1
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Shichino Y, Yamaguchi T, Kashiwagi K, Mito M, Takahashi M, Ito T, Ingolia NT, Kuba K, Iwasaki S. eIF4A1 enhances LARP1-mediated translational repression during mTORC1 inhibition. Nat Struct Mol Biol 2024:10.1038/s41594-024-01321-7. [PMID: 38773334 DOI: 10.1038/s41594-024-01321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/18/2024] [Indexed: 05/23/2024]
Abstract
Eukaryotic translation initiation factor (eIF)4A-a DEAD-box RNA-binding protein-plays an essential role in translation initiation. Recent reports have suggested helicase-dependent and helicase-independent functions for eIF4A, but the multifaceted roles of eIF4A have not been fully explored. Here we show that eIF4A1 enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA pulldown followed by sequencing revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTORC1 inhibition. This selective interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that deletion of EIF4A1 attenuated the translational repression of TOP mRNAs upon mTORC1 inactivation. Moreover, eIF4A1 increases the interaction between TOP mRNAs and LARP1 and, thus, ensures stronger translational repression upon mTORC1 inhibition. Our data show the multimodality of eIF4A1 in modulating protein synthesis through an inhibitory binding partner and provide a unique example of the repressive role of a universal translational activator.
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Affiliation(s)
- Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kazuhiro Kashiwagi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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2
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Xiang X, Deng Q, Zheng Y, He Y, Ji D, Vejlupkova Z, Fowler JE, Zhou L. Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen. BMC PLANT BIOLOGY 2024; 24:348. [PMID: 38684961 PMCID: PMC11057080 DOI: 10.1186/s12870-024-05054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. RESULTS In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type. CONCLUSIONS The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination.
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Affiliation(s)
- Xiaoqin Xiang
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Qianxia Deng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi Zheng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi He
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Dongpu Ji
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Lian Zhou
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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3
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Knop K, Gomez-Moreira C, Galloway A, Ditsova D, Cowling VH. RAM is upregulated during T cell activation and is required for RNA cap formation and gene expression. DISCOVERY IMMUNOLOGY 2023; 3:kyad021. [PMID: 38572449 PMCID: PMC10989996 DOI: 10.1093/discim/kyad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 10/29/2023] [Indexed: 04/05/2024]
Abstract
On T cell activation, upregulation of gene expression produces the protein required for the differentiation and proliferation of effector cell populations. RAM (RNMT-Activating Mini protein/RAMAC/Fam103a1), the cofactor of the RNA cap methyltransferase RNMT (RNA guanosine N-7 cap methyltransferase), is upregulated following activation. Formation of the RNA cap protects RNA during synthesis and guides RNA processing and translation. Using conditional gene deletion, we found that Ram expression stabilizes RNMT protein in T cells and is required for its upregulation on activation. When the Ram gene is deleted in naïve T cells, there are major impacts on activation-induced RNA cap formation and gene expression. Activated T cell proliferation is dependent on increased ribosome production; in Ram knockout T cells, activation-induced expression of ribosomal protein genes and snoRNAs is most severely reduced. Consistent with these changes, Ram deletion resulted in reduced protein synthesis, and reduced growth and proliferation of CD4 T cells. Deletion of Ram results in a similar but milder phenotype to Rnmt deletion, supporting the role of RAM as a RNMT cofactor.
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Affiliation(s)
- Katarzyna Knop
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | | | - Alison Galloway
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Dimitrinka Ditsova
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Victoria H Cowling
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
- School of Cancer Sciences, University of Glasgow, G61 1QH, Glasgow, UK
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4
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Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
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Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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5
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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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6
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Goering R, Arora A, Pockalny MC, Taliaferro JM. RNA localization mechanisms transcend cell morphology. eLife 2023; 12:e80040. [PMID: 36867563 PMCID: PMC9984196 DOI: 10.7554/elife.80040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/24/2023] [Indexed: 03/04/2023] Open
Abstract
RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins (RBPs). Generally, our knowledge of the mechanistic details behind the localization of a given RNA is restricted to a particular cell type. Here, we show that RNA/RBP interactions that regulate RNA localization in one cell type predictably regulate localization in other cell types with vastly different morphologies. To determine transcriptome-wide RNA spatial distributions across the apicobasal axis of human intestinal epithelial cells, we used our recently developed RNA proximity labeling technique, Halo-seq. We found that mRNAs encoding ribosomal proteins (RP mRNAs) were strongly localized to the basal pole of these cells. Using reporter transcripts and single-molecule RNA FISH, we found that pyrimidine-rich motifs in the 5' UTRs of RP mRNAs were sufficient to drive basal RNA localization. Interestingly, the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells. In both cell types, the regulatory activity of this motif was dependent on it being in the 5' UTR of the transcript, was abolished upon perturbation of the RNA-binding protein LARP1, and was reduced upon inhibition of kinesin-1. To extend these findings, we compared subcellular RNAseq data from neuronal and epithelial cells. We found that the basal compartment of epithelial cells and the projections of neuronal cells were enriched for highly similar sets of RNAs, indicating that broadly similar mechanisms may be transporting RNAs to these morphologically distinct locations. These findings identify the first RNA element known to regulate RNA localization across the apicobasal axis of epithelial cells, establish LARP1 as an RNA localization regulator, and demonstrate that RNA localization mechanisms cut across cell morphologies.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Megan C Pockalny
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
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7
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Park J, Kim M, Yi H, Baeg K, Choi Y, Lee YS, Lim J, Kim VN. Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex. Nat Struct Mol Biol 2023; 30:330-338. [PMID: 36849640 DOI: 10.1038/s41594-023-00930-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Deadenylation generally constitutes the first and pivotal step in eukaryotic messenger RNA decay. Despite its importance in posttranscriptional regulations, the kinetics of deadenylation and its regulation remain largely unexplored. Here we identify La ribonucleoprotein 1, translational regulator (LARP1) as a general decelerator of deadenylation, which acts mainly in the 30-60-nucleotide (nt) poly(A) length window. We measured the steady-state and pulse-chased distribution of poly(A)-tail length, and found that deadenylation slows down in the 30-60-nt range. LARP1 associates preferentially with short tails and its depletion results in accelerated deadenylation specifically in the 30-60-nt range. Consistently, LARP1 knockdown leads to a global reduction of messenger RNA abundance. LARP1 interferes with the CCR4-NOT-mediated deadenylation in vitro by forming a ternary complex with poly(A)-binding protein (PABP) and poly(A). Together, our work reveals a dynamic nature of deadenylation kinetics and a role of LARP1 as a poly(A) length-specific barricade that creates a threshold for deadenylation.
