磷酸化蛋白质组研究中的富集策略

蛋白质的磷酸化与去磷酸化过程,调控着包括信号转换、基因表达、细胞周期等诸多细胞过程。因此,对蛋白质磷酸化修饰的分析是蛋白质组研究中的重要内容。但由于磷酸化蛋白的丰度较低,难以用质谱直接检测。为了解决这个问题,改善质谱对磷酸肽的信号响应,需要对磷酸化蛋白质或磷酸肽进行富集。目前主要的富集方法包括免疫沉淀、固相金属离子亲和色谱、金属氧化物/氢氧化物亲和色谱等。     

用蛋白质组学方法解析磷酸化蛋白质

蛋白质磷酸化和去磷酸化这一可逆过程参与了高等真核生物细胞信号转导、细胞分化和细胞生长等重要过程,并与许多疾病、肿瘤的发生密切相关。蛋白质组学技术的不断发展和完善,可以更好、更多地识别和鉴定磷酸化蛋白质,为解析磷酸化蛋白质提供了可能。章综述了用于分离和鉴定磷酸化蛋白质的蛋白质组学方法。     

质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

蛋白质磷酸化修饰的研究进展

蛋白质磷酸化是最常见、最重要的一种蛋白质翻译后修饰方式,它参与和调控生物体内的许多生命活动。通过蛋白质的磷酸化与去磷酸化,调控信号转导、基因表达、细胞周期等诸多细胞过程。随着蛋白质组学技术的发展和应用,蛋白质磷酸化的研究越来越受到广泛的重视。我们介绍了蛋白质磷酸化修饰的主要类型与功能、磷酸化蛋白质分析样品的富集及制备、磷酸化蛋白的鉴定及磷酸化位点的预测、蛋白分离后磷酸化蛋白的检测,及蛋白质磷酸化的分子机制,并综述了近年来国内外的主要相关研究进展。     

杨树蛋白质磷酸化位点预测

以小黑杨磷酸化蛋白质组为研究对象,用人工神经网络表达丝氨酸、苏氨酸等残基位点的磷酸化与氨基酸序列的结构特征之间的非线性关系,建立了BP人工神经网络模型,并用磷酸化数据对所建模型进行训练和分析,得适宜的结构为21×16∶8∶4,拟合准确度为90%,Acc、Sn、Sp、MCC分别为78%、89%、67%、0.57,对比分析结果表明,所建模型具有较强的预测能力。     

蛋白质组中蛋白质磷酸化研究进展

随着后基因组时代的到来 ,对生命体器官、组织或细胞的全部蛋白质的表达、修饰及相互作用的研究已成为蛋白质组学的重要任务。蛋白质磷酸化是细胞内信号转导和酶调控最常见的机制之一 ,人类基因组约 2 %的基因编码 5 0 0种激酶和 10 0种磷酸酶。蛋白质磷酸化和去磷酸化作为原核和真核细胞表达调控的关键环节 ,了解其对功能的影响可以深入理解生命系统在分子水平的调控状况。目前蛋白质组磷酸化研究仍是功能基因组面临的重大课题 ,本文对此作一综述     

原位定量检测磷酸化蛋白质的Duolink PQ技术

很多蛋白质功能的变化往往要借助于特定位置和一定数目的磷酸化变化,因此原位和定量检测将是磷酸化蛋白质分析发展的新方向。一种可原位定量检测磷酸化蛋白质的新技术——Duolink PQ在国内还被了解得很少。本文从原理、方法及应用三个方面对其进行了介绍,并进而对现有磷酸化蛋白质检测的主要技术进行了简要评价。     

蛋白质组氨酸磷酸化研究进展

摘要：蛋白质磷酸化是一种可逆的翻译后修饰,这种翻译后修饰可以改变蛋白质的构象,进而使蛋白质活化或者失活。组氨酸磷酸化在细胞信号传导过程中发挥着重要作用,且组氨酸磷酸化与人类某些疾病密切相关,然而,由于组氨酸磷酸化含有P-N键,具备不稳定性,有关于组氨酸磷酸化的报道远远少于其它磷酸化的报道。本综述系统的总结了组氨酸磷酸化在生物学过程中的作用,以及近些年取得的重要研究进展,以期对深入研究组氨酸磷酸化提供理论参考。     

