一种利用荧光蛋白mNeonGreen2鉴定EI24蛋白拓扑结构的方法（英文）

方便且精准地检测跨膜蛋白拓扑结构,尤其是跨膜片段的氨基(N-)和羧基(C-)端的朝向,有利于发现新的蛋白质与蛋白质之间的相互作用,并进一步揭示蛋白质重要的生物学功能.自组装荧光蛋白已被广泛用于观察蛋白质与蛋白质之间的相互作用、标记细胞内源蛋白质并实现mRNA定位的可视化.本文扩展了自组装荧光蛋白的应用,将自组装荧光蛋白mNeonGreen2与定点标记技术相结合,以确定跨膜蛋白的拓扑结构.通过该方法,第一次清楚地证明了EI24的N端和C端均朝向细胞质方向.此外,该方法可用于确定定位于其他细胞器且结构尚未解析的跨膜蛋白的拓扑结构.     

α-螺旋跨膜蛋白拓扑结构预测方法的评价

在基因组数据中,有20%～30%的产物被预测为跨膜蛋白,本文通过对膜蛋白拓扑结构预测方法进行分析,并评价其结果,为选择更合适的拓扑结构预测方法预测膜蛋白结构。通过对目前已有的拓扑结构预测方法的评价分析,可以为我们在实际工作中提供重要的参考。比如对一个未知拓扑结构的跨膜蛋白序列,我们可以先进行是否含有信号肽的预测,参考Polyphobius和SignalP两种方法,若两种方法预测结果不一致,综合上述对两种方法的评价,Polyphobius预测的综合能力较好,可取其预测的结果,一旦确定含有信号肽,则N端必然位于膜外侧。然后结合序列的长度,判断蛋白是单跨膜还是多重跨膜,即可参照上述评价结果,选择合适的拓扑结构预测方法进行预测。     

枯草杆菌ylmK基因的荧光标记及Ylmk蛋白的亚细胞定位

目的：对枯草杆菌ylmK基因进行3’端荧光标记以便对其产物YlmK蛋白在菌体中的位置进行初步观察。方法：以BS168菌株基因组DNA为模板,PCR扩增ylmK基因的3’端序列,并将其克隆到载体pSGll64中,形成ylmK’-gfpmutl融合,构建重组载体pNC-424;将pNG424转化枯草杆菌168菌株,单交换形成完整的功能性3’端gfpmutl标记的ylmK基因,菌落PCR对阳性转化子BS362进行鉴定,用表面荧光显微镜技术对BS362进行观察。结果：荧光检测结果表明GFP标记的YlmK分布于菌体的外周,在位置上靠近细胞膜并与之平行排列。结论：YlmK是一种膜蛋白。     

拟南芥CAX1转运体蛋白的跨膜拓扑结构预测

目的：对拟南芥的CAX1蛋白进行跨膜结构预测,构建CAX1的跨膜结构模型。方法：以生物信息学工具Signal 3.0、Conpred Ⅱ、TMHMM 2.0、HMMTOP、MEMSAT3、ConPred2分析拟南芥CAX1蛋白的一级序列。结果：模型显示CAX1共有10个跨膜区,分别为氨基酸残基73-93,128-147,163-185,198-219,236-256,286-307,322-344,357-379,387-407,414-432。结论：与现有的资料相印证,此模型可以作为CAX1功能研究的参考模型。     

一种快速纯化蛋白的电洗脱方法

以TB24kDa蛋白为例介绍了一种快速纯化蛋白的电洗脱方法。根据作者实验室先前建立的提取苦荞种子蛋白的方法制备TB324kDa蛋白粗提物,利用阴离子交换层析和改进的电泳洗脱方法对其进行纯化。结果显示：经改进的电洗脱纯化,1mg粗蛋白町以回收得到150μg左右的目的蛋白,同收率为15．32％,纯化效果较理想。     

博尔纳病病毒p24重组蛋白的表达与初步鉴定

博尔纳病病毒(Borna Disease Virus,BDV)是一种嗜神经病毒.研究表明,BDV不仅可以引起马、羊等家畜的自然感染,从啮齿类动物到人以外的灵长类动物均易受到BDV的实验性感染,而且BDV感染还可能与人类的某些精神神经疾病的发生相关.本研究对含有BDV-p24重组质粒PGEX-3X的大肠杆菌表达系统进行了优化表达BDV-p24蛋白,在IPTG 2 mmol/L、3 h表达量最大,同时用BDV-p24单克隆抗体证实了其特异性.从而为建立检测待检血清中BDV-p24特异性抗体的方法提供了实验基础.     

