clustering α3. Hence, we used a C‐terminal GFP‐fused chimera to stabilize the highly insoluble apiRBP and determined its ability to bind U‐rich stretches of RNA. The affinity of apiRBP toward such RNAs is highly dependent on ionic strength, suggesting that the apiRBP–RNA complex is driven by electrostatic interactions. Altogether, apiRBP represents an attractive tool for apicoplast transcriptional studies and for antimalarial drug design.
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Affiliation(s)
- Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Francisco Rivero-Rodríguez
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | | | - Christian Grüttner
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Marian Hernández-Vellisca
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
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9
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García-Mauriño SM, Rivero-Rodríguez F, Velázquez-Cruz A, Hernández-Vellisca M, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. RNA Binding Protein Regulation and Cross-Talk in the Control of AU-rich mRNA Fate. Front Mol Biosci 2017; 4:71. [PMID: 29109951 PMCID: PMC5660096 DOI: 10.3389/fmolb.2017.00071] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/04/2017] [Indexed: 02/06/2023] Open
Abstract
mRNA metabolism is tightly orchestrated by highly-regulated RNA Binding Proteins (RBPs) that determine mRNA fate, thereby influencing multiple cellular functions across biological contexts. Here, we review the interplay between six well-known RBPs (TTP, AUF-1, KSRP, HuR, TIA-1, and TIAR) that recognize AU-rich elements (AREs) at the 3' untranslated regions of mRNAs, namely ARE-RBPs. Examples of the links between their cross-regulations and modulation of their targets are analyzed during mRNA processing, turnover, localization, and translational control. Furthermore, ARE recognition can be self-regulated by several factors that lead to the prevalence of one RBP over another. Consequently, we examine the factors that modulate the dynamics of those protein-RNA transient interactions to better understand the final consequences of the regulation mediated by ARE-RBPs. For instance, factors controlling the RBP isoforms, their conformational state or their post-translational modifications (PTMs) can strongly determine the fate of the protein-RNA complexes. Moreover, mRNA specific sequence and secondary structure or subtle environmental changes are also key determinants to take into account. To sum up, the whole understanding of such a fine tuned regulation is a challenge for future research and requires the integration of all the available structural and functional data by in vivo, in vitro and in silico approaches.
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Affiliation(s)
| | | | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
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10
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Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA. TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 2017; 45:4944-4957. [PMID: 28184449 PMCID: PMC5416816 DOI: 10.1093/nar/gkx102] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/07/2017] [Indexed: 01/01/2023] Open
Abstract
TIA-1 (T-cell restricted intracellular antigen-1) is an RNA-binding protein involved in splicing and translational repression. It mainly interacts with RNA via its second and third RNA recognition motifs (RRMs), with specificity for U-rich sequences directed by RRM2. It has recently been shown that RRM3 also contributes to binding, with preferential binding for C-rich sequences. Here we designed UC-rich and CU-rich 10-nt sequences for engagement of both RRM2 and RRM3 and demonstrated that the TIA-1 RRM23 construct preferentially binds the UC-rich RNA ligand (5΄-UUUUUACUCC-3΄). Interestingly, this binding depends on the presence of Lys274 that is C-terminal to RRM3 and binding to equivalent DNA sequences occurs with similar affinity. Small-angle X-ray scattering was used to demonstrate that, upon complex formation with target RNA or DNA, TIA-1 RRM23 adopts a compact structure, showing that both RRMs engage with the target 10-nt sequences to form the complex. We also report the crystal structure of TIA-1 RRM2 in complex with DNA to 2.3 Å resolution providing the first atomic resolution structure of any TIA protein RRM in complex with oligonucleotide. Together our data support a specific mode of TIA-1 RRM23 interaction with target oligonucleotides consistent with the role of TIA-1 in binding RNA to regulate gene expression.
