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Huang S, Ran Q, Li XM, Bao X, Zheng C, Li XD. MACSPI enables tissue-selective proteomic and interactomic analyses in multicellular organisms. Proc Natl Acad Sci U S A 2024; 121:e2319060121. [PMID: 38753516 PMCID: PMC11126916 DOI: 10.1073/pnas.2319060121] [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: 10/31/2023] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Multicellular organisms are composed of many tissue types that have distinct morphologies and functions, which are largely driven by specialized proteomes and interactomes. To define the proteome and interactome of a specific type of tissue in an intact animal, we developed a localized proteomics approach called Methionine Analog-based Cell-Specific Proteomics and Interactomics (MACSPI). This method uses the tissue-specific expression of an engineered methionyl-tRNA synthetase to label proteins with a bifunctional amino acid 2-amino-5-diazirinylnonynoic acid in selected cells. We applied MACSPI in Caenorhabditis elegans, a model multicellular organism, to selectively label, capture, and profile the proteomes of the body wall muscle and the nervous system, which led to the identification of tissue-specific proteins. Using the photo-cross-linker, we successfully profiled HSP90 interactors in muscles and neurons and identified tissue-specific interactors and stress-related interactors. Our study demonstrates that MACSPI can be used to profile tissue-specific proteomes and interactomes in intact multicellular organisms.
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Affiliation(s)
- Siyue Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Qiao Ran
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiucong Bao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chaogu Zheng
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
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Zou C, Yang T, Zhang J, Chen X, Zhao J, Wu D, Yang C, Liu P, Huang X, Liu J, Xu B. A quantitative proteomic study reveals oxidative stress and synapse-related proteins contributed to TDCIPP exposure induced neurotoxicity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 271:116005. [PMID: 38262093 DOI: 10.1016/j.ecoenv.2024.116005] [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: 11/10/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) has been consistently identified in various environmental media and biological specimens. Current understanding of the in vivo toxicities of TDCIPP is limited, especially for potential for neurotoxic and cognitive impairment effects. To better evaluate the potential adverse effect of the chemical on learning and memory, Sprague Dawley (SD) rats were administered TDCIPP via gavage at doses of 40, 120, and 360 mg/kg/day for a period of 90 days. Quantitative proteomic analysis, immunohistochemistry, and Western blotting were employed to assess alterations in proteins following exposure to TDCIPP. An open field test and the Morris Water Maze were used to assess anxiety and spatial learning memory capacity. Administration of TDCIPP induced anxiety and cognitive impairments in rats. Additionally, a noteworthy decrease in the number of neurons was observed in the hippocampal CA3 and dentate gyrus (DG) regions. Proteomic and bioinformatic analyses revealed dysregulation of numerous hippocampal proteins, particularly those associated with synapses (PKN1) or oxidative stress (GSTM4, NQO1, and BMAL1), which was further confirmed by Western blot analysis. In sum, the cognitive impairment of rats caused by TDCIPP exposure was associated with dysregulation of synaptic and oxidative stress-related proteins.
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Affiliation(s)
- Chunli Zou
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China; College of Public Health, Zunyi Medical University, Zunyi 563000, China
| | - Tingting Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China; College of Public Health, Zunyi Medical University, Zunyi 563000, China
| | - Jiuhong Zhang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Xiao Chen
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Jing Zhao
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Desheng Wu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Chen Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Peiyi Liu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Xinfeng Huang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Jianjun Liu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China.
| | - Benhong Xu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, China.
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Lesanpezeshki L, Qadota H, Darabad MN, Kashyap K, Lacerda CMR, Szewczyk NJ, Benian GM, Vanapalli SA. Investigating the correlation of muscle function tests and sarcomere organization in C. elegans. Skelet Muscle 2021; 11:20. [PMID: 34389048 PMCID: PMC8362255 DOI: 10.1186/s13395-021-00275-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Caenorhabditis elegans has been widely used as a model to study muscle structure and function. Its body wall muscle is functionally and structurally similar to vertebrate skeletal muscle with conserved molecular pathways contributing to sarcomere structure, and muscle function. However, a systematic investigation of the relationship between muscle force and sarcomere organization is lacking. Here, we investigate the contribution of various sarcomere proteins and membrane attachment components to muscle structure and function to introduce C. elegans as a model organism to study the genetic basis of muscle strength. Methods We employ two recently developed assays that involve exertion of muscle forces to investigate the correlation of muscle function to sarcomere organization. We utilized a microfluidic pillar-based platform called NemaFlex that quantifies the maximum exertable force and a burrowing assay that challenges the animals to move in three dimensions under a chemical stimulus. We selected 20 mutants with known defects in various substructures of sarcomeres and compared the physiological function of muscle proteins required for force generation and transmission. We also characterized the degree of sarcomere disorganization using immunostaining approaches. Results We find that mutants with genetic defects in thin filaments, thick filaments, and M-lines are generally weaker, and our assays are successful in detecting the functional changes in response to each sarcomere location tested. We find that the NemaFlex and burrowing assays are functionally distinct informing on different aspects of muscle physiology. Specifically, the burrowing assay has a larger bandwidth in phenotyping muscle mutants, because it could pick ten additional mutants impaired while exerting normal muscle force in NemaFlex. This enabled us to combine their readouts to develop an integrated muscle function score that was found to correlate with the score for muscle structure disorganization. Conclusions Our results highlight the suitability of NemaFlex and burrowing assays for evaluating muscle physiology of C. elegans. Using these approaches, we discuss the importance of the studied sarcomere proteins for muscle function and structure. The scoring methodology we have developed enhances the utility of C. elegans as a genetic model to study muscle function. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-021-00275-4.