荧光假单胞菌2P24中RstA蛋白的功能鉴定

探究荧光假单胞菌2P24中OmpR家族转录因子RstA的功能,明确其对EmhABC外排泵的调控作用及机制。利用共适应分析预测RstA的潜在功能;采用同源重组技术构建rstA、emhABC基因缺失菌株ΔrstA和ΔemhABC,检测野生型、ΔrstA、ΔemhABC对多种抗生素的敏感性;通过qRT-PCR和β-半乳糖苷酶实验检测emhABC在野生型和ΔrstA菌株中的转录、表达水平;表达纯化His-RstA蛋白并经凝胶阻滞实验检测RstA蛋白与emhABC基因启动子区域的结合活性。结果显示,RstA同EmhABC存在共适应性,并预测RstA与多种抗生素胁迫环境的适应相关;ΔrstA和ΔemhABC对多种抗生素耐受性下降;与野生株相比,突变株ΔrstA中emhABC的转录、表达水平均下降超过3倍;成功表达纯化His-RstA蛋白,经凝胶阻滞实验显示重组His-RstA蛋白可与emhABC基因启动子区域特异性结合。OmpR家族转录因子RstA通过结合在emhABC上游启动子区域正向调控EmhABC的表达,并影响荧光假单胞菌2P24的多重耐药性。     

ABC转运蛋白的结构与转运机制

腺苷三磷酸结合盒转运蛋白（ATP-binding cassette transponer,ABC转运蛋白）超家族是一组跨膜蛋白,具有ATP结合区域的单向底物转运泵,以主动转运方式完成多种分子的跨膜转运.ABC转运蛋白的一个亚家族与多药抗性（multidrug resistance,MDR）有关,而多药抗性是临床肿瘤化疗中需要解决的主要问题,所以其结构与转运机制一直是研究的热点.最近几年获得了一些高分辨率的ABC转运蛋白的晶体结构,该文将根据ABC转运蛋白的结构的研究进展对其可能的转运机制进行讨论.     

猪链球菌2型一种新的免疫原性蛋白的鉴定及特性分析

利用免疫蛋白组学方法,鉴定出链球菌2型(Streptococcus suis type2,SS2)江苏分离株HA9801具有免疫反应性的蛋白HM3。应用同源性比对、信号肽预测、跨膜区预测及亚定位预测等生物信息学方法对该蛋白进行分析,结果显示:同源性最高的蛋白为屎肠球菌胞外溶解物结合蛋白(41%);蛋白序列中含有信号肽结构;7-24位氨基酸为该蛋白的跨膜区;预测蛋白定位为除胞质外的未定位置。PCR扩增出该蛋白的一段基因定向克隆到表达载体pET-32a( )中并转化入BL21(DE3)宿主菌。重组菌经IPTG诱导后的SDS-PAGE图谱在46kDa处出现融合蛋白的条带。Westernblot表明,此融合蛋白可被SPF微型猪抗SS2血清所识别,提示该蛋白可作为该菌的亚单位疫苗的候选物。     

糖皮质激素与炎症因子对应急时相反应蛋白SIP24/24p3的协同调控作用及其意义

小鼠应急时相反应蛋白SIP24／24p3有抗炎症和特异性诱导白细胞凋亡的功能,其在体内的表达是高度特异性的。为研究SIP24／24p3的调控因子及机制,我们在小鼠Balb／c3T3和BNL细胞培养中通过灵敏的弱S代谢标记方法检测SIP24／24p3蛋白的表达水平,定量观测分析了糖皮质激素化合物dexamethasone对SIP24／24p3的诱导作用及其与炎症因子白介素6(IL-6)和肿瘤坏死因子α(TNF-α)的协同调控作用。结果显示：(1)在Balb／c3T3和BNL细胞中,dexamethasone对SIP24／24p3都有明显诱导作用,这种诱导作用在BNL细胞中尤其显著;(2)在Balb／c3T3和BNL细胞中dexamethasone与IL-6协同诱导SIP24／24p3;(3)在Balb／c 3T3细胞中dexamethasone与TNF-α对SIP24／24p3有协同诱导效应,而在BNL细胞中dexamethasone与TNF-α对SIP24／24p3的诱导表现为相加效应;(4)在Balb／c3T3和BNL细胞中dexamethasone与IL-6／TNF-α对SIP24／24p3的诱导分别表现出协同和相加效应。多种因子对SIP24／24p3的协同诱导调控有助于阐明其在体内的高度特异表达及机制,SIP24／24p3在不同细胞中的不同表达格局也对体内应急时相反应蛋白在肝脏外和肝脏内的表达方式及诱导机制有提示作用。SIP24／24p3能同时被炎症因子和抗炎症因子诱导的事实显示了其在炎症全过程中的重要作用。     

