A model of whole-body protein turnover based on leucine kinetics in rodents

Use of Mechanistic Nutrition Models to Identify Sustainable Food Animal Production

To feed people in the coming decades, an increase in sustainable animal food production is required. The efficiency of the global food production system is dependent on the knowledge and improvement of its submodels, such as food animal production. Scientists use statistical models to interpret their data, but models are also used to understand systems and to integrate their components. However, empirical models cannot explain systems. Mechanistic models yield insight into the mechanism and provide guidance regarding the exploration of the system. This review offers an overview of models, from simple empirical to more mechanistic models. We demonstrate their applications to amino acid transport, mass balance, whole-tissue metabolism, digestion and absorption, growth curves, lactation, and nutrient excretion. These mechanistic models need to be integrated into a full model using big data from sensors, which represents a new challenge. Soon, training in quantitative and computer science skills will be required to develop, test, and maintain advanced food system models.

Protein Turnover in Epithelial Cells and Mucus along the Gastrointestinal Tract Is Coordinated by the Spatial Location and Microbiota

The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from microbial invasion. The epithelium has one of the highest turnover rates in the body. Using stable isotope labeling, high-resolution mass spectrometry, and computational analysis, we report a comprehensive dataset of the turnover of more than 3,000 and the expression of more than 5,000 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine. The median protein half-life is shorter in the small intestine than in the colon. Differences in protein turnover rates along the intestinal tract can be explained by distinct physiological and immune-related functions between the small and large intestine. An absence of microbiota results in an approximately 1 day longer protein half-life in germ-free animals.

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Dataset of protein turnover rate and expression along the mice intestinal tract

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Protein turnover rate is slower in colon than in small intestine

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Median protein half-life is 1 day longer in germ-free mice

Brain tissue plasticity: protein synthesis rates of the human brain

All tissues undergo continuous reconditioning via the complex orchestration of changes in tissue protein synthesis and breakdown rates. Skeletal muscle tissue has been well studied in this regard, and has been shown to turnover at a rate of 1-2% per day in vivo in humans. Few data are available on protein synthesis rates of other tissues. Because of obvious limitations with regard to brain tissue sampling no study has ever measured brain protein synthesis rates in vivo in humans. Here, we applied stable isotope methodology to directly assess protein synthesis rates in neocortex and hippocampus tissue of six patients undergoing temporal lobectomy for drug-resistant temporal lobe epilepsy (Clinical trial registration: NTR5147). Protein synthesis rates of neocortex and hippocampus tissue averaged 0.17 ± 0.01 and 0.13 ± 0.01%/h, respectively. Brain tissue protein synthesis rates were 3-4-fold higher than skeletal muscle tissue protein synthesis rates (0.05 ± 0.01%/h; P < 0.001). In conclusion, the protein turnover rate of the human brain is much higher than previously assumed.

Carbon stable-isotope tracking in breath for comparative studies of fuel use

Almost half a century ago, researchers demonstrated that the ratio of stable carbon isotopes in exhaled breath of rats and humans could reveal the oxidation of labeled substrates in vivo, opening a new chapter in the study of fuel use, the fate of ingested substrates, and aerobic metabolism. Until recently, the combined use of respirometry and stable-isotope tracer techniques had not been broadly employed to study fuel use in other animal groups. In this review, we summarize the history of this approach in human and animal research and define best practices that maximize its utility. We also summarize several case studies that use stable-isotope measurements of breath to explore the limits of aerobic metabolism and substrate turnover among several species and various physiological states. We highlight the importance of a comparative approach in revealing the profound effects that phylogeny, ecology, and behavior can have in shaping aerobic metabolism and energetics as well as the fundamental biological principles that underlie fuel use and metabolic function across taxa. New analytical equipment and refinement of methodology make the combined use of respirometry and stable-isotope tracer techniques simpler to perform, less costly, and more field ready than ever before.