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Affiliation(s)
- Saboora Waris
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Andrew Sivakumaran
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simone A Beckham
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Fionna E Loughlin
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
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11
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Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-related/like protein (TIAR/TIAL1) are 2 proteins discovered in 1991 as components of cytotoxic T lymphocyte granules. They act in the nucleus as regulators of transcription and pre-mRNA splicing. In the cytoplasm, TIA1 and TIAR regulate and/or modulate the location, stability and/or translation of mRNAs. As knowledge of the different genes regulated by these proteins and the cellular/biological programs in which they are involved increases, it is evident that these antigens are key players in human physiology and pathology. This review will discuss the latest developments in the field, with physiopathological relevance, that point to novel roles for these regulators in the molecular and cell biology of higher eukaryotes.
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Affiliation(s)
- Carmen Sánchez-Jiménez
- a Centro de Biología Molecular Severo Ochoa; Consejo Superior de Investigaciones Científicas; Universidad Autónoma de Madrid (CSIC/UAM); C/Nicolás Cabrera 1 ; Madrid , Spain
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12
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Hennig J, Sattler M. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology. Bioessays 2015; 37:899-908. [DOI: 10.1002/bies.201500033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
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13
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Cruz-Gallardo I, Del Conte R, Velázquez-Campoy A, García-Mauriño SM, Díaz-Moreno I. A Non-Invasive NMR Method Based on Histidine Imidazoles to Analyze the pH-Modulation of Protein-Nucleic Acid Interfaces. Chemistry 2015; 21:7588-95. [PMID: 25846236 DOI: 10.1002/chem.201405538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/19/2015] [Indexed: 12/20/2022]
Abstract
A useful (2) J(N-H) coupling-based NMR spectroscopic approach is proposed to unveil, at the molecular level, the contribution of the imidazole groups of histidines from RNA/DNA-binding proteins on the modulation of binding to nucleic acids by pH. Such protonation/deprotonation events have been monitored on the single His96 located at the second RNA/DNA recognition motif (RRM2) of T-cell intracellular antigen-1 (TIA-1) protein. The pKa values of the His96 ionizable groups were substantially higher in the complexes with short U-rich RNA and T-rich DNA oligonucleotides than those of the isolated TIA-1 RRM2. Herein, the methodology applied to determine changes in pKa of histidine side chains upon DNA/RNA binding, gives valuable information to understand the pH effect on multidomain DNA/RNA-binding proteins that shuttle among different cellular compartments.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Instituto de Bioquímica Vegetal y Fotosíntesis cicCartuja, Universidad de Sevilla - CSIC, Avenida Américo Vespucio 49, 41092 Sevilla (Spain)
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Díaz-Quintana A, García-Mauriño SM, Díaz-Moreno I. Dimerization model of the C-terminal RNA Recognition Motif of HuR. FEBS Lett 2015; 589:1059-66. [PMID: 25841336 DOI: 10.1016/j.febslet.2015.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/10/2015] [Accepted: 03/18/2015] [Indexed: 02/08/2023]
Abstract
Human antigen R (HuR) is a ubiquitous 32 kDa protein comprising three RNA Recognition Motifs (RRMs), whose main function is to bind Adenylate and uridylate Rich Elements (AREs) in 3' UnTranslated Regions (UTRs) of mRNAs. In addition to binding RNA molecules, the third domain (RRM3) is involved in HuR oligomerization and apoptotic signaling. The RRM3 monomer is able to dimerize, with its self-binding affinity being dependent on ionic strength. Here we provide a deeper structural insight into the nature of the encounter complexes leading to the formation of RRM3 dimers by using Brownian Dynamics and Molecular Dynamics. Our computational data show that the initial unspecific encounter follows a downhill pathway until reaching an optimum conformation stabilized by hydrophobic interactions.