Transmembrane-Domain Trapping: A Novel Method for Isolation of cDNAs Encoding Putative Membrane Proteins

We have developed a method that enables us to isolate cDNAsof putative membrane proteins. The system is designed to isolatea cDNA which can provide the transmembrane domain to the extracellularpart of the IL-2 receptor chain. We constructed a p18Mac vectorby putting part of the IL-2 receptor chain cDNA that encodedits signal sequence and extracellular domain, a cDNA cloningsite and a poly(A) additional signal after a strong promoterSR. If a cloned cDNA provides a transmembrane domain in-frame,the extracellular domain of the IL-2 receptor chain will beexpressed on the surface of the transfected cells. Otherwise,the chimeric protein will be either secreted or retained insidethe transfected cells. We made a cDNA library using p18Mac andscreened for cDNA clones which allowed the expression of theextracellular domain of the IL-2 receptor chain on the cellsurface. Of the 2000 clones screened, 5 clones were scored aspositive. Partial sequence analysis revealed that one cloneencoded the amyloid precursor protein, two others encoded mitochondrialproteins and the rest were new. These results suggest the systemis effective in isolating cDNAs encoding putative membrane proteins.     

TMSEG: Novel prediction of transmembrane helices

Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bridged the gap by predicting transmembrane helices (TMHs), but room for improvement remains. Here, we present TMSEG, a novel method identifying TMPs and accurately predicting their TMHs and their topology. The method combines machine learning with empirical filters. Testing it on a non‐redundant dataset of 41 TMPs and 285 soluble proteins, and applying strict performance measures, TMSEG outperformed the state‐of‐the‐art in our hands. TMSEG correctly distinguished helical TMPs from other proteins with a sensitivity of 98 ± 2% and a false positive rate as low as 3 ± 1%. Individual TMHs were predicted with a precision of 87 ± 3% and recall of 84 ± 3%. Furthermore, in 63 ± 6% of helical TMPs the placement of all TMHs and their inside/outside topology was correctly predicted. There are two main features that distinguish TMSEG from other methods. First, the errors in finding all helical TMPs in an organism are significantly reduced. For example, in human this leads to 200 and 1600 fewer misclassifications compared to the second and third best method available, and 4400 fewer mistakes than by a simple hydrophobicity‐based method. Second, TMSEG provides an add‐on improvement for any existing method to benefit from. Proteins 2016; 84:1706–1716. © 2016 Wiley Periodicals, Inc.     

TMED2受miR-5583-5p调控在舌鳞状细胞癌细胞中发挥癌基因作用

舌鳞状细胞癌(tongue squamous cell carcinoma, TSCC)是口腔鳞状细胞癌(oral squamous cell carcinoma, OSCC)中最常见类型,其发病率和死亡率都较高。大量研究表明,microRNA(miRNA)是一类小非编码RNA,可调节靶基因的转录后处理,导致靶mRNA的降解及翻译抑制。然而,关于跨膜p24转运蛋白2(transmembrane p24 trafficking protein 2, TMED2)受miR-5583-5p调控对TSCC细胞Cal-27迁移、侵袭、增殖及上皮间充质转化(epithelial-mesenchymal transition, EMT)能力影响尚不明确。本研究利用数据库,分析TMED2高表达头颈部肿瘤(head and neck cancer, HNC)病人愈后不良,在HNSCC组织中的表达升高(P<0.001)。Western 印迹结果表明,在6例TSCC组织及TSCC细胞系SCC-9、SCC-25和Cal-27中,TMED2蛋白质表达量较癌旁组织及口腔正常上皮细胞中上调,转染TMED2干扰质粒(SiTMED2)的Cal-27细胞中TMED2蛋白质表达量降低,E-钙黏着蛋白(E-cadherin)表达上调,而N-钙黏着蛋白(N-cadherin)和波形蛋白(vimentin)表达下调。迁移与侵袭结果发现,转染SiTMED2的Cal-27细胞穿过小室基底膜细胞数量均低于对照组(P<0.05)。EdU结果显示,转染SiTMED2的Cal-27细胞增殖能力降低(P<0.05)。双荧光素酶结果显示,TMED2存在与miR-5583-5p的结合靶点。荧光定量RT-PCR结果显示,miR-5583-5p在Cal-27细胞中表达量较Hoec细胞中下降,转染过表达miR-5583-5p质粒的Cal-27细胞其表达量升高(P<0.05),过表达miR-5583-5p(miR-5583-5p mimics)后TMED2蛋白表达水平降低(P<0.05)。综上所述,TMED2受miR-5583-5p调控促进舌鳞状细胞癌细胞Cal-27迁移、侵袭、增殖及上皮间充质转化的发生。     

