51
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Kasumov T, Dabkowski ER, Shekar KC, Li L, Ribeiro RF, Walsh K, Previs SF, Sadygov RG, Willard B, Stanley WC. Assessment of cardiac proteome dynamics with heavy water: slower protein synthesis rates in interfibrillar than subsarcolemmal mitochondria. Am J Physiol Heart Circ Physiol 2013; 304:H1201-14. [PMID: 23457012 DOI: 10.1152/ajpheart.00933.2012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Traditional proteomics provides static assessment of protein content, but not synthetic rates. Recently, proteome dynamics with heavy water ((2)H2O) was introduced, where (2)H labels amino acids that are incorporated into proteins, and the synthesis rate of individual proteins is calculated using mass isotopomer distribution analysis. We refine this approach with a novel algorithm and rigorous selection criteria that improve the accuracy and precision of the calculation of synthesis rates and use it to measure protein kinetics in spatially distinct cardiac mitochondrial subpopulations. Subsarcolemmal mitochondria (SSM) and interfibrillar mitochondria (IFM) were isolated from adult rats, which were given (2)H2O in the drinking water for up to 60 days. Plasma (2)H2O and myocardial (2)H-enrichment of amino acids were stable throughout the experimental protocol. Multiple tryptic peptides were identified from 28 proteins in both SSM and IFM and showed a time-dependent increase in heavy mass isotopomers that was consistent within a given protein. Mitochondrial protein synthesis was relatively slow (average half-life of 30 days, 2.4% per day). Although the synthesis rates for individual proteins were correlated between IFM and SSM (R(2) = 0.84; P < 0.0001), values in IFM were 15% less than SSM (P < 0.001). In conclusion, administration of (2)H2O results in stable enrichment of the cardiac precursor amino acid pool, with the use of refined analytical and computational methods coupled with cell fractionation one can measure synthesis rates for cardiac proteins in subcellular compartments in vivo, and protein synthesis is slower in mitochondria located among the myofibrils than in the subsarcolemmal region.
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Affiliation(s)
- Takhar Kasumov
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio 44195, USA.
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52
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Ilchenko S, Previs S, Rachdaoui N, Willard B, McCullough A, Kasumov T. An improved measurement of isotopic ratios by high resolution mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:309-12. [PMID: 23283729 PMCID: PMC3893058 DOI: 10.1007/s13361-012-0536-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 10/17/2012] [Accepted: 11/04/2012] [Indexed: 05/25/2023]
Abstract
The study of protein kinetics requires an accurate measurement of isotopic ratios of peptides. Although Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometers yield accurate mass measurements of analytes, the isotopologue ratios are consistently lower than predicted. Recently, we demonstrated that the magnitude of the spectral error in the FT-ICR mass spectrometer is proportional to the scan duration of ions. Here, we present a novel isotopic ratio extrapolation (IRE) method for obtaining accurate isotopic ratio measurements. Accuracy is achieved by performing scans with different duration and extrapolation of the data to the initial moment of the ion rotation; IRE minimizes the absolute isotopic ratio error to ≤1%. We demonstrate the application of IRE in protein turnover studies using (2)H(2)O-metabolic labeling. Overall, this technique allows accurate measurements of the isotopic ratios of proteolytic peptides, a critical step for enabling routine studies of proteome dynamics.
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Affiliation(s)
- S. Ilchenko
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - S.F. Previs
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - N. Rachdaoui
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - B. Willard
- Department of Research Core Services, Cleveland Clinic, Cleveland, OH 44195
| | - A. McCullough
- Department of Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH 44195
| | - T. Kasumov
- Department of Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH 44195
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53
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Kim TY, Wang D, Kim AK, Lau E, Lin AJ, Liem DA, Zhang J, Zong NC, Lam MPY, Ping P. Metabolic labeling reveals proteome dynamics of mouse mitochondria. Mol Cell Proteomics 2012; 11:1586-94. [PMID: 22915825 PMCID: PMC3518123 DOI: 10.1074/mcp.m112.021162] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/15/2012] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial dysfunction is associated with many human diseases. Mitochondrial damage is exacerbated by inadequate protein quality control and often further contributes to pathogenesis. The maintenance of mitochondrial functions requires a delicate balance of continuous protein synthesis and degradation, i.e. protein turnover. To understand mitochondrial protein dynamics in vivo, we designed a metabolic heavy water ((2)H(2)O) labeling strategy customized to examine individual protein turnover in the mitochondria in a systematic fashion. Mice were fed with (2)H(2)O at a minimal level (<5% body water) without physiological impacts. Mitochondrial proteins were analyzed from 9 mice at each of the 13 time points between 0 and 90 days (d) of labeling. A novel multiparameter fitting approach computationally determined the normalized peak areas of peptide mass isotopomers at initial and steady-state time points and permitted the protein half-life to be determined without plateau-level (2)H incorporation. We characterized the turnover rates of 458 proteins in mouse cardiac and hepatic mitochondria and found median turnover rates of 0.0402 d(-1) and 0.163 d(-1), respectively, corresponding to median half-lives of 17.2 d and 4.26 d. Mitochondria in the heart and those in the liver exhibited distinct turnover kinetics, with limited synchronization within functional clusters. We observed considerable interprotein differences in turnover rates in both organs, with half-lives spanning from hours to months (≈ 60 d). Our proteomics platform demonstrates the first large-scale analysis of mitochondrial protein turnover rates in vivo, with potential applications in translational research.