磷酸化蛋白质组学的新进展及其在肝脏生理和病理机制中的应用

蛋白质磷酸化是最常见的蛋白质翻译后修饰形式。由于蛋白质的磷酸化形式可以被磷酸酶和磷酸激酶进行可逆的调控,所以在众多的生命活动过程中蛋白质的磷酸化修饰起着重要的调控作用,因此对生物体内蛋白质磷酸化修饰的系统研究对于揭示生命科学的奥秘显得十分重要。近年来,随着质谱技术和生物信息学软件以及磷酸化肽段富集方法的发展,利用质谱对生物体内蛋白质磷酸化修饰研究的技术逐渐成熟。肝脏作为人体最重要的代谢和免疫器官,深入研究肝脏细胞内蛋白质磷酸化修饰形式对于理解其功能具有重要指导意义。目前,迅速发展的磷酸化蛋白质组学技术已经被广泛应用到肝脏功能的生物学研究中。这些研究加深了人们对肝脏的生理及病理状态的分子生物学机制的了解。本文综述了当前磷酸化蛋白质组学的研究进展和磷酸化蛋白质组学在肝脏中的研究。     

不同品系小菜蛾成虫脑突触体 蛋白质磷酸化的研究

对小菜蛾Plutella xylostella(L.)敏感品系、抗溴氰菊酯品系、抗杀虫双品系和抗杀螟丹品系的成虫脑突触体蛋白质磷酸化进行了研究比较。结果表明：蛋白质磷酸化在各个品系中的表现是不一样的。cAMP和钙加钙调蛋白对不同品系小菜蛾脑蛋白质磷酸化都有不同程度的刺激作用;3种杀虫剂均对各品系小菜蛾的磷酸化反应有影响,杀虫双、杀螟丹表现为抑制,溴氰菊酯表现为加强。这种影响在敏感品系中表现得比抗性品系中要强烈。     

A Protein Phosphorylation Threshold for Functional Stacking of Plant Photosynthetic Membranes

Phosphorylation of photosystem II (PSII) proteins affects macroscopic structure of thylakoid photosynthetic membranes in chloroplasts of the model plant Arabidopsis. In this study, light-scattering spectroscopy revealed that stacking of thylakoids isolated from wild type Arabidopsis and the mutant lacking STN7 protein kinase was highly influenced by cation (Mg⁺⁺) concentrations. The stacking of thylakoids from the stn8 and stn7stn8 mutants, deficient in STN8 kinase and consequently in light-dependent phosphorylation of PSII, was increased even in the absence of Mg⁺⁺. Additional PSII protein phosphorylation in wild type plants exposed to high light enhanced Mg⁺⁺-dependence of thylakoid stacking. Protein phosphorylation in the plant leaves was analyzed during day, night and prolonged darkness using three independent techniques: immunoblotting with anti-phosphothreonine antibodies; Diamond ProQ phosphoprotein staining; and quantitative mass spectrometry of peptides released from the thylakoid membranes by trypsin. All assays revealed dark/night-induced increase in phosphorylation of the 43 kDa chlorophyll-binding protein CP43, which compensated for decrease in phosphorylation of the other PSII proteins in wild type and stn7, but not in the stn8 and stn7stn8 mutants. Quantitative mass spectrometry determined that every PSII in wild type and stn7 contained on average 2.5±0.1 or 1.4±0.1 phosphoryl groups during day or night, correspondingly, while less than every second PSII had a phosphoryl group in stn8 and stn7stn8. It is postulated that functional cation-dependent stacking of plant thylakoid membranes requires at least one phosphoryl group per PSII, and increased phosphorylation of PSII in plants exposed to high light enhances stacking dynamics of the photosynthetic membranes.     

蛋白质可逆磷酸化调节植物细胞离子跨膜运动研究进展

蛋白激酶和蛋白磷酸酶催化的可逆磷酸化是植物细胞中多种信号转导途径中重要的组成因子.本文对蛋白质可逆磷酸化通过调节多种离子跨膜运动而参与植物细胞激发子信号途径、毒性物质诱导的钙离子内流、盐胁迫适应、气孔运动以及蛋白质可逆磷酸化参与胞外与胞内之间Ca2 状况信息传递,调节花粉管顶端Ca2 离子通道活性进行综述,以揭示蛋白质可逆磷酸化在植物细胞离子跨膜运动中的调控作用,为蛋白质可逆磷酸化调节植物生长发育、响应逆境胁迫等机理的研究提供参考.     

Cold-Shock 310-kD Protein Uncouples Oxidative Phosphorylation in Plant Mitochondria

We studied the effects of cold-shock 310-kD protein (CSP310) isolated from winter rye seedlings on the energetic activity of plant mitochondria. CSP310 was shown to enhance nonphosphorylating respiration and uncoupled oxidative phosphorylation in isolated mitochondria. The uncoupling effect was enhanced with increasing protein concentration. An antibody against CSP310 interfered with the uncoupling effect of CSP310. Free fatty acids were not evidently involved in uncoupling. The physiological role of uncoupling between oxidation and phosphorylation during plant adaptation to low temperatures is discussed.     