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Affiliation(s)
- Antonio Díaz-Quintana
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain.
| | - Sofía M García-Mauriño
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
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15
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Hamdollah Zadeh MA, Amin EM, Hoareau-Aveilla C, Domingo E, Symonds KE, Ye X, Heesom KJ, Salmon A, D'Silva O, Betteridge KB, Williams AC, Kerr DJ, Salmon AHJ, Oltean S, Midgley RS, Ladomery MR, Harper SJ, Varey AHR, Bates DO. Alternative splicing of TIA-1 in human colon cancer regulates VEGF isoform expression, angiogenesis, tumour growth and bevacizumab resistance. Mol Oncol 2015; 9:167-78. [PMID: 25224594 PMCID: PMC4286123 DOI: 10.1016/j.molonc.2014.07.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 02/06/2023] Open
Abstract
The angiogenic capability of colorectal carcinomas (CRC), and their susceptibility to anti-angiogenic therapy, is determined by expression of vascular endothelial growth factor (VEGF) isoforms. The intracellular protein T-cell Intracellular Antigen (TIA-1) alters post-transcriptional RNA processing and binds VEGF-A mRNA. We therefore tested the hypothesis that TIA-1 could regulate VEGF-A isoform expression in colorectal cancers. TIA-1 and VEGF-A isoform expression was measured in colorectal cancers and cell lines. We discovered that an endogenous splice variant of TIA-1 encoding a truncated protein, short TIA-1 (sTIA-1) was expressed in CRC tissues and invasive K-Ras mutant colon cancer cells and tissues but not in adenoma cell lines. sTIA-1 was more highly expressed in CRC than in normal tissues and increased with tumour stage. Knockdown of sTIA-1 or over-expression of full length TIA-1 (flTIA-1) induced expression of the anti-angiogenic VEGF isoform VEGF-A165b. Whereas flTIA-1 selectively bound VEGF-A165 mRNA and increased translation of VEGF-A165b, sTIA-1 prevented this binding. In nude mice, xenografted colon cancer cells over-expressing flTIA-1 formed smaller, less vascular tumours than those expressing sTIA-1, but flTIA-1 expression inhibited the effect of anti-VEGF antibodies. These results indicate that alternative splicing of an RNA binding protein can regulate isoform specific expression of VEGF providing an added layer of complexity to the angiogenic profile of colorectal cancer and their resistance to anti-angiogenic therapy.
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Affiliation(s)
- Maryam A Hamdollah Zadeh
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Elianna M Amin
- Centre for Research in Biomedicine, Faculty of Health and Life Sciences, University of the West of England, Bristol BS16 1QY, UK
| | - Coralie Hoareau-Aveilla
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Enric Domingo
- Molecular and Population Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kirsty E Symonds
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Xi Ye
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Katherine J Heesom
- Proteomics Facility, Faculty of Veterinary and Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew Salmon
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Olivia D'Silva
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Kai B Betteridge
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Ann C Williams
- School of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - David J Kerr
- Nuffield Dept Clinical and Laboratory Sciences, University of Oxford, UK
| | - Andrew H J Salmon
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Sebastian Oltean
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Rachel S Midgley
- Molecular and Population Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Michael R Ladomery
- Centre for Research in Biomedicine, Faculty of Health and Life Sciences, University of the West of England, Bristol BS16 1QY, UK
| | - Steven J Harper
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Alexander H R Varey
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - David O Bates
- Microvascular Research Laboratories, Veterinary Sciences Building, School of Physiology and Pharmacology, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK; Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK.
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RNA recognition and stress granule formation by TIA proteins. Int J Mol Sci 2014; 15:23377-88. [PMID: 25522169 PMCID: PMC4284772 DOI: 10.3390/ijms151223377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 12/05/2014] [Accepted: 12/11/2014] [Indexed: 02/04/2023] Open
Abstract
Stress granule (SG) formation is a primary mechanism through which gene expression is rapidly modulated when the eukaryotic cell undergoes cellular stresses (including heat, oxidative, viral infection, starvation). In particular, the sequestration of specifically targeted translationally stalled mRNAs into SGs limits the expression of a subset of genes, but allows the expression of heatshock proteins that have a protective effect in the cell. The importance of SGs is seen in several disease states in which SG function is disrupted. Fundamental to SG formation are the T cell restricted intracellular antigen (TIA) proteins (TIA-1 and TIA-1 related protein (TIAR)), that both directly bind to target RNA and self-associate to seed the formation of SGs. Here a summary is provided of the current understanding of the way in which TIA proteins target specific mRNA, and how TIA self-association is triggered under conditions of cellular stress.
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