1
|
Schwenzer H, Abdel Mouti M, Neubert P, Morris J, Stockton J, Bonham S, Fellermeyer M, Chettle J, Fischer R, Beggs AD, Blagden SP. LARP1 isoform expression in human cancer cell lines. RNA Biol 2021; 18:237-247. [PMID: 32286153 PMCID: PMC7928056 DOI: 10.1080/15476286.2020.1744320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 01/07/2023] Open
Abstract
LARP1 is an oncogenic RNA-binding protein required for ribosome biogenesis and cancer cell survival. From published in vitro studies, there is disparity over which of two different LARP1 protein isoforms (termed the long LI-LARP1 and short SI-LARP1) is the canonical. Here, after conducting a series of biochemical and cellular assays, we conclude that LI-LARP1 (NM_033551.3 > NP_056130.2) is the dominantly expressed form. We observe that SI-LARP1 (NM_015315.5> NP_056130.2) is epigenetically repressed and that this repression is evolutionarily conserved in all but a small subclade of mammalian species. As with other LARP family members, there are multiple potential LARP1 mRNA isoforms that appear to be censored within the nucleus. The capacity of the cell to modulate splicing and expression of these apparently 'redundant' mRNAs hints at contextually specific mechanisms of LARP1 expression.
Collapse
Affiliation(s)
| | | | - Pia Neubert
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Joanne Stockton
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew D. Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | | |
Collapse
|
3
|
Simon M, Richard EM, Wang X, Shahzad M, Huang VH, Qaiser TA, Potluri P, Mahl SE, Davila A, Nazli S, Hancock S, Yu M, Gargus J, Chang R, Al-sheqaih N, Newman WG, Abdenur J, Starr A, Hegde R, Dorn T, Busch A, Park E, Wu J, Schwenzer H, Flierl A, Florentz C, Sissler M, Khan SN, Li R, Guan MX, Friedman TB, Wu DK, Procaccio V, Riazuddin S, Wallace DC, Ahmed ZM, Huang T, Riazuddin S. Mutations of human NARS2, encoding the mitochondrial asparaginyl-tRNA synthetase, cause nonsyndromic deafness and Leigh syndrome. PLoS Genet 2015; 11:e1005097. [PMID: 25807530 PMCID: PMC4373692 DOI: 10.1371/journal.pgen.1005097] [Citation(s) in RCA: 87] [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: 12/26/2014] [Accepted: 02/23/2015] [Indexed: 12/31/2022] Open
Abstract
Here we demonstrate association of variants in the mitochondrial asparaginyl-tRNA synthetase NARS2 with human hearing loss and Leigh syndrome. A homozygous missense mutation ([c.637G>T; p.Val213Phe]) is the underlying cause of nonsyndromic hearing loss (DFNB94) and compound heterozygous mutations ([c.969T>A; p.Tyr323*] + [c.1142A>G; p.Asn381Ser]) result in mitochondrial respiratory chain deficiency and Leigh syndrome, which is a neurodegenerative disease characterized by symmetric, bilateral lesions in the basal ganglia, thalamus, and brain stem. The severity of the genetic lesions and their effects on NARS2 protein structure cosegregate with the phenotype. A hypothetical truncated NARS2 protein, secondary to the Leigh syndrome mutation p.Tyr323* is not detectable and p.Asn381Ser further decreases NARS2 protein levels in patient fibroblasts. p.Asn381Ser also disrupts dimerization of NARS2, while the hearing loss p.Val213Phe variant has no effect on NARS2 oligomerization. Additionally we demonstrate decreased steady-state levels of mt-tRNAAsn in fibroblasts from the Leigh syndrome patients. In these cells we show that a decrease in oxygen consumption rates (OCR) and electron transport chain (ETC) activity can be rescued by overexpression of wild type NARS2. However, overexpression of the hearing loss associated p.Val213Phe mutant protein in these fibroblasts cannot complement the OCR and ETC defects. Our findings establish lesions in NARS2 as a new cause for nonsyndromic hearing loss and Leigh syndrome. Mitochondrial respiratory chain (MRC) disease represents a large and heterogeneous group of energy deficiency disorders. Here we report three mutations in NARS2, a mitochondrial asparaginyl-tRNA synthetase, associated with non-syndromic hearing loss (NSHL) and Leigh syndrome in two independent families. Located in the predicted catalytic domain of the protein, missense mutation p.(Val213Phe) results in NSHL (DFNB94) while compound heterozygous mutation (p.Tyr323*; p.Asn381Ser) is leading to Leigh syndrome with auditory neuropathy. In vivo analysis deemed p.Tyr323* mutant protein to be unstable. Co-immunoprecipitation assays show that p.Asn381Ser mutant disrupts the dimerization ability of NARS2. Leigh syndrome patient fibroblasts exhibit a decreased steady-state level of mt-tRNAAsn. In addition, in these cells, the mitochondrial respiratory chain is deficient, including significantly decreased oxygen consumption rates and electron transport chain activities. These functions can be partially restored with over-expression of wild-type NARS2 but not with p.Val213Phe mutant protein. Our study provides new insights into the genes that are necessary for the function of brain and inner ear sensory cells in humans.
