植物与病原菌互作的蛋白质组学研究进展

深入认识植物与病原菌的识别方式、亲和性或非亲和性的互作模式,对于揭示植物-病原菌互作机制研究具有重要意义.利用蛋白质组学方法研究病原菌侵染植物过程,分析相关的基因和蛋白,有助于从分子水平上探究植物-病原菌相互作用机制.本文概述了植物-病原菌的互作机制,系统介绍了差异蛋白质组学分析方法在植物-病原真菌、植物-病原细菌两类互作系统中的应用,分析了植物与病原菌互作过程中可能涉及的差异表达功能蛋白,并对当前蛋白质组学技术在植物与病原菌互作研究中存在的诸多问题进行了探讨.     

Proteomic Characterization of Acyclovir-Induced Nephrotoxicity in a Mouse Model

Acyclovir (ACV) is an effective and widely used antiviral agent. However, its clinical application is limited by severe nephrotoxicity. We assessed ACV-induced nephrotoxicity and identified the differentially expressed proteins using mass spectrometry-based proteomic analysis. In total, 30 ICR mice were intraperitoneally administrated ACV (150 or 600 mg/kg per day) for 9 days. After administration of ACV, levels of serum creatinine and urea nitrogen increased significantly. In addition, mouse kidneys exhibited histopathological changes and reduced expression levels of vascular endothelial growth factor (VEGF) and its receptor VEGFR2. In the proteomic analysis, more than 1,000 proteins were separated by two-dimensional polyacrylamide gel electrophoresis, and a total of 20 proteins were up- or down-regulated in the ACV group compared with the saline group. Among these, six proteins (MHC class II antigen, glyoxalase 1, peroxiredoxin 1, αB-crystallin, fibroblast growth factor receptor 1-IIIb, and cytochrome c oxidase subunit Vb) were identified in association with ACV-induced nephrotoxicity. These findings were confirmed by Western blotting analysis. The differential expression levels of α-BC, Prx1, Glo I and CcO Vb suggest that oxidative damage and mitochondrial injury may be involved in ACV-induced nephrotoxicity. Furthermore, VEGF and FGF may play a role in tissue repair and the restoration process following ACV nephrotoxicity.     

Proteomic Profiling of Mouse Helper T Cell Differentiation

Helper T cell differentiation is a key process in the regulation of adaptive immune responses. Here, mouse Th1 and Th2 cells are profiled using high‐throughput proteomics to increase the understanding of the molecular biology of Th differentiation to support the design of prophylactic and therapeutic intervention strategies for (infectious) diseases. Protein profiling of Th1/Th2 differentiated cells results in the quantification of almost 6000 proteins of which 41 are differentially expressed at FDR < 0.1, and 19 at the FDR < 0.05 level, respectively. Differential protein expression analysis identifies a number of the expected canonical Th differentiation markers, and gene set analysis using the REACTOME database and a hypergeometric test (FDR < 0.05) confirms that helper T cell pathways are the top sets that are differentially expressed. Additionally, by network analysis, many differentially expressed proteins are associated with the Th1 and Th2 pathways. Data are available via PRIDE database with identifier PXD004532.     

Proteomic Analysis of Mouse Hypothalamus under Simulated Microgravity

Exposure to altered microgravity during space travel induces changes in the brain and these are reflected in many of the physical behavior seen in the astronauts. The vulnerability of the brain to microgravity stress has been reviewed and reported. Identifying microgravity-induced changes in the brain proteome may aid in understanding the impact of the microgravity environment on brain function. In our previous study we have reported changes in specific proteins under simulated microgravity in the hippocampus using proteomics approach. In the present study the profiling of the hypothalamus region in the brain was studied as a step towards exploring the effect of microgravity in this region of the brain. Hypothalamus is the critical region in the brain that strictly controls the pituitary gland that in turn is responsible for the secretion of important hormones. Here we report a 2-dimensional gel electrophoretic analysis of the mouse hypothalamus in response to simulated microgravity. Lowered glutathione and differences in abundance expression of seven proteins were detected in the hypothalamus of mice exposed to microgravity. These changes included decreased superoxide dismutase-2 (SOD-2) and increased malate dehydrogenase and peroxiredoxin-6, reflecting reduction of the antioxidant system in the hypothalamus. Taken together the results reported here indicate that oxidative imbalance occurred in the hypothalamus in response to simulated microgravity.     

