AXONAL TRANSPORT OF PROTEINS IN THE HYPOTHALAMO-NEUROHYPOPHYSIAL SYSTEM OF THE RAT

—Axonal transport of proteins in the hypothalamo-neurohypophysial system of the rat was studied after a local injection of [³⁵S]cysteine in the region of the supraoptic nucleus. The migration of labelled proteins was followed by measuring the specific radioactivity of the proteins in various parts of the hypothalamo-neurohypophysial tract. Between 2 and 4 h after the isotope injection there was a sharp increase in the protein-bound specific radioactivity of the posterior pituitary lobe, demonstrating that a transport of ³⁵S-labelled proteins had occurred from the supraoptic nucleus to the neurohypophysis. The rate of the transport was 2-3 mm/h. During the first 24 h after the injection a continuous accumulation of labelled material occurred in the neural lobe. Considerable radioactivity could still be recovered 6 days after the isotope injection. Fractionation of the neurohypophysial proteins by polyacrylamide gel electrophoresis revealed that approximately 90 per cent of the radioactivity of the soluble proteins was recovered in a single protein fraction. Labelling of this fraction was not observed until 2 h after isotope injection. The radioactivity increased markedly up to 4 h. It is suggested that this protein component is involved in the neurohypophysial response to osmotic stress since the protein disappeared from the posterior lobe upon dehydration of the rat.     

Amino-acid-type selective isotope labeling of proteins expressed in Baculovirus-infected insect cells useful for NMR studies

Culture conditions for successful amino–acid-type selective isotope labeling of proteins expressed in Baculovirus-infected insect cells are described. The method was applied to the selective labeling of the catalytic domain of c-Abl kinase with ¹⁵N-phenylalanine, ¹⁵N-glycine, ¹⁵N-tyrosine or ¹⁵N-valine. For the essential amino acids phenylalanine, tyrosine and valine high ¹⁵N-label incorporation rates of 90% and approximately the expected number of resonances in the HSQC spectra were observed, which was not the case for the non-essential amino acid glycine. The method should be applicable to amino-acid-type selective isotope labeling of other recombinant proteins which have not been amenable to NMR analysis.     

A direct introduction of <Superscript>18</Superscript>O isotopes into peptides and proteins for quantitative mass spectroscopy analysis

A method for direct introduction of ¹⁸O isotopes into carboxyl groups of peptides and proteins via the exchange with H₂ ¹⁸O in the presence of TFA is described. The isotope label is sufficiently stable in a wide pH range. Since the compounds labeled by this method retain their physicochemical characteristics, they can be used as an internal standard in quantitative assay of authentic compounds in the analyzed objects by means of mass spectrometry. This method is applicable to quantitative analysis of peptides and proteins in biological environments, as well as for quantitative kinetic studies of metabolism and enzyme activity. The quantitative analysis of polypeptides and proteins is combined with trypsinolysis. When necessary, the isotope label can be simultaneously introduced into all peptides and proteins in a control biosample, making it applicable as a standard for comparative analysis of experimental biosamples.     

CSN-5, a Component of the COP9 Signalosome Complex,Regulates the Levels of UNC-96 and UNC-98, Two Components of M-lines in Caenorhabditis elegans Muscle

In Caenorhabditis elegans two M-line proteins, UNC-98 and UNC-96, are involved in myofibril assembly and/or maintenance, especially myosin thick filaments. We found that CSN-5, a component of the COP9 signalosome complex, binds to UNC-98 and -96 using the yeast two-hybrid method. These interactions were confirmed by biochemical methods. The CSN-5 protein contains a Mov34 domain. Although one other COP9 signalosome component, CSN-6, also has a Mov34 domain, CSN-6 did not interact with UNC-98 or -96. Anti-CSN-5 antibody colocalized with paramyosin at A-bands in wild type and colocalized with abnormal accumulations of paramyosin found in unc-98, -96, and -15 (encodes paramyosin) mutants. Double knockdown of csn-5 and -6 could slightly suppress the unc-96 mutant phenotype. In the double knockdown of csn-5 and -6, the levels of UNC-98 protein were increased and the levels of UNC-96 protein levels were slightly reduced, suggesting that CSN-5 promotes the degradation of UNC-98 and that CSN-5 stabilizes UNC-96. In unc-15 and unc-96 mutants, CSN-5 protein was reduced, implying the existence of feed back regulation from myofibril proteins to CSN-5 protein levels. Taken together, we found that CSN-5 functions in muscle cells to regulate UNC-98 and -96, two M-line proteins.     

Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein

Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise ²H isotope shift measurements for ¹³C^??, ¹³C^??, ¹³C??, ¹⁵N, and ¹H^N have been obtained by using a mixed sample of protonated and uniformly perdeuterated ??-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil ²H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.     

Membranes of animal cells. V. Biosynthesis of the surface membrane during the cell cycle

KB cells grown in suspension culture were synchronized by using a double thymidine block. At various times throughout the life cycle aliquots of cells were pulsed with ¹⁴C-L-leucine, ¹⁴C-D-glucosamine and ¹⁴C-choline for one hour periods. Surface membranes, cell particulates and soluble proteins were isolated and their ¹⁴C specific activities were determined. It was found that there was a marked increase in the rate of incorporation into surface membrane just after division. The pattern of incorporation was the same for all three isotopic precursors. The rate of incorporation of isotopic precursors into soluble proteins was constant throughout the cycle. Some increase in rate of incorporation of isotope into the particulate fraction was observed during division.     

Enhanced production and isotope enrichment of recombinant glycoproteins produced in cultured mammalian cells

NMR studies of post-translationally modified proteins are complicated by the lack of an efficient method to produce isotope enriched recombinant proteins in cultured mammalian cells. We show that reducing the glucose concentration and substituting glutamate for glutamine in serum-free medium increased cell viability while simultaneously increasing recombinant protein yield and the enrichment of non-essential amino acids compared to culture in unmodified, serum-free medium. Adding dichloroacetate, a pyruvate dehydrogenase kinase inhibitor, further improves cell viability, recombinant protein yield, and isotope enrichment. We demonstrate the method by producing partially enriched recombinant Thy1 glycoprotein from Lec1 Chinese hamster ovary (CHO) cells using U-¹³C-glucose and ¹⁵N-glutamate as labeled precursors. This study suggests that uniformly ¹⁵N,¹³C-labeled recombinant proteins may be produced in cultured mammalian cells starting from a mixture of labeled essential amino acids, glucose, and glutamate.     

THE INCORPORATION OF RADIOACTIVE AMINO ACIDS INTO BRAIN SUBCELLULAR PROTEINS DURING TRAINING

—Total proteins, free amino acids, tritiated water and subcellular proteins of mouse brain were examined for changes in radioactivity during operant conditioning after subcutaneous administration of labelled amino acids. The conditioning was based on appetitive learning, using sweetened milk as a reward. During training and incorporation for 20-30 min, both [³H]leucine and [1-¹⁴C]leucine underwent a significant increase in catabolism, resulting in a decreased radioactivity in the free amino acids. [2-²H]Methionine underwent a rapid loss of isotope, so that 90% of the radioactivity was in the form of tritiated water at the end of training, and this phenomenon masked any possible effect of training. The brain uptake of [³⁵S]methionine increased during the training, resulting in an increased radioactivity in the proteins. Uptake of [³H]lysine increased slightly during training only after 1 h incorporation and not after 20 or 30 min, as judged from a time course of radioactivity in the free amino acids. Incorporation into nuclear proteins increased selectively during 20 min, and into nuclear and cytosol proteins after 60 min incorporations. It is concluded that changes in the observed rate of incorporation of a precursor into brain subcellular proteins under the influence of behaviour might be the result of changes in precursor catabolism or uptake, or both, and that each amino acid behaves in a different way. Even the same amino acid gives different results depending on the isotope and its position in the amino acid.     

HE TURNOVER RATE OF TUBULIN IN RAT BRAIN

The turnover rate of tubulin in rat brain was determined from the decay in specific radioactivity of the protein after pulse-labeling. When precursors were administered by a parenteral route, the shortest half-life, 9.8 days, was obtained with [¹⁴C]NaHCO₃; the longer half-lives obtained with [U-¹⁴C]glucose or [4,5-³H]leucine suggest significant reutilization of label. Furthermore, with leucine as precursor maximal specific radioactivity of tubulin was not obtained until eight days after administration of label. Labeling and decay kinetics obtained with [4,5-³H]leucine were markedly different when the isotope was administered directly into the lateral ventricle. The difference between the turnover rates of the -α and β subunits of tubulin purified by means of high resolution polyacrylamide gel electrophoresis was not statistically significant. A half-life for tubulin of 6.2 days was measured by continuous intravenous infusion of [U-¹⁴C]tyrosine.     

