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Zhang Y, Zhang Y, Song J, Cheng X, Zhou C, Huang S, Zhao W, Zong Z, Yang L. Targeting the "tumor microenvironment": RNA-binding proteins in the spotlight in colorectal cancer therapy. Int Immunopharmacol 2024; 131:111876. [PMID: 38493688 DOI: 10.1016/j.intimp.2024.111876] [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: 01/31/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer and has the second highest mortality rate among cancers. The development of CRC involves both genetic and epigenetic abnormalities, and recent research has focused on exploring the ex-transcriptome, particularly post-transcriptional modifications. RNA-binding proteins (RBPs) are emerging epigenetic regulators that play crucial roles in post-transcriptional events. Dysregulation of RBPs can result in aberrant expression of downstream target genes, thereby affecting the progression of colorectal tumors and the prognosis of patients. Recent studies have shown that RBPs can influence CRC pathogenesis and progression by regulating various components of the tumor microenvironment (TME). Although previous research on RBPs has primarily focused on their direct regulation of colorectal tumor development, their involvement in the remodeling of the TME has not been systematically reported. This review aims to highlight the significant role of RBPs in the intricate interactions within the CRC tumor microenvironment, including tumor immune microenvironment, inflammatory microenvironment, extracellular matrix, tumor vasculature, and CRC cancer stem cells. We also highlight several compounds under investigation for RBP-TME-based treatment of CRC, including small molecule inhibitors such as antisense oligonucleotides (ASOs), siRNAs, agonists, gene manipulation, and tumor vaccines. The insights gained from this review may lead to the development of RBP-based targeted novel therapeutic strategies aimed at modulating the TME, potentially inhibiting the progression and metastasis of CRC.
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Affiliation(s)
- Yiwei Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; Queen Mary School, Nanchang University, 330006 Nanchang, China
| | - Yujun Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China
| | - Jingjing Song
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; School of Ophthalmology and Optometry of Nanchang University, China
| | - Xifu Cheng
- School of Ophthalmology and Optometry of Nanchang University, China
| | - Chulin Zhou
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Shuo Huang
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Wentao Zhao
- The 3rd Clinical Department of China Medical University, 10159 Shenyang, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China.
| | - Lingling Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China.
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2
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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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3
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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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4
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Legrand N, Dixon DA, Sobolewski C. AU-rich element-binding proteins in colorectal cancer. World J Gastrointest Oncol 2019; 11:71-90. [PMID: 30788036 PMCID: PMC6379757 DOI: 10.4251/wjgo.v11.i2.71] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/11/2018] [Accepted: 01/01/2019] [Indexed: 02/05/2023] Open
Abstract
Trans-acting factors controlling mRNA fate are critical for the post-transcriptional regulation of inflammation-related genes, as well as for oncogene and tumor suppressor expression in human cancers. Among them, a group of RNA-binding proteins called “Adenylate-Uridylate-rich elements binding proteins” (AUBPs) control mRNA stability or translation through their binding to AU-rich elements enriched in the 3’UTRs of inflammation- and cancer-associated mRNA transcripts. AUBPs play a central role in the recruitment of target mRNAs into small cytoplasmic foci called Processing-bodies and stress granules (also known as P-body/SG). Alterations in the expression and activities of AUBPs and P-body/SG assembly have been observed to occur with colorectal cancer (CRC) progression, indicating the significant role AUBP-dependent post-transcriptional regulation plays in controlling gene expression during CRC tumorigenesis. Accordingly, these alterations contribute to the pathological expression of many early-response genes involved in prostaglandin biosynthesis and inflammation, along with key oncogenic pathways. In this review, we summarize the current role of these proteins in CRC development. CRC remains a major cause of cancer mortality worldwide and, therefore, targeting these AUBPs to restore efficient post-transcriptional regulation of gene expression may represent an appealing therapeutic strategy.
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Affiliation(s)
- Noémie Legrand
- Department of Microbiology, Faculty of Medicine, University of Geneva, Geneva CH-1211, Switzerland
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, and University of Kansas Cancer Center, Kansas City, KS 66045, United States
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva CH-1211, Switzerland
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5
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Structural characterization of a novel KH-domain containing plant chloroplast endonuclease. Sci Rep 2018; 8:13750. [PMID: 30214061 PMCID: PMC6137056 DOI: 10.1038/s41598-018-31142-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 08/02/2018] [Indexed: 11/08/2022] Open
Abstract
Chlamydomonas reinhardtii is a single celled alga that undergoes apoptosis in response to UV-C irradiation. UVI31+, a novel UV-inducible DNA endonuclease in C. reinhardtii, which normally localizes near cell wall and pyrenoid regions, gets redistributed into punctate foci within the whole chloroplast, away from the pyrenoid, upon UV-stress. Solution NMR structure of the first putative UV inducible endonuclease UVI31+ revealed an α1–β1–β2–α2–α3–β3 fold similar to BolA and type II KH-domain ubiquitous protein families. Three α−helices of UVI31+ constitute one side of the protein surface, which are packed to the other side, made of three-stranded β–sheet, with intervening hydrophobic residues. A twenty-three residues long polypeptide stretch (D54-H76) connecting β1 and β2 strands is found to be highly flexible. Interestingly, UVI31+ recognizes the DNA primarily through its β–sheet. We propose that the catalytic triad residues involving Ser114, His95 and Thr116 facilitate DNA endonuclease activity of UVI31+. Further, decreased endonuclease activity of the S114A mutant is consistent with the direct participation of Ser114 in the catalysis. This study provides the first structural description of a plant chloroplast endonuclease that is regulated by UV-stress response.
