Glutamine Transport in Rat Brain Synaptic and Non-Synaptic Mitochondria

Glutamine transport into rat brain mitochondria (synaptic and non-synaptic) was monitored by the uptake of [³H]glutamine as well as by mitochondrial swelling. The uptake is inversely correlated to medium osmolarity, temperature-dependent, saturable and inhibited by mersalyl, and glutamine is upconcentrated in the mitochondria. These results indicate that glutamine is transported into an osmotically active space by a protein catalyzed mechanism. The uptake is slightly higher in synaptic mitochondria than in non-synaptic ones. It is inhibited both by rotenone and the protonophore carbonyl cyanide p-trifluoromethoxyphenylhydrazone, the latter at pH 6.5, showing that the transport is activated by an electrochemical proton gradient. The K⁺/H⁺ ionophore nigericin also inhibits the uptake at pH 6.5 in the presence of external K⁺, which indicates that glutamine, at least in part, is taken up by a proton symport transporter. In addition, glutamine uptake as measured by the swelling technique revealed an additional glutamine transport activity with at least 10 times higher K_m value. This uptake is inhibited by valinomycin in the presence of K⁺ and is thus also activated by the membrane potential. Otherwise, the two methods show similar results. These data indicate that glutamine transport in brain mitochondria cannot be described by merely a simple electroneutral uniport mechanism, but are consistent with the uptake of both the anionic and the zwitterionic glutamine.     

The Activities of Some Energy-Metabolising Enzymes in Nonsynaptic (Free) and Synaptic Mitochondria Derived from Selected Brain Regions

Abstract: The enzyme complement of two different mitochondrial preparations from adult rat brain has been studied. One population of mitochondria (synaptic) is prepared by the lysis of synaptosomes, the other (nonsynaptic or free) by separation from homogenates. These populations have been prepared from distinct regions of the brain: cortex, striatum, and pons and medulla oblongata. The following enzymes have been measured: pyruvate dehydrogenase (EC 1.2.4.1), citrate synthase (EC 4.1.3.7), NAD-linked isocitrate dehydrogenase (EC 1.1.1.41), NADP-linked isocitrate dehydrogenase (EC 1.1.1.42), fumarase (EC 4.2.1.2), NAD-linked malate dehydrogenase (EC 1.1.1.37), D-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30), and mitochondrially bound hexokinase (EC 2.7.1.1) and creatine kinase (EC 2.7.3.2). The nonsynaptic (free) mitochondria show higher enzyme specific activities in the regions studied than the corresponding values recorded for the synaptic mitochondria. The significance of these observations is discussed in the light of the different metabolic activities of the two populations of mitochondria and the compartmentation of the metabolic activities of the brain.     

Proteomic and Metabolic Analyses of S49 Lymphoma Cells Reveal Novel Regulation of Mitochondria by cAMP and Protein Kinase A

Cyclic AMP (cAMP), acting via protein kinase A (PKA), regulates many cellular responses, but the role of mitochondria in such responses is poorly understood. To define such roles, we used quantitative proteomic analysis of mitochondria-enriched fractions and performed functional and morphologic studies of wild-type (WT) and kin⁻ (PKA-null) murine S49 lymphoma cells. Basally, 75 proteins significantly differed in abundance between WT and kin⁻ S49 cells. WT, but not kin⁻, S49 cells incubated with the cAMP analog 8-(4-chlorophenylthio)adenosine cAMP (CPT-cAMP) for 16 h have (a) increased expression of mitochondria-related genes and proteins, including ones in pathways of branched-chain amino acid and fatty acid metabolism and (b) increased maximal capacity of respiration on branched-chain keto acids and fatty acids. CPT-cAMP also regulates the cellular rate of ATP-utilization, as the rates of both ATP-linked respiration and proton efflux are decreased in WT but not kin⁻ cells. CPT-cAMP protected WT S49 cells from glucose or glutamine deprivation, In contrast, CPT-cAMP did not protect kin⁻ cells or WT cells treated with the PKA inhibitor H89 from glutamine deprivation. Under basal conditions, the mitochondrial structure of WT and kin⁻ S49 cells is similar. Treatment with CPT-cAMP produced apoptotic changes (i.e. decreased mitochondrial density and size and loss of cristae) in WT, but not kin⁻ cells. Together, these findings show that cAMP acts via PKA to regulate multiple aspects of mitochondrial function and structure. Mitochondrial perturbation thus likely contributes to cAMP/PKA-mediated cellular responses.     

Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate

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神经元突触前可塑性的结构及分子基础

突触可塑性是神经元间信息传递的重要生理调控机制,它包括突触前可塑性和突触后可塑性.突触前可塑性是指通过对神经递质释放过程的干预、修饰,调节突触强度的过程.突触强度的变化,是通过影响量子的大小,活动区的个数和囊泡释放概率来实现的.而突触前囊泡活动尤为重要：从转运、搭靠、融合至内吞进入下一轮循环,每一步都是由一群互相作用的蛋白质共同完成的.     

Quantitative Proteomics of Human Heart Samples Collected In Vivo Reveal the Remodeled Protein Landscape of Dilated Left Atrium Without Atrial Fibrillation

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Highlights

• •Proteomes measured from human heart biopsies collected in-vivo covers >7000 cardiac proteins and highlight hundreds of chamber-specific molecular signatures that meaningfully reflect the specialized functions of the respective chambers.
• •Protein quantification from freshly collected biopsies is preferential to necropsy samples because of unspecific post-mortem protein degradation in the latter.
• •Increased abundances of proteins associated with sustained atrial fibrillation are not a sufficient condition to generate the disease state.
• •Protein abundance differences between atria and ventricle primarily originate at the level of gene regulation and reflect a functional need.

     

蛋白质质谱分析的无标记定量算法研究进展

作为发现疾病相关生物标志物的重要途径,定量研究已成为蛋白质组学的热点问题.随着实验方法的发展和改进,定量数据处理算法也在不断更新和完善.将现有的无标记定量方法归纳为需要/不需要鉴定结果两类方法,分析比较了两类方法的异同及优缺点,详细讨论了所涉及的主要算法,总结了一些常用的无标记定量软件及对应的网络资源.展望了无标记定量数据分析的未来研究方向.     

18O标记法在定量蛋白质组学中的应用

基于质谱技术去识别和检测蛋白质表达差异是一个热点,有助于生物过程和体系的分子机制的研究。近年来各种基于质谱技术的定量蛋白质组学研究方法发展较快,相对其他方法而言,18O标记法是一种较为理想、相对容易实现并且在不断完善的体外标记方法,最近在定量蛋白质组学研究中应用较多。现对18O标记法原理、特点以及技术方法的优化和应用进展进行综述。     

Regional Development of Glutamate Dehydrogenase in the at Brain

The development of glutamate dehydrogenase enzyme activity in rat brain regions has been followed from the late foetal stage to the adult and through to the aged (greater than 2 years) adult. In the adult brain the enzyme activity was greatest in the medulla oblongata and pons greater than midbrain = hypothalamus greater than cerebellum = striatum = cortex. In the aged adult brain, glutamate dehydrogenase activity was significantly lower in the medulla oblongata and pons when compared to the 90-day-old adult value, but not in other regions. The enzyme-specific activity of nonsynaptic (free) mitochondria purified from the medulla oblongata and pons of 90-day-old animals was about twice that of mitochondria purified from the striatum and the cortex. The specific activity of the enzyme in synaptic mitochondria purified from the above three brain regions, however, remained almost constant.     