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Affiliation(s)
- Leila Lesanpezeshki
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Hiroshi Qadota
- Department of Pathology, Emory University, Atlanta, GA, 30322, USA
| | | | - Karishma Kashyap
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Carla M R Lacerda
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Nathaniel J Szewczyk
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, United Kingdom & National Institute for Health Research Nottingham Biomedical Research Centre, Derby, DE22 3DT, UK.,Ohio Musculoskeletal and Neurological Institute (OMNI) and Department of Biomedical Sciences, Ohio University, Athens, OH, 45701, USA
| | - Guy M Benian
- Department of Pathology, Emory University, Atlanta, GA, 30322, USA
| | - Siva A Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, 79409, USA.
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Qadota H, Matsunaga Y, Bagchi P, Lange KI, Carrier KJ, Pols WV, Swartzbaugh E, Wilson KJ, Srayko M, Pallas DC, Benian GM. Protein phosphatase 2A is crucial for sarcomere organization in Caenorhabditis elegans striated muscle. Mol Biol Cell 2018; 29:2084-2097. [PMID: 29949401 PMCID: PMC6232960 DOI: 10.1091/mbc.e18-03-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 01/06/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a heterotrimer composed of single catalytic and scaffolding subunits and one of several possible regulatory subunits. We identified PPTR-2, a regulatory subunit of PP2A, as a binding partner for the giant muscle protein UNC-89 (obscurin) in Caenorhabditis elegans. PPTR-2 is required for sarcomere organization when its paralogue, PPTR-1, is deficient. PPTR-2 localizes to the sarcomere at dense bodies and M-lines, colocalizing with UNC-89 at M-lines. PP2A components in C. elegans include one catalytic subunit LET-92, one scaffolding subunit (PAA-1), and five regulatory subunits (SUR-6, PPTR-1, PPTR-2, RSA-1, and CASH-1). In adult muscle, loss of function in any of these subunits results in sarcomere disorganization. rsa-1 mutants show an interesting phenotype: one of the two myosin heavy chains, MHC A, localizes as closely spaced double lines rather than single lines. This "double line" phenotype is found in rare missense mutants of the head domain of MHC B myosin, such as unc-54(s74). Analysis of phosphoproteins in the unc-54(s74) mutant revealed two additional phosphoserines in the nonhelical tailpiece of MHC A. Antibodies localize PPTR-1, PAA-1, and SUR-6 to I-bands and RSA-1 to M-lines and I-bands. Therefore, PP2A localizes to sarcomeres and functions in the assembly or maintenance of sarcomeres.
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Affiliation(s)
- Hiroshi Qadota
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Yohei Matsunaga
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA 30322
| | - Karen I. Lange
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Karma J. Carrier
- Department of Biochemistry and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | | | | | | | - Martin Srayko
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - David C. Pallas
- Department of Biochemistry and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | - Guy M. Benian
- Department of Pathology, Emory University, Atlanta, GA 30322
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Butkevich E, Klopfenstein DR, Schmidt CF. Game of Zones: how actin-binding proteins organize muscle contraction. WORM 2016; 5:e1161880. [PMID: 27383012 PMCID: PMC4911971 DOI: 10.1080/21624054.2016.1161880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 02/26/2016] [Indexed: 11/22/2022]
Abstract
Locomotion of C. elegans requires coordinated, efficient transmission of forces generated on the molecular scale by myosin and actin filaments in myocytes to dense bodies and the hypodermis and cuticle enveloping body wall muscles. The complex organization of the acto-myosin scaffold with its accessory proteins provides a fine-tuned machinery regulated by effectors that guarantees that sarcomere units undergo controlled, reversible cycles of contraction and relaxation. Actin filaments in sarcomeres dynamically undergo polymerization and depolymerization. In a recent study, the actin-binding protein DBN-1, the C. elegans ortholog of human drebrin and drebrin-like proteins, was discovered to stabilize actin in muscle cells. DBN-1 reversibly changes location between actin filaments and myosin-rich regions during muscle contraction. Mutations in DBN-1 result in mislocalization of other actin-binding proteins. Here we discuss implications of this finding for the regulation of sarcomere actin stability and the organization of other actin-binding proteins.