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Affiliation(s)
- Joha Park
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Myeonghwan Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hyerim Yi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Stanford University School of Medicine, Stanford, CA, USA
| | - Kyungmin Baeg
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
| | - Yongkuk Choi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Yale School of Medicine, New Haven, CT, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.
- School of Biological Sciences, Seoul National University, Seoul, Korea.
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8
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Pongprayoon W, Panya A, Jaresitthikunchai J, Phaonakrop N, Roytrakul S. Phosphoprotein Profile of Rice ( Oryza sativa L.) Seedlings under Osmotic Stress after Pretreatment with Chitosan. PLANTS (BASEL, SWITZERLAND) 2022; 11:2729. [PMID: 36297750 PMCID: PMC9611960 DOI: 10.3390/plants11202729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
This study aims to identify novel chitosan (CTS)-responsive phosphoproteins in Leung Pratew 123 (LPT123) and Khao Dawk Mali 105 (KDML105) as drought-sensitive rice cultivars and differences in the CTS response. Rice seeds were soaked in CTS solution before germination, and 2- and 4-week-old rice seedlings sprayed with CTS before osmotic stress comprised the following four groups: (1) seedlings treated with distilled water; (2) seedlings treated with CTS; (3) seedlings pretreated with distilled water and subjected to osmotic stress; and (4) seedlings pretreated with CTS and subjected to osmotic stress. Phosphoproteins of leaf tissues were enriched using immobilized metal affinity chromatography (IMAC) before tryptic digestion and analysis via LC-MS. Phosphoprotein profiling analyses led to the identification of 4721 phosphoproteins representing 1052 and 1040 unique phosphoproteins in the LPT123 and KDML105 seedlings, respectively. In response to CTS pretreatment before osmotic stress, 22 differently expressed proteins were discovered, of which 10 and 12 were identified in the LPT123 and KDML105, respectively. These proteins are typically involved in signaling, transport, protein folding, protein degradation, and metabolism. This study provides fruitful data to understand the signal transduction mechanisms of rice seedlings pretreated with CTS before exposure to osmotic stress.
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Affiliation(s)
- Wasinee Pongprayoon
- Department of Biology, Faculty of Science, Burapha University, 169 Longhaad Bangsaen Rd, Saensook, Mueang, Chonburi 20131, Thailand
| | - Atikorn Panya
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Janthima Jaresitthikunchai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
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9
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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10
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Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum. Int J Biol Macromol 2022; 224:1101-1117. [DOI: 10.1016/j.ijbiomac.2022.10.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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11
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Schneider C, Erhard F, Binotti B, Buchberger A, Vogel J, Fischer U. An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs. Cell Rep 2022; 41:111467. [DOI: 10.1016/j.celrep.2022.111467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/14/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
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12
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Farooq Z, Kusuma F, Burke P, Dufour CR, Lee D, Tabatabaei N, Toboz P, Radovani E, Greenblatt J, Rehman J, Class J, Khoutorsky A, Fonseca BD, Richner JM, Mercier E, Bourque G, Giguère V, Subramaniam AR, Han J, Tahmasebi S. The amino acid sensor GCN2 suppresses Terminal Oligopyrimidine (TOP) mRNA translation via La-related Protein 1 (LARP1). J Biol Chem 2022; 298:102277. [PMID: 35863436 PMCID: PMC9396407 DOI: 10.1016/j.jbc.2022.102277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
La-related protein 1 (LARP1) has been identified as a key translational inhibitor of terminal oligopyrimidine (TOP) mRNAs downstream of the nutrient sensing protein kinase complex, mTORC1. LARP1 exerts this inhibitory effect on TOP mRNA translation by binding to the mRNA cap and the adjacent 5′TOP motif, resulting in the displacement of the cap-binding protein eIF4E from TOP mRNAs. However, the involvement of additional signaling pathway in regulating LARP1-mediated inhibition of TOP mRNA translation is largely unexplored. In the present study, we identify a second nutrient sensing kinase GCN2 that converges on LARP1 to control TOP mRNA translation. Using chromatin-immunoprecipitation followed by massive parallel sequencing (ChIP-seq) analysis of activating transcription factor 4 (ATF4), an effector of GCN2 in nutrient stress conditions, in WT and GCN2 KO mouse embryonic fibroblasts, we determined that LARP1 is a GCN2-dependent transcriptional target of ATF4. Moreover, we identified GCN1, a GCN2 activator, participates in a complex with LARP1 on stalled ribosomes, suggesting a role for GCN1 in LARP1-mediated translation inhibition in response to ribosome stalling. Therefore, our data suggest that the GCN2 pathway controls LARP1 activity via two mechanisms: ATF4-dependent transcriptional induction of LARP1 mRNA and GCN1-mediated recruitment of LARP1 to stalled ribosomes.
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Affiliation(s)
- Zeenat Farooq
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Fedho Kusuma
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Phillip Burke
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Catherine R Dufour
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Duckgue Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Phoenix Toboz
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Jacob Class
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Arkady Khoutorsky
- Department of Anesthesia and Faculty of Dentistry, McGill University, Montreal, QC H3A 0G1, Canada
| | | | - Justin M Richner
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Eloi Mercier
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jaeseok Han
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea.
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
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13
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Martin ET, Blatt P, Nguyen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Dev Cell 2022; 57:883-900.e10. [PMID: 35413237 PMCID: PMC9011129 DOI: 10.1016/j.devcel.2022.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/11/2022] [Accepted: 03/10/2022] [Indexed: 01/26/2023]
Abstract
Ribosomal defects perturb stem cell differentiation, and this is the cause of ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discover that three DExD/H-box proteins govern ribosome biogenesis (RiBi) and Drosophila oogenesis. Loss of these DExD/H-box proteins, which we name Aramis, Athos, and Porthos, aberrantly stabilizes p53, arrests the cell cycle, and stalls germline stem cell (GSC) differentiation. Aramis controls cell-cycle progression by regulating translation of mRNAs that contain a terminal oligo pyrimidine (TOP) motif in their 5' UTRs. We find that TOP motifs confer sensitivity to ribosome levels that are mediated by La-related protein (Larp). One such TOP-containing mRNA codes for novel nucleolar protein 1 (Non1), a conserved p53 destabilizing protein. Upon a sufficient ribosome concentration, Non1 is expressed, and it promotes GSC cell-cycle progression via p53 degradation. Thus, a previously unappreciated TOP motif in Drosophila responds to reduced RiBi to co-regulate the translation of ribosomal proteins and a p53 repressor, coupling RiBi to GSC differentiation.