MPTP慢性帕金森病小鼠纹状体差异蛋白质的研究

目的分离、鉴定MPTP诱导慢性帕金森病模型小鼠纹状体差异表达的蛋白质,对MPTP慢性PD动物模型的特异性蛋白质组进行初步探讨,为PD的发病机制提供一定的蛋白质组学依据。方法成功建立MPTP诱导慢性帕金森病小鼠模型,提取模型组和对照组小鼠脑纹状体蛋白质,分别以固相pH梯度等电聚焦为第一向,SDS-PAGE垂直电泳为第二向进行2-DE。图像分析软件PDQUEST8.0分析电泳图谱找出差异表达蛋白,运用MALDI-TOF MS质谱鉴定;其肽质量指纹图（PMF）经MS Fit检索。结果比较MPTP诱导慢性PD模型小鼠和正常对照小鼠纹状体二向电泳图,发现12个蛋白表达异常,最终鉴定出其中4个蛋白质：线粒体裂殖调节因子1（mitochondrial fission regulator 1）、类泛素样蛋白3前体（ubiquitin-like protein 3 precursor）表达下调;S100蛋白A10（proteinS100-A10）、Lin-7 homolog B为新出现点。结论初步鉴定出MPTP慢性PD模型小鼠纹状体部分差异表达蛋白,所发现4个表达异常的蛋白质与帕金森病线粒体的损伤和兴奋性神经毒性密切相关,与PD的发病机制相符,为深入研究帕金森病病理机制奠定了基础。     

原位鼻咽癌裸鼠模型血清蛋白质组学的研究

利用我室建立的原位鼻咽癌裸鼠模型,建立了稳定性较好的鼻咽癌裸鼠血清蛋白质2-DE方法,并比较了原位鼻咽癌裸鼠血清与对照组裸鼠血清蛋白质2-DE图谱之间的差异.与正常裸鼠血清比较,原位鼻咽癌裸鼠模型组血清增加了4个蛋白质点.利用MALDI-TOF质谱技术对血清差异蛋白点进行鉴定,发现SAA-1前体(serumamyloidA-1 protein precursor)在鼻咽癌裸鼠模型组血清中明显高表达,为寻找鼻咽癌血清生物标志物提供了有利的线索.     

Hydrophobic Interactions Stabilize the Basigin-MCT1 Complex

Previous reports demonstrated that monocarboxylate transporter-1 (MCT1) interacts with Basigin. It was hypothesized that the two proteins interact via the transmembrane domain of Basigin, specifically through the glutamate residue within the domain. We therefore sought to test this hypothesis and determine which amino acids of the Basigin protein are necessary for the interaction with MCT1. Probes consisting of the full-length putative transmembrane domain, as well as small regions of the domain, were generated for use in ELISA binding assays using endogenous mouse MCT1. Site directed mutagenesis of candidate residues was performed and probes were generated for ELISA analyses to determine the specific residues involved. The data suggest that hydrophobic residues at the N- and C-termini of the putative transmembrane domain of Basigin interact with MCT1, but the glutamate plays no role. The previously proposed hypothesis is partially correct, in that the putative transmembrane domain of Basigin does interact with MCT1.     

Evisceration of Mouse Vitreous and Retina for Proteomic Analyses

While the mouse retina has emerged as an important genetic model for inherited retinal disease, the mouse vitreous remains to be explored. The vitreous is a highly aqueous extracellular matrix overlying the retina where intraocular as well as extraocular proteins accumulate during disease.^1-3 Abnormal interactions between vitreous and retina underlie several diseases such as retinal detachment, proliferative diabetic retinopathy, uveitis, and proliferative vitreoretinopathy.^1,4 The relative mouse vitreous volume is significantly smaller than the human vitreous (Figure 1), since the mouse lens occupies nearly 75% of its eye.⁵ This has made biochemical studies of mouse vitreous challenging. In this video article, we present a technique to dissect and isolate the mouse vitreous from the retina, which will allow use of transgenic mouse models to more clearly define the role of this extracellular matrix in the development of vitreoretinal diseases.     