Mercury determination in blood by gas chromatography-mass spectrometry

A stable isotope dilution gas chromatography-mass spectrometry method using¹⁹⁶Hg as an internal standard is described for determining Hg in blood. In this method, the blood samples are not subjected to any digestion to avoid the loss of Hg. A solution of 0.6M HCl is used to free Hg present in blood from proteins. The pH of the solution is adjusted to 9 using borate buffer and Hg chelated using lithiumbis(trifluoroethyl)dithiocarbamate. All isotope ratio measurements are made using an organic mass spectrometer. Overall precision values for the five major Hg isotopes relative to²⁰²Hg are 1.6–2.3% when 10 ng samples of chelated Hg are analyzed. No appreciable memory or carryover effect is observed when two synthetic mixtures differing in¹⁹⁶Hg/²⁰²Hg ratios by a factor of 30 are sequentially analyzed. The method is validated by determining Hg in blood samples using isotope dilution GC-MS.     

Alp/Enigma Family Proteins Cooperate in Z-Disc Formation and Myofibril Assembly

The Drosophila Alp/Enigma family protein Zasp52 localizes to myotendinous junctions and Z-discs. It is required for terminal muscle differentiation and muscle attachment. Its vertebrate ortholog ZASP/Cypher also localizes to Z-discs, interacts with α-actinin through its PDZ domain, and is involved in Z-disc maintenance. Human mutations in ZASP cause myopathies and cardiomyopathies. Here we show that Drosophila Zasp52 is one of the earliest markers of Z-disc assembly, and we use a Zasp52-GFP fusion to document myofibril assembly by live imaging. We demonstrate that Zasp52 is required for adult Z-disc stability and pupal myofibril assembly. In addition, we show that two closely related proteins, Zasp66 and the newly identified Zasp67, are also required for adult Z-disc stability and are participating with Zasp52 in Z-disc assembly resulting in more severe, synergistic myofibril defects in double mutants. Zasp52 and Zasp66 directly bind to α-actinin, and they can also form a ternary complex. Our results indicate that Alp/Enigma family members cooperate in Z-disc assembly and myofibril formation; and we propose, based on sequence analysis, a novel class of PDZ domain likely involved in α-actinin binding.     

Myofibril MgATPase activities and energy metabolism in cardiomyopathic mice with diastolic dysfunction

To study the genomic physiology of cardiac myofibril proteins in the heart, we have successfully created a cardiac troponin I (cTnI; a myofibril protein) gene knockout mouse model using gene targeting techniques. The phenotype of the cTnI gene knockout mouse is a cardiomyopathy with diastolic dysfunction resulting in sudden death in neonates. In the present studies, energy metabolism was analyzed in myocardial cells from cTnI-null hearts. Myofibril MgATPase activities were determined in myocardial cells from either wild-type or cTnI mutant mouse hearts. Furthermore, the quantity and quality of the mitochondria in wild-type and cTnI mutant animals were counted and analyzed. Our results demonstrate that damaged relaxation and increased Ca²⁺-independent force production in cTnI-null hearts is in part related to the increased myofibril MgATPase activities accompanied by an increase in mitochondria quantity and mitochondrial ATPase activities. These data indicate that cardiomyopathies with diastolic dysfunction are different from cardiomyopathies caused by systolic dysfunction. The former involves the damage of cardiac relaxation due to increased MgATPase activities and increased Ca²⁺-independent force production inside of myofilaments, while the latter involves the damage of systolic contraction due to decreased MgATPase activities and decreased force production.     

Abstracts: Albany 2005, The 14th Conversation

Abstract

We report a cost efficient approach for amino-acid-type selective isotope labeling of proteins expressed in Leishmania tarentolae. The method provides an economically advantageous alternative to recently established protocol for isotopic labeling using expensive synthetic media. The method is based on cultivation of the L. tarentolae expression strain in a cheap complex medium supplemented with labeled amino acid(s). In this protocol, a labeled amino acid is deliberately diluted in the medium of undefined composition, which leads to a low-level isotope enrichment upon protein over-expression. The economic advantage of the protocol is achieved by avoiding large volumes of expensive synthetic medium. Decreased sensitivity of a NMR experiment due to low-level isotope enrichment is compensated by a five- to seven-fold increase of the yield of the recombinant protein in complex medium as compared to that in the synthetic medium. In addition, the decreased sensitivity can be compensated by using a higher magnetic field, cryo-detection system or higher number of transients during the NMR data acquisition. We show that enrichment as low as 5% does not compromise a NMR experiment and makes preparation of the recombinant proteins over- expressed in L. tarentolae economically viable. The method is demonstrated by selective labeling of the ～27 kDa enhanced green fluorescent protein (EGFP) with ¹⁵N-labeled valine.     