Serum ferritin is an important inflammatory disease marker, as it is mainly a leakage product from damaged cells

"Serum ferritin" presents a paradox, as the iron storage protein ferritin is not synthesised in serum yet is to be found there. Serum ferritin is also a well known inflammatory marker, but it is unclear whether serum ferritin reflects or causes inflammation, or whether it is involved in an inflammatory cycle. We argue here that serum ferritin arises from damaged cells, and is thus a marker of cellular damage. The protein in serum ferritin is considered benign, but it has lost (i.e. dumped) most of its normal complement of iron which when unliganded is highly toxic. The facts that serum ferritin levels can correlate with both disease and with body iron stores are thus expected on simple chemical kinetic grounds. Serum ferritin levels also correlate with other phenotypic readouts such as erythrocyte morphology. Overall, this systems approach serves to explain a number of apparent paradoxes of serum ferritin, including (i) why it correlates with biomarkers of cell damage, (ii) why it correlates with biomarkers of hydroxyl radical formation (and oxidative stress) and (iii) therefore why it correlates with the presence and/or severity of numerous diseases. This leads to suggestions for how one might exploit the corollaries of the recognition that serum ferritin levels mainly represent a consequence of cell stress and damage.

Protein turnover on the scale of the proteome

Protein turnover is a neglected dimension in postgenomic studies, defining the dynamics of changes in protein expression and forging a link between transcriptome, proteome and metabolome. Recent advances in postgenomic technologies have led to the development of new proteomic techniques to measure protein turnover on a proteome-wide scale. These methods are driven by stable isotope metabolic labeling of cells in culture or in intact animals. This review considers the merits and difficulties of different methods that allow access to proteome dynamics.

Dietary protein content affects isotopic carbon and nitrogen turnover

RATIONALE

Isotopic turnover quantifies the metabolic renewal process of elements in organs and excreta. Knowledge of the isotopic turnover of animal organs and excreta is necessary for diet reconstruction via stable isotope analysis, as used in animal ecology, palaeontology and food authentication. Effects of dietary protein content on the isotopic carbon and nitrogen turnover (i.e. delay, representing the time between ingestion and start of renewal, and half-life) are unknown for most mammalian organs and excreta.

METHODS

To examine the effect of dietary protein content on turnover (delay and turnover rate), we fed 18 rats either a diet at protein maintenance or above protein maintenance, and quantified their isotopic carbon and nitrogen turnover in ten organs and excreta. These included the excreta faeces and urine, the visceral organs blood plasma, liver, kidney, lung and spleen, the cerebral tissue brain, and the muscular tissues heart and muscle. For data analysis, we used piecewise linear/non-linear exponential modelling that allows quantifying delay and turnover rate simultaneously.

RESULTS

Delays were ~0.5 days for carbon and nitrogen turnover and were not affected by dietary protein content. Half-lives during the following reaction progress were in the range of 1 to 45 days, increasing from excreta to visceral organs to muscular and cerebral organs. Rats fed the higher protein amount had 30% shorter nitrogen half-lives, and 20% shorter carbon half-lives.

CONCLUSIONS

The renewal times of organs and excreta depend on the dietary protein content. Hence, isotopic diet reconstruction is confronted with variation in half-lives within the same organ or excrement, altering the time window through which information can be perceived.