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6
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Sofi S, Fitzgerald JC, Jähn D, Dumoulin B, Stehling S, Kuhn H, Ufer C. Functional characterization of naturally occurring genetic variations of the human guanine-rich RNA sequence binding factor 1 (GRSF1). Biochim Biophys Acta Gen Subj 2018; 1862:866-876. [DOI: 10.1016/j.bbagen.2017.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/12/2017] [Accepted: 12/22/2017] [Indexed: 10/18/2022]
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7
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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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8
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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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9
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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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10
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Scheiba RM, de Opakua AI, Díaz-Quintana A, Cruz-Gallardo I, Martínez-Cruz LA, Martínez-Chantar ML, Blanco FJ, Díaz-Moreno I. The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets. RNA Biol 2015; 11:1250-61. [PMID: 25584704 DOI: 10.1080/15476286.2014.996069] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human antigen R (HuR) is a 32 kDa protein with 3 RNA Recognition Motifs (RRMs), which bind to Adenylate and uridylate Rich Elements (AREs) of mRNAs. Whereas the N-terminal and central domains (RRM1 and RRM2) are essential for AREs recognition, little is known on the C-terminal RRM3 beyond its implication in HuR oligomerization and apoptotic signaling. We have developed a detergent-based strategy to produce soluble RRM3 for structural studies. We have found that it adopts the typical RRM fold, does not interact with the RRM1 and RRM2 modules, and forms dimers in solution. Our NMR measurements, combined with Molecular Dynamics simulations and Analytical Ultracentrifugation experiments, show that the protein dimerizes through a helical region that contains the conserved W261 residue. We found that HuR RRM3 binds to 5'-mer U-rich RNA stretches through the solvent exposed side of its β-sheet, located opposite to the dimerization site. Upon mimicking phosphorylation by the S318D replacement, RRM3 mutant shows less ability to recognize RNA due to an electrostatic repulsion effect with the phosphate groups. Our study brings new insights of HuR RRM3 as a domain involved in protein oligomerization and RNA interaction, both functions regulated by 2 surfaces on opposite sides of the RRM domain.
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Key Words
- AREs, Adenylate and uridylate Rich Elements
- AU, Analytical Ultracentrifugation
- CARM1, Coactivator associated Arginine Methyltransferase 1
- CD, Circular Dichroism
- Cdk1, Cyclin-dependent kinase 1
- Chk2, Checkpoint kinase 2
- ELAV1, Embryonic Lethal Abnormal Vision system human homolog 1
- EMSA, Electrophoretic Mobility Shift Assay
- FIR, FBP-Interacting Repressor
- FL, Full-Length, HNS, HuR Nucleocytoplasmic Shuttling Sequence
- HSQC, Heteronuclear Single-Quantum Correlation
- HuR, Human antigen R
- Human antigen R (HuR)
- MD, Molecular Dynamics
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhauser Effect
- Nuclear Magnetic Resonance (NMR)
- PCA, Principal Component Analysis
- PKCα, Protein Kinase C α
- PKCδ, Protein Kinase C δ
- PMSF, PhenylMethylSulfonyl Fluoride
- PTB, Polypyrimidine Tract Binding protein
- RBPs, RNA Binding Proteins
- RNA binding
- RNA binding protein (RBP)
- RNA recognition motif (RRM)
- RRMs, RNA Recognition Motifs
- SPR, Surface Plasmon Resonance
- Serine Phosphorylation
- WT, Wild-Type
- dimerization
- hnRNP1, heterogeneous nuclear RiboNucleoprotein C protein
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Affiliation(s)
- Rafael M Scheiba
- a Instituto de Bioquímica Vegetal y Fotosíntesis; cicCartuja ; Sevilla , Spain
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11
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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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12
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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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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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Cruz-Gallardo I, Aroca Á, Gunzburg MJ, Sivakumaran A, Yoon JH, Angulo J, Persson C, Gorospe M, Karlsson BG, Wilce JA, Díaz-Moreno I. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain. RNA Biol 2014; 11:766-76. [PMID: 24824036 DOI: 10.4161/rna.28801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein-nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5' TOPs (5' terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Menachem J Gunzburg
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Andrew Sivakumaran
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Je-Hyun Yoon
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - Jesús Angulo
- Instituto de Investigaciones Químicas; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain; School of Pharmacy; University of East Anglia; Norwich Research Park; Norwich, UK
| | - Cecilia Persson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - B Göran Karlsson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Jacqueline A Wilce
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
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15
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Wang I, Hennig J, Jagtap PKA, Sonntag M, Valcárcel J, Sattler M. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1. Nucleic Acids Res 2014; 42:5949-66. [PMID: 24682828 PMCID: PMC4027183 DOI: 10.1093/nar/gku193] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.
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Affiliation(s)
- Iren Wang
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Miriam Sonntag
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
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