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Affiliation(s)
- Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Elaine Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sangeetha Selvam
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Hyun Ah M Yoon
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; Albany Medical College, Albany, NY 12208, USA
| | - Tyler Pocchiari
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; SUNY Upstate Medical University, Syracuse, NY 13210-2375, USA
| | - Shamsi Emtenani
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Andrea Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
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14
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Desi N, Tong QY, Teh V, Chan JJ, Zhang B, Tabatabaeian H, Tan HQ, Kapeli K, Jin W, Lim CY, Kwok ZH, Tan HT, Wang S, Siew BE, Lee KC, Chong CS, Tan KK, Yang H, Kappei D, Yeo GW, Chung MCM, Tay Y. Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis. Cell Mol Life Sci 2022; 79:147. [PMID: 35195778 PMCID: PMC11072786 DOI: 10.1007/s00018-021-04093-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we identify LARP1 as one of the most upregulated RBPs in colorectal cancer (CRC) and demonstrate its oncogenic properties. We perform LARP1:RNA interactome profiling and unveil a previously unexplored role for LARP1 in targeting the 3'UTR of oncogenes in CRC. Notably, we identify the proto-oncogenic transcription factor MYC as a key LARP1-regulated target. Our data show that LARP1 positively modulates MYC expression by associating with its 3'UTR. In addition, antisense oligonucleotide-mediated blocking of the interaction between LARP1 and the MYC 3'UTR reduces MYC expression and in vitro CRC growth. Furthermore, a systematic analysis of LARP1:protein interactions reveals IGF2BP3 and YBX1 as LARP1-interacting proteins that also regulate MYC expression and CRC development. Finally, we demonstrate that MYC reciprocally modulates LARP1 expression by targeting its enhancer. In summary, our data reveal a critical, previously uncharacterized role of LARP1 in promoting CRC tumorigenesis, validate its direct regulation of the proto-oncogene MYC and delineate a model of the positive feedback loop between MYC and LARP1 that promotes CRC growth and development.
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Affiliation(s)
- Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Qing Yun Tong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Velda Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Division of Pulmonary and Critical Care, Boston University, Boston, MA, 02118, USA
| | - Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei-En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok-Chung Lee
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon-Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, San Diego, USA
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
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15
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Xu X, Ahmed T, Wang L, Cao X, Zhang Z, Wang M, Lv Y, Kanwal S, Tariq M, Lin R, Zhang H, Huang Y, Peng H, Lin D, Shi X, Geng D, Liu B, Zhang X, Yi W, Qin Y, Esteban MA, Qin B. The mTORC1-eIF4F axis controls paused pluripotency. EMBO Rep 2022; 23:e53081. [PMID: 34866316 PMCID: PMC8811634 DOI: 10.15252/embr.202153081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) can self-renew indefinitely and maintain pluripotency. Inhibition of mechanistic target of rapamycin (mTOR) by the kinase inhibitor INK128 is known to induce paused pluripotency in mESCs cultured with traditional serum/LIF medium (SL), but the underlying mechanisms remain unclear. In this study, we demonstrate that mTOR complex 1 (mTORC1) but not complex 2 (mTORC2) mediates mTOR inhibition-induced paused pluripotency in cells grown in both SL and 2iL medium (GSK3 and MEK inhibitors and LIF). We also show that mTORC1 regulates self-renewal in both conditions mainly through eIF4F-mediated translation initiation that targets mRNAs of both cytosolic and mitochondrial ribosome subunits. Moreover, inhibition of mitochondrial translation is sufficient to induce paused pluripotency. Interestingly, eIF4F also regulates maintenance of pluripotency in an mTORC1-independent but MEK/ERK-dependent manner in SL, indicating that translation of pluripotency genes is controlled differently in SL and 2iL. Our study reveals a detailed picture of how mTOR governs self-renewal in mESCs and uncovers a context-dependent function of eIF4F in pluripotency regulation.
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Affiliation(s)
- Xueting Xu
- School of Life SciencesUniversity of Science and Technology of ChinaHefeiChina,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Tanveer Ahmed
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Lulu Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Xintao Cao
- Key Laboratory of RNA BiologyInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Zeyu Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Ming Wang
- Guangdong Key Laboratory of Genome Stability and Human Disease PreventionDepartment of Biochemistry & Molecular BiologyShenzhen University Health Science CenterShenzhenChina
| | - Yuan Lv
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,University of Chinese Academy of SciencesBeijingChina,Laboratory of Integrative BiologyGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Shahzina Kanwal
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Integrative BiologyGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Muqddas Tariq
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Runxia Lin
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,University of Chinese Academy of SciencesBeijingChina
| | - Hui Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Yinghua Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Hao Peng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,University of Chinese Academy of SciencesBeijingChina
| | - Danni Lin
- School of Life SciencesUniversity of Science and Technology of ChinaHefeiChina,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Xue Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,University of Chinese Academy of SciencesBeijingChina
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Stability and Human Disease PreventionDepartment of Biochemistry & Molecular BiologyShenzhen University Health Science CenterShenzhenChina
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina,University of Chinese Academy of SciencesBeijingChina
| | - Wen Yi
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Yan Qin
- Key Laboratory of RNA BiologyInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Miguel A Esteban
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina,University of Chinese Academy of SciencesBeijingChina,Laboratory of Integrative BiologyGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Institute of Stem Cells and RegenerationChinese Academy of SciencesBeijingChina,Joint School of Life SciencesGuangzhou Institutes of Biomedicine and Health and Guangzhou Medical UniversityGuangzhouChina
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Center, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Laboratory of Metabolism and Cell FateGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina,University of Chinese Academy of SciencesBeijingChina,Joint School of Life SciencesGuangzhou Institutes of Biomedicine and Health and Guangzhou Medical UniversityGuangzhouChina
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16
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Jurgens AP, Popović B, Wolkers MC. T cells at work: How post-transcriptional mechanisms control T cell homeostasis and activation. Eur J Immunol 2021; 51:2178-2187. [PMID: 34180545 PMCID: PMC8457102 DOI: 10.1002/eji.202049055] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/07/2021] [Indexed: 12/19/2022]
Abstract
T cells are central players of the adaptive immune system by protecting us from recurring infections and by killing malignant cells. Protective T cell responses rely on the concerted production of effector molecules such as cytolytic mediators, granzymes, and perforins, as well as pro-inflammatory cytokines and chemokines. Once activated, T cells drastically change their gene expression and rapidly respond to insults by producing ample amounts of effector molecules. In the absence of antigen, T cells remain in a quiescent state and survey our body for possible pathogenic insults. Resting T cells are, however, not inert, but continuously regulate their protein production to survive and to be prepared for possible re-infections. Here, we review our current knowledge on the regulation of gene expression in activated and quiescent T cells. We specifically focus on post-transcriptional mechanisms that define the protein output and that allow dormant cells to undergo active signaling and selective translation, keeping them poised for activation. Finally, we discuss which signals drive T cell survival and their preparedness to respond to insults and which mechanisms are involved in these processes.
