1
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Porat J, Vakiloroayaei A, Remnant BM, Talebi M, Cargill T, Bayfield MA. Crosstalk between the tRNA methyltransferase Trm1 and RNA chaperone La influences eukaryotic tRNA maturation. J Biol Chem 2023; 299:105326. [PMID: 37805140 PMCID: PMC10652106 DOI: 10.1016/j.jbc.2023.105326] [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: 05/15/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
tRNAs undergo an extensive maturation process involving posttranscriptional modifications often associated with tRNA structural stability and promoting the native fold. Impaired posttranscriptional modification has been linked to human disease, likely through defects in translation, mitochondrial function, and increased susceptibility to degradation by various tRNA decay pathways. More recently, evidence has emerged that bacterial tRNA modification enzymes can act as tRNA chaperones to guide tRNA folding in a manner independent from catalytic activity. Here, we provide evidence that the fission yeast tRNA methyltransferase Trm1, which dimethylates nuclear- and mitochondrial-encoded tRNAs at G26, can also promote tRNA functionality in the absence of catalysis. We show that WT and catalytic-dead Trm1 are active in an in vivo tRNA-mediated suppression assay and possess RNA strand annealing and dissociation activity in vitro, similar to previously characterized RNA chaperones. Trm1 and the RNA chaperone La have previously been proposed to function synergistically in promoting tRNA maturation, yet we surprisingly demonstrate that La binding to nascent pre-tRNAs decreases Trm1 tRNA dimethylation in vivo and in vitro. Collectively, these results support the hypothesis for tRNA modification enzymes that combine catalytic and noncatalytic activities to promote tRNA maturation, as well as expand our understanding of how La function can influence tRNA modification.
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2
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Soengas-Gonda E, Pérez de la Fuente R, Arteche-López A, Gómez-Cano MDLÁ, Quesada-Espinosa JF, Palma Milla C, Lezana Rosales JM, Mayo de Andrés S, Sánchez-Calvín MT, Gómez-Rodríguez MJ, Sierra Tomillo O, Juarez Rufian A, Ramos Gomez P, Herrero-Forte C, Fenollar-Cortés M, Cotarelo-Pérez C, García Ron A, Pérez Rodríguez O, Oancea-Ionescu R, Moreno-García M. Expanding the Phenotypic Spectrum of Alazami Syndrome: Two Unrelated Spanish Families. Neuropediatrics 2023; 54:31-36. [PMID: 36126956 DOI: 10.1055/a-1947-8411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alazami syndrome is a rare disorder with an autosomal recessive inheritance caused by pathogenic biallelic variants in the LARP7 gene. Clinically, it is mainly characterized by short stature, intellectual disability, and dysmorphic facial features. However, the phenotype is not yet well-defined because less than 50 cases have been described to date. Here, we report three new patients from two unrelated Spanish families who, in addition to the defined features of Alazami syndrome, also exhibit unique features that broaden the phenotypic spectrum of the syndrome. Moreover, we describe the novel frameshift variant c.690_699delins27 in the LARP7 gene, in which loss of function is a known mechanism of Alazami syndrome.
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Affiliation(s)
- Emma Soengas-Gonda
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | - Rubén Pérez de la Fuente
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - Ana Arteche-López
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - María de Los Ángeles Gómez-Cano
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Pediatrics, Endocrinology Unit, 12 de Octubre University Hospital, Madrid, Spain
| | - Juan Francisco Quesada-Espinosa
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - Carmen Palma Milla
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - José Miguel Lezana Rosales
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - Sonia Mayo de Andrés
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - María Teresa Sánchez-Calvín
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | - María José Gómez-Rodríguez
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
| | | | | | | | - Clara Herrero-Forte
- Clinical Genetics, Clinical Analysis Service, Molecular Diagnostics Unit, Institute of Laboratory Medicine (UDM-IML), Clinico San Carlos University Hospital, Madrid, Spain.,San Carlos Clinical Research Institute (IdISSC), Madrid, Spain
| | - Maria Fenollar-Cortés
- Clinical Genetics, Clinical Analysis Service, Molecular Diagnostics Unit, Institute of Laboratory Medicine (UDM-IML), Clinico San Carlos University Hospital, Madrid, Spain.,San Carlos Clinical Research Institute (IdISSC), Madrid, Spain
| | - Carmen Cotarelo-Pérez
- Clinical Genetics, Clinical Analysis Service, Molecular Diagnostics Unit, Institute of Laboratory Medicine (UDM-IML), Clinico San Carlos University Hospital, Madrid, Spain.,San Carlos Clinical Research Institute (IdISSC), Madrid, Spain
| | - Adrián García Ron
- Neuropaediatrics Unit, Child and Adolescent Institute, Clinico San Carlos University Hospital, Madrid, Spain
| | | | - Raluca Oancea-Ionescu
- Clinical Genetics, Clinical Analysis Service, Molecular Diagnostics Unit, Institute of Laboratory Medicine (UDM-IML), Clinico San Carlos University Hospital, Madrid, Spain.,San Carlos Clinical Research Institute (IdISSC), Madrid, Spain