定量蛋白质组学分析方法及应用

蛋白质组学经历了近10年的发展,现在已经初具规模。但是由于它是动态地观察生物体不断变化的所有蛋白质,所以技术难度非常之大。为使研究简化并更具针对性,人们着重进行比较蛋白质组学的研究。为了具体量化这些蛋白质的变化产生了定量蛋白质组学,近几年各种标记技术的进步使得该学科得以迅猛发展。     

定量蛋白质组学分析PknG在分枝杆菌中的功能

丝氨酸苏氨酸蛋白激酶G(PknG)是分枝杆菌中一个类似于真核生物蛋白激酶C的蛋白质,对结核分枝杆菌的生长和新陈代谢等生理过程,以及结核分枝杆菌的耐药和在宿主细胞中的存活都起着重要的调节作用.本文在耻垢分枝杆菌(Mycobacterium smegmatis)mc2155中构建了过表达结核分枝杆菌PknG的重组菌株PknG-mc2155,并发现PknG-mc2155的生长速度慢于mc2155.应用化学修饰结合LC-LC-MS/MS的定量蛋白质组学方法,在mc2155和PknG-mc2155中鉴定到了176种有差异表达的蛋白,其中152种蛋白在PknG-mc2155中表达下调,24种蛋白表达上调.这些差异表达的蛋白参与了多个细胞过程,包括代谢、蛋白翻译等.基于这些结果,我们推测PknG-mc2155生长速度慢的原因是因为代谢相关酶如GlpK,ALD和DesA1等蛋白表达的下调;而Ag85A,Ag85C,SecA2等蛋白的上调则增强细菌的感染性;另外KatG蛋白的下调提示PknG的过表达增强了菌株的抗药性.代谢组学分析发现谷氨酸和谷氨酰胺在PknG-mc2155中的水平低于在mc2155中水平,证实了PknG影响谷氨酰胺的稳态平衡.利用蛋白质磷酸化分析,我们发现PknG的苏氨酸残基T-320上有一个自磷酸化修饰,而且在PknG-mc2155菌株中,也鉴定到gltA和glmM上的磷酸化修饰,显示gltA和glmM是PknG的底物.本研究为理解PknG的功能和作用机制提供了新的依据和解释,为深入研究PknG在结核分枝杆菌中的功能奠定了基础,我们的结果也表明蛋白质组学技术是系统研究细菌蛋白质功能的重要工具.     

深度学习方法在生物质谱及蛋白质组学中的应用

深度学习是近年来机器学习领域最热门的研究方向,尤其是在图像及语音识别、自然语言处理、自动驾驶等方面取得了突破性进展．生物质谱是当今生命科学领域重要的研究工具,尤其在蛋白质组学、代谢组学、生物制药等领域发挥着关键作用．近年来,基于深度学习方法的发展,以生物质谱为核心的蛋白质组学大数据分析将迎来发展新契机．本文综述了深度学习方法在生物质谱数据解析及蛋白质组学研究方面的最新应用．     

Mitochondria in the pathogenesis of diabetes:a proteomic view

Diabetes mellitus is a complex metabolic disordercharacterized by chronic hyperglycemia due to absolute or relative lack of insulin.Though great efforts have been made to investigate the pathogenesis of diabetes,the underlying mechanism behind the development of diabetes and its complications remains unexplored.Cumulative evidence has linked mitochondrial modification to the pathogenesis of diabetes and its complications and they are also observed in various tissues affected by diabetes.Proteomics is an attractive tool for the study of diabetes since it allows researchers to compare normal and diabetic samples by identifying and quantifying the differentially expressed proteins in tissues,cells or organelles.Great progress has already been made in mitochondrial proteomics to elucidate the role of mitochondria in the pathogenesis of diabetes and its complications.Further studies on the changes of mitochondrial protein specifically post-translational modifications during the diabetic state using proteomic tools,would provide more information to better understand diabetes.     