A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions

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Proteomic Characterization of Primary Mouse Hepatocytes in Collagen Monolayer and Sandwich Culture

Dedifferentiation of primary hepatocytes in vitro makes their application in long‐term studies difficult. Embedding hepatocytes in a sandwich of extracellular matrix is reported to delay the dedifferentiation process to some extent. In this study, we compared the intracellular proteome of primary mouse hepatocytes (PMH) in conventional monolayer cultures (ML) to collagen sandwich culture (SW) after 1 day and 5 days of cultivation. Quantitative proteome analysis of PMH showed no differences between collagen SW and ML cultures after 1 day. Glycolysis and gluconeogenesis were strongly affected by long‐term cultivation in both ML and SW cultures. Interestingly, culture conditions had no effect on cellular lipid metabolism. After 5 days, PMH in collagen SW and ML cultures exhibit characteristic indications of oxidative stress. However, in the SW culture the defense system against oxidative stress is significantly up‐regulated to deal with this, whereas in the ML culture a down‐regulation of these important enzymes takes place. Regarding the multiple effects of ROS and oxidative stress in cells, we conclude that the down‐regulation of these enzymes seem to play a role in the loss of hepatic function observed in the ML cultivation. In addition, enzymes of the urea cycle were clearly down‐regulated in ML culture. Proteomics confirms lack in oxidative stress defense mechanisms as the major characteristic of hepatocytes in monolayer cultures compared to sandwich cultures. J. Cell. Biochem. 119: 447–454, 2018. © 2017 Wiley Periodicals, Inc.     

Genetic Interactions between the Members of the SMN-Gemins Complex in Drosophila

The SMN-Gemins complex is composed of Gemins 2–8, Unrip and the survival motor neuron (SMN) protein. Limiting levels of SMN result in the neuromuscular disorder, spinal muscular atrophy (SMA), which is presently untreatable. The most-documented function of the SMN-Gemins complex concerns the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). Despite multiple genetic studies, the Gemin proteins have not been identified as prominent modifiers of SMN-associated mutant phenotypes. In the present report, we make use of the Drosophila model organism to investigate whether viability and motor phenotypes associated with a hypomorphic Gemin3 mutant are enhanced by changes in the levels of SMN, Gemin2 and Gemin5 brought about by various genetic manipulations. We show a modifier effect by all three members of the minimalistic fly SMN-Gemins complex within the muscle compartment of the motor unit. Interestingly, muscle-specific overexpression of Gemin2 was by itself sufficient to depress normal motor function and its enhanced upregulation in all tissues leads to a decline in fly viability. The toxicity associated with increased Gemin2 levels is conserved in the yeast S. pombe in which we find that the cytoplasmic retention of Sm proteins, likely reflecting a block in the snRNP assembly pathway, is a contributing factor. We propose that a disruption in the normal stoichiometry of the SMN-Gemins complex depresses its function with consequences that are detrimental to the motor system.     

Proteomic Analysis of Clathrin Interactions in Trypanosomes Reveals Dynamic Evolution of Endocytosis

Endocytosis is a vital cellular process maintaining the cell surface, modulating signal transduction and facilitating nutrient acquisition. In metazoa, multiple endocytic modes are recognized, but for many unicellular organisms the process is likely dominated by the ancient clathrin‐mediated pathway. The endocytic system of the highly divergent trypanosomatid Trypanosoma brucei exhibits many unusual features, including a restricted site of internalization, dominance of the plasma membrane by GPI‐anchored proteins, absence of the AP2 complex and an exceptionally high rate. Here we asked if the proteins subtending clathrin trafficking in trypanosomes are exclusively related to those of higher eukaryotes or if novel, potentially taxon‐specific proteins operate. Co‐immunoprecipitation identified twelve T. brucei clathrin‐associating proteins (TbCAPs), which partially colocalized with clathrin. Critically, eight TbCAPs are restricted to trypanosomatid genomes and all of these are required for robust cell proliferation. A subset, TbCAP100, TbCAP116, TbCAP161 and TbCAP334, were implicated in distinct endocytic steps by detailed analysis of knockdown cells. Coupled with the absence of orthologs for many metazoan and fungal endocytic factors, these data suggest that clathrin interactions in trypanosomes are highly lineage‐specific, and indicate substantial evolutionary diversity within clathrin‐mediated endocytosis mechanisms across the eukaryotes.     