| | - Marta Moreno-García
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain.,Department of Genetics, 12 de Octubre University Hospital, Madrid, Spain
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3
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Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila. Nat Commun 2022; 13:7332. [PMID: 36443289 PMCID: PMC9705548 DOI: 10.1038/s41467-022-34796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
Nascent pre-tRNAs are transcribed by RNA polymerase III and immediately bound by La proteins on the UUU-3'OH sequence, using a tandem arrangement of the La motif and an adjacent RNA recognition motif-1 (RRM1), resulting in protection from 3'-exonucleases and promotion of pre-tRNA folding. The Tetrahymena thermophila protein Mlp1 has been previously classified as a genuine La protein, despite the predicted absence of the RRM1. We find that Mlp1 functions as a La protein through binding of pre-tRNAs, and affects pre-tRNA processing in Tetrahymena thermophila and when expressed in fission yeast. However, unlike in other examined eukaryotes, depletion of Mlp1 results in 3'-trailer stabilization. The 3'-trailers in Tetrahymena thermophila are uniquely short relative to other examined eukaryotes, and 5'-leaders have evolved to disfavour pre-tRNA leader/trailer pairing. Our data indicate that this variant Mlp1 architecture is linked to an altered, novel mechanism of tRNA processing in Tetrahymena thermophila.
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4
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Bayfield MA, Vinayak J, Kerkhofs K, Mansouri-Noori F. La proteins couple use of sequence-specific and non-specific binding modes to engage RNA substrates. RNA Biol 2021; 18:168-177. [PMID: 30777481 PMCID: PMC7928037 DOI: 10.1080/15476286.2019.1582955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
La shuttles between the nucleus and cytoplasm where it binds nascent RNA polymerase III (pol III) transcripts and mRNAs, respectively. La protects the 3' end of pol III transcribed RNA precursors, such as pre-tRNAs, through the use of a well-characterized UUU-3'OH binding mode. La proteins are also RNA chaperones, and La-dependent RNA chaperone activity is hypothesized to promote pre-tRNA maturation and translation at cellular and viral internal ribosome entry sites via binding sites distinct from those used for UUU-3'OH recognition. Since the publication of La-UUU-3'OH co-crystal structures, biochemical and genetic experiments have expanded our understanding of how La proteins use UUU-3'OH-independent binding modes to make sequence-independent contacts that can increase affinity for ligands and promote RNA remodeling. Other recent work has also expanded our understanding of how La binds mRNAs through contacts to the poly(A) tail. In this review, we focus on advances in the study of La protein-RNA complex surfaces beyond the description of the La-UUU-3'OH binding mode. We highlight recent advances in the functions of expected canonical nucleic acid interaction surfaces, a heightened appreciation of disordered C-terminal regions, and the nature of sequence-independent RNA determinants in La-RNA target binding. We further discuss how these RNA binding modes may have relevance to the function of the La-related proteins.
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Affiliation(s)
- Mark A. Bayfield
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jyotsna Vinayak
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Kyra Kerkhofs
- Department of Biology, York University, Toronto, Ontario, Canada
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5
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Abstract
RNA-binding proteins are important regulators of RNA metabolism and are of critical importance in all steps of the gene expression cascade. The role of aberrantly expressed RBPs in human disease is an exciting research field and the potential application of RBPs as a therapeutic target or a diagnostic marker represents a fast-growing area of research.Aberrant overexpression of the human RNA-binding protein La has been found in various cancer entities including lung, cervical, head and neck, and chronic myelogenous leukaemia. Cancer-associated La protein supports tumour-promoting processes such as proliferation, mobility, invasiveness and tumour growth. Moreover, the La protein maintains the survival of cancer cells by supporting an anti-apoptotic state that may cause resistance to chemotherapeutic therapy.The human La protein represents a multifunctional post-translationally modified RNA-binding protein with RNA chaperone activity that promotes processing of non-coding precursor RNAs but also stimulates the translation of selective messenger RNAs encoding tumour-promoting and anti-apoptotic factors. In our model, La facilitates the expression of those factors and helps cancer cells to cope with cellular stress. In contrast to oncogenes, able to initiate tumorigenesis, we postulate that the aberrantly elevated expression of the human La protein contributes to the non-oncogenic addiction of cancer cells. In this review, we summarize the current understanding about the implications of the RNA-binding protein La in cancer progression and therapeutic resistance. The concept of exploiting the RBP La as a cancer drug target will be discussed.