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Affiliation(s)
- Anouk P. Jurgens
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Branka Popović
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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17
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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18
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Jia JJ, Lahr RM, Solgaard MT, Moraes BJ, Pointet R, Yang AD, Celucci G, Graber TE, Hoang HD, Niklaus M, Pena IA, Hollensen AK, Smith EM, Chaker-Margot M, Anton L, Dajadian C, Livingstone M, Hearnden J, Wang XD, Yu Y, Maier T, Damgaard CK, Berman AJ, Alain T, Fonseca BD. mTORC1 promotes TOP mRNA translation through site-specific phosphorylation of LARP1. Nucleic Acids Res 2021; 49:3461-3489. [PMID: 33398329 PMCID: PMC8034618 DOI: 10.1093/nar/gkaa1239] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 11/29/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
LARP1 is a key repressor of TOP mRNA translation. It binds the m7Gppp cap moiety and the adjacent 5'TOP motif of TOP mRNAs, thus impeding the assembly of the eIF4F complex on these transcripts. mTORC1 controls TOP mRNA translation via LARP1, but the details of the mechanism are unclear. Herein we elucidate the mechanism by which mTORC1 controls LARP1's translation repression activity. We demonstrate that mTORC1 phosphorylates LARP1 in vitro and in vivo, activities that are efficiently inhibited by rapamycin and torin1. We uncover 26 rapamycin-sensitive phospho-serine and -threonine residues on LARP1 that are distributed in 7 clusters. Our data show that phosphorylation of a cluster of residues located proximally to the m7Gppp cap-binding DM15 region is particularly sensitive to rapamycin and regulates both the RNA-binding and the translation inhibitory activities of LARP1. Our results unravel a new model of translation control in which the La module (LaMod) and DM15 region of LARP1, both of which can directly interact with TOP mRNA, are differentially regulated: the LaMod remains constitutively bound to PABP (irrespective of the activation status of mTORC1), while the C-terminal DM15 'pendular hook' engages the TOP mRNA 5'-end to repress translation, but only in conditions of mTORC1 inhibition.
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Affiliation(s)
- Jian-Jun Jia
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael T Solgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bruno J Moraes
- GABBA PhD Program, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
- PrimerGen Ltd, Viseu, Portugal
| | - Roberta Pointet
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - An-Dao Yang
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Giovanna Celucci
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Marius R Niklaus
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Anne K Hollensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ewan M Smith
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Leonie Anton
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christopher Dajadian
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Mark Livingstone
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Jaclyn Hearnden
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Xu-Dong Wang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yonghao Yu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christian K Damgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tommy Alain
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- PrimerGen Ltd, Viseu, Portugal
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19
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Zhou L, Vejlupkova Z, Warman C, Fowler JE. A Maize Male Gametophyte-Specific Gene Encodes ZmLARP6c1, a Potential RNA-Binding Protein Required for Competitive Pollen Tube Growth. FRONTIERS IN PLANT SCIENCE 2021; 12:635244. [PMID: 33719310 PMCID: PMC7947365 DOI: 10.3389/fpls.2021.635244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Members of the La-related protein family (LARPs) contain a conserved La module, which has been associated with RNA-binding activity. Expression of the maize gene GRMZM2G323499/Zm00001d018613, a member of the LARP family, is highly specific to pollen, based on both transcriptomic and proteomic assays. This suggests a pollen-specific RNA regulatory function for the protein, designated ZmLARP6c1 based on sequence similarity to the LARP6 subfamily in Arabidopsis. To test this hypothesis, a Ds-GFP transposable element insertion in the ZmLarp6c1 gene (tdsgR82C05) was obtained from the Dooner/Du mutant collection. Sequencing confirmed that the Ds-GFP insertion is in an exon, and thus likely interferes with ZmLARP6c1 function. Tracking inheritance of the insertion via its endosperm-expressed GFP indicated that the mutation was associated with reduced transmission from a heterozygous plant when crossed as a male (ranging from 0.5 to 26.5% transmission), but not as a female. Furthermore, this transmission defect was significantly alleviated when less pollen was applied to the silk, reducing competition between mutant and wild-type pollen. Pollen grain diameter measurements and nuclei counts showed no significant differences between wild-type and mutant pollen. However, in vitro, mutant pollen tubes were significantly shorter than those from sibling wild-type plants, and also displayed altered germination dynamics. These results are consistent with the idea that ZmLARP6c1 provides an important regulatory function during the highly competitive progamic phase of male gametophyte development following arrival of the pollen grain on the silk. The conditional, competitive nature of the Zmlarp6c1::Ds male sterility phenotype (i.e., reduced ability to produce progeny seed) points toward new possibilities for genetic control of parentage in crop production.
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Affiliation(s)
- Lian Zhou
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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20
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Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. Controversies around the function of LARP1. RNA Biol 2021; 18:207-217. [PMID: 32233986 PMCID: PMC7928164 DOI: 10.1080/15476286.2020.1733787] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.