Isotopic and modeling investigation of long-term protein turnover in rat tissues

Fractional synthesis rates (FSR) of tissue proteins (P) are usually measured using labeled amino acid (AA) tracer methods over short periods of time under acute, particular conditions. By combining the long-term and non-steady-state (15)N labeling of AA and P tissue fractions with compartmental modeling, we have developed a new isotopic approach to investigate the degree of compartmentation of P turnover in tissues and to estimate long-term FSR values under sustained and averaged nutritional and physiological conditions. We measured the rise-to-plateau kinetics of nitrogen isotopic enrichments (δ(15)N) in the AA and P fractions of various tissues in rats for 2 mo following a slight increase in diet δ(15)N. Using these δ(15)N kinetics and a numerical method based on a two-compartment model, we determined reliable FSR estimates for tissues in which P turnover is adequately represented by such a simple precursor-product model. This was the case for kidney, liver, plasma, and muscle, where FSR estimates were 103, 101, 58, and 11%/day, respectively. Conversely, we identified tissues, namely, skin and small intestine, where P turnover proved to be too complex to be represented by a simple two-compartment model, evidencing the higher level of subcompartmentation of the P and/or AA metabolism in these tissues. The present results support the value of this new approach in gaining cognitive and practical insights into tissue P turnover and propose new and integrated FSR values over all individual precursor AA and all diurnal variations in P kinetics.

Proteome dynamics: revisiting turnover with a global perspective

Although bulk protein turnover has been measured with the use of stable isotope labeled tracers for over half a century, it is only recently that the same approach has become applicable to the level of the proteome, permitting analysis of the turnover of many proteins instead of single proteins or an aggregated protein pool. The optimal experimental design for turnover studies is dependent on the nature of the biological system under study, which dictates the choice of precursor label, protein pool sampling strategy, and treatment of data. In this review we discuss different approaches and, in particular, explore how complexity in experimental design and data processing increases as we shift from unicellular to multicellular systems, in particular animals.

A proteomics strategy for determining the synthesis and degradation rates of individual proteins in fish

In order to study the protein dynamics in the tissues of fish we have developed a proteomics-based strategy to determine the rates of synthesis and degradation of individual proteins. We have demonstrated the feasibility of this approach by measuring the turnover of multiple isoforms of parvalbumin (β1-7) in the skeletal muscle of common carp (Cyprinus carpio). A stable isotope-labelled amino acid ([(2)H(7)] l-leucine) was administered to the carp via the diet and its incorporation into the isoforms of parvalbumin in muscle over time was monitored by LC-MS analysis of signature peptides. The relative isotope abundance was calculated and used to deconvolute the data. The β7 parvalbumin isoform had a rate of synthesis that was greater than the rate of degradation. In contrast the rate of degradation of the β5 isoform exceeded its rate of synthesis, whilst the analysis revealed that the other parvalbumin β-isoforms (β1, β2, β3, β4 and β6) had a rate of synthesis that was equal to the rate of degradation. This work has addressed a number of technical challenges and represents the first study to use proteomic approaches to measure the turnover of individual proteins in fish.

Proteomics moves from expression to turnover: update and future perspective

Proteomics is a rapidly developing discipline that seeks to understand the role of proteins in the wider biological context. In order to take a holistic view of a biological system, it is vital that we can elucidate the dynamics of the proteome. In this article, we have outlined the recent advances in experimental strategies for measuring protein synthesis and degradation on a proteome-wide scale. The application of mass spectrometry and non-mass spectrometric-based approaches in this field of research has been discussed. The article also explores the challenges associated with these types of analyses and the development of appropriate bioinformatic resources for interrogating the complex datasets that are generated.

A weak link in metabolism: the metabolic capacity for glycine biosynthesis does not satisfy the need for collagen synthesis

In a previous paper, we pointed out that the capability to synthesize glycine from serine is constrained by the stoichiometry of the glycine hydroxymethyltransferase reaction, which limits the amount of glycine produced to be no more than equimolar with the amount of C 1 units produced. This constraint predicts a shortage of available glycine if there are no adequate compensating processes. Here, we test this prediction by comparing all reported fl uxes for the production and consumption of glycine in a human adult. Detailed assessment of all possible sources of glycine shows that synthesis from serine accounts for more than 85% of the total, and that the amount of glycine available from synthesis, about 3 g/day, together with that available from the diet, in the range 1.5-3.0 g/day, may fall significantly short of the amount needed for all metabolic uses, including collagen synthesis by about 10 g per day for a 70 kg human. This result supports earlier suggestions in the literature that glycine is a semi-essential amino acid and that it should be taken as a nutritional supplement to guarantee a healthy metabolism.