A proteomic approach to identification of transmembrane proteins and membrane-anchored proteins of Arabidopsis thaliana by peptide sequencing.

A proteomic approach was developed for the identification of membrane-bound proteins of Arabidopsis thaliana. A subcellular fraction enriched in vacuolar membranes was prepared from 4-week-old plants and was washed with various agents to remove peripheral membrane proteins and contaminating soluble proteins. The remaining membrane-bound proteins were then subjected to proteomic analysis. Given that these proteins were resolved poorly by standard two-dimensional gel electrophoresis, we subjected them instead to SDS-polyacrylamide gel electrophoresis and to protein digestion within gel slices with lysylendopeptidase. The resulting peptides were separated by reverse-phase high-performance liquid chromatography and subjected to Edman sequencing. From the 163 peptide peaks analyzed, 69 peptide sequences were obtained, 64 of which were informative. The proteins corresponding to these peptide sequences were identified as belonging to 42 families, including two subfamilies, by comparison with the protein sequences predicted from annotation of the A. thaliana genome. A total of 34 proteins was identified definitively with protein-specific peptide sequences. Transmembrane proteins detected in the membrane fraction included transporters, channels, receptors, and unknown molecules, whereas the remaining proteins, categorized as membrane-anchored proteins, included small GTPases, GTPase binding proteins, heat shock protein 70-like proteins, ribosomal proteins, and unknown proteins. These membrane-anchored proteins are likely attached to membranes by hydrophobic anchor molecules or through tight association with other membrane-bound proteins. This proteomic approach has thus proved effective for the identification of membrane-bound proteins.     

Autocrine GM-CSF transcription in the leukemic progenitor cell line KG1a is mediated by the transcription factor ETS1 and is negatively regulated through SECTM1 mediated ligation of CD7

Background

CD7 expression is found on ~ 30% of acute myeloblastic leukemias (AML). The leukemic progenitor cell line KG1a (CD7 +) constitutively expresses GM-CSF while the parental KG1 (CD7-) cell line does not. This study focuses on the molecular basis of CD7 mediated GM-CSF regulation.

Methods

KG1a cells were treated with recombinant SECTM1-Fc protein, the PI3K kinase inhibitors wortmannin, LY292004, or PI4K activator spermine. Stable KG1-CD7 +, KG1a-shCD7, KG1a-shETS1 as well as KG1a-GFP, KG1a-PKCβII-GFP cell lines were generated and the levels of CD7, GM-CSF and ETS-1 mRNA and protein were compared by real-time-PCR, western blotting, flow cytometry and ELISA.

Results

SECTM1 is expressed in Human Bone Marrow Endothelial Cells (HBMEC) and its expression can be upregulated by both IFN-γ. KG1a cells demonstrated high expression levels of CD7 and ETS-1 allowing a constitutative signaling through the PI3K/Atk pathway to promote GM-CSF expression, while KG1 cells with low expression of CD7 and ETS-1 showed low GM-CSF expression. On KG1a cells GM-CSF expression could be negatively regulated by PI3K inhibitors or by recombinant SECTM1-Fc. Overexpression of CD7 in KG1 cells was insufficient to promote GM-CSF expression, while silencing of CD7 or ETS-1 resulted in reduced GM-CSF expression levels. Differentiation capable KG1a cells overexpressing PKCβII illustrated complete loss of CD7, but maintained normal levels of both ETS-1 and GM-CSF expression.

Conclusion

These findings add an additional layer to the previously described autocrine/paracrine signaling between leukemic progenitor cells and the bone marrow microenvironment and highlight a role for SECTM1 in both normal and malignant hematopoiesis.

General Significance

This work shows that SECTM1 secreted from bone marrow stromal cells may interact with CD7 to influence GM-CSF expression in leukemic cells.