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Affiliation(s)
- Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, USA
| | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université De Montréal, Montreal, Quebec, Canada
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21
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Al-Ashtal HA, Rubottom CM, Leeper TC, Berman AJ. The LARP1 La-Module recognizes both ends of TOP mRNAs. RNA Biol 2021; 18:248-258. [PMID: 31601159 PMCID: PMC7927982 DOI: 10.1080/15476286.2019.1669404] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/22/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022] Open
Abstract
La-Related Protein 1 (LARP1) is an RNA-binding protein that regulates the stability and translation of mRNAs encoding the translation machinery, including ribosomal proteins and translation factors. These mRNAs are characterized by a 5'-terminal oligopyrimidine (TOP) motif that coordinates their temporal and stoichiometric expression. While LARP1 represses TOP mRNA translation via the C-terminal DM15 region, the role of the N-terminal La-Module in the recognition and translational regulation of TOP mRNAs remains elusive. Herein we show that the LARP1 La-Module also binds TOP motifs, although in a cap-independent manner. We also demonstrate that it recognizes poly(A) RNA. Further, our data reveal that the LARP1 La-Module can simultaneously engage TOP motifs and poly(A) RNA. These results evoke an intriguing molecular mechanism whereby LARP1 could regulate translation and stabilization of TOP transcripts.
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Affiliation(s)
- Hiba A. Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney M. Rubottom
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas C. Leeper
- Department of Chemistry & Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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22
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Smith EM, Benbahouche N, Morris K, Wilczynska A, Gillen S, Schmidt T, Meijer H, Jukes-Jones R, Cain K, Jones C, Stoneley M, Waldron J, Bell C, Fonseca B, Blagden S, Willis A, Bushell M. The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction. Nucleic Acids Res 2021; 49:458-478. [PMID: 33332560 PMCID: PMC7797073 DOI: 10.1093/nar/gkaa1189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 11/16/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal oligopyrimidine tract (TOP) at their 5'ends, although the mechanisms by which this occurs downstream of mTOR signalling are still unclear. We used RNA-binding protein (RBP) capture to identify changes in the protein-RNA interaction landscape following mTOR inhibition. Upon mTOR inhibition, the binding of LARP1 to a number of mRNAs, including TOP-containing mRNAs, increased. Importantly, non-TOP-containing mRNAs bound by LARP1 are in a translationally-repressed state, even under control conditions. The mRNA interactome of the LARP1-associated protein PABPC1 was found to have a high degree of overlap with that of LARP1 and our data show that PABPC1 is required for the association of LARP1 with its specific mRNA targets. Finally, we demonstrate that mRNAs, including those encoding proteins critical for cell growth and survival, are translationally repressed when bound by both LARP1 and PABPC1.
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Affiliation(s)
- Ewan M Smith
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Nour El Houda Benbahouche
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Katherine Morris
- MRC Toxicology Unit, University of Cambridge, Leicester LE1 9HN, UK
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Sarah Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Hedda A Meijer
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Kelvin Cain
- MRC Toxicology Unit, University of Cambridge, Leicester LE1 9HN, UK
| | - Carolyn Jones
- MRC Toxicology Unit, University of Cambridge, Leicester LE1 9HN, UK
| | - Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Leicester LE1 9HN, UK
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Cameron Bell
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK
| | | | - Sarah Blagden
- Department of Oncology, University of Oxford, Oxford, OX3 7LE, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester LE1 9HN, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
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23
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Zhang Y, Cai W, Zou Y, Zhang H. Knockdown of KCNQ1OT1 Inhibits Proliferation, Invasion, and Drug Resistance by Regulating miR-129-5p-Mediated LARP1 in Osteosarcoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7698767. [PMID: 32953888 PMCID: PMC7487100 DOI: 10.1155/2020/7698767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
KCNQ1OT1 exerts an important role in various cancers, but its role in osteosarcoma (OS) and the potential mechanism remain to be clarified. In the present research, we aimed to explore the effect of KCNQ1OT1 on osteosarcoma and further explore the special molecular mechanism. The expression of KCNQ1OT1 was analyzed in tumor and adjacent tissues of 30 patients with osteosarcoma by RT-PCR. Cell proliferation and invasion were explored using MTT and transwell assay, respectively. Luciferase reporter analysis and pull-down assay were performed to determine the binding activity of KCNQ1OT1 and miR-129-5p. The result revealed that KCNQ1OT1 was highly expressed in osteosarcoma tissues and cells. KCNQ1OT1-siRNA inhibited the proliferation, invasion, and drug resistance of osteosarcoma cells. The luciferase reporter assay and pull-down assay demonstrated that KCNQ1OT1 directly interact with miR-129-5p. In addition, miR-129-5p binds to LARP1 directly, and LARP1 promoted the proliferation, invasion, and drug resistance of osteosarcoma cells. What is more, KCNQ1OT1 promoted proliferation, invasion, and drug resistance via inhibiting the expression of miR-129-5p and further promoting the expression of miR-129-5p-mediated LARP1. Collectively, it suggests that downregulation of KCNQ1OT1 inhibits proliferation, invasion, and drug resistance by regulating miR-129-5p-mediated LARP1 in osteosarcoma cells.
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Affiliation(s)
- Yunfei Zhang
- Department of Pathology, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
| | - Wei Cai
- Department of Pathology, People's Hospital of Gansu Province, Lanzhou, 73000 Gansu Province, China
| | - Yuli Zou
- Department of Emergency, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
| | - Hong Zhang
- Department of Pathology, Affiliated Hospital of Northwest Minzu University, Second Provincial People's Hospital of Gansu, Lanzhou, 73000 Gansu Province, China
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24
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TOP mRNPs: Molecular Mechanisms and Principles of Regulation. Biomolecules 2020; 10:biom10070969. [PMID: 32605040 PMCID: PMC7407576 DOI: 10.3390/biom10070969] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.
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25
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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: 3] [Impact Index Per Article: 0.8] [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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26
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Hoxhaj G, Manning BD. The PI3K-AKT network at the interface of oncogenic signalling and cancer metabolism. Nat Rev Cancer 2020; 20:74-88. [PMID: 31686003 PMCID: PMC7314312 DOI: 10.1038/s41568-019-0216-7] [Citation(s) in RCA: 1004] [Impact Index Per Article: 251.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 02/06/2023]
Abstract
The altered metabolic programme of cancer cells facilitates their cell-autonomous proliferation and survival. In normal cells, signal transduction pathways control core cellular functions, including metabolism, to couple the signals from exogenous growth factors, cytokines or hormones to adaptive changes in cell physiology. The ubiquitous, growth factor-regulated phosphoinositide 3-kinase (PI3K)-AKT signalling network has diverse downstream effects on cellular metabolism, through either direct regulation of nutrient transporters and metabolic enzymes or the control of transcription factors that regulate the expression of key components of metabolic pathways. Aberrant activation of this signalling network is one of the most frequent events in human cancer and serves to disconnect the control of cell growth, survival and metabolism from exogenous growth stimuli. Here we discuss our current understanding of the molecular events controlling cellular metabolism downstream of PI3K and AKT and of how these events couple two major hallmarks of cancer: growth factor independence through oncogenic signalling and metabolic reprogramming to support cell survival and proliferation.