蛋白磷酸化修饰在植物-病原微生物互作中的作用研究进展

蛋白磷酸化修饰是植物细胞信号调控的普遍机制。植物-病原微生物互作过程中, 关键调控蛋白的磷酸化状态影响免疫信号的激活。多种病原微生物通过干扰宿主蛋白的磷酸化状态攻击免疫系统, 以提高致病性。该文对植物免疫调控过程中关键元件的磷酸化修饰及其在免疫信号中的调控作用进行了综述。研究植物-病原菌互作过程中关键蛋白的磷酸化修饰, 有助于深入探讨植物-病原微生物互作的分子机理。该文将为寻找广谱抗病的新途径提供理论依据。     

植物响应非生物胁迫的磷酸化修饰组学研究进展

植物具有固着生活的特点,高温、低温、干旱和盐等生境中常见的非生物胁迫会严重影响植物的生长发育。蛋白质磷酸化是植物应对非生物胁迫的重要机制,主要通过蛋白质的磷酸化和去磷酸化修饰来调控植物细胞对外界胁迫的应激反应,在植物细胞快速传递胁迫信号并激活对胁迫环境的形态、生理和分子水平适应机制的过程中起重要作用。该文主要介绍了植物磷酸化蛋白质的富集、检测和鉴定技术,并对近年来国内外有关植物响应高温、低温、干旱、淹水、盐、养分亏缺和元素毒害等非生物胁迫的磷酸化修饰蛋白组学研究进展进行综述。     

Thylakoid Protein Phosphorylation in Higher Plant Chloroplasts Optimizes Electron Transfer under Fluctuating Light