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Affiliation(s)
- Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
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6
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Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
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7
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The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Mol Cell 2020; 77:1014-1031.e13. [DOI: 10.1016/j.molcel.2020.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/25/2019] [Accepted: 12/26/2019] [Indexed: 12/12/2022]
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8
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Abstract
La proteins have well-established roles in the maturation of RNA polymerase III transcripts, including pre-tRNAs. In addition to protecting the 3' end of pre-tRNAs from exonuclease digestion, La proteins also promote the native fold of the pre-tRNA using RNA chaperone activity. tRNA-mediated suppression in the fission yeast S. pombe has been an invaluable tool in determining the mechanistic basis by which La proteins promote the maturation of defective pre-tRNAs that benefit from RNA chaperone activity. More recently, tRNA-mediated suppression has been adapted to test for RNA chaperone function in the La-related proteins and in the promoting of tRNA function by tRNA modification enzymes. Thus tRNA-mediated suppression can be a useful assay for the investigation of various proteins hypothesized to promote tRNA folding through RNA chaperone related activities.
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9
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Sommer G, Sendlmeier C, Heise T. Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La. Methods Mol Biol 2020; 2106:121-136. [PMID: 31889254 DOI: 10.1007/978-1-0716-0231-7_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
It is well established that the RNA-binding protein La has RNA chaperone activity. Recent work suggests that the La protein has two distinct RNA chaperone domains (RCD-A and RCD-B) assisting structural changes in diverse groups of RNA molecules such as RNA polymerase III transcripts (e.g., pre-tRNA, U6 snRNA), cellular messenger, and viral RNAs. In this protocol we focus on the RNA chaperone domain RCD-B, which is located in the carboxy-terminal domain of La. It has been shown that this RNA chaperone domain assists structural changes in predicted RNA hairpins folded in the 5'-untranslated regions of cyclin D1 and Bcl2 mRNAs. Besides RNA helicases, which are implicated in melting RNA hairpin structures in an ATP-dependent manner, RNA chaperones fulfil a similar function in an ATP-independent manner. Aiming to study the RNA chaperon activity of La, we established a La-dependent molecular beacon-based RNA chaperone assay and systematically tested the various salt conditions. Herein we describe the assay format and design to study the salt dependency of RNA chaperones. This protocol can be easily adapted to test the RNA chaperone activity of other RNA-binding proteins and to optimize assay conditions.
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Affiliation(s)
- Gunhild Sommer
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital of Regensburg, Regensburg, Germany
| | - Christina Sendlmeier
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital of Regensburg, Regensburg, Germany
| | - Tilman Heise
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital of Regensburg, Regensburg, Germany.
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10
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Vinayak J, Marrella SA, Hussain RH, Rozenfeld L, Solomon K, Bayfield MA. Human La binds mRNAs through contacts to the poly(A) tail. Nucleic Acids Res 2019; 46:4228-4240. [PMID: 29447394 PMCID: PMC5934636 DOI: 10.1093/nar/gky090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.
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Affiliation(s)
- Jyotsna Vinayak
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Stefano A Marrella
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Rawaa H Hussain
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Leonid Rozenfeld
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Karine Solomon
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
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11
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Yin W, Chen J, Wang G, Zhang D. MicroRNA‑106b functions as an oncogene and regulates tumor viability and metastasis by targeting LARP4B in prostate cancer. Mol Med Rep 2019; 20:951-958. [PMID: 31173237 PMCID: PMC6625195 DOI: 10.3892/mmr.2019.10343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer (PCa) is the most common malignancy among males worldwide, and is one of the leading causes of cancer‑related mortality. MicroRNAs (miRs) are a type of endogenous, noncoding RNA that serve a key role in pathological processes, and have been demonstrated to be involved in the formation and progression of PCa. Previous studies have reported that miR‑106b acts as an oncogene; however, the specific effects of miR‑106b on PCa have not been fully elucidated. The present study aimed to investigate the role and underlying molecular mechanisms of miR‑106b in the initiation and progression of PCa. In this study, miR‑106b was reported to be overexpressed and la‑related protein 4B (LARP4B) was downregulated in PCa tissues compared with paracancerous tissues. In addition, LARP4B was identified as a target gene of miR‑106b by bioinformatics prediction analysis and a dual luciferase reporter gene assay. Furthermore, MTT, wound healing and Transwell assays were performed to evaluate PCa cell viability, and migration and invasive abilities. The data revealed that inhibition of miR‑106b significantly suppressed the viability, migration and invasion of PCa cells. In addition, inhibition of miR‑106b significantly suppressed the mRNA and protein expression of cancer‑related genes, including matrix metalloproteinase‑2, cluster of differentiation 44 and Ki‑67, and increased that of the tumor suppressor, mothers against decapentaplegic homolog 2. Collectively, the findings of the present study indicated that miR‑106b may target LAR4B to inhibit cancer cell viability, migration and invasion, and may be considered as a novel therapeutic target in PCa.