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Affiliation(s)
- Gerta Hoxhaj
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Brendan D Manning
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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27
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Cassidy KC, Lahr RM, Kaminsky JC, Mack S, Fonseca BD, Das SR, Berman AJ, Durrant JD. Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Structure 2019; 27:1771-1781.e5. [PMID: 31676287 PMCID: PMC7269035 DOI: 10.1016/j.str.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/06/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m7G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m7G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m7GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.
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Affiliation(s)
- Kevin C Cassidy
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jesse C Kaminsky
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Stephanie Mack
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1 ON, Canada
| | - Subha R Das
- Department of Chemistry and Center for Nucleic Acids Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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28
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Pacheco S, Kaminsky JC, Kochnev IK, Durrant JD. PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. J Chem Inf Model 2019; 59:4087-4092. [PMID: 31580061 PMCID: PMC6849643 DOI: 10.1021/acs.jcim.9b00703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Molecular dynamics (MD) simulations
reveal molecular motions at
atomic resolution. Recent advances in high-performance computing now
enable microsecond-long simulations capable of sampling a wide range
of biologically relevant events. But the disk space required to store
an MD trajectory increases with simulation length and system size,
complicating collaborative sharing and visualization. To overcome
these limitations, we created PCAViz, an open-source toolkit for sharing
and visualizing MD trajectories via the web browser. PCAViz includes
two components: the PCAViz Compressor, which compresses and saves
simulation data; and the PCAViz Interpreter, which decompresses the
data in users’ browsers and feeds it to any of several browser-based
molecular-visualization libraries (e.g., 3Dmol.js, NGL Viewer, etc.).
An easy-to-install WordPress plugin enables “plug-and-play”
trajectory visualization. PCAViz will appeal to a broad audience of
researchers and educators. The source code is available at http://durrantlab.com/pcaviz/, and the WordPress plugin is available via the official WordPress
Plugin Directory.
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Affiliation(s)
- Sayuri Pacheco
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Jesse C Kaminsky
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Iurii K Kochnev
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Jacob D Durrant
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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29
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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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30
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Valvezan AJ, Manning BD. Molecular logic of mTORC1 signalling as a metabolic rheostat. Nat Metab 2019; 1:321-333. [PMID: 32694720 DOI: 10.1038/s42255-019-0038-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/24/2019] [Indexed: 02/05/2023]
Abstract
The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) serves as a key conduit between growth signals and the metabolic processes underlying cell growth. The activation state of mTORC1 is controlled by intracellular nutrients and energy, as well as exogenous hormones and growth factors, thereby integrating local and systemic growth signals. Here we discuss the molecular logic of the mTORC1 signalling network and its importance in coupling growth signals to the control of cellular metabolism. After activation, mTORC1 promotes the conversion of available nutrients and energy into the major macromolecular species contributing to cellular mass, including proteins, nucleic acids and lipids, while suppressing the autophagic recycling of these macromolecules back into their nutrient constituents. Given that uncoupling of mTORC1 from its normal regulatory inputs contributes to many diseases-including cancer, genetic tumour syndromes, metabolic diseases, autoimmune diseases and neurological disorders-understanding the molecular logic of the mTORC1 network and how to modulate it may present therapeutic opportunities for treatment of a broad range of diseases and potentially even for the extension of lifespan.
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Affiliation(s)
- Alexander J Valvezan
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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31
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Translation of Human β-Actin mRNA is Regulated by mTOR Pathway. Genes (Basel) 2019; 10:genes10020096. [PMID: 30700035 PMCID: PMC6410274 DOI: 10.3390/genes10020096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 01/09/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) kinase is a well-known master regulator of growth-dependent gene expression in higher eukaryotes. Translation regulation is an important function of the mTORC1 pathway that controls the synthesis of many ribosomal proteins and translation factors. Housekeeping genes such as β-actin (ACTB) are widely used as negative control genes in studies of growth-dependent translation. Here we demonstrate that translation of both endogenous and reporter ACTB mRNA is inhibited in the presence of mTOR kinase inhibitor (Torin1) and under amino acid starvation. Notably, 5’UTR and promoter of ACTB are sufficient for the mTOR-dependent translational response, and the degree of mTOR-sensitivity of ACTB mRNA translation is cell type-dependent.
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32
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Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays 2018; 40:e1800133. [PMID: 30264543 DOI: 10.1002/bies.201800133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/27/2018] [Indexed: 11/08/2022]
Abstract
DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
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33
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Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication. J Virol 2018; 92:JVI.00563-18. [PMID: 29769334 DOI: 10.1128/jvi.00563-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/07/2018] [Indexed: 12/23/2022] Open
Abstract
Viral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, using in vitro and cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCE Following infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the family Reoviridae encode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the family Reoviridae diverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Using in vitro and cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the family Reoviridae assort and replicate their genomes.
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34
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Abstract
Translation is a key step in the regulation of gene expression and one of the most energy-consuming processes in the cell. In response to various stimuli, multiple signaling pathways converge on the translational machinery to regulate its function. To date, the roles of phosphoinositide 3-kinase (PI3K)/AKT and the mitogen-activated protein kinase (MAPK) pathways in the regulation of translation are among the best understood. Both pathways engage the mechanistic target of rapamycin (mTOR) to regulate a variety of components of the translational machinery. While these pathways regulate protein synthesis in homeostasis, their dysregulation results in aberrant translation leading to human diseases, including diabetes, neurological disorders, and cancer. Here we review the roles of the PI3K/AKT and MAPK pathways in the regulation of mRNA translation. We also highlight additional signaling mechanisms that have recently emerged as regulators of the translational apparatus.