Proteomic Analysis of the Multimeric Nuclear Egress Complex of Human Cytomegalovirus

Herpesviral capsids are assembled in the host cell nucleus before being translocated into the cytoplasm for further maturation. The crossing of the nuclear envelope represents a major event that requires the formation of the nuclear egress complex (NEC). Previous studies demonstrated that human cytomegalovirus (HCMV) proteins pUL50 and pUL53, as well as their homologs in all members of Herpesviridae, interact with each other at the nuclear envelope and form the heterodimeric core of the NEC. In order to characterize further the viral and cellular protein content of the multimeric NEC, the native complex was isolated from HCMV-infected human primary fibroblasts at various time points and analyzed using quantitative proteomics. Previously postulated components of the HCMV-specific NEC, as well as novel potential NEC-associated proteins such as emerin, were identified. In this regard, interaction and colocalization between emerin and pUL50 were confirmed by coimmunoprecipitation and confocal microscopy analyses, respectively. A functional validation of viral and cellular NEC constituents was achieved through siRNA-mediated knockdown experiments. The important role of emerin in NEC functionality was demonstrated by a reduction of viral replication when emerin expression was down-regulated. Moreover, under such conditions, reduced production of viral proteins and deregulation of viral late cytoplasmic maturation were observed. Combined, these data prove the functional importance of emerin as an NEC component, associated with pUL50, pUL53, pUL97, p32/gC1qR, and further regulatory proteins. Summarized, our findings provide the first proteomics-based characterization and functional validation of the HCMV-specific multimeric NEC.Viruses are tightly linked to the regulatory processes governing the metabolic state of their host cells. This regulatory linkage is reflected by viral activation or silencing of gene expression and productive replication in response to cellular changes in signaling, cell cycle, apoptosis, differentiation, and other parameters. Viruses also tend to exert a strong influence on regulatory cellular pathways and the developmental fate of virus-infected tissues (1, 2). These examples of virus-cell interregulation have been studied in detail, but in many cases the essential molecular mechanisms are still poorly understood. In the field of herpesviruses, profound efforts in molecular research have been undertaken to characterize those direct protein–protein interactions that regulate cross-talk between the virus and its host. Multi-protein complexes composed of both viral and cellular constituents were identified in several stages of herpesviral lytic replication. In particular, detailed studies on the replication of human cytomegalovirus (HCMV)¹ in primary fibroblasts and other permissive cell types have provided very interesting insights into the nature of chimeric multi-protein complexes. These examples were described for viral entry, viral response to intrinsic immunity, intracellular transport of viral products, nucleocytoplasmic egress of viral capsids, and other processes (3–6). In classical approaches, protein–protein interaction was studied by means of approved methods including yeast two-hybrid, coimmunoprecipitation (CoIP), and pulldown analyses with purified proteins. More recently, very sensitive methods have been introduced into this field, such as proteomic analysis using tandem mass spectrometry (MS/MS), confocal imaging techniques, surface plasmon resonance analysis, and others.During HCMV replication, the translocation of genome-containing viral capsids from the nucleus to the cytoplasm (nuclear egress) is one of the most crucial steps. In this process, the nuclear envelope represents a barrier consisting of three distinct elements: nuclear membranes, nuclear pores, and the proteinaceous network of the nuclear lamina. The viral capsids traverse the nuclear envelope by budding through nuclear membranes. Importantly, HCMV capsids access the inner nuclear membrane by overcoming the proteinaceous network of the nuclear lamina. To regulate the serial steps in this procedure, a multimeric protein complex is formed, termed the nuclear egress complex (NEC) (4, 7). One of the main tasks of the NEC is the distortion of the nuclear lamina. Our recent studies identified the formation of lamina-depleted areas that result from the recruitment of sophisticated enzymatic activities to these specific sites at the lamina (8). Viral and cellular effectors, such as protein kinases, a proline cis/trans isomerase, and possibly further regulatory proteins, are involved in this process (4). It is commonly accepted that the core NEC is composed of two viral proteins, namely, pUL50 and pUL53 (9–13). Moreover, the association of pUL50–pUL53 with a number of viral and cellular proteins supports the concept of a multimeric NEC that may include the viral protein kinase pUL97, multi-ligand binding protein p32/gC1qR, lamin B receptor, and protein kinase C (PKC) (14).In this work, we first confirmed the major role played by pUL50 and pUL53 in NEC formation. The pUL50–pUL53 core NEC was then used as bait for the identification of other NEC components at different time points post-infection. Quantitative MS-based proteomics confirmed known members of the multimeric NEC and also identified the cellular inner nuclear membrane protein emerin as a novel NEC constituent. Importantly, colocalization of emerin with the HCMV-specific NEC and its interaction with pUL50 were demonstrated for the first time. Knockdown experiments provided functional validation of the importance of emerin and other NEC proteins for HCMV replication. Together, these data provide an extended mechanistic model for the composition and function of the HCMV-specific NEC.