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Affiliation(s)
- Weiqi Yin
- Department of Urology, Ningbo First Hospital, Ningbo, Zhejiang 315010, P.R. China
| | - Junfeng Chen
- Department of Urology, Ningbo First Hospital, Ningbo, Zhejiang 315010, P.R. China
| | - Guoyao Wang
- Department of Urology, Ningbo First Hospital, Ningbo, Zhejiang 315010, P.R. China
| | - Dongxu Zhang
- Department of Urology, Ningbo First Hospital, Ningbo, Zhejiang 315010, P.R. China
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12
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Yang Y, Eichhorn CD, Wang Y, Cascio D, Feigon J. Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE. Nat Chem Biol 2019; 15:132-140. [PMID: 30559425 PMCID: PMC6339579 DOI: 10.1038/s41589-018-0188-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023]
Abstract
Among RNA 5'-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second nonenzymatic role as a core component of the 7SK ribonuclear protein (RNP), an essential regulator of RNA transcription. We report 2.0- and 2.1-Å X-ray crystal structures of the human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5'-hairpin-single-stranded RNA region, thus explaining MePCE's specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition-state geometry. Unexpectedly, binding experiments showed that MePCE has higher affinity for capped versus uncapped 7SK, and kinetic data support a model of slow product release. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.
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Affiliation(s)
- Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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13
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Marrella SA, Brown KA, Mansouri-Noori F, Porat J, Wilson DJ, Bayfield MA. An interdomain bridge influences RNA binding of the human La protein. J Biol Chem 2018; 294:1529-1540. [PMID: 30530494 DOI: 10.1074/jbc.ra118.003995] [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: 05/23/2018] [Revised: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
La proteins are RNA chaperones that perform various functions depending on distinct RNA-binding modes and their subcellular localization. In the nucleus, they help process UUU-3'OH-tailed nascent RNA polymerase III transcripts, such as pre-tRNAs, whereas in the cytoplasm they contribute to translation of poly(A)-tailed mRNAs. La accumulation in the nucleus and cytoplasm is controlled by several trafficking elements, including a canonical nuclear localization signal in the extreme C terminus and a nuclear retention element (NRE) in the RNA recognition motif 2 (RRM2) domain. Previous findings indicate that cytoplasmic export of La due to mutation of the NRE can be suppressed by mutations in RRM1, but the mechanism by which the RRM1 and RRM2 domains functionally cooperate is poorly understood. In this work, we use electromobility shift assays (EMSA) to show that mutations in the NRE and RRM1 affect binding of human La to pre-tRNAs but not UUU-3'OH or poly(A) sequences, and we present compensatory mutagenesis data supporting a direct interaction between the RRM1 and RRM2 domains. Moreover, we use collision-induced unfolding and time-resolved hydrogen-deuterium exchange MS analyses to study the conformational dynamics that occur when this interaction is intact or disrupted. Our results suggest that the intracellular distribution of La may be linked to its RNA-binding modes and provide the first evidence for a direct protein-protein interdomain interaction in La proteins.
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Affiliation(s)
- Stefano A Marrella
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Kerene A Brown
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Farnaz Mansouri-Noori
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jennifer Porat
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada.
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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14
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SUMO Modification of the RNA-Binding Protein La Regulates Cell Proliferation and STAT3 Protein Stability. Mol Cell Biol 2017; 38:MCB.00129-17. [PMID: 29084811 DOI: 10.1128/mcb.00129-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
The cancer-associated RNA-binding protein La is posttranslationally modified by phosphorylation and sumoylation. Sumoylation of La regulates not only the trafficking of La in neuronal axons but also its association with specific mRNAs. Depletion of La in various types of cancer cell lines impairs cell proliferation; however, the molecular mechanism whereby La supports cell proliferation is not clearly understood. In this study, we address the question of whether sumoylation of La contributes to cell proliferation of HEK293 cells. We show that HEK293 cells stably expressing green fluorescent protein (GFP)-tagged wild-type La (GFP-LaWT) grow faster than cells expressing a sumoylation-deficient mutant La (GFP-LaSD), suggesting a proproliferative function of La in HEK293 cells. Further, we found that STAT3 protein levels were reduced in GFP-LaSD cells due to an increase in STAT3 ubiquitination and that overexpression of STAT3 partially restored cell proliferation. Finally, we present RNA sequencing data from RNA immunoprecipitations (RIPs) and report that mRNAs associated with the cell cycle and ubiquitination are preferentially bound by GFP-LaWT and are less enriched in GFP-LaSD RIPs. Taken together, results of our study support a novel mechanism whereby sumoylation of La promotes cell proliferation by averting ubiquitination-mediated degradation of the STAT3 protein.