Effects of Aluminum and Calcium on Acetyl-CoA Metabolism in Rat Brain Mitochondria

Abstract: Al complexes are known to accumulate in extra- and intracellular compartments of the brain in the course of different encephalopathies. In this study possible effects of Al accumulation in the cytoplasmic compartment on mitochondrial metabolism were investigated. Al, like Ca, inhibited pyruvate utilization as well as citrate and oxoglutarate accumulation by whole brain mitochondria. Potencies of Ca²⁺_total effects were 10–20 times stronger than those of Al. Al decreased mitochondrial acetyl-CoA content in a concentration-dependent manner, along with an equivalent rise of free CoA level, whereas Ca caused loss of both intermediates from mitochondria. In the absence of P_i in the medium, Ca had no effect on mitochondrial metabolism, whereas Al lost its ability to suppress pyruvate utilization and acetyl-CoA content in Ca-free conditions. Verapamil potentiated, whereas ruthenium red reversed, Ca-evoked suppression of mitochondrial metabolism. On the other hand, in Ca-supplemented medium, Al partially overcame the inhibitory influence of verapamil. Accordingly, verapamil increased mitochondrial Ca levels much more strongly than Al. However, Al partially reversed the verapamil-evoked rise of Ca²⁺_total level. These data indicate that Al accumulated in cytoplasm in the form of the Al(PO₄)OH⁻ complex may inhibit mitochondrial functions by an increase of intramitochondrial [Ca²⁺]_total resulting from the Al-evoked rise of cytoplasmic [Ca²⁺]_free, as well as from inhibitory interference with the verapamil binding site on the Na⁺/Ca²⁺ antiporter.     

Mitochondria in the pathogenesis of diabetes: a proteomic view

Diabetes mellitus is a complex metabolic disorder characterized by chronic hyperglycemia due to absolute or relative lack of insulin. Though great efforts have been made to investigate the pathogenesis of diabetes, the underlying mechanism behind the development of diabetes and its complications remains unexplored. Cumulative evidence has linked mitochondrial modification to the pathogenesis of diabetes and its complications and they are also observed in various tissues affected by diabetes. Proteomics is an attractive tool for the study of diabetes since it allows researchers to compare normal and diabetic samples by identifying and quantifying the differentially expressed proteins in tissues, cells or organelles. Great progress has already been made in mitochondrial proteomics to elucidate the role of mitochondria in the pathogenesis of diabetes and its complications. Further studies on the changes of mitochondrial protein specifically post-translational modifications during the diabetic state using proteomic tools, would provide more information to better understand diabetes.     

Age-Dependent Variations in Peroxide-Utilizing Enzymes from Rat Brain Mitochondria and Cytoplasm

Abstract: The location of peroxide-utilizing enzymes has been studied in rat brain. Glutathione peroxidase and glutathione reductase distributions indicate that both enzymes are located in the cytoplasm and in the matrix space of "synaptosomal" and "free" mitochondria. On the other hand, catalase distribution parallels that of NADH-cytochrome c reductase (rotenone-insensitive), and appears to be associated with the outer membrane of brain mitochondria. Whereas no gross age-dependent changes in various marker enzymes were found, a gradual but significant increase in glutathione peroxidase from the soluble fraction of free mitochondria was detected. The consequences of such increase are discussed with regard to the reducing potential of the cell.     

Targeted and Untargeted Proteomics Approaches in Biomarker Development

An enormous amount of research effort has been devoted to biomarker discovery and validation. With the completion of the human genome, proteomics is now playing an increasing role in this search for new and better biomarkers. Here, what leads to successful biomarker development is reviewed and how these features may be applied in the context of proteomic biomarker research is considered. The “fit‐for‐purpose” approach to biomarker development suggests that untargeted proteomic approaches may be better suited for early stages of biomarker discovery, while targeted approaches are preferred for validation and implementation. A systematic screening of published biomarker articles using MS‐based proteomics reveals that while both targeted and untargeted technologies are used in proteomic biomarker development, most researchers do not combine these approaches. i) The reasons for this discrepancy, (ii) how proteomic technologies can overcome technical challenges that seem to limit their translation into the clinic, and (iii) how MS can improve, complement, or replace existing clinically important assays in the future are discussed.     

