Characterization of early autophagy signaling by quantitative phosphoproteomics

Under conditions of nutrient shortage autophagy is the primary cellular mechanism ensuring availability of substrates for continuous biosynthesis. Subjecting cells to starvation or rapamycin efficiently induces autophagy by inhibiting the MTOR signaling pathway triggering increased autophagic flux. To elucidate the regulation of early signaling events upon autophagy induction, we applied quantitative phosphoproteomics characterizing the temporal phosphorylation dynamics after starvation and rapamycin treatment. We obtained a comprehensive atlas of phosphorylation kinetics within the first 30 min upon induction of autophagy with both treatments affecting widely different cellular processes. The identification of dynamic phosphorylation already after 2 min demonstrates that the earliest events in autophagy signaling occur rapidly after induction. The data was subjected to extensive bioinformatics analysis revealing regulated phosphorylation sites on proteins involved in a wide range of cellular processes and an impact of the treatments on the kinome. To approach the potential function of the identified phosphorylation sites we performed a screen for MAP1LC3-interacting proteins and identified a group of binding partners exhibiting dynamic phosphorylation patterns. The data presented here provide a valuable resource on phosphorylation events underlying early autophagy induction.     

组氨酸磷酸化修饰的鉴定方法及应用

蛋白质磷酸化是广受关注的翻译后修饰类型之一,组氨酸磷酸化作为一种非常见的磷酸化修饰,最早被发现在细菌和低等真核生物信号传导的级联反应中起关键作用.近年来研究显示,其在肿瘤发生发展过程中也可能扮演了重要角色.由于磷酸化组氨酸的化学不稳定性、低丰度、亚化学计量性质、缺乏特异性的富集试剂,导致研究手段缺乏,限制了人们对磷酸化...     

The current state of the art of quantitative phosphoproteomics and its applications to diabetes research

Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.     

Recent findings and technological advances in phosphoproteomics for cells and tissues

Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.     

酪氨酸磷酸化在精子获能中的作用

获能是精子发生顶体反应以及与卵子结合之前所必需的生理过程.研究发现在精子获能过程中伴随有蛋白质的磷酸化特别是酪氨酸的磷酸化.主要对酪氨酸磷酸化蛋白在精子获能过程中的作用及其存在的部位进行归纳总结,为进一步阐明精子获能分子机制奠定基础.     

Super-SILAC: current trends and future perspectives

Stable isotope labeling with amino acids in cell culture (SILAC) has risen as a powerful quantification technique in mass spectrometry (MS)–based proteomics in classical and modified forms. Previously, SILAC was limited to cultured cells because of the requirement of active protein synthesis; however, in recent years, it was expanded to model organisms and tissue samples. Specifically, the super-SILAC technique uses a mixture of SILAC-labeled cells as a spike-in standard for accurate quantification of unlabeled samples, thereby enabling quantification of human tissue samples. Here, we highlight the recent developments in super-SILAC and its application to the study of clinical samples, secretomes, post-translational modifications and organelle proteomes. Finally, we propose super-SILAC as a robust and accurate method that can be commercialized and applied to basic and clinical research.     

Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways

Protein phosphorylation is a central regulatory mechanism of cell signaling pathways. This highly controlled biochemical process is involved in most cellular functions, and defects in protein kinases and phosphatases have been implicated in many diseases, highlighting the importance of understanding phosphorylation-mediated signaling networks. However, phosphorylation is a transient modification, and phosphorylated proteins are often less abundant. Therefore, the large-scale identification and quantification of phosphoproteins and their phosphorylation sites under different conditions are one of the most interesting and challenging tasks in the field of proteomics. Both 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry serve as key phosphoproteomic technologies in combination with prefractionation, such as enrichment of phosphorylated proteins/peptides. Recently, new possibilities for quantitative phosphoproteomic analysis have been offered by technical advances in sample preparation, enrichment, separation, instrumentation, quantification and informatics. In this article, we present an overview of several strategies for quantitative phosphoproteomics and discuss how phosphoproteomic analysis can help to elucidate signaling pathways that regulate various cellular processes.     

Cancer imaging with CEA antibodies: historical and current perspectives.

This article reviews the history and status of cancer imaging with radiolabeled antibodies against carcinoembryonic antigen (CEA). Although CEA and many other cancer-associated antigens are not distinct for neoplasia, the quantitative increase of these markers in malignant tissues provides a sufficient differential for selective antibody targeting. Animal studies with xenografted human tumors provided the first evidence of the prospects of this technology, followed by initial clinical success with purified goat whole IgG antibodies to CEA, labeled with 131I and with the use of dual-isotope subtraction methods. Subsequently, improved and earlier imaging could be accomplished with monoclonal antibody fragments, which then would permit the use of shorter-lived radionuclides, such as 111In, 123I, and 99mTc. The preferred use of a monoclonal anti-CEA IgG Fab' fragment, labeled with 99mTc by a recently developed, simple and rapid kit, has enabled the detection of small lesions, including those in the liver, within 4 h of injection. By means of SPECT imaging, a high sensitivity and specificity for RAID could be achieved.     

线粒体呼吸功能与精子活力、核DNA损伤的相关性分析

为探讨线粒体呼吸功能与精子活力、核DNA损伤程度之间的相关性,按WHO标准收集34例不同活力的精液标本,采用蔗糖差速离心法或密度梯度离心法提取精子线粒体,通过铂氧电极-溶氧仪测定线粒体呼吸耗氧率并计算状态III呼吸、状态IV呼吸、呼吸控制率（RCR）、磷氧比（P／0）及氧化磷酸化效率（0PR）;应用精子染色质扩散（sperm chromatin dispersion,SCD）实验检测精子DNA损伤情况。结果表明：不同活力精子线粒体状态Ⅲ呼吸耗氧量之间具有显著差异俨〈0．01）;弱精子症组RcR和OPR与正常对照组比较,分别降低了17．03％（P〈0．05）和40．74％（P〈0。01）;精子DNA损伤程度与精子活力、状态III呼吸及OPR均呈极显著负相关（r值分别是-0．812、-0．788和-0．696）。以上结果提示：精子线粒体呼吸耗氧和氧化磷酸化功能与精子活力之间存在着密切的联系;精子DNA（包括mtDNA）损伤可能影响精子的正常功能。     

Sperm motility in the horseshoe crab. III. Isolation and characterization of a sperm motility initiating peptide

Sperm motility in Limulus is initiated by a sperm motility initiating factor (SMI) that emanates from Limulus eggs. This report describes the partial purification of SMI (greater than 230-fold purification with respect to protein content) with 40% recovery. SMI appears to be a hydrophobic peptide of 500–2,000 MW. Although probably not purified to homogeneity, SMI is estimated to be active at a concentration of less than 0.2 μM.     

Sperm competition mechanisms in birds: models and data

This study presents three models to explain the mechanism oflast male sperm precedence in birds. Because passive loss ofsperm from the female reproductive tract occurs, all modelsincorporate this process. The three models are passive spermloss alone, stratification with passive sperm loss, and displacementwith passive sperm loss. With two inseminations containing thesame number of sperm, the models make the following predictions.For passive sperm loss alone, (1) differential paternity ispositively and linearly related to the time interval betweeninseminations, (2) with a slope that is equal to rate of lossof sperm from the female reproductive tract, (3) with an interceptthat is the same as the differential fertilizing capacity betweenthe semen of the two inseminations, and (4) the ratio of offspringfrom two inseminations remains constant over time. For stratification,(1) the relationship between differential paternity and theinterval between inseminations is nonlinear and exhibits a "brokenstick" pattern, with a substantial first-insemination precedencefor short intervals, and (2) the proportion of offspring fatheredby the first insemination increases over time. For displacement,the relationship between differential paternity and the intervalbetween inseminations is nonlinear and also exhibits a "brokenstick" pattern, but in contrast to the stratification model,sperm from the last insemination have precedence. Data fromthree experimental studies of the domestic fowl and one forthe turkey provide the opportunity to test these models, albeitto different extents. The data from all studies are consistentwith the passive sperm-loss model, except that one aspect ofone data set provided ambiguous support for stratification.None of the data provided any support for the displacement model.     

Sperm competitiveness in frogs: slow and steady wins the race

When sperm compete to fertilize available ova, selection is expected to favour ejaculate traits that contribute to a male''s fertilization success. While there is much evidence to show that selection favours increased numbers of sperm, only a handful of empirical studies have examined how variation in sperm form and function contributes to competitive fertilization success. Here, we examine selection acting on sperm form and function in the externally fertilizing myobatrachid frog, Crinia georgiana. Using in vitro fertilization techniques and controlling for variation in the number of sperm contributed by males in competitive situations, we show that males with a greater proportion of motile sperm, and motile sperm with slower swimming velocities, have an advantage when competing for fertilizations. Sperm morphology and the degree of genetic similarity between putative sires and the female had no influence on competitive fertilization success. These unusual patterns of selection might explain why frog sperm typically exhibit relatively slow swimming speeds and sustained longevity.     

Characterizing phosphoproteins and phosphoproteomes using mass spectrometry.

The reversible phosphorylation of proteins plays a major role in many vital cellular processes by modulating protein function and transmitting signals within cellular pathways and networks. Because phosphorylation is dynamic and the sites of modification cannot be predicted by an organism's genome, proteomic measurements are required to identify sites of and changes in the phosphorylation state of proteins. The low stoichiometry of phosphorylation sites that accompany the multifarious nature of protein phosphorylation in biological systems continues to challenge the dynamic range of present mass spectrometry (MS) technologies and proteomic measurements, despite the preponderance of research and analytical methods devoted to this area. This review addresses some of the strategies and limitations involving the use of MS to map and quantify changes in protein phosphorylation sites for samples that range from a single protein to an entire proteome, and presents several compelling reasons as to why comprehensive phosphorylation site analysis has proven to be so elusive without a hypothesis-driven experimental approach to elicit more meaningful and confident results.     

Bacterial phosphoproteomic analysis reveals the correlation between protein phosphorylation and bacterial pathogenicity

Increasing evidence shows that protein phosphorylation on serine, threonine and tyrosine residues is a major regulatory post-translational modification in the bacteria. This review focuses on the implications of bacterial phosphoproteome in bacterial pathogenicity and highlights recent development of methods in phosphoproteomics and the connectivity of the phosphorylation networks. Recent technical developments in the high accuracy mass spectrometry have dramatically transformed proteomics and made it possible the characterization of a few exhaustive site-specific bacterial phosphoproteomes. The high abundance of tyrosine phosphorylations in a few bacterial phosphoproteomes suggests their roles in the pathogenicity, especially in the case of pathogen-host interactions; the high abundance of multi-phosphorylation sites in bacterial phosphoprotein is a compensation of the relatively small phosphorylation size and an indicator of the delicate regulation of protein functions.     

Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives

Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.