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15
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Vakiloroayaei A, Shah NS, Oeffinger M, Bayfield MA. The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets. Nucleic Acids Res 2017; 45:11341-11355. [PMID: 28977649 PMCID: PMC5737608 DOI: 10.1093/nar/gkx764] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs have critical roles in biological processes, and RNA chaperones can promote their folding into the native shape required for their function. La proteins are a class of highly abundant RNA chaperones that contact pre-tRNAs and other RNA polymerase III transcripts via their common UUU-3′OH ends, as well as through less specific contacts associated with RNA chaperone activity. However, whether La proteins preferentially bind misfolded pre-tRNAs or instead engage all pre-tRNA substrates irrespective of their folding status is not known. La deletion in yeast is synthetically lethal when combined with the loss of tRNA modifications predicted to contribute to the native pre-tRNA fold, such as the N2, N2-dimethylation of G26 by the methyltransferase Trm1p. In this work, we identify G26 containing pre-tRNAs that misfold in the absence of Trm1p and/or La (Sla1p) in Schizosaccharomyces pombe cells, then test whether La preferentially associates with such tRNAs in vitro and in vivo. Our data suggest that La does not discriminate a native from misfolded RNA target, and highlights the potential challenges faced by RNA chaperones in preferentially binding defective substrates.
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Affiliation(s)
- Ana Vakiloroayaei
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Neha S Shah
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada.,Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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16
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Brogie JE, Price DH. Reconstitution of a functional 7SK snRNP. Nucleic Acids Res 2017; 45:6864-6880. [PMID: 28431135 PMCID: PMC5499737 DOI: 10.1093/nar/gkx262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 01/29/2023] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro. Stably associated P-TEFb was highly inhibited, but could still be released and activated by HIV-1 Tat. Notably, P-TEFb association with both in vitro-reconstituted and cellular snRNPs led to similar changes in SHAPE reactivities, confirming that 7SK undergoes a P-TEFb-dependent structural change. We determined that the xRRM of LARP7 binds to the 3΄ stem loop of 7SK and inhibits the methyltransferase activity of MEPCE through a C-terminal MEPCE interaction domain (MID). Inhibition of MEPCE is dependent on the structure of the 3΄ stem loop and the closed form of 7SK RNA. This study provides important insights into intramolecular interactions within the 7SK snRNP.
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Affiliation(s)
- John E Brogie
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
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17
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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18
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Castro JM, Horn DA, Pu X, Lewis KA. Recombinant expression and purification of the RNA-binding LARP6 proteins from fish genetic model organisms. Protein Expr Purif 2017; 134:147-153. [PMID: 28400296 DOI: 10.1016/j.pep.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The RNA-binding proteins that comprise the La-related protein (LARP) superfamily have been implicated in a wide range of cellular functions, from tRNA maturation to regulation of protein synthesis. To more expansively characterize the biological function of the LARP6 subfamily, we have recombinantly expressed the full-length LARP6 proteins from two teleost fish, platyfish (Xiphophorus maculatus) and zebrafish (Danio rerio). The yields of the recombinant proteins were enhanced to >2 mg/L using a tandem approach of an N-terminal His6-SUMO tag and an iterative solubility screening assay to identify structurally stabilizing buffer components. The domain topologies of the purified fish proteins were probed with limited proteolysis. The fish proteins contain an internal, protease-resistant 40 kDa domain, which is considerably more stable than the comparable domain from the human LARP6 protein. The fish proteins are therefore a lucrative model system in which to study both the evolutionary divergence of this family of La-related proteins and the structure and conformational dynamics of the domains that comprise the LARP6 protein.
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Affiliation(s)
- José M Castro
- Department of Chemistry and Biochemistry, Texas State University, 601 University Dr., San Marcos, TX, 78666, United States
| | - Daniel A Horn
- Department of Chemistry and Biochemistry, Texas State University, 601 University Dr., San Marcos, TX, 78666, United States
| | - Xinzhu Pu
- Department of Chemistry and Biochemistry, Texas State University, 601 University Dr., San Marcos, TX, 78666, United States
| | - Karen A Lewis
- Department of Chemistry and Biochemistry, Texas State University, 601 University Dr., San Marcos, TX, 78666, United States.
