On the Rate of Synthesis of Individual Proteins within and between Different Striated Muscles of the Rat

The application of proteomics in muscle exercise physiology

INTRODUCTION

Exercise offers protection from non-communicable diseases and extends healthspan by offsetting natural physiological declines that occur in older age. Striated muscle is the largest bodily organ; it underpins the capacity for physical work, and the responses of muscle to exercise convey the health benefits of a physically active lifestyle. Proteomic surveys of muscle provide a means to study the protective effects of exercise and this review summaries some key findings from literature listed in PubMed during the last 10 years that have led to new insight in muscle exercise physiology.

AREAS COVERED

'Bottom-up' analyses involving liquid-chromatography tandem mass spectrometry (LC-MS/MS) of peptide digests have become the mainstay of proteomic studies and have been applied to muscle mitochondrial fractions. Enrichment techniques for post-translational modifications, including phosphorylation, acetylation and ubiquitination, have evolved and the analysis of site-specific modifications has become a major area of interest in exercise proteomics. Finally, we consider emergent techniques for dynamic analysis of muscle proteomes that offer new insight to protein turnover and the contributions of synthesis and degradation to changes in protein abundance in response to exercise training.

EXPERT OPINION

Burgeoning methods for dynamic proteome profiling offer new opportunities to study the mechanisms of muscle adaptation.

Dynamic Profiling of Protein Mole Synthesis Rates during C2C12 Myoblast Differentiation

Mole (MSR) and fractional (FSR) synthesis rates of proteins during C2C12 myoblast differentiation are investigated. Myoblast cultures supplemented with D₂ O during 0-24 h or 72-96 h of differentiation are analyzed by LC-MS/MS to calculate protein FSR and MSR after samples are spiked with yeast alcohol dehydrogenase (ADH1). Profiling of 153 proteins detected 70 significant (p ≤ 0.05, FDR ≤ 1%) differences in abundance between cell states. Early differentiation is enriched by clusters of ribosomal and heat shock proteins, whereas later differentiation is associated with actin filament binding. The median (first-third quartile) FSR (%/h) during early differentiation 4.1 (2.7-5.3) is approximately twofold greater than later differentiation 1.7 (1.0-2.2), equating to MSR of 0.64 (0.38-1.2) and 0.28 (0.1-0.5) fmol h^-1  µg^-1 total protein, respectively. MSR corresponds more closely with abundance data and highlights proteins associated with glycolytic processes and intermediate filament protein binding that are not evident among FSR data. Similarly, MSR during early differentiation accounts for 78% of the variation in protein abundance during later differentiation, whereas FSR accounts for 4%. Conclusively, the interpretation of protein synthesis data differs when reported in mole or fractional terms, which has consequences when studying the allocation of cellular resources.

Fractional Synthesis Rates of Individual Proteins in Rat Soleus and Plantaris Muscles

Differences in the protein composition of fast- and slow-twitch muscle may be maintained by different rates of protein turnover. We investigated protein turnover rates in slow-twitch soleus and fast-twitch plantaris of male Wistar rats (body weight 412 ± 69 g). Animals were assigned to four groups (n = 3, in each), including a control group (0 d) and three groups that received deuterium oxide (D₂O) for either 10 days, 20 days or 30 days. D₂O administration was initiated by an intraperitoneal injection of 20 μL of 99% D₂O-saline per g body weight, and maintained by provision of 4% (v/v) D₂O in the drinking water available ad libitum. Soluble proteins from harvested muscles were analysed by liquid chromatography–tandem mass spectrometry and identified against the SwissProt database. The enrichment of D₂O and rate constant (k) of protein synthesis was calculated from the abundance of peptide mass isotopomers. The fractional synthesis rate (FSR) of 44 proteins in soleus and 34 proteins in plantaris spanned from 0.58%/day (CO1A1: Collagen alpha-1 chain) to 5.40%/day NDRG2 (N-myc downstream-regulated gene 2 protein). Eight out of 18 proteins identified in both muscles had a different FSR in soleus than in plantaris (p < 0.05).

Actin Mutations and Their Role in Disease

Actin is a widely expressed protein found in almost all eukaryotic cells. In humans, there are six different genes, which encode specific actin isoforms. Disease-causing mutations have been described for each of these, most of which are missense. Analysis of the position of the resulting mutated residues in the protein reveals mutational hotspots. Many of these occur in regions important for actin polymerization. We briefly discuss the challenges in characterizing the effects of these actin mutations, with a focus on cardiac actin mutations.

