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Melby JA, Brown KA, Gregorich ZR, Roberts DS, Chapman EA, Ehlers LE, Gao Z, Larson EJ, Jin Y, Lopez JR, Hartung J, Zhu Y, McIlwain SJ, Wang D, Guo W, Diffee GM, Ge Y. High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms. Proc Natl Acad Sci U S A 2023; 120:e2222081120. [PMID: 37126723 PMCID: PMC10175728 DOI: 10.1073/pnas.2222081120] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023] Open
Abstract
Single-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell proteomics for the analysis of proteoforms arising from genetic mutations, alternative splicing, and post-translational modifications. Herein, we have developed a highly sensitive functionally integrated top-down proteomics method for the comprehensive analysis of proteoforms from single cells. We applied this method to single muscle fibers (SMFs) to resolve their heterogeneous functional and proteomic properties at the single-cell level. Notably, we have detected single-cell heterogeneity in large proteoforms (>200 kDa) from the SMFs. Using SMFs obtained from three functionally distinct muscles, we found fiber-to-fiber heterogeneity among the sarcomeric proteoforms which can be related to the functional heterogeneity. Importantly, we detected multiple isoforms of myosin heavy chain (~223 kDa), a motor protein that drives muscle contraction, with high reproducibility to enable the classification of individual fiber types. This study reveals single muscle cell heterogeneity in large proteoforms and establishes a direct relationship between sarcomeric proteoforms and muscle fiber types, highlighting the potential of top-down proteomics for uncovering the molecular underpinnings of cell-to-cell variation in complex systems.
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Affiliation(s)
- Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Zachery R. Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI53706
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Lauren E. Ehlers
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Zhan Gao
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
| | - Eli J. Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Justin R. Lopez
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Jared Hartung
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI53705
| | | | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI53706
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
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Solaro RJ. Widely cited publications of Michael Bárány in 1964 and 1967 as tipping points in understanding myosin molecular motors. Arch Biochem Biophys 2022; 727:109319. [PMID: 35709967 DOI: 10.1016/j.abb.2022.109319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
In 1964 Michael Bárány and colleagues published a paper ((M. Bárány, E. Gaetjens, K. Bárány, Karp E. Arch Biochem Biophys 106(1964)280-93. http://10.1016/0003-9861(64)90,189-4)) that has been one of the most cited papers in Archives of Biochemistry and Biophysics. This was followed in 1967 by another most cited paper (M. Bárány. J Gen Physiol 50(1967)197-218. https://doi.org/10.1085/jgp.50.6.197). I have commemorated these achievements as tipping points in the understanding of myosin motors in muscle function. Tipping points are generally defined as a temporal point in which a series of progressive advances (in this case the understanding of the relations between myosin ATP hydrolysis and muscle function) inspire more expansive, wide-ranging, significant changes. I first concisely summarize the background against which the papers came to publication as well as the unimaginable personal challenges faced by Michael and Kate Bárány. A final section summarizes the impact of these publications as key steps in the progression of contemporary understanding of diverse control of myosin ATPase activity with focus on the thick filaments in cardiac homeostasis, disorders, and as targets for therapeutic applications in translational investigations.
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Affiliation(s)
- R John Solaro
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, College of Medicine, University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, IL, USA.