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19
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Brown KA, Sharifi S, Hussain R, Donaldson L, Bayfield MA, Wilson DJ. Distinct Dynamic Modes Enable the Engagement of Dissimilar Ligands in a Promiscuous Atypical RNA Recognition Motif. Biochemistry 2016; 55:7141-7150. [PMID: 27959512 DOI: 10.1021/acs.biochem.6b00995] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes. In particular, binding of the single-stranded RNA induces helical "unwinding" in a region of the CTD previously hypothesized to play an important role in La and La-related protein-associated RNA remodeling, while the same region becomes less dynamic upon engagement with the double-stranded HCV RNA. Binding of double-stranded RNA also involves less penetration into the RRM2 binding pocket and more engagement with the unstructured C-terminus of the La CTD. The complementarity between TRESI-HDX and Δδ nuclear magnetic resonance measurements for ligand binding analysis is also explored.
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Affiliation(s)
- Kerene A Brown
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
| | - Samel Sharifi
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Rawaa Hussain
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Logan Donaldson
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
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20
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Seetharaman S, Flemyng E, Shen J, Conte MR, Ridley AJ. The RNA-binding protein LARP4 regulates cancer cell migration and invasion. Cytoskeleton (Hoboken) 2016; 73:680-690. [PMID: 27615744 PMCID: PMC5111583 DOI: 10.1002/cm.21336] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
Abstract
LARP4 is a La-related RNA-binding protein implicated in regulating mRNA translation, which interacts with poly(A)-binding protein (PABP). We previously identified LARP4 in an RNAi screen as one of several genes that regulate the shape of PC3 prostate cancer cells. Here we show that LARP4 depletion induces cell elongation in PC3 cells and MDA-MB-231 breast cancer cells. LARP4 depletion increases cell migration and invasion, as well as inducing invasive cell protrusions in 3D Matrigel. Conversely, LARP4 over-expression reduces cell elongation and increases cell circularity. LARP4 mutations are found in a variety of cancers. Introduction of some of these cancer-associated mutations, including a truncation mutant, into LARP4 enhances its effects on cell morphology. The truncation mutant shows enhanced interaction with PABP. We propose that LARP4 inhibits migration and invasion of cancer cells, and that some cancer-associated mutations stimulate these effects of LARP4. © 2016 The Authors. Cytoskeleton Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Shailaja Seetharaman
- Randall Division of Cell and Molecular BiophysicsKing's College LondonNew Hunt's House, Guy's CampusLondonSE1 1ULUnited Kingdom
| | - Ella Flemyng
- Randall Division of Cell and Molecular BiophysicsKing's College LondonNew Hunt's House, Guy's CampusLondonSE1 1ULUnited Kingdom
| | - Jiazhen Shen
- Randall Division of Cell and Molecular BiophysicsKing's College LondonNew Hunt's House, Guy's CampusLondonSE1 1ULUnited Kingdom
| | - Maria R. Conte
- Randall Division of Cell and Molecular BiophysicsKing's College LondonNew Hunt's House, Guy's CampusLondonSE1 1ULUnited Kingdom
| | - Anne J. Ridley
- Randall Division of Cell and Molecular BiophysicsKing's College LondonNew Hunt's House, Guy's CampusLondonSE1 1ULUnited Kingdom
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21
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Chen DF, Lin C, Wang HL, Zhang L, Dai L, Jia SN, Zhou R, Li R, Yang JS, Yang F, Clegg JS, Nagasawa H, Yang WJ. An La-related protein controls cell cycle arrest by nuclear retrograde transport of tRNAs during diapause formation in Artemia. BMC Biol 2016; 14:16. [PMID: 26941127 PMCID: PMC4778291 DOI: 10.1186/s12915-016-0239-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/18/2016] [Indexed: 08/30/2023] Open
Abstract
Background In eukaryotes, tRNA trafficking between the nucleus and cytoplasm is a complex process connected with cell cycle regulation. Such trafficking is therefore of fundamental importance in cell biology, and disruption of this process has grave consequences for cell viability and survival. To cope with harsh habitats, Artemia has evolved a special reproductive mode to release encysted embryos in which cell division can be maintained in a dormancy state for a long period. Results Using Artemia as a peculiar model of the cell cycle, an La-related protein from Artemia, named Ar-Larp, was found to bind to tRNA and accumulate in the nucleus, leading to cell cycle arrest and controlling the onset of diapause formation in Artemia. Furthermore, exogenous gene expression of Ar-Larp could induce cell cycle arrest in cancer cells and suppress tumor growth in a xenograft mouse model, similar to the results obtained in diapause embryos of Artemia. Our study of tRNA trafficking indicated that Ar-Larp controls cell cycle arrest by binding to tRNAs and influencing their retrograde movement from the cytoplasm to the nucleus, which is connected to pathways involved in cell cycle checkpoints. Conclusions These findings in Artemia offer new insights into the mechanism underlying cell cycle arrest regulation, as well as providing a potentially novel approach to study tRNA retrograde movement from the cytoplasm to the nucleus. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dian-Fu Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.,Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Cheng Lin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Hong-Liang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Li Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Li Dai