Use of labelled methionine to investigate the contribution of muscle proteins to egg production in zebra finches

Many bird species show a loss of female muscle mass at the time of egg formation. In this study we investigated whether there was a causal link between the loss in muscle condition and the formation of egg proteins by feeding ³⁵S-methionine to female zebra finches to label muscle proteins. When these birds subsequently bred the isotope was transferred to the egg proteins: isotope loss from female muscle tissue was significantly greater in birds which had bred than in control groups which had not.     

Gas chromatography-mass spectrometry determination of [15N]ammonia enrichment in blood and urine

A rapid gas chromatography-mass spectrometry method for [¹⁵N]ammonia analysis is deseribed which is based on the formation of [¹⁵N]glutamic acid from ammonia and analysis of isotopic abundance in the N-trifluoroacetyl-n-butylester glutamate derivative. Mean recovery of [¹⁵N]ammonia added to either plasma or urine was greater than 99% with a relative standard deviation of less than 10%. The method can be applied to the determination of extremely low levels of ammonia through an isotope dilution technique. The [¹⁵N]ammonia abundance of blood and urine was determined in an adult following on oral dose (500 mg) of ¹⁵NH₄Cl. A peak isotopic abundance of 13 atoms% excess was reached by 30 min. Urinary excretion of [¹⁵N]ammonia during the first 4 h after administration of the isotope amounted to 4.1% of the isotope administered.     

Selective <Superscript>15</Superscript>N labeling of barstar in a T7 polymerase system

The T7 RNA polymerase system for selective protein labeling, previously optimized for the time of introducing the ¹⁵N amino acid relative to the inducer (IPTG) and host polymerase inhibitor (rifampicin), was further improved by the use of a special growth medium enriched in particular amino acids and by administration of an aminotransferase inhibitor (α-aminooxyacetic acid); the latter prevented isotope redistribution (as required by NMR studies) even with readily metabolized leucine. The approach is shown to be successful for selective labeling of barstar with [¹⁵N]Trp and [¹⁵N]Leu; it can be used with any proteins expressed in the T7 system.     

Genetic dissection of novel myopathy models reveals a role of CapZα and Leiomodin 3 during myofibril elongation

Myofibrils within skeletal muscle are composed of sarcomeres that generate force by contraction when their myosin-rich thick filaments slide past actin-based thin filaments. Although mutations in components of the sarcomere are a major cause of human disease, the highly complex process of sarcomere assembly is not fully understood. Current models of thin filament assembly highlight a central role for filament capping proteins, which can be divided into three protein families, each ascribed with separate roles in thin filament assembly. CapZ proteins have been shown to bind the Z-disc protein α-actinin to form an anchoring complex for thin filaments and actin polymerisation. Subsequent thin filaments extension dynamics are thought to be facilitated by Leiomodins (Lmods) and thin filament assembly is concluded by Tropomodulins (Tmods) that specifically cap the pointed end of thin filaments. To study thin filament assembly in vivo, single and compound loss-of-function zebrafish mutants within distinct classes of capping proteins were analysed. The generated lmod3- and capza1b-deficient zebrafish exhibited aspects of the pathology caused by variations in their human orthologs. Although loss of the analysed main capping proteins of the skeletal muscle, capza1b, capza1a, lmod3 and tmod4, resulted in sarcomere defects, residual organised sarcomeres were formed within the assessed mutants, indicating that these proteins are not essential for the initial myofibril assembly. Furthermore, detected similarity and location of myofibril defects, apparent at the peripheral ends of myofibres of both Lmod3- and CapZα-deficient mutants, suggest a function in longitudinal myofibril growth for both proteins, which is molecularly distinct to the function of Tmod4.     

