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Lehmann S, Bass JJ, Barratt TF, Ali MZ, Szewczyk NJ. Functional phosphatome requirement for protein homeostasis, networked mitochondria, and sarcomere structure in C. elegans muscle. J Cachexia Sarcopenia Muscle 2017; 8:660-672. [PMID: 28508547 PMCID: PMC5566650 DOI: 10.1002/jcsm.12196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 12/08/2016] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Skeletal muscle is central to locomotion and metabolic homeostasis. The laboratory worm Caenorhabditis elegans has been developed into a genomic model for assessing the genes and signals that regulate muscle development and protein degradation. Past work has identified a receptor tyrosine kinase signalling network that combinatorially controls autophagy, nerve signal to muscle to oppose proteasome-based degradation, and extracellular matrix-based signals that control calpain and caspase activation. The last two discoveries were enabled by following up results from a functional genomic screen of known regulators of muscle. Recently, a screen of the kinome requirement for muscle homeostasis identified roughly 40% of kinases as required for C. elegans muscle health; 80 have identified human orthologues and 53 are known to be expressed in skeletal muscle. To complement this kinome screen, here, we screen most of the phosphatases in C. elegans. METHODS RNA interference was used to knockdown phosphatase-encoding genes. Knockdown was first conducted during development with positive results also knocked down only in fully developed adult muscle. Protein homeostasis, mitochondrial structure, and sarcomere structure were assessed using transgenic reporter proteins. Genes identified as being required to prevent protein degradation were also knocked down in conditions that blocked proteasome or autophagic degradation. Genes identified as being required to prevent autophagic degradation were also assessed for autophagic vesicle accumulation using another transgenic reporter. Lastly, bioinformatics were used to look for overlap between kinases and phosphatases required for muscle homeostasis, and the prediction that one phosphatase was required to prevent mitogen-activated protein kinase activation was assessed by western blot. RESULTS A little over half of all phosphatases are each required to prevent abnormal development or maintenance of muscle. Eighty-six of these phosphatases have known human orthologues, 57 of which are known to be expressed in human skeletal muscle. Of the phosphatases required to prevent abnormal muscle protein degradation, roughly half are required to prevent increased autophagy. CONCLUSIONS A significant portion of both the kinome and phosphatome are required for establishing and maintaining C. elegans muscle health. Autophagy appears to be the most commonly triggered form of protein degradation in response to disruption of phosphorylation-based signalling. The results from these screens provide measurable phenotypes for analysing the combined contribution of kinases and phosphatases in a multi-cellular organism and suggest new potential regulators of human skeletal muscle for further analysis.
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Affiliation(s)
- Susann Lehmann
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Joseph J Bass
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Thomas F Barratt
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Mohammed Z Ali
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
| | - Nathaniel J Szewczyk
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Medical School, University of Nottingham, Royal Derby Hospital, Derby, DE22 3DT, UK
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Zugasti O, Thakur N, Belougne J, Squiban B, Kurz CL, Soulé J, Omi S, Tichit L, Pujol N, Ewbank JJ. A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes. BMC Biol 2016; 14:35. [PMID: 27129311 PMCID: PMC4850687 DOI: 10.1186/s12915-016-0256-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/18/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Caenorhabditis elegans has emerged over the last decade as a useful model for the study of innate immunity. Its infection with the pathogenic fungus Drechmeria coniospora leads to the rapid up-regulation in the epidermis of genes encoding antimicrobial peptides. The molecular basis of antimicrobial peptide gene regulation has been previously characterized through forward genetic screens. Reverse genetics, based on RNAi, provide a complementary approach to dissect the worm's immune defenses. RESULTS We report here the full results of a quantitative whole-genome RNAi screen in C. elegans for genes involved in regulating antimicrobial peptide gene expression. The results will be a valuable resource for those contemplating similar RNAi-based screens and also reveal the limitations of such an approach. We present several strategies, including a comprehensive class clustering method, to overcome these limitations and which allowed us to characterize the different steps of the interaction between C. elegans and the fungus D. coniospora, leading to a complete description of the MAPK pathway central to innate immunity in C. elegans. The results further revealed a cross-tissue signaling, triggered by mitochondrial dysfunction in the intestine, that suppresses antimicrobial peptide gene expression in the nematode epidermis. CONCLUSIONS Overall, our results provide an unprecedented system's level insight into the regulation of C. elegans innate immunity. They represent a significant contribution to our understanding of host defenses and will lead to a better comprehension of the function and evolution of animal innate immunity.