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Hoh JFY. Myosin heavy chains in extraocular muscle fibres: Distribution, regulation and function. Acta Physiol (Oxf) 2021; 231:e13535. [PMID: 32640094 DOI: 10.1111/apha.13535] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
This review examines kinetic properties and distribution of the 11 isoforms of myosin heavy chain (MyHC) expressed in extraocular muscle (EOM) fibre types and the regulation and function of these MyHCs. Although recruitment and discharge characteristics of ocular motoneurons during fixation and eye movements are well documented, work directly linking these properties with motor unit contractile speed and MyHC composition is lacking. Recruitment of motor units according to Henneman's size principle has some support in EOMs but needs consolidation. Both neurogenic and myogenic mechanisms regulate MyHC expression as in other muscle allotypes. Developmentally, multiply-innervated (MIFs) and singly-innervated fibres (SIFs) are derived presumably from distinct myoblast lineages, ending up expressing MyHCs in the slow and fast ends of the kinetic spectrum respectively. They modulate the synaptic inputs of their motoneurons through different retrogradely transported neurotrophins, thereby specifying their tonic and phasic impulse patterns. Immunohistochemical analyses of EOMs regenerating in situ and in limb muscle beds suggest that the very impulse patterns driving various ocular movements equip effectors with appropriate MyHC compositions and speeds to accomplish their tasks. These experiments also suggest that satellite cells of SIFs and MIFs are distinct lineages expressing different MyHCs during regeneration. MyHC compositions and functional characteristics of orbital fibres show longitudinal variations that facilitate linear ocular rotation during saccades. Palisade endings on global MIFs are postulated to respond to active and passive tensions by triggering axon reflexes that play important roles during fixation, saccades and vergence. How EOMs implement Listings law during ocular rotation is discussed.
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Affiliation(s)
- Joseph F. Y. Hoh
- Discipline of Physiology and the Bosch Institute School of Medical Sciences Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
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Li Y, Wu T, Wu C, Wang Q, Ma P, Shao Y, Yu H, Hu Y. Eugenol-loaded chitosan emulsion holds the texture of chilled hairtail (Trichiurus lepturus) better: mechanism exploration by proteomic analysis. Food Funct 2020; 11:7509-7522. [DOI: 10.1039/d0fo01135e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Eugenol-loaded chitosan emulsion (ELCE) has been proved to have an excellent antibacterial property.
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Affiliation(s)
- Yuan Li
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Tiantian Wu
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Chunhua Wu
- College of Food Science
- Fujian Agriculture and Forestry University
- Fuzhou 350002
- China
| | - Qin Wang
- Department of Nutrition and Food Science
- College of Agriculture and Nature Resources
- University of Maryland
- College Park
- USA
| | - Peihua Ma
- Department of Nutrition and Food Science
- College of Agriculture and Nature Resources
- University of Maryland
- College Park
- USA
| | - Ying Shao
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Haixia Yu
- Ocean Research Center of Zhoushan
- Zhejiang University
- Zhoushan 316021
- China
| | - Yaqin Hu
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
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Schiaffino S, Reggiani C, Murgia M. Fiber type diversity in skeletal muscle explored by mass spectrometry-based single fiber proteomics. Histol Histopathol 2019; 35:239-246. [PMID: 31612964 DOI: 10.14670/hh-18-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian skeletal muscles are composed of a variety of muscle fibers with specialized functional properties. Slow fibers are suited for long lasting and low intensity contractile activity, while various subtypes of fast fibers are optimized to produce high force and power even with a significant fatigue. The functional specialization of muscle fibers is based on selective gene expression regulation, which provides each fiber with a specific protein complement. The recent refinement of small-scale sample preparation, combined with the development of mass spectrometers characterized by high sensitivity, sequencing speed and mass accuracy, has allowed the characterization of the proteome of single muscle fibers with an unprecedented resolution. In the last few years, the first studies on the global proteomics of individual fibers of different types have been published. In this short review we discuss the methodological advancements which have opened the way to single fiber proteomics and the discovery power of this approach. We provide examples of how specific features of single fibers can be overlooked when whole muscle or multi-fiber samples are analyzed and can only be detected when a single fiber proteome is analyzed. Thus, novel subtype-specific metabolic features, most prominently mitochondrial specialization of fiber types have been revealed by single fiber proteomics. In the same way, specific adaptive responses of single fibers to aging or loss of neural input have been detected when single fibers were individually analyzed. We conclude that the fiber type-resolved proteomes represent a powerful tool which can be applied to a variety of physiological and pathological conditions.
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Affiliation(s)
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute for Kinesiology Research, Science and Research Center of Koper, Koper, Slovenia
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Max-Planck-Institute of Biochemistry, Martinsried, Germany
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Abstract
The second of two special issues on contractile systems charts further progress towards an understanding of myofilament regulation.
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Affiliation(s)
- Henk L Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Richard L Moss
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI
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