激光捕获显微切割技术结合18O标记定量蛋白质组技术在胃癌标志物筛查中的应用研究

建立一种更加精确地分离鉴定胃癌特异肿瘤标志物的定量蛋白质组学技术．首先采用激光捕获显微切割技术(LCM)纯化胃腺癌细胞及胃黏膜良性上皮细胞,将裂解的样本总蛋白经过1D SDS-PAGE预分离,然后采用¹⁸O/¹⁶O分别标记两种样本酶切后的多肽混合物．结合纳升级液相色谱(Nano-HPLC-MS/MS)定量地鉴定胃癌细胞和胃黏膜良性上皮细胞的差异表达蛋白．共筛选出78个差异表达蛋白,其中42个蛋白质在胃癌组织中表达上调,36个蛋白质下调．Western blot 技术验证了其中几个差异蛋白(moesin, periostin, annexin A2, annexin A4)的表达,与蛋白质组学研究的结果一致．LCM技术结合¹⁸O稳定同位素标记的定量蛋白质组学技术,为研究胃癌发生机制、筛选胃癌的分子标志物提供了新的思路,亦为诸如胃癌等复杂体系蛋白质的分离鉴定提供了新的技术选择．     

Chromium isotopic composition of core‐top planktonic foraminifera

The chromium isotope system (⁵³Cr/⁵²Cr expressed as δ⁵³Cr relative to NIST SRM 979) is potentially a powerful proxy for the redox state of the ocean–atmosphere system, but a lack of temporally continuous, well‐calibrated archives has limited its application to date. Marine carbonates could potentially serve as a common and continuous Cr isotope archive. Here, we present the first evaluation of planktonic foraminiferal calcite as an archive of seawater δ⁵³Cr. We show that single foraminiferal species from globally distributed core tops yielded variable δ⁵³Cr, ranging from 0.1‰ to 2.5‰. These values do not match with the existing measurements of seawater δ⁵³Cr. Further, within a single core‐top, species with similar water column distributions (i.e., depth habitats) yielded variable δ⁵³Cr values. In addition, mixed layer and thermocline species do not consistently exhibit decreasing trends in δ⁵³Cr as expected based on current understanding of Cr cycling in the ocean. These observations suggest that either seawater δ⁵³Cr is more heterogeneous than previously thought or that there is significant and species‐dependent Cr isotope fractionation during foraminiferal calcification. Given that the δ⁵³Cr variability is comparable to that observed in geological samples throughout Earth's history, interpreting planktonic foraminiferal δ⁵³Cr without calibrating modern foraminifera further, and without additional seawater measurements, would lead to erroneous conclusions. Our core‐top survey clearly indicates that planktonic foraminifera are not a straightforward δ⁵³Cr archive and should not be used to study marine redox evolution without additional study. It likewise cautions against the use of δ⁵³Cr in bulk carbonate or other biogenic archives pending further work on vital effects and the geographic heterogeneity of the Cr isotope composition of seawater.     

Isotope alteration caused by changes in biochemical composition of sedimentary organic matter

Stable carbon (C) and nitrogen (N) isotope ratios of sedimentary organic matter (OM) can reflect the biogeochemical history of aquatic ecosystems. However, diagenetic processes in sediments may alter isotope records of OM via microbial activity and preferential degradation of isotopically distinct organic components. This study investigated the isotope alteration caused by preferential degradation in surface sediments sampled from a eutrophic reservoir in Germany. Sediments were treated sequentially with hot water extraction, hydrochloric acid hydrolysis, hydrogen peroxide oxidation and di-sodium peroxodisulfate oxidation to chemically simulate preferential degradation pathways of sedimentary OM. Residue and extracts from each extraction step were analyzed using elemental analyzer-isotope ratio mass spectrometry and solid-state ¹³C nuclear magnetic resonance spectroscopy. Our results show that stable C and N isotope ratios reacted differently to changes in the biochemical composition of sedimentary OM. Preferential degradation of proteins and carbohydrates resulted in a 1.2‰ depletion of ¹³C, while the isotope composition of ¹⁵N remained nearly the same. Sedimentary δ¹⁵N values were notably altered when lignins and lipids were oxidized from residual sediments. Throughout the sequential fractionation procedure, δ¹³C was linearly correlated with the C:N of residual sediments. This finding demonstrates that changes in biochemical composition caused by preferential degradation altered δ¹³C values of sedimentary OM, while this trend was not observed for δ¹⁵N values. Our study identifies the influence of preferential degradation on stable C isotope ratios and provide additional insight into the isotope alteration caused by post-depositional processes.