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Proteomes
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Striated Muscle Proteomics
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Striated Muscle Proteomics

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (29 February 2016) | Viewed by 53632

Special Issue Editor

Prof. Dr. Jatin G. Burniston

E-Mail Website
Guest Editor
Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
Interests: dynamic proteome profiling; proteome responses to exercise; striated muscle proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We warmly invite contributions of original research or review articles that enhance understanding regarding striated muscle biology. Striated muscle is a fascinating tissue that exhibits profound plasticity in response to mechanical loading, nutrition and exogenous agents. Skeletal muscle undergoes a complex developmental process that creates mature multinucleate fibres exhibiting a broad range of different phenotypes. In response to endurance exercise, muscle can more than double its mitochondrial content, whereas resistance exercise stimulates protein accretion and substantial myofibre hypertrophy. Interestingly, cardiac muscle is exposed to a continuous rhythmic workload yet pathological and physiological stimuli result in discrete forms of cardiac hypertrophy.

Muscle is the target of monogenic diseases, including muscular dystrophies and complex polygenic diseases such as type 2 diabetes. Similarly, cardiomyopathies occur due to inherited or environmental factors and are often progressive processes that coincide with other complicated risk factors such as low exercise capacity, hypertension and dyslipidaemia. Therefore, understanding the deterioration of cardiac performance is a particularly challenging area of research. Indeed, from adulthood to old-age the natural decline in muscle mass and cardiac function negatively impact individuals’ functional independence and health-span.

Striated muscle is a technically challenging substrate for proteomic investigation and so we also welcome methodological articles that aim to address muscle-specific issues. For example, approximately half of the protein content of skeletal muscle is accounted for by just 10 proteins, and the dynamic range of muscle protein abundance is second only to blood plasma. Therefore, deep mining of the muscle proteome is particularly challenging. Similarly, the broad diversity in muscle phenotype is underpinned by complex patterns of expression of protein isoforms and splice variants, many of which share high levels of sequence homology, which makes peptide-level studies challenging.

We hope this special issue will serve as a point of reference for burgeoning themes in striated muscle proteomics.

Dr. Jatin G Burniston Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Adaptation to exercise
  • Anabolic agents
  • Cancer cachexia
  • Cardiac muscle
  • Cardiomyopathy
  • Disuse atrophy
  • Insulin resistance
  • Muscle development
  • Muscle mitochondria
  • Muscle wasting
  • Muscular dystrophy
  • Myofibre phenotyping
  • Physiological/ Pathological cardiac hypertrophy
  • Sarcopenia

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Published Papers (8 papers)

