蛋白质亚细胞定位预测中的序列编码技术

蛋白质序列的编码是亚细胞定位预测问题中的关键技术之一。该文较为详细地介绍了目前已有的蛋白质序列编码算法;并指出了序列编码中存在的一些问题及可能的发展方向。     

荧光蛋白标签对gD囊膜蛋白在BHK-21细胞亚细胞定位的影响

【目的】探究荧光蛋白标签对马疱疹病毒I型(Equine herpes virus type 1,EHV-1)gD囊膜蛋白亚细胞定位的影响。【方法】以EHV-1基因组为模板利用PCR扩增gD全基因,分别克隆至pAcGFP1-C1和p Ds Red2-N1质粒,构建p Ac-GFP-gD(GFP-gD)和p Ds-gD-Red(gD-Red)重组质粒;将GFP基因插入gD基因信号肽序列之后并克隆至PVAX-1质粒,构建PVAX-S-GFP-gD’(S-GFP-gD’)重组质粒;将Flag标签序列与gD囊膜蛋白N端序列融合后并克隆至p VAX-1表达载体,构建p VAX-Flag-gD(Flag-gD)重组质粒。将4种不同重组真核表达质粒分别转染BHK-21细胞,通过激光共聚焦显微镜对不同融合蛋白gD进行亚细胞定位。【结果】成功构建4种不同的融合蛋白gD真核表达载体;在BHK-21细胞单独表达时,不同融合蛋白gD绝大部分都定位于高尔基体,极少量定位于细胞核内。【结论】不同插入位点的荧光蛋白标签对gD囊膜蛋白亚细胞定位无明显影响,这对今后研究其它蛋白亚细胞定位提供参考。     

Comprehensive studies on subcellular localizations and cell death-inducing activities of eight GFP-tagged apoptosis-related caspases

By using green fluorescent protein fusion, we investigated the subcellular localization of all the caspases that have been cloned from humans and implicated in the execution of apoptosis. We divided these caspases into three groups according to subcellular localization. The first group includes caspase-1, -3, -6, -7, and -9, which are expressed mainly in the cytoplasm with various levels of nuclear localization depending on the cell type. The second group has a single member, caspase-2, which is primarily localized in the nucleus. The nuclear localization was demonstrated to be mediated by a nuclear localization signal near the NH(2)-terminus of the prodomain. The third group includes caspase-8 and -10, which have a cytoplasmic distribution. These two members have potent, rapid cell death-inducing activity and are prone to make aggregates when overexpressed. Their prodomains formed marked fibrous structures in the cytoplasm whose localization seemed distinct from organelles or cytoskeletons. None of the GFP-caspases examined in this study showed a predominant mitochondrial localization as has been reported for some caspases.     

三套荧光显微成像系统在光敏剂亚细胞定位研究中的应用比较

目的：对三套荧光显微成像系统在国产新型光敏剂HMME亚细胞定位研究中的应用特点及适用范围进行了比较与评价。方法：分别应用LSCM、CCD、ICCD荧光显微成像系统,选择特异性细胞器荧光探针Rhodamine-123、DIOC6(3)标记细胞内线粒体和内质网。采用细胞器-细胞荧光强度比值法,对HMME进行单细胞内分布的定性与定量研究。结果：LSCM和CCD成像系统能采集到浓度达到160μg／ml时的HMME的荧光图像,获得荧光探针图像信息显示所标记的细胞内线粒体和内质网平均荧光强度比值(J1/J2值)都明显高于细胞内J1/J2值。而ICCD成像系统只需HMME浓度为5μg/ml,荧光图像特点都呈胞浆中荧光强度较高且分布不均,细胞核区荧光较弱的中空现象。ICCD系统对细胞器探针荧光图像在空间分辨上不理想。结论：LSCM与CCD成像系统限于其探测灵敏度,对于弱荧光性光敏剂,适用于其高孵育浓度条件下的亚细胞定位研究。二者获得的结果相一致：孵育24h,HMME在鼠肺内皮细胞线粒体和内质网有分布而几乎不进入细胞核。ICCD成像系统可不受孵育浓度条件的限制,实现光敏剂极微弱荧光的有效探测,但空间分辨率较低。     

Expression,subcellular localization and protein‑protein interaction of four isoforms of EcR/USP in the common cutworm