Tracking the oxidative kinetics of carbohydrates, amino acids and fatty acids in the house sparrow using exhaled 13CO2

Clinicians commonly measure the 13CO2 in exhaled breath samples following administration of a metabolic tracer (breath testing) to diagnose certain infections and metabolic disorders. We believe that breath testing can become a powerful tool to investigate novel questions about the influence of ecological and physiological factors on the oxidative fates of exogenous nutrients. Here we examined several predictions regarding the oxidative kinetics of specific carbohydrates, amino acids and fatty acids in a dietary generalist, the house sparrow (Passer domesticus). After administering postprandial birds with 20 mg of one of seven 13C-labeled tracers, we measured rates of 13CO2 production every 15 min over 2 h. We found that sparrows oxidized exogenous amino acids far more rapidly than carbohydrates or fatty acids, and that different tracers belonging to the same class of physiological fuels had unique oxidative kinetics. Glycine had a mean maximum rate of oxidation (2021 nmol min−1) that was significantly higher than that of leucine (351 nmol min−1), supporting our prediction that nonessential amino acids are oxidized more rapidly than essential amino acids. Exogenous glucose and fructose were oxidized to a similar extent (5.9% of dose), but the time required to reach maximum rates of oxidation was longer for fructose. The maximum rates of oxidation were significantly higher when exogenous glucose was administered as an aqueous solution (122 nmol min−1), rather than as an oil suspension (93 nmol min−1), supporting our prediction that exogenous lipids negatively influence rates of exogenous glucose oxidation. Dietary fatty acids had the lowest maximum rates of oxidation (2-6 nmol min−1), and differed significantly in the extent to which each was oxidized, with 0.73%, 0.63% and 0.21% of palmitic, oleic and stearic acid tracers oxidized, respectively.

Metabolic Models of Ruminant Metabolism: Recent Improvements and Current Status

The NC-1009 regional research project has two broad goals of quantifying the properties of feeds and the metabolic interactions among nutrients that influence nutrient availability for milk production and that alter synthesis of milk, and using those quantitative relationships to challenge and refine computer-based nutrition systems for dairy cattle. The objective of this paper was to review progress in modeling. Significant progress has been made in model refinements over the past 10 yr as exemplified by the most recent NRC model (2001) and work on the Molly model of Baldwin and colleagues (1987). These models have different objectives but share many properties. The level of aggregation of the NRC model (2001) does not allow detailed analyses of specific metabolic reactions that affect nutritional efficiency. The Baldwin model is aggregated at the pathway level and is therefore amenable to assessment with a broad range of biological measurements. Recent improvements to that model include the addition of an ingredient based input scheme, use of in situ data to set ruminal protein degradation rates, and refinement of the representation of mammary cell numbers and activity. Although the Baldwin model appears to be appropriate structurally, several parameters are known to be inadequate. Predictions of ruminal N metabolism and total-tract starch digestions have similar accuracy as the NRC model. However, the NRC more accurately predicts total-tract fiber digestion and both models significantly overpredict total-tract lipid digestion. These errors contribute to overpredictions of weight retention when simulating full lactations with the Baldwin model and may result in performance prediction errors with the NRC model. Limitations remain in the descriptions of metabolism and metabolic regulation of the splanchnic, viscera, adipose tissue, body muscle, and mammary tissue. Integration of genetic control mechanisms can expand these efforts to assist genetic selection as well as feeding management decisions.