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Research

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5588 KiB  
Article
Calcium Homeostasis and Muscle Energy Metabolism Are Modified in HspB1-Null Mice
by Brigitte Picard, Malek Kammoun, Mohammed Gagaoua, Christiane Barboiron, Bruno Meunier, Christophe Chambon and Isabelle Cassar-Malek
Proteomes 2016, 4(2), 17; https://doi.org/10.3390/proteomes4020017 - 4 May 2016
Cited by 20 | Viewed by 6291
Abstract
Hsp27—encoded by HspB1—is a member of the small heat shock proteins (sHsp, 12–43 kDa (kilodalton)) family. This protein is constitutively present in a wide variety of tissues and in many cell lines. The abundance of Hsp27 is highest in skeletal muscle, indicating [...] Read more.
Hsp27—encoded by HspB1—is a member of the small heat shock proteins (sHsp, 12–43 kDa (kilodalton)) family. This protein is constitutively present in a wide variety of tissues and in many cell lines. The abundance of Hsp27 is highest in skeletal muscle, indicating a crucial role for muscle physiology. The protein identified as a beef tenderness biomarker was found at a crucial hub in a functional network involved in beef tenderness. The aim of this study was to analyze the proteins impacted by the targeted invalidation of HspB1 in the Tibialis anterior muscle of the mouse. Comparative proteomics using two-dimensional gel electrophoresis revealed 22 spots that were differentially abundant between HspB1-null mice and their controls that could be identified by mass spectrometry. Eighteen spots were more abundant in the muscle of the mutant mice, and four were less abundant. The proteins impacted by the absence of Hsp27 belonged mainly to calcium homeostasis (Srl and Calsq1), contraction (TnnT3), energy metabolism (Tpi1, Mdh1, PdhB, Ckm, Pygm, ApoA1) and the Hsp proteins family (HspA9). These data suggest a crucial role for these proteins in meat tenderization. The information gained by this study could also be helpful to predict the side effects of Hsp27 depletion in muscle development and pathologies linked to small Hsps. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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1977 KiB  
Article
Age- and Activity-Related Differences in the Abundance of Myosin Essential and Regulatory Light Chains in Human Muscle
by James N. Cobley, Zulezwan Ab. Malik, James P. Morton, Graeme L. Close, Ben J. Edwards and Jatin G. Burniston
Proteomes 2016, 4(2), 15; https://doi.org/10.3390/proteomes4020015 - 8 Apr 2016
Cited by 11 | Viewed by 6875
Abstract
Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry) are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance [...] Read more.
Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry) are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance knowledge regarding age- and activity-dependent changes in human muscle. We report a label-free, semi-automated and time efficient LC-MS proteomic workflow for phenotyping the myofibrillar proteome. Application of this workflow in old and young as well as trained and untrained human skeletal muscle yielded several novel observations that were subsequently verified by multiple reaction monitoring (MRM). We report novel data demonstrating that human ageing is associated with lesser myosin light chain 1 content and greater myosin light chain 3 content, consistent with an age-related reduction in type II muscle fibers. We also disambiguate conflicting data regarding myosin regulatory light chain, revealing that age-related changes in this protein more closely reflect physical activity status than ageing per se. This finding reinforces the need to control for physical activity levels when investigating the natural process of ageing. Taken together, our data confirm and extend knowledge regarding age- and activity-related phenotypes. In addition, the MRM transitions described here provide a methodological platform that can be fine-tuned to suite multiple research needs and thus advance myofibrillar phenotyping. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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1856 KiB  
Article
On the Rate of Synthesis of Individual Proteins within and between Different Striated Muscles of the Rat
by Stuart Hesketh, Kanchana Srisawat, Hazel Sutherland, Jonathan Jarvis and Jatin Burniston
Proteomes 2016, 4(1), 12; https://doi.org/10.3390/proteomes4010012 - 15 Mar 2016
Cited by 10 | Viewed by 5478
Abstract
The turnover of muscle protein is responsive to different (patho)-physiological conditions but little is known about the rate of synthesis at the level of individual proteins or whether this varies between different muscles. We investigated the synthesis rate of eight proteins (actin, albumin, [...] Read more.
The turnover of muscle protein is responsive to different (patho)-physiological conditions but little is known about the rate of synthesis at the level of individual proteins or whether this varies between different muscles. We investigated the synthesis rate of eight proteins (actin, albumin, ATP synthase alpha, beta enolase, creatine kinase, myosin essential light chain, myosin regulatory light chain and tropomyosin) in the extensor digitorum longus, diaphragm, heart and soleus of male Wistar rats (352 ± 30 g body weight). Animals were assigned to four groups (n = 3, in each), including a control and groups that received deuterium oxide (2H2O) for 4 days, 7 days or 14 days. Deuterium labelling was initiated by an intraperitoneal injection of 10 μL/g body weight of 99.9% 2H2O-saline, and was maintained by administration of 5% (v/v) 2H2O in drinking water provided ad libitum. Homogenates of the isolated muscles were analysed by 2-dimensional gel electrophoresis and matrix-assisted laser desorption ionisation time of flight mass spectrometry. Proteins were identified against the SwissProt database using peptide mass fingerprinting. For each of the eight proteins investigated, the molar percent enrichment (MPE) of 2H and rate constant (k) of protein synthesis was calculated from the mass isotopomer distribution of peptides based on the amino acid sequence and predicted number of exchangeable C–H bonds. The average MPE (2.14% ± 0.2%) was as expected and was consistent across muscles harvested at different times (i.e., steady state enrichment was achieved). The synthesis rate of individual proteins differed markedly within each muscle and the rank-order of synthesis rates differed among the muscles studied. After 14 days the fraction of albumin synthesised (23% ± 5%) was significantly (p < 0.05) greater than for other muscle proteins. These data represent the first attempt to study the synthesis rates of individual proteins across a number of different striated muscles. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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1430 KiB  
Article
Comparing Simplification Strategies for the Skeletal Muscle Proteome
by Bethany Geary, Iain S. Young, Phillip Cash, Phillip D. Whitfield and Mary K. Doherty
Proteomes 2016, 4(1), 10; https://doi.org/10.3390/proteomes4010010 - 2 Mar 2016
Cited by 2 | Viewed by 4984
Abstract
Skeletal muscle is a complex tissue that is dominated by the presence of a few abundant proteins. This wide dynamic range can mask the presence of lower abundance proteins, which can be a confounding factor in large-scale proteomic experiments. In this study, we [...] Read more.
Skeletal muscle is a complex tissue that is dominated by the presence of a few abundant proteins. This wide dynamic range can mask the presence of lower abundance proteins, which can be a confounding factor in large-scale proteomic experiments. In this study, we have investigated a number of pre-fractionation methods, at both the protein and peptide level, for the characterization of the skeletal muscle proteome. The analyses revealed that the use of OFFGEL isoelectric focusing yielded the largest number of protein identifications (>750) compared to alternative gel-based and protein equalization strategies. Further, OFFGEL led to a substantial enrichment of a different sub-population of the proteome. Filter-aided sample preparation (FASP), coupled to peptide-level OFFGEL provided more confidence in the results due to a substantial increase in the number of peptides assigned to each protein. The findings presented here support the use of a multiplexed approach to proteome characterization of skeletal muscle, which has a recognized imbalance in the dynamic range of its protein complement. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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2820 KiB  
Article
Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology
by Atul S. Deshmukh
Proteomes 2016, 4(1), 6; https://doi.org/10.3390/proteomes4010006 - 4 Feb 2016
Cited by 24 | Viewed by 10026
Abstract
Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused [...] Read more.
Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence, of altered protein expressions profiles and/or their posttranslational modifications (PTMs). Mass spectrometry (MS)-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle proteomics are challenging. This review describes the technical limitations of skeletal muscle proteomics as well as emerging developments in proteomics workflow with respect to samples preparation, liquid chromatography (LC), MS and computational analysis. These technologies have not yet been fully exploited in the field of skeletal muscle proteomics. Future studies that involve state-of-the-art proteomics technology will broaden our understanding of exercise-induced adaptations as well as molecular pathogenesis of insulin resistance. This could lead to the identification of new therapeutic targets. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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4076 KiB  
Article
Concurrent Label-Free Mass Spectrometric Analysis of Dystrophin Isoform Dp427 and the Myofibrosis Marker Collagen in Crude Extracts from mdx-4cv Skeletal Muscles
by Sandra Murphy, Margit Zweyer, Rustam R. Mundegar, Michael Henry, Paula Meleady, Dieter Swandulla and Kay Ohlendieck
Proteomes 2015, 3(3), 298-327; https://doi.org/10.3390/proteomes3030298 - 16 Sep 2015
Cited by 27 | Viewed by 7714
Abstract
The full-length dystrophin protein isoform of 427 kDa (Dp427), the absence of which represents the principal abnormality in X-linked muscular dystrophy, is difficult to identify and characterize by routine proteomic screening approaches of crude tissue extracts. This is probably related to its large [...] Read more.
The full-length dystrophin protein isoform of 427 kDa (Dp427), the absence of which represents the principal abnormality in X-linked muscular dystrophy, is difficult to identify and characterize by routine proteomic screening approaches of crude tissue extracts. This is probably related to its large molecular size, its close association with the sarcolemmal membrane, and its existence within a heterogeneous glycoprotein complex. Here, we used a careful extraction procedure to isolate the total protein repertoire from normal versus dystrophic mdx-4cv skeletal muscles, in conjunction with label-free mass spectrometry, and successfully identified Dp427 by proteomic means. In contrast to a considerable number of previous comparative studies of the total skeletal muscle proteome, using whole tissue proteomics we show here for the first time that the reduced expression of this membrane cytoskeletal protein is the most significant alteration in dystrophinopathy. This agrees with the pathobiochemical concept that the almost complete absence of dystrophin is the main defect in Duchenne muscular dystrophy and that the mdx-4cv mouse model of dystrophinopathy exhibits only very few revertant fibers. Significant increases in collagens and associated fibrotic marker proteins, such as fibronectin, biglycan, asporin, decorin, prolargin, mimecan, and lumican were identified in dystrophin-deficient muscles. The up-regulation of collagen in mdx-4cv muscles was confirmed by immunofluorescence microscopy and immunoblotting. Thus, this is the first mass spectrometric study of crude tissue extracts that puts the proteomic identification of dystrophin in its proper pathophysiological context. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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Review