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Sheng-Nan Jia
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Rong Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China
| | - Ran Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, People's Republic of China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fan Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - James S Clegg
- Section of Molecular and Cellular Biology and Bodega Marine Laboratory, University of California, Davis, Bodega Bay, California, 94923, USA
| | - Hiromichi Nagasawa
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.,Department of Biological Chemistry, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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22
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Li Y, Collins M, Geiser R, Bakkar N, Riascos D, Bowser R. RBM45 homo-oligomerization mediates association with ALS-linked proteins and stress granules. Sci Rep 2015; 5:14262. [PMID: 26391765 PMCID: PMC4585734 DOI: 10.1038/srep14262] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/21/2015] [Indexed: 12/12/2022] Open
Abstract
The aggregation of RNA-binding proteins is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBM45 is an RNA-binding protein that forms cytoplasmic inclusions in neurons and glia in ALS and FTLD. To explore the role of RBM45 in ALS and FTLD, we examined the contribution of the protein’s domains to its function, subcellular localization, and interaction with itself and ALS-linked proteins. We find that RBM45 forms homo-oligomers and physically associates with the ALS-linked proteins TDP-43 and FUS in the nucleus. Nuclear localization of RBM45 is mediated by a bipartite nuclear-localization sequence (NLS) located at the C-terminus. RBM45 mutants that lack a functional NLS accumulate in the cytoplasm and form TDP-43 positive stress granules. Moreover, we identify a novel structural element, termed the homo-oligomer assembly (HOA) domain, that is highly conserved across species and promote homo-oligomerization of RBM45. RBM45 mutants that fail to form homo-oligomers exhibit significantly reduced association with ALS-linked proteins and inclusion into stress granules. These results show that RMB45 may function as a homo-oligomer and that its oligomerization contributes to ALS/FTLD RNA-binding protein aggregation.
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Affiliation(s)
- Yang Li
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Mahlon Collins
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Rachel Geiser
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Nadine Bakkar
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - David Riascos
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Robert Bowser
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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23
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Deragon JM, Bousquet-Antonelli C. The role of LARP1 in translation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:399-417. [PMID: 25892282 DOI: 10.1002/wrna.1282] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
The LARP1 proteins form an evolutionarily homogeneous subgroup of the eukaryotic superfamily of La-Motif (LAM) containing factors. Members of the LARP1 family are found in most protists, fungi, plants, and animals. We review here evidence suggesting that LARP1 are key versatile messenger RNA (mRNA)-binding proteins involved in regulating important biological processes such as gametogenesis, embryogenesis, sex determination, and cell division in animals, as well as acclimation to stress in yeasts and plants. LARP1 proteins perform all these essential tasks likely by binding to key mRNAs and regulating their stability and/or translation. In human, the impact of LARP1 over cell division and proliferation is potentially under the control of the TORC1 complex. We review data suggesting that LARP1 is a direct target of this master signaling hub. TOR-dependent LARP1 phosphorylation could specifically enhance the translation of TOP mRNAs providing a way to promote translation, growth, and proliferation. Consequently, LARP1 is found to be significantly upregulated in many malignant cell types. In plants, LARP1 was found to act as a cofactor of the heat-induced mRNA degradation process, an essential acclimation strategy leading to the degradation of more than 4500 mRNAs coding for growth and development housekeeping functions. In Saccharomyces cerevisiae, the LARP1 proteins (Slf1p and Sro9p) are important, among other things, for copper resistance and oxidative stress survival. LARP1 proteins are therefore emerging as critical ancient mRNA-binding factors that evolved common as well as specific targets and regulatory functions in all eukaryotic lineages.
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Affiliation(s)
- Jean-Marc Deragon
- CNRS, LGDP-UMR5096, Perpignan, France.,University of Perpignan, LGDP-UMR5096, Perpignan, France
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24
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Martino L, Pennell S, Kelly G, Busi B, Brown P, Atkinson RA, Salisbury NJH, Ooi ZH, See KW, Smerdon SJ, Alfano C, Bui TTT, Conte MR. Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module. Nucleic Acids Res 2015; 43:645-60. [PMID: 25488812 PMCID: PMC4288179 DOI: 10.1093/nar/gku1287] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023] Open
Abstract
The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3' UUUOH sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5' UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs.