Ecdysone receptor (EcR) and ultraspiracle (USP) form heterodimers to mediate ecdysteroid signaling during molting and metamorphosis. Various EcR/USP heterodimers have been reported. However, it is unclear what kind of EcR/USP combination is adopted by lepidopteran insects during the larval?pupal metamorphosis and whether the EcR/USP heterodimer varies among different tissues. To address these questions, two isoforms of each EcR and USP were cloned from the common cutworm, their messenger RNA expression patterns were examined by real‐time quantitative polymerase chain reaction in different tissues during the larval–pupal metamorphosis and in the midgut in response to hormonal induction. Furthermore, their subcellular localization and protein?protein interaction were explored by transient expression and far‐western blotting, respectively. All the four genes were significantly up‐regulated in prepuae and/or pupae. The expression profiles of EcRB1 and USP1 were nearly identical to each other in the epidermis, fat body and midgut, and a similar situation also applied to EcRA and USP2. The three genes responded to 20‐hydroxyecdysone (20E) induction except for USP2, and USP1 could be up‐regulated by both 20E and juvenile hormone. The four proteins mainly localized in the nucleus and the nuclear localization was promoted by 20E. The protein?protein interaction between each EcR and USP was found in vitro. These results suggest that two types of EcR/USP heterodimer (EcRA/USP2 and EcRB1/USP1) may exist simultaneously in the common cutworm, and the latter should play more important roles during the larval?pupal metamorphosis. In addition, the types of EcR/USP heterodimer do not vary in the tissues which undergo histolysis and regeneration during metamorphosis.     

Activity and subcellular distribution of protein kinase C (PKC) in muscle and brain of force-fed zinc-deficient rats

The purpose of the present study was to investigate, in force-fed rats, whether alimentary zinc (Zn) deficiency affects the activity of the Zn-metalloenzyme protein kinase C (PKC). The in vivo activity of PKC was determined by measuring the subcellular distribution of the enzyme between the cytosolic and the particulate fraction in brain and muscle. For this purpose, 24 male Sprague-Dawley rats with an average live mass of 126 g were divided into 2 groups of 12 animals each. The Zn-deficient and the control rats received a semisynthetic casein diet with a Zn content of 1.2 and 24.1 ppm, respectively. All animals were fed four times daily by gastric tube in order to ensure that the depleted animals also received adequate nutrients and to synchronize the feed intake exactly. After 12 d, the depleted rats were in a state of severe Zn deficiency, as demonstrated by a 70% lower serum Zn concentration and a 66% reduction in the serum activity of alkaline phosphatase. Neither the cytosolic nor the particulate fraction of the thigh muscle showed any difference between the depleted and the control animals as regards PKC activity/g of muscle. The specific activity of PKC/mg of protein in the cytosolic fraction of the muscle was not affected by alimentary zinc deficiency, whereas the specific activity of PKC in the particulate fraction of the muscle was reduced by a significant 10% in Zn deficiency (150±12 vs 135±14 pmol P/min/mg protein). In the brain, neither the cytosolic nor the particulate fraction revealed any difference in PKC activity/g of fresh weight or in the specific activity/mg of protein between the control and the Zn-deficient rats.     

Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences

Eukaryote peroxisomes, plant glyoxysomes and trypanosomal glycosomes belong to the microbody family of organelles that compartmentalise a variety of biochemical processes. The interaction between the PTS1 signal and its cognate receptor Pex5 initiates the major import mechanism for proteins into the matrix of these organelles. Relying on the analysis of amino acid sequence variability of known PTS1-targeted proteins and PTS1-containing peptides that interact with Pex5 in the yeast two-hybrid assay, on binding site studies of the Pex5-ligand complex crystal structure, 3D models and sequences of Pex5 proteins from various taxa, we derived the requirements for a C-terminal amino acid sequence to interact productively with Pex5. We found evidence that, at least the 12 C-terminal residues of a given substrate protein are implicated in PTS1 signal recognition. This motif can be structurally and functionally divided into three regions: (i) the C-terminal tripeptide, (ii) a region interacting with the surface of Pex5 (about four residues further upstream), and (iii) a polar, solvent-accessible and unstructured region with linker function (the remaining five residues). Specificity differences are confined to taxonomic subgroups (metazoa and fungi) and are connected with amino acid type preferences in region 1 and deviating hydrophobicity patterns in region 2.     