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4019 KiB  
Review
Role of Protein Carbonylation in Skeletal Muscle Mass Loss Associated with Chronic Conditions
by Esther Barreiro
Proteomes 2016, 4(2), 18; https://doi.org/10.3390/proteomes4020018 - 6 May 2016
Cited by 43 | Viewed by 6551
Abstract
Muscle dysfunction, characterized by a reductive remodeling of muscle fibers, is a common systemic manifestation in highly prevalent conditions such as chronic heart failure (CHF), chronic obstructive pulmonary disease (COPD), cancer cachexia, and critically ill patients. Skeletal muscle dysfunction and impaired muscle mass [...] Read more.
Muscle dysfunction, characterized by a reductive remodeling of muscle fibers, is a common systemic manifestation in highly prevalent conditions such as chronic heart failure (CHF), chronic obstructive pulmonary disease (COPD), cancer cachexia, and critically ill patients. Skeletal muscle dysfunction and impaired muscle mass may predict morbidity and mortality in patients with chronic diseases, regardless of the underlying condition. High levels of oxidants may alter function and structure of key cellular molecules such as proteins, DNA, and lipids, leading to cellular injury and death. Protein oxidation including protein carbonylation was demonstrated to modify enzyme activity and DNA binding of transcription factors, while also rendering proteins more prone to proteolytic degradation. Given the relevance of protein oxidation in the pathophysiology of many chronic conditions and their comorbidities, the current review focuses on the analysis of different studies in which the biological and clinical significance of the modifications induced by reactive carbonyls on proteins have been explored so far in skeletal muscles of patients and animal models of chronic conditions such as COPD, disuse muscle atrophy, cancer cachexia, sepsis, and physiological aging. Future research will elucidate the specific impact and sites of reactive carbonyls on muscle protein content and function in human conditions. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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Other