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35
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Fonseca BD, Lahr RM, Damgaard CK, Alain T, Berman AJ. LARP1 on TOP of ribosome production. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1480. [PMID: 29722158 DOI: 10.1002/wrna.1480] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
The ribosome is an essential unit of all living organisms that commands protein synthesis, ultimately fuelling cell growth (accumulation of cell mass) and cell proliferation (increase in cell number). The eukaryotic ribosome consists of 4 ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs). Despite its fundamental role in every living organism, our present understanding of how higher eukaryotes produce the various ribosome components is incomplete. Uncovering the mechanisms utilized by human cells to generate functional ribosomes will likely have far-reaching implications in human disease. Recent biochemical and structural studies revealed La-related protein 1 (LARP1) as a key new player in RP production. LARP1 is an RNA-binding protein that belongs to the LARP superfamily; it controls the translation and stability of the mRNAs that encode RPs and translation factors, which are characterized by a 5' terminal oligopyrimidine (5'TOP) motif and are thus known as TOP mRNAs. The activity of LARP1 is regulated by the mammalian target of rapamycin complex 1 (mTORC1): a eukaryotic protein kinase complex that integrates nutrient sensing with mRNA translation, particularly that of TOP mRNAs. In this review, we provide an overview of the role of LARP1 in the control of ribosome production in multicellular eukaryotes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Bruno D Fonseca
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Roni M Lahr
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | | | - Tommy Alain
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Andrea J Berman
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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36
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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37
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Blagden S, Abdel Mouti M, Chettle J. Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1432. [PMID: 28762650 PMCID: PMC5763387 DOI: 10.1002/wrna.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/12/2017] [Accepted: 06/12/2017] [Indexed: 01/04/2023]
Abstract
RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network. This network regulates survival and chemotherapy resistance in the contemporary context of the cancer cell. There is emerging evidence that cancers become dependent on PTGR factors for their survival. Further understanding of this network may identify innovative therapeutic targets as well as yield crucial insights into the hard-wiring of many malignancies, including ovarian cancer. WIREs RNA 2018, 9:e1432. doi: 10.1002/wrna.1432 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Mechanisms RNA in Disease and Development > RNA in Disease.
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38
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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: 87] [Impact Index Per Article: 12.4] [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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39
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The molecular basis of mTORC1-regulated translation. Biochem Soc Trans 2017; 45:213-221. [PMID: 28202675 DOI: 10.1042/bst20160072] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022]
Abstract
The mammalian target of rapamycin (mTOR) signaling pathway is a master regulator of cell growth throughout eukaryotes. The pathway senses nutrient and other growth signals, and then orchestrates the complex systems of anabolic and catabolic metabolism that underpin the growth process. A central target of mTOR signaling is the translation machinery. mTOR uses a multitude of translation factors to drive the bulk production of protein that growth requires, but also to direct a post-transcriptional program of growth-specific gene expression. This review will discuss current understanding of how mTOR controls these mechanisms and their functions in growth control.
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40
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Hong S, Freeberg MA, Han T, Kamath A, Yao Y, Fukuda T, Suzuki T, Kim JK, Inoki K. LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs. eLife 2017; 6:e25237. [PMID: 28650797 PMCID: PMC5484620 DOI: 10.7554/elife.25237] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/15/2017] [Indexed: 12/15/2022] Open
Abstract
The RNA binding protein, LARP1, has been proposed to function downstream of mTORC1 to regulate the translation of 5'TOP mRNAs such as those encoding ribosome proteins (RP). However, the roles of LARP1 in the translation of 5'TOP mRNAs are controversial and its regulatory roles in mTORC1-mediated translation remain unclear. Here we show that LARP1 is a direct substrate of mTORC1 and Akt/S6K1. Deep sequencing of LARP1-bound mRNAs reveal that non-phosphorylated LARP1 interacts with both 5' and 3'UTRs of RP mRNAs and inhibits their translation. Importantly, phosphorylation of LARP1 by mTORC1 and Akt/S6K1 dissociates it from 5'UTRs and relieves its inhibitory activity on RP mRNA translation. Concomitantly, phosphorylated LARP1 scaffolds mTORC1 on the 3'UTRs of translationally-competent RP mRNAs to facilitate mTORC1-dependent induction of translation initiation. Thus, in response to cellular mTOR activity, LARP1 serves as a phosphorylation-sensitive molecular switch for turning off or on RP mRNA translation and subsequent ribosome biogenesis.
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Affiliation(s)
- Sungki Hong
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Mallory A Freeberg
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States
| | - Ting Han
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Avani Kamath
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Yao Yao
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Tomoko Fukuda
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Tsukasa Suzuki
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - John K Kim
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, United States
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, Ann Arbor, United States
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, United States
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
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41
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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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42
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Lahr RM, Fonseca BD, Ciotti GE, Al-Ashtal HA, Jia JJ, Niklaus MR, Blagden SP, Alain T, Berman AJ. La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs. eLife 2017. [PMID: 28379136 DOI: 10.7554/elife.24146.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 5'terminal oligopyrimidine (5'TOP) motif is a cis-regulatory RNA element located immediately downstream of the 7-methylguanosine [m7G] cap of TOP mRNAs, which encode ribosomal proteins and translation factors. In eukaryotes, this motif coordinates the synchronous and stoichiometric expression of the protein components of the translation machinery. La-related protein 1 (LARP1) binds TOP mRNAs, regulating their stability and translation. We present crystal structures of the human LARP1 DM15 region in complex with a 5'TOP motif, a cap analog (m7GTP), and a capped cytidine (m7GpppC), resolved to 2.6, 1.8 and 1.7 Å, respectively. Our binding, competition, and immunoprecipitation data corroborate and elaborate on the mechanism of 5'TOP motif binding by LARP1. We show that LARP1 directly binds the cap and adjacent 5'TOP motif of TOP mRNAs, effectively impeding access of eIF4E to the cap and preventing eIF4F assembly. Thus, LARP1 is a specialized TOP mRNA cap-binding protein that controls ribosome biogenesis.
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Affiliation(s)
- Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Gabrielle E Ciotti
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Hiba A Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Jian-Jun Jia
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Marius R Niklaus
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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43
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Lahr RM, Fonseca BD, Ciotti GE, Al-Ashtal HA, Jia JJ, Niklaus MR, Blagden SP, Alain T, Berman AJ. La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs. eLife 2017; 6:e24146. [PMID: 28379136 PMCID: PMC5419741 DOI: 10.7554/elife.24146] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/04/2017] [Indexed: 01/07/2023] Open
Abstract
The 5'terminal oligopyrimidine (5'TOP) motif is a cis-regulatory RNA element located immediately downstream of the 7-methylguanosine [m7G] cap of TOP mRNAs, which encode ribosomal proteins and translation factors. In eukaryotes, this motif coordinates the synchronous and stoichiometric expression of the protein components of the translation machinery. La-related protein 1 (LARP1) binds TOP mRNAs, regulating their stability and translation. We present crystal structures of the human LARP1 DM15 region in complex with a 5'TOP motif, a cap analog (m7GTP), and a capped cytidine (m7GpppC), resolved to 2.6, 1.8 and 1.7 Å, respectively. Our binding, competition, and immunoprecipitation data corroborate and elaborate on the mechanism of 5'TOP motif binding by LARP1. We show that LARP1 directly binds the cap and adjacent 5'TOP motif of TOP mRNAs, effectively impeding access of eIF4E to the cap and preventing eIF4F assembly. Thus, LARP1 is a specialized TOP mRNA cap-binding protein that controls ribosome biogenesis.