Characterization of traumatic brain injury in human brains reveals distinct cellular and molecular changes in contusion and pericontusion

Traumatic brain injury (TBI) contributes to fatalities and neurological disabilities worldwide. While primary injury causes immediate damage, secondary events contribute to long‐term neurological defects. Contusions (Ct) are primary injuries correlated with poor clinical prognosis, and can expand leading to delayed neurological deterioration. Pericontusion (PC) (penumbra), the region surrounding Ct, can also expand with edema, increased intracranial pressure, ischemia, and poor clinical outcome. Analysis of Ct and PC can therefore assist in understanding the pathobiology of TBI and its management. This study on human TBI brains noted extensive neuronal, astroglial and inflammatory changes, alterations in mitochondrial, synaptic and oxidative markers, and associated proteomic profile, with distinct differences in Ct and PC. While Ct displayed petechial hemorrhages, thrombosis, inflammation, neuronal pyknosis, and astrogliosis, PC revealed edema, vacuolation of neuropil, axonal loss, and dystrophic changes. Proteomic analysis demonstrated altered immune response, synaptic, and mitochondrial dysfunction, among others, in Ct, while PC displayed altered regulation of neurogenesis and cytoskeletal architecture, among others. TBI brains displayed oxidative damage, glutathione depletion, mitochondrial dysfunction, and loss of synaptic proteins, with these changes being more profound in Ct. We suggest that analysis of markers specific to Ct and PC may be valuable in the evaluation of TBI pathobiology and therapeutics.

     

The Effect of γ-Aminobutyric Acid on Substrate-Level Phosphorylation in Brain Mitochondria

Abstract: A consequence of the metabolism of γ-aminobutyric acid (GABA) via the "GABA shunt" should be a decreased rate of substrate-level phos- phorylation of GDP to GTP. ³²P₁ labeling of nucleotides was, therefore, studied in uncoupled brain mitochondria with α-ketoglutarate or a-ketoglutarate + GABA as substrates. The addition of an equimolar amount of GABA resulted in an approximately 50% reduction of the final specific activity of all mitochondrial nucleotides. This effect was completely reversed by aminooxyacetic acid. GABA did not affect the time course of nucleotide labeling. Although delineation of the mechanism involved requires further study, these preliminary results suggest an important modulatory role of GABA in the intermediary metabolism of brain mitochondria.     

Quantitative Proteomics by SWATH‐MS Suggest an Association Between Circulating Exosomes and Maternal Metabolic Changes in Gestational Diabetes Mellitus

Several factors including placental hormones (PH) released from the human placenta have been associated with the development of insulin resistance and gestational diabetes mellitus (GDM). However, circulating levels of PH does not correlate well with maternal insulin sensitivity across gestation, suggesting that other, previously unrecognized, mechanisms may be involved. The levels of circulating exosomes are higher in GDM compared to normal. GDM derived exosomes produce greater release of pro‐inflammatory cytokines from endothelial cells compared to exosomes from normal, suggesting that their contents may differ compared to normal pregnancies. Using a quantitative, information‐independent acquisition (Sequential Windowed Acquisition of All Theoretical Mass Spectra [SWATH]) approach, differentially abundant circulating exosome proteins are identified in women with normal glucose tolerance (NGT) and GDM at the time of GDM diagnosis. A total of 78 statistically significant proteins in the relative expression of exosomal proteins in GDM are compared with NGT. Bioinformatic analysis shows that the exosomal proteins in GDM target pathways are mainly associated with energy production, inflammation, and metabolism. Finally, an independent cohort of patients is used to validate some of the proteins identified by SWATH. The data obtained may be of utility in elucidating the underlying physiological mechanisms associated with insulin resistance in GDM.