Several proteins of photosystem II (PSII) and its light-harvesting antenna (LHCII) are reversibly phosphorylated according to light quantity and quality. Nevertheless, the interdependence of protein phosphorylation, nonphotochemical quenching, and efficiency of electron transfer in the thylakoid membrane has remained elusive. These questions were addressed by investigating in parallel the wild type and the stn7, stn8, and stn7 stn8 kinase mutants of Arabidopsis (Arabidopsis thaliana), using the stn7 npq4, npq4, npq1, and pgr5 mutants as controls. Phosphorylation of PSII-LHCII proteins is strongly and dynamically regulated according to white light intensity. Yet, the changes in phosphorylation do not notably modify the relative excitation energy distribution between PSII and PSI, as typically occurs when phosphorylation is induced by “state 2” light that selectively excites PSII and induces the phosphorylation of both the PSII core and LHCII proteins. On the contrary, under low-light conditions, when excitation energy transfer from LHCII to reaction centers is efficient, the STN7-dependent LHCII protein phosphorylation guarantees a balanced distribution of excitation energy to both photosystems. The importance of this regulation diminishes at high light upon induction of thermal dissipation of excitation energy. Lack of the STN7 kinase, and thus the capacity for equal distribution of excitation energy to PSII and PSI, causes relative overexcitation of PSII under low light but not under high light, leading to disturbed maintenance of fluent electron flow under fluctuating light intensities. The physiological relevance of the STN7-dependent regulation is evidenced by severely stunted phenotypes of the stn7 and stn7 stn8 mutants under strongly fluctuating light conditions.Several proteins of PSII and its light-harvesting antenna (LHCII) are reversibly phosphorylated by the STN7 and STN8 kinase-dependent pathways according to the intensity and quality of light (Bellafiore et al., 2005; Bonardi et al., 2005). The best-known phosphorylation-dependent phenomenon in the thylakoid membrane is the state transition: a regulatory mechanism that modulates the light-harvesting capacity between PSII and PSI. According to the traditional view, “state 1” prevails when plants are exposed to far-red light (state 1 light), which selectively excites PSI. Alternatively, thylakoids are in “state 2” when plants are exposed to blue or red light (state 2 light), favoring PSII excitation. In state 1, the yield of fluorescence from PSII is higher in comparison with state 2 (for review, see Allen and Forsberg, 2001). State transitions are dependent on the phosphorylation of LHCII proteins (Bellafiore et al., 2005) and their association with PSI proteins, particularly PSI-H (Lunde et al., 2000). Under state 2 light, both the PSII core and LHCII proteins are strongly phosphorylated, whereas the state 1 light induces dephosphorylation of both the PSII core and LHCII phosphoproteins (Piippo et al., 2006; Tikkanen et al., 2006). In nature, however, such extreme changes in light quality rarely occur. The intensity of light, on the contrary, fluctuates frequently in all natural habitats occupied by photosynthetic organisms, thus constantly modulating the extent of thylakoid protein phosphorylation in a highly dynamic manner (Tikkanen et al., 2008a).The regulation of PSII-LHCII protein phosphorylation by the quantity of light is much more complex than the regulatory circuits induced by the state 1 and state 2 lights. Whereas changes in light quality induce a concurrent increase or decrease in the phosphorylation levels of both the PSII core (D1, D2, and CP43) and LHCII (Lhcb1 and Lhcb2) proteins, the changes in white light intensity may influence the kinetics of PSII core and LHCII protein phosphorylation in higher plant chloroplasts even in opposite directions (Tikkanen et al., 2008a). Indeed, it is well documented that low light (LL; i.e. lower than that generally experienced during growth) induces strong phosphorylation of LHCII but relatively weak phosphorylation of the PSII core proteins. Exposure of plants to high light (HL) intensities, on the contrary, promotes the phosphorylation of PSII core proteins but inhibits the activity of the LHCII kinase, leading to dephosphorylation of LHCII proteins (Rintamäki et al., 2000; Hou et al., 2003).Thylakoid protein phosphorylation induces dynamic migrations of PSII-LHCII proteins along the thylakoid membrane (Bassi et al., 1988; Iwai et al., 2008) and modulation of thylakoid ultrastructure (Chuartzman et al., 2008). According to the traditional state transition theory, the phosphorylation of LHCII proteins decreases the antenna size of PSII and increases that of PSI, which is reflected as a quenched fluorescence emission from PSII. Alternatively, subsequent dephosphorylation of LHCII increases the antenna size of PSII and decreases that of PSI, which in turn is seen as increased PSII fluorescence (Bennett et al., 1980; Allen et al., 1981; Allen and Forsberg, 2001). This view was recently challenged based on studies with thylakoid membrane fractions, revealing that modulations in the relative distribution of excitation energy between PSII and PSI by LHCII phosphorylation specifically occur in the areas of grana margins, where both PSII and PSI function under the same antenna system, and the energy distribution between the photosystems is regulated via a more subtle mechanism than just the robust migration of phosphorylated LHCII (Tikkanen et al., 2008b). It has also been reported that most of the PSI reaction centers are located in the grana margins in a close vicinity to PSII-LHCII-rich grana thylakoids (Kaftan et al., 2002), providing a perfect framework for the regulation of excitation energy distribution from LHCII to both PSII and PSI.When considering the natural light conditions, the HL intensities are the only known light conditions that in higher plant chloroplasts specifically dephosphorylate only the LHCII proteins but not the PSII core proteins. However, such light conditions do not lead to enhanced function of PSII. Instead, the HL conditions strongly down-regulate the function of PSII via nonphotochemical quenching of excitation energy (NPQ) and PSII photoinhibition (for review, see Niyogi, 1999). On the other hand, after dark acclimation of leaves and relaxation of NPQ, PSII functions much more efficiently when plants/leaves are transferred to LL despite strong phosphorylation of LHCII, as compared with the low phosphorylation state of LHCII upon transfer to HL conditions.The delicate regulation of thylakoid protein phosphorylation in higher plant chloroplasts according to prevailing light intensity is difficult to integrate with the traditional theory of state transitions (i.e. the regulation of the absorption cross-section of PSII and PSI by reversible phosphorylation of LHCII). Moreover, besides LHCII proteins, reversible phosphorylation of the PSII core proteins may also play a role in dynamic light acclimation of plants. Recently, we demonstrated that the PSII core protein phosphorylation is a prerequisite for controlled turnover of the PSII reaction center protein D1 upon photodamage (Tikkanen et al., 2008a). This, however, does not exclude the possibility that the strict regulation of PSII core protein phosphorylation is also connected to the regulation of light harvesting and photosynthetic electron transfer. Moreover, the interactions between PSII and LHCII protein phosphorylation, nonphotochemical quenching, and cyclic electron flow around PSI in the regulation of photosynthetic electron transfer reactions remain poorly understood. To gain a deeper insight into such regulatory networks, we explored the effect of strongly fluctuating white light on chlorophyll (chl) fluorescence in Arabidopsis (Arabidopsis thaliana) mutants differentially deficient in PSII-LHCII protein phosphorylation and/or the regulatory systems of NPQ.     