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Affiliation(s)
- Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Bruno D Fonseca
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Gabrielle E Ciotti
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Hiba A Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Jian-Jun Jia
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Marius R Niklaus
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Tommy Alain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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44
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Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation. Trends Biochem Sci 2017; 42:369-382. [PMID: 28268044 DOI: 10.1016/j.tibs.2017.02.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/27/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Abstract
Eukaryotic cells determine the final protein output of their genetic program not only by controlling transcription but also by regulating the localization, translation and turnover rates of their mRNAs. Ultimately, the fate of any given mRNA is determined by the ensemble of all associated RNA-binding proteins (RBPs), non-coding RNAs and metabolites collectively known as the messenger ribonucleoprotein particle (mRNP). Although many mRNA-associated factors have been identified over the past years, little is known about the composition of individual mRNPs and the cooperation of their constituents. In this review we discuss recent progress that has been made on how this 'mRNP code' is established on individual transcripts and how it is interpreted during gene expression in eukaryotic cells.
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45
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Alam N, Zimmerman L, Wolfson NA, Joseph CG, Fierke CA, Schueler-Furman O. Structure-Based Identification of HDAC8 Non-histone Substrates. Structure 2016; 24:458-68. [PMID: 26933971 PMCID: PMC5590822 DOI: 10.1016/j.str.2016.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 11/17/2022]
Abstract
HDAC8 is a member of the family of histone deacetylases (HDACs) that catalyze the deacetylation of acetyl lysine residues within histone and non-histone proteins. The recent identification of novel non-histone HDAC8 substrates such as SMC3, ERRα, and ARID1A indicates a complex functionality of this enzyme in cellular homeostasis. To discover additional HDAC8 substrates, we developed a comprehensive, structure-based approach based on Rosetta FlexPepBind, a protocol that evaluates peptide-binding ability to a receptor from structural models of this interaction. Here we adapt this protocol to identify HDAC8 substrates using peptide sequences extracted from proteins with known acetylated sites. The many new in vitro HDAC8 peptide substrates identified in this study suggest that numerous cellular proteins are HDAC8 substrates, thus expanding our view of the acetylome and its regulation by HDAC8.
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Affiliation(s)
- Nawsad Alam
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Lior Zimmerman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Noah A Wolfson
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Caleb G Joseph
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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46
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Hopkins TG, Mura M, Al-Ashtal HA, Lahr RM, Abd-Latip N, Sweeney K, Lu H, Weir J, El-Bahrawy M, Steel JH, Ghaem-Maghami S, Aboagye EO, Berman AJ, Blagden SP. The RNA-binding protein LARP1 is a post-transcriptional regulator of survival and tumorigenesis in ovarian cancer. Nucleic Acids Res 2016; 44:1227-46. [PMID: 26717985 PMCID: PMC4756840 DOI: 10.1093/nar/gkv1515] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/12/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are increasingly identified as post-transcriptional drivers of cancer progression. The RBP LARP1 is an mRNA stability regulator, and elevated expression of the protein in hepatocellular and lung cancers is correlated with adverse prognosis. LARP1 associates with an mRNA interactome that is enriched for oncogenic transcripts. Here we explore the role of LARP1 in epithelial ovarian cancer, a disease characterized by the rapid acquisition of resistance to chemotherapy through the induction of pro-survival signalling. We show, using ovarian cell lines and xenografts, that LARP1 is required for cancer cell survival and chemotherapy resistance. LARP1 promotes tumour formation in vivo and maintains cancer stem cell-like populations. Using transcriptomic analysis following LARP1 knockdown, cross-referenced against the LARP1 interactome, we identify BCL2 and BIK as LARP1 mRNA targets. We demonstrate that, through an interaction with the 3' untranslated regions (3' UTRs) of BCL2 and BIK, LARP1 stabilizes BCL2 but destabilizes BIK with the net effect of resisting apoptosis. Together, our data indicate that by differentially regulating the stability of a selection of mRNAs, LARP1 promotes ovarian cancer progression and chemotherapy resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Autoantigens/genetics
- Autoantigens/metabolism
- Blotting, Western
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Cell Line, Tumor
- Cell Survival/drug effects
- Cell Survival/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- HeLa Cells
- Humans
- Interleukin Receptor Common gamma Subunit/deficiency
- Interleukin Receptor Common gamma Subunit/genetics
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Microscopy, Confocal
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Protein Binding
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Survival Analysis
- Transplantation, Heterologous
- SS-B Antigen
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Affiliation(s)
- Thomas G Hopkins
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Manuela Mura
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Hiba A Al-Ashtal
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Normala Abd-Latip
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Katrina Sweeney
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Haonan Lu
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Justin Weir
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Mona El-Bahrawy
- Department of Histopathology, Imperial College Healthcare NHS Trust, London W12 0NN, UK
| | - Jennifer H Steel
- Imperial College Experimental Cancer Medicine Centre, Division of Cancer, Imperial College Academic Health Science Centre, London W12 0NN, UK
| | - Sadaf Ghaem-Maghami
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK
| | - Eric O Aboagye
- Comprehensive Cancer Imaging Centre, Imperial College, Du Cane Road, London W12 0NN, UK
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sarah P Blagden
- Ovarian Cancer Action Research Centre, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0HS, UK Department of Oncology, University of Oxford, Old Road, Oxford OX3 7LE, UK
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Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules 2015; 5:2701-22. [PMID: 26501340 PMCID: PMC4693254 DOI: 10.3390/biom5042701] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 01/09/2023] Open
Abstract
The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.
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Affiliation(s)
- Chara Stavraka
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
| | - Sarah Blagden
- Ovarian Cancer Research Centre, Institute for Reproductive and Developmental Biology, Imperial College, Du Cane Road, London W12 0HS, UK.
- Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LE, UK.
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