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689 KiB  
Commentary
Will Quantitative Proteomics Redefine Some of the Key Concepts in Skeletal Muscle Physiology?
by Agnieszka Gizak and Dariusz Rakus
Proteomes 2016, 4(1), 2; https://doi.org/10.3390/proteomes4010002 - 11 Jan 2016
Cited by 4 | Viewed by 4832
Abstract
Molecular and cellular biology methodology is traditionally based on the reasoning called “the mechanistic explanation”. In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach [...] Read more.
Molecular and cellular biology methodology is traditionally based on the reasoning called “the mechanistic explanation”. In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach requires precise knowledge about all parameters of a studied system. However, in practice, due to the systems’ complexity, this requirement is rarely, if ever, accomplished. Typically, it is limited to a quantitative or semi-quantitative measurements of selected parameters (e.g., concentrations of some metabolites), and a qualitative or semi-quantitative description of expression/post-translational modifications changes within selected proteins. A quantitative proteomics approach gives a possibility of quantitative characterization of the entire proteome of a biological system, in the context of the titer of proteins as well as their post-translational modifications. This enables not only more accurate testing of novel hypotheses but also provides tools that can be used to verify some of the most fundamental dogmas of modern biology. In this short review, we discuss some of the consequences of using quantitative proteomics to verify several key concepts in skeletal muscle physiology. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics)
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