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Affiliation(s)
- Tae-Young Kim
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Ding Wang
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Allen K. Kim
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Edward Lau
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Amanda J. Lin
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - David A. Liem
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jun Zhang
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nobel C. Zong
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Maggie P. Y. Lam
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Peipei Ping
- From the §Departments of Physiology and Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
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54
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Price JC, Khambatta CF, Li KW, Bruss MD, Shankaran M, Dalidd M, Floreani NA, Roberts LS, Turner SM, Holmes WE, Hellerstein MK. The effect of long term calorie restriction on in vivo hepatic proteostatis: a novel combination of dynamic and quantitative proteomics. Mol Cell Proteomics 2012; 11:1801-14. [PMID: 22984287 PMCID: PMC3518108 DOI: 10.1074/mcp.m112.021204] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/31/2012] [Indexed: 11/06/2022] Open
Abstract
Calorie restriction (CR) promotes longevity. A prevalent mechanistic hypothesis explaining this effect suggests that protein degradation, including mitochondrial autophagy, is increased with CR, removing damaged proteins and improving cellular fitness. At steady state, increased catabolism must be balanced by increasing mitochondrial biogenesis and protein synthesis, resulting in faster protein replacement rates. To test this hypothesis, we measured replacement kinetics and relative concentrations of hundreds of proteins in vivo in long-term CR and ad libitum-fed mice using metabolic (2)H(2)O-labeling combined with the Stable Isotope Labeling in Mammals protocol and LC-MS/MS analysis of mass isotopomer abundances in tryptic peptides. CR reduced absolute synthesis and breakdown rates of almost all measured hepatic proteins and prolonged the half-lives of most (≈ 80%), particularly mitochondrial proteins (but not ribosomal subunits). Proteins with related functions exhibited coordinated changes in relative concentration and replacement rates. In silico expression pathway interrogation allowed the testing of potential regulators of altered network dynamics (e.g. peroxisome proliferator-activated receptor gamma coactivator 1-alpha). In summary, our combination of dynamic and quantitative proteomics suggests that long-term CR reduces mitochondrial biogenesis and mitophagy. Our findings contradict the theory that CR increases mitochondrial protein turnover and provide compelling evidence that cellular fitness is accompanied by reduced global protein synthetic burden.
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55
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Claydon AJ, Beynon R. Proteome dynamics: revisiting turnover with a global perspective. Mol Cell Proteomics 2012; 11:1551-65. [PMID: 23125033 DOI: 10.1074/mcp.o112.022186] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
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.
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Affiliation(s)
- Amy J Claydon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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56
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Li L, Willard B, Rachdaoui N, Kirwan JP, Sadygov RG, Stanley WC, Previs S, McCullough AJ, Kasumov T. Plasma proteome dynamics: analysis of lipoproteins and acute phase response proteins with 2H2O metabolic labeling. Mol Cell Proteomics 2012; 11:M111.014209. [PMID: 22393261 PMCID: PMC3394944 DOI: 10.1074/mcp.m111.014209] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 02/16/2012] [Indexed: 11/06/2022] Open
Abstract
Understanding the pathologies related to the regulation of protein metabolism requires methods for studying the kinetics of individual proteins. We developed a (2)H(2)O metabolic labeling technique and software for protein kinetic studies in free living organisms. This approach for proteome dynamic studies requires the measurement of total body water enrichments by GC-MS, isotopic distribution of the tryptic peptide by LC-MS/MS, and estimation of the asymptotical number of deuterium incorporated into a peptide by software. We applied this technique to measure the synthesis rates of several plasma lipoproteins and acute phase response proteins in rats. Samples were collected at different time points, and proteins were separated by a gradient gel electrophoresis. (2)H labeling of tryptic peptides was analyzed by ion trap tandem mass spectrometry (LTQ MS/MS) for measurement of the fractional synthesis rates of plasma proteins. The high sensitivity of LTQ MS in zoom scan mode in combination with (2)H label amplification in proteolytic peptides allows detection of the changes in plasma protein synthesis related to animal nutritional status. Our results demonstrate that fasting has divergent effects on the rate of synthesis of plasma proteins, increasing synthesis of ApoB 100 but decreasing formation of albumin and fibrinogen. We conclude that this technique can effectively measure the synthesis of plasma proteins and can be used to study the regulation of protein homeostasis under physiological and pathological conditions.