Investigation of selenium distribution in subcellular fractions of human liver by neutron activation analysis

Selenium is an important and essential trace element to living systems. In the article, two methods of instrumental neutron activation analysis and hydride generation-atomic fluorescence spectrometry were applied to determine Se in biological samples and the accuracy was evaluated by several reference materials. The subcellular distribution of selenium in human liver samples, which were obtained from normal subjects who had an accidental death, was investigated by differential centrifugation combined with INAA. Selenium was mainly enriched in mitochondria, nuclei, and cytosol. Almost half of the total Se content existed in nuclei as a result of the large amount in liver and the high Se concentration. Generally, the highest Se concentration in the mitochondrial fractions of each liver sample suggested that Se had important functions in this liver component.     

Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect.

Support Vector Machine (SVM), which is one class of learning machines, was applied to predict the subcellular location of proteins by incorporating the quasi-sequence-order effect (Chou [2000] Biochem. Biophys. Res. Commun. 278:477-483). In this study, the proteins are classified into the following 12 groups: (1) chloroplast, (2) cytoplasm, (3) cytoskeleton, (4) endoplasmic reticulum, (5) extracellular, (6) Golgi apparatus, (7) lysosome, (8) mitochondria, (9) nucleus, (10) peroxisome, (11) plasma membrane, and (12) vacuole, which account for most organelles and subcellular compartments in an animal or plant cell. Examinations for self-consistency and jackknife testing of the SVMs method were conducted for three sets consisting of 1,911, 2,044, and 2,191 proteins. The correct rates for self-consistency and the jackknife test values achieved with these protein sets were 94 and 83% for 1,911 proteins, 92 and 78% for 2,044 proteins, and 89 and 75% for 2,191 proteins, respectively. Furthermore, tests for correct prediction rates were undertaken with three independent testing datasets containing 2,148 proteins, 2,417 proteins, and 2,494 proteins producing values of 84, 77, and 74%, respectively.     

Expression of EGFP/SDCT1 fusion protein, subcellular localization signal analysis, tissue distribution and electrophysiological function study

A main pathway for energy ATP production inhuman body is by tricarboxylic acid cycle (Krebs cy-cle). Sodium-dependent dicarboxylate co-transporterprotein (SDCT, NaDC, NaC) is an organic aniontransporter protein family responsible for trans-mem- for 30 s, and extension 72℃ for 2 min; followed bybrane transport of Krebs cycle intermediate metabolite final extension 72℃ for 7 min. PCR products weresuch as succinate and citrate. They predominantly lo- …     

Kinase activity and subcellular distribution of a chimeric green fluorescent protein-tagged Janus kinase 2

Summary Janus kinase 2 (JAK2) is an essential intracellular signal transducer for numerous cytokines and hormones. To examine how JAK2 structural modifications can affect cellular physiology, we created expression vectors for chimeric proteins containing an enhanced green fluorescent protein (EGFP) fused to rat JAK2 (EGFP/rJAK2), and a kinase-inactive variant, EGFP/rJAK2(K882E). The properties of EGFP/rJAK2 were examined following transient transfection of COS-7 cells. EGFP/rJAK2 was expressed throughout the cell, and was found in subcellular membrane, cytosolic and nuclear fractions. Interestingly, EGFP/rJAK2 phosphorylated other proteins in situ without additional cytokine stimulation. Furthermore, despite a much higher level of tyrosine phosphorylation arising from in situ autophosphorylation, the in vitro radiolabelling autokinase activity of EGFP/rJAK2 was significantly less than that of the endogenous JAK2. These results reveal a technical limitation of the application of the “conventional” in vitro radiolabelling autokinase assay to hyperphosphorylated forms of the enzyme and illustrate the potential weaknesses in individual assays commonly used to determine JAK2’s enzymatic activity and subcellular distribution. We also suggest that the EGFP/rJAK2 model can be very useful in studying JAK2-related cancers, because its ubiquitous distribution and abnormal constitutive hyperphosphorylation may distinguish it from the cytokine-regulated, membrane-proximal form of JAK2 associated with normal physiology.     