Endurance-Type Exercise Increases Bulk and Individual Mitochondrial Protein Synthesis Rates in Rats

Physical activity increases muscle protein synthesis rates. However, the impact of exercise on the coordinated up- and/or downregulation of individual protein synthesis rates in skeletal muscle tissue remains unclear. The authors assessed the impact of exercise on mixed muscle, myofibrillar, and mitochondrial protein synthesis rates as well as individual protein synthesis rates in vivo in rats. Adult Lewis rats either remained sedentary (n = 3) or had access to a running wheel (n = 3) for the last 2 weeks of a 3-week experimental period. Deuterated water was injected and subsequently administered in drinking water over the experimental period. Blood and soleus muscle were collected and used to assess bulk mixed muscle, myofibrillar, and mitochondrial protein synthesis rates using gas chromatography–mass spectrometry and individual muscle protein synthesis rates using liquid chromatography–mass spectrometry (i.e., dynamic proteomic profiling). Wheel running resulted in greater myofibrillar (3.94 ± 0.26 vs. 3.03 ± 0.15%/day; p < .01) and mitochondrial (4.64 ± 0.24 vs. 3.97 ± 0.26%/day; p < .05), but not mixed muscle (2.64 ± 0.96 vs. 2.38 ± 0.62%/day; p = .71) protein synthesis rates, when compared with the sedentary condition. Exercise impacted the synthesis rates of 80 proteins, with the difference from the sedentary condition ranging between −64% and +420%. Significantly greater synthesis rates were detected for F1-ATP synthase, ATP synthase subunit alpha, hemoglobin, myosin light chain-6, and synaptopodin-2 (p < .05). The skeletal muscle protein adaptive response to endurance-type exercise involves upregulation of mitochondrial protein synthesis rates, but it is highly coordinated as reflected by the up- and downregulation of various individual proteins across different bulk subcellular protein fractions.

Calculation of the Protein Turnover Rate Using the Number of Incorporated 2H Atoms and Proteomics Analysis of a Single Labeled Sample

Rate constant estimation with heavy water requires a long-term experiment with data collection at multiple time points (3-4 weeks for mitochondrial proteome dynamics in mice and much longer in other species). When tissue proteins are analyzed, this approach requires euthanizing animals at each time point or multiple tissue biopsies in humans. Although short-term protocols are available, they require knowledge of the maximum number of isotope labels (N) and accurate quantification of observed ²H-enrichment in the peptide. The high-resolution accurate mass spectrometers used for proteome dynamics studies are characterized by a systematic spectral error that compromises these measurements. To circumvent these issues, we developed a simple algorithm for the rate constant calculation based on a single labeled sample and comparable unlabeled (time 0) sample. The algorithm determines N for all proteogenic amino acids from a long-term experiment to calculate the predicted plateau ²H-labeling of peptides for a short-term protocol and estimates the rate constant based on the measured baseline and the predicted plateau ²H-labeling of peptides. The method was validated based on the rate constant estimation in a long-term experiment in mice and dogs. The improved 2 time-point method enables the rate constant calculation with less than 10% relative error compared to the bench-marked multi-point method in mice and dogs and allows us to detect diet-induced subtle changes in ApoAI turnover in mice. In conclusion, we have developed and validated a new algorithm for protein rate constant calculation based on 2-time point measurements that could also be applied to other biomolecules.

Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise

It is generally accepted that muscle adaptation to resistance exercise (REX) training is underpinned by contraction-induced, increased rates of protein synthesis and dietary protein availability. By using dynamic proteome profiling (DPP), we investigated the contribution of both synthesis and breakdown to changes in abundance on a protein-by-protein basis in human skeletal muscle. Age-matched, overweight males consumed 9 d of a high-fat, low-carbohydrate diet during which time they either undertook 3 sessions of REX or performed no exercise. Precursor enrichment and the rate of incorporation of deuterium oxide into newly synthesized muscle proteins were determined by mass spectrometry. Ninety proteins were included in the DPP, with 28 proteins exhibiting significant responses to REX. The most common pattern of response was an increase in turnover, followed by an increase in abundance with no detectable increase in protein synthesis. Here, we provide novel evidence that demonstrates that the contribution of synthesis and breakdown to changes in protein abundance induced by REX differ on a protein-by-protein basis. We also highlight the importance of the degradation of individual muscle proteins after exercise in human skeletal muscle.-Camera, D. M., Burniston, J. G., Pogson, M. A., Smiles, W. J., Hawley, J. A. Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise.