A novel regulatory role of TRAPPC9 in L-plastin-mediated osteoclast actin ring formation

Trafficking protein particle complex 9 (TRAPPC9) is a major subunit of the TRAPPII complex. TRAPPC9 has been reported to bind nuclear factor κB kinase subunit β (IKKβ) and NF-kB-inducing kinase (NIK) where it plays a role in the canonical and noncanonical of nuclear factor-κB (NF-kB) signaling pathways, receptively. The role of TRAPPC9 in protein trafficking and cytoskeleton organization in osteoclast (OC) has not been studied yet. In this study, we examined the mRNA expression of TRAPPC9 during OC differentiation. Next, we examined the colocalization of TRAPPC9 with cathepsin-K, known to mediate OC resorption suggesting that TRAPPC9 mediates the trafficking pathway within OC. To identify TRAPPC9 protein partners important for OC-mediated cytoskeleton re-organization, we conducted immunoprecipitation of TRAPPC9 in mature OCs followed by mass spectrometry analysis. Our data showed that TRAPPC9 binds various protein partners. One protein with high recovery rate is L-plastin (LPL). LPL localizes at the podosomes and reported to play a crucial role in actin aggregation thereby actin ring formation and OC function. Although the role of LPL in OC-mediated bone resorption has not fully reported in detail. Here, first, we confirmed the binding of LPL to TRAPPC9 and, then, we investigated the potential regulatory role of TRAPPC9 in LPL-mediated OC cytoskeleton reorganization. We assessed the localization of TRAPPC9 and LPL in OC and found that TRAPPC9 is colocalized with LPL at the periphery of OC. Next, we determined the effect of TRAPPC9 overexpression on LPL recruitment to the actin ring using a viral system. Interestingly, our data showed that TRAPPC9 overexpression promotes the recruitment of LPL to the actin ring when compared with control cultures. In addition, we observed that TRAPPC9 overexpression reorganizes actin clusters/aggregates and regulates vinculin recruitment into the OC periphery to initiate podosome formation.     

Properties of amphotericin B channels in a lipid bilayer

Properties of individual ionic channels formed by polyene antibiotic Amphotericin B were studied on brain phospholipid membranes containing cholesterol. The ionic channels have a closed state and an open one (with conductance of about 6.5 pS in 2 M KCl). The conductance value of an open channel is independent of cholesterol concentration in the membrane and of pH in the range from 3.5 to 8.0. The voltage-current characteristics of a single channel are superlinear. Zero current potential value in the case of different KCl concentrations in the two solutions indicates preferential but not ideal anionic selectivity of a single channel. Channel conductivity grows as the electrolyte concentration is increased and tends to a limiting value at high concentrations. A simple model having only one site for an ion was shown to represent satisfactorily an open channel behaviour under different conditions. An individual ionic channel performs a large number of transitions between the open and closed states during its life-time of several minutes. Rate constants of these transitions depend on the kind and concentration of salt in aqueous solutions. The switching system functioning is not influenced by an ion situated inside the pore.     

Measuring Proteome Dynamics in Vivo: AS EASY AS ADDING WATER?

Proteomics investigations typically yield information regarding static gene expression profiles. The central issues that limit the study of proteome dynamics include how to (i) administer a labeled amino acid in vivo, (ii) measure the isotopic labeling of a protein(s) (which may be low), and (iii) reliably interpret the precursor/product labeling relationships. In this study, we demonstrate the potential of quantifying proteome dynamics by coupling the administration of stable isotopes with mass spectrometric assays. Although the direct administration of a labeled amino acid(s) is typically used to measure protein synthesis, we explain the application of labeled water, comparing ²H₂O versus H₂¹⁸O for measuring albumin biosynthesis in vivo. This application emphasizes two distinct advantages of using labeled water over a labeled amino acid(s). First, in long term studies (e.g. days or weeks), it is not practical to continuously administer a labeled amino acid(s); however, in the presence of labeled water, organisms will generate labeled amino acids. Second, to calculate rates of protein synthesis in short term studies (e.g. hours), one must utilize a precursor/product labeling ratio; when using labeled water it is possible to reliably identify and easily measure the precursor labeling (i.e. water). We demonstrate that labeled water permits studies of protein synthesis (e.g. albumin synthesis in mice) during metabolic “steady-state” or “non-steady-state” conditions, i.e. integrating transitions between the fed and fasted state or during an acute perturbation (e.g. following a meal), respectively. We expect that the use of labeled water is applicable to wide scale investigations of proteome dynamics and can therein be used to obtain a functional image of gene expression in vivo.Proteomics investigations typically yield information regarding static gene expression profiles; i.e. current “state-of-the-art” research programs lack measurements of proteome dynamics (1–3). This deficiency is unfortunate because the ability to measure rates of protein synthesis and breakdown will likely facilitate the identification of biomarkers of disease and yield novel insight regarding underlying homeostatic abnormalities (3, 4). For example, by measuring the concentration of circulating aminotransferase and the synthesis/secretion of albumin, one might be able to determine the degree of liver damage and assess whether hepatic function is compromised, respectively (5). Also, it should be possible to determine the influence of specific factors on the regulation of protein synthesis; e.g. does a therapeutic agent stimulate insulin biosynthesis?Classic studies of protein biosynthesis have measured the incorporation of a labeled amino acid(s) into a protein(s) of interest and estimated a synthesis rate by using a “precursor/product labeling ratio” (6). Because modern proteomics technologies can rapidly separate and quantify individual proteins from complex mixtures, investigators have started to exploit the use of stable isotope tracers in mass spectrometry-based studies of proteome kinetics. However, the ability to study protein dynamics in vivo presents unique challenges (3, 4, 7–13); e.g. how does one (i) administer an isotope (typically a labeled amino acid) over a prolonged period and (ii) determine the true precursor labeling (because the amino acid will be rapidly turned over and its labeling will be diluted)? We have demonstrated how to quantify protein synthesis using ²H₂O in vivo (10, 11); the advantages are that the tracer can be given orally, body water is a homogeneous pool with a relatively slow turnover, and the organism will continuously generate ²H-labeled amino acids (consequently one can study free living subjects, including humans (9, 11, 14)). The assumption of the method is that the equilibration between ²H in body water and a free amino acid(s) is faster than the rate of incorporation of an amino acid(s) into a newly made protein(s); preferably, the labeling of a free amino acid(s) should remain constant regardless of the metabolic status. We have validated that assumption by measuring the time-dependent labeling of alanine in vivo during the administration of ²H₂O and by measuring the incorporation of ²H-labeled alanine into plasma albumin and total tissue proteins using gas chromatography-mass spectrometry methods (10, 11, 15). Subsequent reports support our observations (12, 13).In this study, we demonstrate (as a model example) the application of our ²H₂O-based approach for measuring albumin biosynthesis in vivo in mice during long term and short term investigations. Namely, we recently demonstrated how to obtain relatively precise measurements of mass isotopomer profiles of peptides and other relatively large molecules by developing a novel approach for integrating the data (16, 17). Our method allowed us to detect shifts in the isotope distribution profile of albumin-derived peptides from mice given ²H₂O (17). In the current report, parallel studies examined the use of H₂¹⁸O because it offers potential advantages over ²H₂O, especially during acute studies that involve perturbations such as consumption of a meal. For example, the cleavage of a protein will immediately add a labeled oxygen atom into the carboxyl group of a free amino acid; resonance effects will distribute the label over both carboxyl oxygens. Although repeated cleavage is required to achieve maximal labeling of both oxygens, cleavage of tRNA-bound amino acids will also contribute to the labeling of the carboxyl oxygen (18–21). The synthesis of a new protein(s) then results in the stable incorporation of ¹⁸O into the peptide bond; indeed, the oxygen in peptide bonds accounts for a majority of the total oxygen in a protein (18, 19), making it potentially easier to describe precursor/product labeling relationships (6). Finally, during the development of this work pitfalls were identified; thus we discuss strategies to circumvent potential problems.     

Plasma proteome dynamics: analysis of lipoproteins and acute phase response proteins with 2H2O metabolic labeling

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.     

Assessing the reversibility of the anaplerotic reactions of the propionyl-CoA pathway in heart and liver

While a number of studies underline the importance of anaplerotic pathways for hepatic biosynthetic functions and cardiac contractile activity, much remains to be learned about the sites and regulation of anaplerosis in these tissues. As part of a study on the regulation of anaplerosis from propionyl-CoA precursors in rat livers and hearts, we investigated the degree of reversibility of the reactions of the propionyl-CoA pathway. Label was introduced into the pathway via NaH13CO3, [U-13C3]propionate, or [U-13C3]lactate + [U-13C3]pyruvate, under various concentrations of propionate. The mass isotopomer distributions of propionyl-CoA, methylmalonyl-CoA, and succinyl-CoA revealed that, in intact livers and hearts, (i) the propionyl-CoA carboxylase reaction is slightly reversible only at low propionyl-CoA flux, (ii) the methylmalonyl-CoA racemase reaction keeps the methylmalonyl-CoA enantiomers in isotopic equilibrium under all conditions tested, and (iii) the methylmalonyl-CoA mutase reaction is reversible, but its reversibility decreases as the flow of propionyl-CoA increases. The thermodynamic dis-equilibrium of the combined reactions of the propionyl-CoA pathway explains the effectiveness of anaplerosis from propionyl-CoA precursors such as heptanoate.     

Assay of the concentration and (13)C isotopic enrichment of propionyl-CoA,methylmalonyl-CoA,and succinyl-CoA by gas chromatography-mass spectrometry

We developed gas chromatography-mass spectrometry assays for the concentration and mass isotopomer distribution of propionyl-CoA, methylmalonyl-CoA, and succinyl-CoA in tissues. The assays involves perchloric acid extraction of the tissue, spiking the extract with [(2)H(5)]propionyl-CoA and [(2)H(4)]succinyl-CoA internal standards, and isolation of short-chain acyl-CoA fraction on an oligonucleotide purification cartridge. Propionyl-CoA is reacted with sarcosine and the formed N-propionylsarcosine is assayed as its pentafluorobenzyl derivative. Methylmalonyl-CoA and succinyl-CoA are hydrolyzed and the corresponding acids assayed as tert-butyl dimethylsilyl derivatives. The assay was applied to a study of [U-(13)C(3)]propionate metabolism in perfused rat livers. While propionyl-CoA is only M3 labeled, succinyl-CoA is M3, M2, and M1 labeled because of isotopic exchanges in the citric acid cycle. Methylmalonyl-CoA is M3 and M2 labeled, reflecting reversal of S-methylmalonyl-CoA mutase. Thus, our assays allow measuring the turnover of the coenzyme A derivatives involved in anaplerosis of the citric acid cycle via precursors of propionyl-CoA, i.e., propionate, odd-chain fatty acids, isoleucine, threonine, and valine.     