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Affiliation(s)
- Eugenia Butkevich
- Georg August University, Third Institute of Physics - Biophysics , Göttingen, Germany
| | - Dieter R Klopfenstein
- Georg August University, Third Institute of Physics - Biophysics , Göttingen, Germany
| | - Christoph F Schmidt
- Georg August University, Third Institute of Physics - Biophysics , Göttingen, Germany
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Xu Y, Taru H, Jin Y, Quinn CC. SYD-1C, UNC-40 (DCC) and SAX-3 (Robo) function interdependently to promote axon guidance by regulating the MIG-2 GTPase. PLoS Genet 2015; 11:e1005185. [PMID: 25876065 PMCID: PMC4398414 DOI: 10.1371/journal.pgen.1005185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 03/30/2015] [Indexed: 12/13/2022] Open
Abstract
During development, axons must integrate directional information encoded by multiple guidance cues and their receptors. Axon guidance receptors, such as UNC-40 (DCC) and SAX-3 (Robo), can function individually or combinatorially with other guidance receptors to regulate downstream effectors. However, little is known about the molecular mechanisms that mediate combinatorial guidance receptor signaling. Here, we show that UNC-40, SAX-3 and the SYD-1 RhoGAP-like protein function interdependently to regulate the MIG-2 (Rac) GTPase in the HSN axon of C. elegans. We find that SYD-1 mediates an UNC-6 (netrin) independent UNC-40 activity to promote ventral axon guidance. Genetic analysis suggests that SYD-1 function in axon guidance requires both UNC-40 and SAX-3 activity. Moreover, the cytoplasmic domains of UNC-40 and SAX-3 bind to SYD-1 and SYD-1 binds to and negatively regulates the MIG-2 (Rac) GTPase. We also find that the function of SYD-1 in axon guidance is mediated by its phylogenetically conserved C isoform, indicating that the role of SYD-1 in guidance is distinct from its previously described roles in synaptogenesis and axonal specification. Our observations reveal a molecular mechanism that can allow two guidance receptors to function interdependently to regulate a common downstream effector, providing a potential means for the integration of guidance signals.
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Affiliation(s)
- Yan Xu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Hidenori Taru
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yishi Jin
- Division of Biological Sciences, Section of Neurobiology, and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Christopher C. Quinn
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
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Nahabedian JF, Qadota H, Stirman JN, Lu H, Benian GM. Bending amplitude - a new quantitative assay of C. elegans locomotion: identification of phenotypes for mutants in genes encoding muscle focal adhesion components. Methods 2012; 56:95-102. [PMID: 22126736 PMCID: PMC3299906 DOI: 10.1016/j.ymeth.2011.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 11/09/2011] [Accepted: 11/14/2011] [Indexed: 10/15/2022] Open
Abstract
The nematode Caenorhabditis elegans uses striated muscle in its body wall for locomotion. The myofilament lattice is organized such that all the thin filament attachment structures (dense bodies, analogous to Z-disks) and thick filament organizing centers (M-lines) are attached to the muscle cell membrane. Thus, the force of muscle contraction is transmitted through these structures and allows locomotion of the worm. Dense bodies and M-lines are compositionally similar to focal adhesions and costameres, and are based on integrin and associated proteins. Null mutants for many of the newly discovered dense body and M-line proteins do not have obvious locomotion defects when observed casually, or when assayed by counting the number of times a worm moves back and forth in liquid. We hypothesized that many of these proteins, located as they are in muscle focal adhesions, function in force transmission, but we had not used an appropriate or sufficiently sensitive assay to reveal this function. Recently, we have developed a new quantitative assay of C. elegans locomotion that measures the maximum bending amplitude of an adult worm as it moves backwards. The assay had been used to reveal locomotion defects for null mutants of genes encoding ATN-1 (α-actinin) and PKN-1 (protein kinase N). Here, we describe the details of this method, and apply it to 21 loss of function mutants in 17 additional genes, most of which encode components of muscle attachment structures. As compared to wild type, mutants in 11 genes were found to have less ability to bend, and mutants in one gene were found to have greater ability to bend. Loss of function mutants for eight proteins had been reported to have normal locomotion (ZYX-1 (zyxin), ALP-1 (Enigma), DIM-1, SCPL-1), or locomotion that was not previously investigated (FRG-1 (FRG1), KIN-32 (focal adhesion kinase), LIM-8), or had only slightly decreased locomotion (PFN-3 (profilin)).
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Affiliation(s)
- John F Nahabedian
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
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Benian GM, Epstein HF. Caenorhabditis elegans muscle: a genetic and molecular model for protein interactions in the heart. Circ Res 2011; 109:1082-95. [PMID: 21998299 DOI: 10.1161/circresaha.110.237685] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The nematode Caenorhabditis elegans has become established as a major experimental organism with applications to many biomedical research areas. The body wall muscle cells are a useful model for the study of human cardiomyocytes and their homologous structures and proteins. The ability to readily identify mutations affecting these proteins and structures in C elegans and to be able to rigorously characterize their genotypes and phenotypes at the cellular and molecular levels permits mechanistic studies of the responsible interactions relevant to the inherited human cardiomyopathies. Future work in C elegans muscle holds great promise in uncovering new mechanisms in the pathogenesis of these cardiac disorders.
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Affiliation(s)
- Guy M Benian
- Department of Pathology, Emory University, Atlanta, GA 30322, USA.
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