Turnover of stable carbon isotopes in the muscle, liver, and breath CO2 of alpacas (Lama pacos)

Stable carbon isotope analysis of animal liver and muscle has become a widespread tool for investigating dietary ecology. Nonetheless, stable carbon isotope turnover of these tissues has not been studied in large mammals except with isotopically labelled tracer methodologies, which do not produce carbon half-lives analogous to those derived from naturalistic diet-switch experiments. To address this gap, we studied turnover of carbon isotopes in the liver, muscle, and breath CO2 of alpacas (Lama pacos) by switching them from a C3 grass diet to an isonitrogenous C4 grass diet. Breath samples as well as liver and muscle biopsies were collected and analyzed for up to 72 days to monitor the incorporation of the C4-derived carbon. The data suggest half-lives of 2.8, 37.3, and 178.7 days for alpaca breath CO2, liver, and muscle, respectively. Alpaca liver and muscle carbon half-lives are about 6 times longer than those of gerbils, which is about what would be expected given their size. In contrast, breath CO2 turnover does not scale readily with body mass. We also note that the breath CO2 and liver data are better described using a multiple-pool exponential decay model than a single-pool model.

Challenging the Assumptions in Estimating Protein Fractional Synthesis Rate Using a Model of Rodent Protein Turnover

Published estimates of protein fractional synthetic rate vary widely (Johnson et al., 1999a). Contributing to the large standard deviation for FSR are physiological and methodological differences that do not account for changes in specific radioactivities of I, E, T, and P. Current methods for estimating FSR are based on four assumptions which may not be valid. The first assumption, that the free amino acid pool is homogenous and reflects the specific radioactivity of the true precursor pool (aminoacyl tRNA), can cause FSR estimates to increase by up to 8%/d. The second assumption, that recycling has an insignificant effect on FSR estimates, could result in decreases in estimates of FSR from 10 to 20%/d. The third assumption, that the protein pool is homogeneous and will not change over time, results in a 4-10%/d change using the flooding dose method. The fourth assumption, that growth will not affect estimated FSR over a short experimental time, is true if aminoacyl tRNA specific radioactivity is used to estimate FSR. Otherwise, estimates can vary 4-5%/d. Although specific radioactivity of aminoacyl tRNA is difficult to measure, the first and fourth assumptions are valid if aminoacyl tRNA specific radioactivity is used. Using a model of protein turnover, as described in this paper, to interpret specific radioactivity data allows the inclusion of all four assumptions and the potential to better quantify changes in FSR under different physiological conditions.

A rodent model of protein turnover used to design an experiment for measuring the rates of channeling, recycling and protein synthesis

We described previously a mechanistic model of whole-body protein turnover in rodents. Channeling was defined as the flow of amino acids from the extracellular compartment to aminoacyl tRNA and protein synthesis. Recycling was defined as the flow of amino acids from protein degradation to aminoacyl tRNA (protein synthesis) without mixing with the intracellular pool of amino acids. In this paper, the model is applied to tissues and whole body and is used to develop an experimental protocol for estimating protein fractional synthesis rate, recycling and channeling. Channeling, recycling and protein synthesis must be estimated simultaneously because changes in specific radioactivities over time are highly dependent on the rate of protein synthesis. Injection-specific radioactivities, body weights and experimental variation were used with the model to generate data at different rates of recycling and channeling. The data generated were then used to determine the best time points and experimental method to estimate percentages of recycling, channeling and protein synthesis rate by the iterative Method of Maximum Likelihood. Specific radioactivity at each time point was based on simulated data from three rodents at each of six time points. Predicted protein synthesis rates were within 5%/d of observed rates for all methods. Predicted rates of recycling and channeling were generally within 15% of observed rates except recycling in muscle at high channeling and high recycling. Standard deviations of the predictions of percentages of channeling and recycling were between 0.148 and 44.5% for the pulse dose method, 0.0655 and 197% for the continuous infusion method and 0.351 and 962% for the flooding dose method. The experimental design that yields the best estimates of channeling, recycling and protein synthesis is the pulse dose. Changes in amino acid specific radioactivities in the extracellular, aminoacyl tRNA and protein pools were greatest and should be measured at 2, 6, 10, 40, 70 and 100 min in the pulse method.