Differential proteome analysis of hagfish dental and somatic skeletal muscles

Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics

The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

Toxic effects of two brominated flame retardants BDE-47 and BDE-183 on the survival and protein expression of the tubificid Monopylephorus limosus

The toxic effects of two brominated diphenyl ethers (BDE), BDE-47, and BDE-183, on a benthic oligochaete tubificid, Monopylephorus limosus were studied under laboratory conditions. Investigated responses included survival, growth, and protein expression profiles, at BDE concentrations of 1, 10, 100, and 700 ng/g on a dry soil weight basis, with isooctane as the carrier solvent. Body weight losses among treatments were insignificant after 8 weeks of exposure. The 8-wk LC(50) of BDE-47 and -183 were 2311 and 169 ng/g, respectively. By applying multivariate analysis techniques, protein expression patterns were compared and correlated with stressful sources of long-term culture, carrier solvent, BDE-47 and -183. The treatment of 8-wk 100 ng/g BDE-47 was most closely clustered to the 10 ng/g BDE-183 treatment, based on the 40 examined protein spots. This indicated that BDE-183 was more potent to M. limosus, than was BDE-47. The 2-wk and 8-wk controls clustered into different groups indicating the occurrence of physiological changes due to long-term laboratory culture. Additionally, solvent effect was shown by grouping the isooctane carrier to different clusters. With further characterization by principle component analysis, it was found that the separation was mainly contributed by the 2nd principal-component. And, the primarily inhibitory variation was at spots 2 (UMP-CMP kinase) and 40 (plasma retinol-binding protein precursor) in the 8-wk groups. On the contrary, protein spots 16 (cell division control protein 2 homolog) and 24 (mitochondrial DNA mismatch repair protein) showed stimulatory variation. In all, the observed proteomic responses suggest that BDEs disrupted metabolic function in M. limosus and multivariate analysis tool offers significant potential for the assessment of various stress sources at biochemical level.

Seasonal changes in atrophy-associated proteins of the sonic muscle in the big-snout croaker, Johnius macrorhynus (Pisces, Sciaenidae), identified by using a proteomic approach

In most sciaenids, males possess sonic muscles and produce sound through the contraction of these muscles and amplification of the swim bladder. The sonic muscles in some fishes exhibit seasonal changes in size. For example, they are hypertrophic in the spawning season, and atrophic in the non-spawning months. The protein profiles of the sonic muscle, red muscle, and white muscle in the Johnius macrorhynus were shown by two-dimensional electrophoresis (2-DE) and were compared to reveal differential protein expressions. About 80 up-regulated protein spots in the sonic muscle, and 30 spots related to six contractile proteins (fast muscle myosin heavy chain, skeletal alpha actin, alpha actin cardiac, tropomyosin, myosin light chain 2, and myosin light chain 3), four energy metabolic enzymes (enolase, acyl-CoA synthetase, creatine kinase, and cytochrome P450 monooxygenase), and two miscellaneous proteins (DEAD box protein and cyclin H) were identified. Seasonal hypertrophy and atrophy of the sonic muscles related to the reproductive cycle were verified in male big-snout croaker. The contents of some proteins were significantly different in the muscles under these conditions. The levels of cytochrome P450 monooxygenase, fast muscle myosin heavy chain, DEAD box proteins, isocitrate dehydrogenase, and creatine kinase were up-regulated in the hypertrophic muscle, but the levels of alpha actin cardiac, myosin light 2, and myosin light 3 were lower than in the atrophic muscle. Potential reasons for these differences in protein expression related to physiological adaptation are discussed.

A NMR-based metabolomic approach for differentiation of hagfish dental and somatic skeletal muscles

The hagfish dental muscle is a large and specialized element of the feeding apparatus that helps ingest food. This muscle has enzymatic activities and contractile properties different from the hagfish somatic skeletal muscle. To verify the functional relevance of protein alterations, we examined the metabolomic differentiation of hagfish dental and somatic skeletal muscles using ¹H-nuclear magnetic resonance (NMR)-based metabolomics and multivariate analysis that separated hagfish dental and somatic muscles by principal component analysis and partial least squares for discriminant analysis. Our analysis of assigned metabolites showed that anserine and taurine levels were higher in dental muscle, but creatine, fructose, glucose, glycerate, pyruvate, and succinate levels were higher in somatic muscle. We concluded that the primary energy sources of dental and somatic muscles are related to the citric acid cycle and the anaerobic glycolysis and metabolism of creatine. Thus, ¹H-NMR-based metabolomics can be integrated with the previous proteomic approach to derive biochemical and physiological information about hagfish muscles.