Collapse
Affiliation(s)
- Mariella Simon
- Department of Developmental and Cellular Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, United States of America
- CHOC Childrens’, Division of Metabolics, Orange, California, United States of America
| | - Elodie M. Richard
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Mohsin Shahzad
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Vincent H. Huang
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Tanveer A. Qaiser
- National Center for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sarah E. Mahl
- Division of Pediatric Otolaryngology Head & Neck Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Antonio Davila
- Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sabiha Nazli
- National Center for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Saege Hancock
- Trovagene, San Diego, California, United States of America
| | - Margret Yu
- Marshall B Ketchum University, Fullerton, California, United States of America
| | - Jay Gargus
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Richard Chang
- CHOC Childrens’, Division of Metabolics, Orange, California, United States of America
| | - Nada Al-sheqaih
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, United Kingdom
| | - William G. Newman
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, United Kingdom
| | - Jose Abdenur
- CHOC Childrens’, Division of Metabolics, Orange, California, United States of America
| | - Arnold Starr
- Department of Neurology and Neurobiology, University of California, Irvine, Irvine, California, United States of America
| | - Rashmi Hegde
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Anke Busch
- Institute of Molecular Biology, Mainz, Germany
| | - Eddie Park
- Department of Developmental and Cellular Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, United States of America
| | - Jie Wu
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Hagen Schwenzer
- Architecture et Réactivité de l’ARN, CNRS, University of Strasbourg, IBMC, Strasbourg, France
| | - Adrian Flierl
- Parkinson’s Institute and Clinical Center, Sunnyvale, California, United States of America
| | - Catherine Florentz
- Architecture et Réactivité de l’ARN, CNRS, University of Strasbourg, IBMC, Strasbourg, France
| | - Marie Sissler
- Architecture et Réactivité de l’ARN, CNRS, University of Strasbourg, IBMC, Strasbourg, France
| | - Shaheen N. Khan
- National Center for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ronghua Li
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Min-Xin Guan
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Doris K. Wu
- Section on Sensory Cell Regeneration and Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vincent Procaccio
- Biochemistry and Genetics Department, UMR CNRS 6214–INSERM U1083, CHU Angers, Angers, France
| | - Sheikh Riazuddin
- Jinnah Hospital Complex, Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- University of Lahore, Lahore, Pakistan
- Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- * E-mail: (TH); (SR)
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
- * E-mail: (TH); (SR)
| |
Collapse
|
4
|
Lo WS, Gardiner E, Xu Z, Lau CF, Wang F, Zhou JJ, Mendlein JD, Nangle LA, Chiang KP, Yang XL, Au KF, Wong WH, Guo M, Zhang M, Schimmel P. Human tRNA synthetase catalytic nulls with diverse functions. Science 2014; 345:328-32. [PMID: 25035493 PMCID: PMC4188629 DOI: 10.1126/science.1252943] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic efficiency in higher organisms depends on mechanisms to create multiple functions from single genes. To investigate this question for an enzyme family, we chose aminoacyl tRNA synthetases (AARSs). They are exceptional in their progressive and accretive proliferation of noncatalytic domains as the Tree of Life is ascended. Here we report discovery of a large number of natural catalytic nulls (CNs) for each human AARS. Splicing events retain noncatalytic domains while ablating the catalytic domain to create CNs with diverse functions. Each synthetase is converted into several new signaling proteins with biological activities "orthogonal" to that of the catalytic parent. We suggest that splice variants with nonenzymatic functions may be more general, as evidenced by recent findings of other catalytically inactive splice-variant enzymes.
Collapse
Affiliation(s)
- Wing-Sze Lo
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Elisabeth Gardiner
- The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA. aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Zhiwen Xu
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Ching-Fun Lau
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Feng Wang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Jie J Zhou
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - John D Mendlein
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Leslie A Nangle
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Kyle P Chiang
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Xiang-Lei Yang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kin-Fai Au
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Min Guo
- The Scripps Laboratories for tRNA Synthetase Research, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mingjie Zhang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Paul Schimmel
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA. The Scripps Laboratories for tRNA Synthetase Research, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|