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Affiliation(s)
- Ling Li
- From the Departments of ‡Research Core Services and
| | | | - Nadia Rachdaoui
- §School of Medicine, Case Western Reserve University, Cleveland, Ohio 44195
| | - John P. Kirwan
- ¶Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, Ohio 44195
| | - Rovshan G. Sadygov
- the ‖Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, and
| | - William C. Stanley
- the **Division of Cardiology, Department of Medicine, University of Maryland Medical Center, Baltimore, Maryland 21201-1595
| | - Stephen Previs
- §School of Medicine, Case Western Reserve University, Cleveland, Ohio 44195
| | | | - Takhar Kasumov
- ¶Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, Ohio 44195
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57
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Guan S, Price JC, Ghaemmaghami S, Prusiner SB, Burlingame AL. Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling. Anal Chem 2012; 84:4014-21. [PMID: 22444387 DOI: 10.1021/ac203330z] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein turnover studies on a proteome scale based on metabolic isotopic labeling can provide a systematic understanding of mechanisms for regulation of protein abundances and their transient behaviors. At this time, these large-scale studies typically utilize a simple kinetic model to extract protein dynamic information. Although many high-quality, protein isotope incorporation data are available from those experiments, accurate and additionally useful protein dynamic information cannot be extracted from the experimental data by use of the simple kinetic models. In this paper, we describe a formal connection between data obtained from elemental isotope labeling experiments and the well-known compartment modeling, and we demonstrate that an appropriate application of a compartment model to turnover of proteins from mammalian tissues can indeed lead to a better fitting of the experimental data.
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Affiliation(s)
- Shenheng Guan
- Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, California 94158-2517, USA.
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58
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Zhou H, Li W, Wang SP, Mendoza V, Rosa R, Hubert J, Herath K, McLaughlin T, Rohm RJ, Lassman ME, Wong KK, Johns DG, Previs SF, Hubbard BK, Roddy TP. Quantifying apoprotein synthesis in rodents: coupling LC-MS/MS analyses with the administration of labeled water. J Lipid Res 2012; 53:1223-31. [PMID: 22389331 DOI: 10.1194/jlr.d021295] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stable isotope tracer studies of apoprotein flux in rodent models present difficulties as they require working with small volumes of plasma. We demonstrate the ability to measure apoprotein flux by administering either (2)H- or (18)O-labeled water to mice and then subjecting samples to LC-MS/MS analyses; we were able to simultaneously determine the labeling of several proteolytic peptides representing multiple apoproteins. Consistent with relative differences reported in the literature regarding apoprotein flux in humans, we found that the fractional synthetic rate of apoB is greater than apoA1 in mice. In addition, the method is suitable for quantifying acute changes in protein flux: we observed a stimulation of apoB production in mice following an intravenous injection of Intralipid and a decrease in apoB production in mice treated with an inhibitor of microsomal triglyceride transfer protein. In summary, we demonstrate a high-throughput method for studying apoprotein kinetics in rodent models. Although notable differences exist between lipoprotein profiles that are observed in rodents and humans, we expect that the method reported here has merit in studies of dyslipidemia as i) rodent models can be used to probe target engagement in cases where one aims to modulate apoprotein production and ii) the approach should be adaptable to studies in humans.
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Affiliation(s)
- Haihong Zhou
- Atherosclerosis, Merck Research Laboratories, Rahway, NJ 07065, USA
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59
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Price JC, Holmes WE, Li KW, Floreani NA, Neese RA, Turner SM, Hellerstein MK. Measurement of human plasma proteome dynamics with (2)H(2)O and liquid chromatography tandem mass spectrometry. Anal Biochem 2011; 420:73-83. [PMID: 21964502 DOI: 10.1016/j.ab.2011.09.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 09/06/2011] [Indexed: 11/18/2022]
Abstract
Dysfunction of protein turnover is a feature of many human diseases, and proteins are substrates in important biological processes. Currently, no method exists for the measurement of global protein turnover (i.e., proteome dynamics) that can be applied in humans. Here we describe the use of metabolic labeling with deuterium ((2)H) from (2)H(2)O and liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of mass isotopomer patterns to measure protein turnover. We show that the positions available for (2)H label incorporation in vivo can be calculated using peptide sequence. The isotopic incorporation values calculated by combinatorial analysis of mass isotopomer patterns in peptides correlate very closely with values established for individual amino acids. Inpatient and outpatient heavy water labeling protocols resulted in (2)H label incorporation sufficient for reproducible quantitation in humans. Replacement rates were similar for peptides deriving from the same protein. Using a kinetic model to account for the time course of each individual's (2)H(2)O enrichment curves, dynamics of approximately 100 proteins with half-lives ranging from 0.4 to 40 days were measured using 8 μl of plasma. The measured rates were consistent with literature values. This method can be used to measure in vivo proteome homeostasis in humans in disease and during therapeutic interventions.
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