Protein Phosphorylation in Astrocytes Mediated by Protein Kinase C: Comparison with Phosphorylation by Cyclic AMP-Dependent Protein Kinase

The protein kinase C activator, phorbol 12-myristate 13-acetate (PMA), has been found recently to transform cultured astrocytes from flat, polygonal cells into stellate-shaped, process-bearing cells. Studies were conducted to determine the effect of PMA on protein phosphorylation in astrocytes and to compare this pattern of phosphorylation with that elicited by dibutyryl cyclic AMP (dbcAMP), an activator of the cyclic AMP-dependent protein kinase which also affects astrocyte morphology. Exposure to PMA increased the amount of 32P incorporation into several phosphoproteins, including two cytosolic proteins with molecular weights of 30,000 (pI 5.5 and 5.7), an acidic 80,000 molecular weight protein (pI 4.5) present in both the cytosolic and membrane fractions, and two cytoskeletal proteins with molecular weights of 60,000 (pI 5.3) and 55,000 (pI 5.6), identified as vimentin and glial fibrillary acidic protein, respectively. Effects of PMA on protein phosphorylation were not observed in cells depleted of protein kinase C. In contrast to the effect observed with PMA, treatment with dbcAMP decreased the amount of 32P incorporation into the 80,000 protein. Like PMA, treatment with dbcAMP increased the 32P incorporation into the proteins with molecular weights of 60,000, 55,000 and 30,000, although the magnitude of this effect was different. The effect of dbcAMP on protein phosphorylation was still observed in cells depleted of protein kinase C. The results suggest that PMA, via the activation of protein kinase C, can alter the phosphorylation of a number of proteins in astrocytes, and some of these same phosphoproteins are also phosphorylated by the cyclic AMP-dependent mechanisms.     

植物类受体蛋白激酶的研究进展

植物类受体蛋白激酶(receptor-like protein kinase,RLKs)通过胞外结构域识别病原信号分子,发生磷酸化、去磷酸化反应而开启或关闭下游靶蛋白,调节植物固有免疫反应,诱导抗病防御反应.目前对植物类受体蛋白激酶的功能、信号传导和配体识别等方面的研究已成为该领域的重点.本文对近年来国内外有关植物类受体蛋白激酶的结构、功能及其在植物抗病防御反应中的作用研究进行综述,为今后进一步深入研究植物类受体蛋白激酶的生理生化功能及应用提供参考.     

蛋白质磷酸化作用的结构基础

蛋白质可逆磷酸化涉及到几乎所有细胞活动的调节.着重探讨了影响蛋白激酶作用专一性的几个因素和磷酸化影响蛋白质功能的结构基础及作用机制.     

Calmodulin-Dependent Protein Phosphorylation in Synaptic Junctions

Synaptic junctions (SJs) from rat forebrain were examined for Ca2+/calmodulin (CaM)-dependent kinase activity and compared to synaptic plasma membrane (SPM) and postsynaptic density (PSD) fractions. The kinase activity in synaptic fractions was examined for its capacity to phosphorylate endogenous proteins or exogenous synapsin I, in the presence or absence of Ca2+ plus CaM. When assayed for endogenous protein phosphorylation, SJs contained approximately 25-fold greater amounts of Ca2+/CAM-dependent kinase activity than SPMs, and fivefold more activity than PSDs. When kinase activities were measured by phosphorylation of exogenous synapsin I, SJs contained fourfold more activity than SPMs, and 10-fold more than PSDs. The phosphorylation of SJ proteins of 60- and 50-kilodalton (major PSD protein) polypeptides were greatly stimulated by Ca2+/CaM; levels of phosphorylation for these proteins were 23- and 17-fold greater than basal levels, respectively. Six additional proteins whose phosphorylation was stimulated 6-15-fold by Ca2+/CAM were identified in SJs. These proteins include synapsin I, and proteins of 240, 207, 170, 140, and 54 kilodaltons. The 54-kilodalton protein is a highly phosphorylated form of the major PSD protein and the 170-kilodalton component is a cell-surface glycoprotein of the postsynaptic membrane that binds concanavalin A. The CaM-dependent kinase in SJ fractions phosphorylated endogenous phosphoproteins at serine and/or threonine residues. Ca2+-dependent phosphorylation in SJ fractions was strictly dependent on exogenous CaM, even though SJs contained substantial amounts of endogenous CaM (15 micrograms CaM/mg SJ protein). Exogenous CaM, after being functionally incorporated into SJs, was rapidly removed by sequential washings. These observations suggest that the SJ-associated CaM involved in regulating Ca2+-dependent protein phosphorylation may be in dynamic equilibrium with the cytoplasm. These findings indicate that a brain CaM-dependent kinase(s) and substrate proteins are concentrated at SJs and that CaM-dependent protein phosphorylation may play an important role in mechanisms that underlie synaptic communication.