How do ionic channel properties depend on the structure of polyene antibiotic molecules?

A study has been made of the properties of ionic channels formed in phospholipid-cholesterol bilayers by polyene antibiotics of various molecular structures. Properties of channels created by natural antibiotics with different structures of the lactone ring (amphotericin B-nystatin-mycoheptin) as well as by some derivatives of amphotericin B modified with respect to the amino and carboxyl groups are compared. Neutralization of one or both charges of the amphotericin B molecule (both by chemical modification and by pH shift) increases the probability of the channel to be in a nonconducting state. An increase of cholesterol concentration in the membrane produces an opposite effect. It is assumed that the electrostatic interaction of the amino group of an antibiotic molecule with the carboxyl group of an adjacent one stabilized the channel. Conductance and selectivity of an open channel are not influenced by changes in the charged groups. These properties strongly depend on the structure of the polar chain of the lactone ring. For example, the appearance of one more carbonyl group in the mycoheptin molecule results in a sharply decreasing anion permeability of channels. An antibiotic concentration which is necessary to observe single channels depends on the polyene chain structure: this is about 10(-7) M for tetraene nystatin and 2.10(-8) M for heptaene amphotericin B an mycoheptin.     

Transient permeability induced by alkyl derivatives of amphotericin B in lipid membranes

Individual ionic channels were shown to be formed in the brain cholesterol containing phospholipid membranes by two-sided addition of the amphotericin B alkyl derivatives. At concentrations between 10(-8) and 10(-7) M, the resulting conductance appeared to be transient. Existence of different antibiotic assemblies was justified by the kinetic analysis of the membrane conductance decline following the antibiotic washing out. In order to account for the transient characteristics of the induced conductance, it was proposed that the antibiotic oligomers incorporate into the membrane from the aqueous phase, form channels aggregating with cholesterol, and then dissociate in the bilayer into non-active degraded oligomeric or monomeric forms.     

Peroxisomal fatty acid oxidation is a substantial source of the acetyl moiety of malonyl-CoA in rat heart

Little is known about the sources of acetyl-CoA used for the synthesis of malonyl-CoA, a key regulator of mitochondrial fatty acid oxidation in the heart. In perfused rat hearts, we previously showed that malonyl-CoA is labeled from both carbohydrates and fatty acids. This study was aimed at assessing the mechanisms of incorporation of fatty acid carbons into malonyl-CoA. Rat hearts were perfused with glucose, lactate, pyruvate, and a fatty acid (palmitate, oleate or docosanoate). In each experiment, substrates were (13)C-labeled to yield singly or/and doubly labeled acetyl-CoA. The mass isotopomer distribution of malonyl-CoA was compared with that of the acetyl moiety of citrate, which reflects mitochondrial acetyl-CoA. In the presence of labeled glucose or lactate/pyruvate, the (13)C labeling of malonyl-CoA was up to 2-fold lower than that of mitochondrial acetyl-CoA. However, in the presence of a fatty acid labeled in its first acetyl moiety, the (13)C labeling of malonyl-CoA was up to 10-fold higher than that of mitochondrial acetyl-CoA. The labeling of malonyl-CoA and of the acetyl moiety of citrate is compatible with peroxisomal beta-oxidation forming C(12) and C(14) acyl-CoAs and contributing >50% of the fatty acid-derived acetyl groups that end up in malonyl-CoA. This fraction increases with the fatty acid chain length. By supplying acetyl-CoA for malonyl-CoA synthesis, peroxisomal beta-oxidation may participate in the control of mitochondrial fatty acid oxidation in the heart. In addition, this pathway may supply some acyl groups used in protein acylation, which is increasingly recognized as an important regulatory mechanism for many biochemical processes.     

Determination of the accessible surface of globular proteins by means of tritium planigraphy

Results are presented for proteins with known three-dimensional structure (lysozyme, myoglobin, ribonuclease), which show that the probability of label incorporation upon bombardment by hot tritium atoms may be quantitatively linked with the surface area of the protein accessible to water molecules. Possible deviations from simple linear dependency caused by particular mechanisms of label introduction are discussed. The data obtained in experiments with model systems were used to determine the accessible surface area of human serum albumin, for which structural data is not sufficiently accurate to allow estimation of accessible surface area. Experimental data correlate reasonably well with estimations based on conventional concepts of the relationship between accessible surface area and molecular weight for globular proteins. Correspondence to: A. V. Volynskaya