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Affiliation(s)
- Olivier Zugasti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
- Present address: Institut de Biologie du Développement de Marseille, CNRS, UMR6216, Case 907, Marseille, France
| | - Nishant Thakur
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
| | - Jérôme Belougne
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
| | - Barbara Squiban
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
- Present address: Section of Hematology/Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - C Léopold Kurz
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
- Present address: Institut de Biologie du Développement de Marseille, CNRS, UMR6216, Case 907, Marseille, France
| | - Julien Soulé
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
- Present address: Institut de Genomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Shizue Omi
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France
| | - Laurent Tichit
- Institut de Mathématiques de Marseille, Aix Marseille Université, I2M Centrale Marseille, CNRS UMR 7373, 13453, Marseille, France
| | - Nathalie Pujol
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France.
| | - Jonathan J Ewbank
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288, Marseille, France.
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Etheridge T, Rahman M, Gaffney CJ, Shaw D, Shephard F, Magudia J, Solomon DE, Milne T, Blawzdziewicz J, Constantin-Teodosiu D, Greenhaff PL, Vanapalli SA, Szewczyk NJ. The integrin-adhesome is required to maintain muscle structure, mitochondrial ATP production, and movement forces in Caenorhabditis elegans. FASEB J 2014; 29:1235-46. [PMID: 25491313 PMCID: PMC4396603 DOI: 10.1096/fj.14-259119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/11/2014] [Indexed: 01/19/2023]
Abstract
The integrin-adhesome network, which contains >150 proteins, is mechano-transducing and located at discreet positions along the cell-cell and cell-extracellular matrix interface. A small subset of the integrin-adhesome is known to maintain normal muscle morphology. However, the importance of the entire adhesome for muscle structure and function is unknown. We used RNA interference to knock down 113 putative Caenorhabditis elegans homologs constituting most of the mammalian adhesome and 48 proteins known to localize to attachment sites in C. elegans muscle. In both cases, we found >90% of components were required for normal muscle mitochondrial structure and/or proteostasis vs. empty vector controls. Approximately half of these, mainly proteins that physically interact with each other, were also required for normal sarcomere and/or adhesome structure. Next we confirmed that the dystrophy observed in adhesome mutants associates with impaired maximal mitochondrial ATP production (P < 0.01), as well as reduced probability distribution of muscle movement forces compared with wild-type animals. Our results show that the integrin-adhesome network as a whole is required for maintaining both muscle structure and function and extend the current understanding of the full complexities of the functional adhesome in vivo.—Etheridge, T., Rahman, M., Gaffney, C. J., Shaw, D., Shephard, F., Magudia, J., Solomon, D. E., Milne, T., Blawzdziewicz, J., Constantin-Teodosiu, D., Greenhaff, P. L., Vanapalli, S. A., Szewczyk, N. J. The integrin-adhesome is required to maintain muscle structure, mitochondrial ATP production, and movement forces in Caenorhabditis elegans.
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Affiliation(s)
- Timothy Etheridge
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Mizanur Rahman
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Christopher J Gaffney
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Debra Shaw
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Freya Shephard
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Jignesh Magudia
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Deepak E Solomon
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Thomas Milne
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Jerzy Blawzdziewicz
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Dumitru Constantin-Teodosiu
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Paul L Greenhaff
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Siva A Vanapalli
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Nathaniel J Szewczyk
- *Department of Sport and Health Science, College of Life and Environmental Sciences, and College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, United Kingdom; Departments of Chemical Engineering and Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA; Medical Research Council/Arthritis Research UK Centre for Musculoskeletal Ageing Research, Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, United Kingdom; and School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
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