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Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Simon Pennell
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Baptiste Busi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biology, École Normale Supérieure de Lyon, CEDEX 07, France
| | - Paul Brown
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Nicholas J H Salisbury
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Zi-Hao Ooi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Kang-Wei See
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Stephen J Smerdon
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Caterina Alfano
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
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25
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Kuehnert J, Sommer G, Zierk AW, Fedarovich A, Brock A, Fedarovich D, Heise T. Novel RNA chaperone domain of RNA-binding protein La is regulated by AKT phosphorylation. Nucleic Acids Res 2015; 43:581-94. [PMID: 25520193 PMCID: PMC4288197 DOI: 10.1093/nar/gku1309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 01/13/2023] Open
Abstract
The cellular function of the cancer-associated RNA-binding protein La has been linked to translation of viral and cellular mRNAs. Recently, we have shown that the human La protein stimulates IRES-mediated translation of the cooperative oncogene CCND1 in cervical cancer cells. However, there is little known about the underlying molecular mechanism by which La stimulates CCND1 IRES-mediated translation, and we propose that its RNA chaperone activity is required. Herein, we show that La binds close to the CCND1 start codon and demonstrate that La's RNA chaperone activity can change the folding of its binding site. We map the RNA chaperone domain (RCD) within the C-terminal region of La in close proximity to a novel AKT phosphorylation site (T389). Phosphorylation at T389 by AKT-1 strongly impairs its RNA chaperone activity. Furthermore, we demonstrate that the RCD as well as T389 is required to stimulate CCND1 IRES-mediated translation in cells. In summary, we provide a model whereby a novel interplay between RNA-binding, RNA chaperoning and AKT phosphorylation of La protein regulates CCND1 IRES-mediated translation.
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Affiliation(s)
- Julia Kuehnert
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gunhild Sommer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Avery W Zierk
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alena Fedarovich
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alexander Brock
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Dzmitry Fedarovich
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tilman Heise
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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Rijal K, Maraia RJ, Arimbasseri AG. A methods review on use of nonsense suppression to study 3' end formation and other aspects of tRNA biogenesis. Gene 2014; 556:35-50. [PMID: 25447915 DOI: 10.1016/j.gene.2014.11.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/26/2022]
Abstract
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Aneeshkumar G Arimbasseri
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Gaidamakov S, Maximova OA, Chon H, Blewett NH, Wang H, Crawford AK, Day A, Tulchin N, Crouch RJ, Morse HC, Blitzer RD, Maraia RJ. Targeted deletion of the gene encoding the La autoantigen (Sjögren's syndrome antigen B) in B cells or the frontal brain causes extensive tissue loss. Mol Cell Biol 2014; 34:123-31. [PMID: 24190965 PMCID: PMC3911279 DOI: 10.1128/mcb.01010-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/09/2013] [Accepted: 10/23/2013] [Indexed: 11/20/2022] Open
Abstract
La antigen (Sjögren's syndrome antigen B) is a phosphoprotein associated with nascent precursor tRNAs and other RNAs, and it is targeted by autoantibodies in patients with Sjögren's syndrome, systemic lupus erythematosus, and neonatal lupus. Increased levels of La are associated with leukemias and other cancers, and various viruses usurp La to promote their replication. Yeast cells (Saccharomyces cerevisiae and Schizosaccharomyces pombe) genetically depleted of La grow and proliferate, whereas deletion from mice causes early embryonic lethality, raising the question of whether La is required by mammalian cells generally or only to surpass a developmental stage. We developed a conditional La allele and used it in mice that express Cre recombinase in either B cell progenitors or the forebrain. B cell Mb1(Cre) La-deleted mice produce no B cells. Consistent with αCamKII Cre, which induces deletion in hippocampal CA1 cells in the third postnatal week and later throughout the neocortex, brains develop normally in La-deleted mice until ∼5 weeks and then lose a large amount of forebrain cells and mass, with evidence of altered pre-tRNA processing. The data indicate that La is required not only in proliferating cells but also in nondividing postmitotic cells. Thus, La is essential in different cell types and required for normal development of various tissue types.
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Affiliation(s)
- Sergei Gaidamakov
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Olga A. Maximova
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hyongi Chon
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Nathan H. Blewett
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Hongsheng Wang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda K. Crawford
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda Day
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalie Tulchin
- Department of Pathology, Mount Sinai School of Medicine, New York, New York, USA
| | - Robert J. Crouch
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Herbert C. Morse
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert D. Blitzer
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, USA
| | - Richard J. Maraia
- Intramural Research Programs of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Commissioned Corps, U.S. Public Health Service, Washington, DC, USA
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