The subcellular distribution of carotenoids in Neurospora crassa

The intracellular localization of carotenoids in the fungus Neurospora crassa was examined after completion of photoinduced biosynthesis of these pigments. Differential centrifugation of cell homogenates yielded subcellular fractions which were characterized by activities of several marker enzymes for cell constituents and in part purified by subsequent sucrose density gradient centrifugation. Most (ca 58%) of the carotenoids were found to be localized in lipid globules, but substantial amounts are also associated with two membrane fractions that were rich in membranes of the endoplasmic reticulum as indicated by high activities of NADPH- and NADH—cytochrome c reductase. These results, along with the coincidence in the distribution of both carotenoids and activities of specific marker enzymes in the sucrose density gradients, led to the conclusion that apart from lipid globules, carotenoids are also localized in membranes of the endoplasmic reticulum.     

两个大豆GmSBP基因的特征、亚细胞定位及对非生物胁迫的响应

我国南方春大豆种子发育过程中,常处于高温、高湿季节,加之种子本身富含蛋白(约40%)和脂肪(约20%),导致南方春大豆种子易劣变。本项目组前期差异蛋白质组学研究发现蔗糖结合蛋白在高温高湿胁迫168 h时在种子田间劣变抗性品种湘豆3号发育种子中呈下调表达。为进一步从分子水平了解Gm SBP基因表达以及响应高温高湿胁迫的特性,本研究利用RT-PCR技术从大豆扩增出两个Gm SBP基因(Gm SBP2和Gm SBPL)。两个基因编码的蛋白均为亲水性,不完整的膜蛋白。荧光定量PCR分析表明:在高温高湿条件下,种子田间劣变不抗品种宁镇1号和抗性品种湘豆3号发育种子中Gm SBP2和Gm SBPL基因表达量均受高温高湿胁迫影响,也会导致种子中蔗糖和可溶性糖含量变化。在籽粒发育过程中,Gm SBP2和Gm SBPL基因表达量在花后30 d左右达到最高,对应时期的蔗糖和可溶性糖含量也达到最大值。组织特异性显示Gm SBP和Gm SBPL基因在不同组织间存在差异表达。亚细胞定位结果表明Gm SBP2和Gm SBPL蛋白均定位在细胞膜和细胞质中。以上结果表明Gm SBP2和Gm SBPL基因可能参与了植物非生物胁迫的应答过程,这将从一个侧面丰富我们对大豆种子田间劣变性和劣变抗性的认识。     

Compartmentalization of membrane trafficking,glucose transport,glycolysis, actin,tubulin and the proteasome in the cytoplasmic droplet/Hermes body of epididymal sperm

Discovered in 1909 by Retzius and described mainly by morphology, the cytoplasmic droplet of sperm (renamed here the Hermes body) is conserved among all mammalian species but largely undefined at the molecular level. Tandem mass spectrometry of the isolated Hermes body from rat epididymal sperm characterized 1511 proteins, 43 of which were localized to the structure in situ by light microscopy and two by quantitative electron microscopy localization. Glucose transporter 3 (GLUT-3) glycolytic enzymes, selected membrane traffic and cytoskeletal proteins were highly abundant and concentrated in the Hermes body. By electron microscope gold antibody labelling, the Golgi trafficking protein TMED7/p27 localized to unstacked flattened cisternae of the Hermes body, as did GLUT-3, the most abundant protein. Its biogenesis was deduced through the mapping of protein expression for all 43 proteins during male germ cell differentiation in the testis. It is at the terminal step 19 of spermiogenesis that the 43 characteristic proteins accumulated in the nascent Hermes body.     

镉在互花米草中积累、转运及亚细胞的分布

研究了在不同Cd浓度(0、5、100、200μg·g-1)处理下,互花米草花序、叶、茎、根茎、须根中Cd含量、积累量、转运特征,及Cd在互花米草体内的亚细胞分布。结果表明,Cd在互花米草不同器官中的积累能力存在较大差异。茎、根茎、须根中Cd含量及积累量随处理浓度的增加而升高,其中须根中Cd含量及积累量均高于其他器官。Cd处理浓度为100gμ·g-1时,花序和叶中Cd含量达到最大值,分别为8.65和7.82μg·g-1。在Cd处理浓度为200μg·g-1时,须根中Cd含量可高达390.00μg·g-1,积累量达3200μg·株-1。Cd在互花米草体内转运能力极低,绝大部分Cd积累在地下部位。Cd在互花米草亚细胞中的分布规律为细胞壁>胞液>细胞器。随着Cd处理浓度的增加,Cd在细胞壁中的分配比例增大,胞液中Cd分布比例则相应减小,细胞壁和胞液相互协调,增强互花米草对重金属Cd的耐性。