Temperate Stutzerimonas Phage Encoding Toxin-Antitoxin System Genes Represents a Novel Genus

Stutzerimonas have been extensively studied due to their remarkable metabolic and physiological diversity.However,research on its phages is currently limited.In this study,we isolated a novel double-stranded DNA(dsDNA)phage,vB_SstM-PG1,from the marine environment that infects Stutzerimonas stutzeri G1.Its dsDNA genome is 37204 bp long with a G/C content of 64.14%and encodes 54 open reading frames.The phage possesses a tail packaging structure that is different from known Stutzerimonas stutzeri phages and exhibits structural protein characteristics similar to those of temperate phages.In addition,two genes of toxin-antitoxin system,including YdaS_antitoxin and HEPN_SAV_6107,were found in the vB_SstM-PG1 genome and play important roles in regulating host growth and metabolism.With phylogenetic tree and comparative genomic analysis,it has been determined that vB_SstM-PG1 is not closely related to any phages previously identified in the GenBank database.Instead,it has a connection with enigmatic,uncultured viruses.Specifically,the vB_SstM-PG1 virus exhibits an average nucleotide identity of over 70%with six uncultivated viruses identified in the IMG/VR v4 database.This significant finding has resulted in the identification of a novel viral genus known as Metabovirus.

一株新型杀鲑气单胞菌烈性类T4噬菌体Asfd-1的分离鉴定和生物学特性分析

噬菌体是自然界中最普遍的生物之一,其专一性裂解细菌的能力在针对耐药菌感染治疗方面具有很大的应用前景。杀鲑气单胞菌(Aeromonas salmonicide)是水产养殖业中一种主要病原菌,其引发的疖疮病是一种常见的水产养殖动物疾病,具有高死亡率和高发病率,一旦爆发,将给水产养殖业带来重大的经济损失。该研究以杀鲑气单胞菌MF663675.1为宿主菌,从深圳海鲜市场的污水中,采用双层琼脂平板法分离纯化得到单个噬菌体,通过电镜对其表观形态特征进行观察,并运用生物信息的方法进一步确定其基因型特征及遗传分类地位。研究结果表明,分离出的烈性噬菌体命名为Asfd-1,噬菌斑呈圆形,轮廓分明、透明,直径约1mm。电镜观察显示,Asfd-1具有对称的二十面体头部,以及长度为51 nm的收缩尾部。基因组测序和基因对比分析表明,Asfd-1含双链脱氧核糖核酸(dsDNA),全基因组大小为168 962 bp,鸟嘌呤(G)和胞嘧啶(C)所占的比例为41.53%,共编码263个开放阅读框和16个转移核糖核酸(tRNA)序列,Genbank登录号为MK577502。根据国际病毒分类委员会规定的病毒分类方法,与同源的Aeromonas phage 31 GCA_000862645.1和Aeromonas phiSA4GCA_002710125.1全基因组对比结果显示,Asfd-1是新型噬菌体。综合电镜观察结果及系统进化树分析,Asfd-1属于肌尾科下的T4噬菌体属、肌尾噬菌体科、有尾噬菌体目的新成员。该研究可为应用噬菌体治疗细菌感染提供进一步的参考。

Screening of Proteins Interacting with Nonstructural 1 Protein of H5N1 Avian Influenza Virus from T7-phage Display Library

Avian influenza virus（AIV） nonstructural 1（NS1） gene was amplified by real-time polymerse chain reac tion（RT-PCR） and inserted into pET28a, then transformed into E. coli BL21（DE3） competent cell. With the induction of isopropyl-β-D-thiogalactoside（IPTG） and the purification of Ni-NTA column, we finally obtained purified NS1 protein. T7-phage display system was used to screen the proteins that interacted with NS1 from lung cell cDNA li brary. The selected positive clones were identified by DNA sequencing and analyzed by BLAST program in Gene Bank. Two proteins were obtained as NS1 binding proteins, Homo sapiens nucleolar and coiled-body phosphoprotein 1（NOLC1） and Homo sapiens similar to colon cancer-associated antigen. By co-immunoprecipitation and other me thods, Homo sapiens NOLC1 was found to interact with the NS1 protein, the results would provide the basis for fur ther studying biological function of NS1 protein.

Screening and Identification of a Targeting Peptide to nGLP-1R from Phage Display Peptide Library

In order to provide the structure information for designing new exendin-4 analogues, a phage display peptide library was screened by targeting the N-terminal extracellular domain of GLP-1R（nGLP-1R）. After four rounds of selection, nine sequences were obtained, four of them have higher affinity for nGLP-1R than the others. We chose two of them named X and Y peptides. Islet β-cell proliferation assay suggested that X and Y peptides didn＇t have any activity to increase islet β-cell proliferation. In other words, X and Y peptides were not agonists to GLP-1R. However, the conservative motifs of X and Y peptides provided us useful information to design new exendin-4 analogues.

Identification and Characterization of Peptides Binding AgEG1 from a Phage Display Library

Endoglucanases are the main cellulolytic enzymes digestion as well as its good kinetic properties make it an attractive of Anoplophora glabripennis. Their high activities in cellulose target for development of cellulase inhibitors. In this study, random pepfide phage display technology was employed to identify peptides that bound the AgEG1, a member of endoglucanase isozymes. Phage clones with peptide LPPNPTK and XPP （X is residue T, L, A or H） motif frequently occurred in the selected phage population and showed a higher phage recovery than other clones. Peptide LPPNPTK was chemically synthesized and characterized tor its binding activities to AgEG1. The synthetic peptide exhibited high specificity for AgEG1. The peptide LPPNPTK has the potential to be developed into inhibitors of the endoglucanase of A. glabripennis.

The Structural Proteins of Bdellovibrio bacteriovorus Bacteriophage MAC-1

In the present investigation the structural proteins associated with MAC-1 bacteriophage have been characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE);tandem mass spectrometry of protein bands from SDS-PAGE gel;from the open reading frames (ORFs) deduced from MAC-1 genome sequence and amino acid sequence homology searches from the Uniprot database (up000002418). Results have led to the identification of at least three structural proteins associated with MAC-1 phage genome. They are: capsid protein (~55,000-daltons);spike protein (~22,000-daltons) and a low molecular weight DNA binding protein (~4000-dal- tons). In addition, two other minor proteins were tentatively identified as replicative and scaffold proteins based on two to three unique peptides from mass spectrometry data. However, other proteins coded (ORFs) by phage genome remain to be identified.

Biological Effects of Chlamydiaphage phi CPG1 Capsid Protein Vp1 on Chlamydia Trachomatis In Vitro and In Vivo

The researches on chlamydia in recent years show that chlamydia bacteriophage may be a potential and effective means to solve the clinical infection of chlamydia trachomatis（Ct）. We investigated the biological effect of chlamydiaphage phi CPG1 capsid protein Vp1 on Ct both in Mc Coy cells and genital tract of mice. Different concentrations of Vp1 were co-incubated with Ct E serotype strain in Mc Coy cells. Female BALB/c mice were used to establish Ct E strain-induced urogenital infection model. They were randomly divided into five groups and given different treatments on the fifth day after Ct inoculation. Animals in groups 1 and 2 were given 30 μL different concentrations of Vp1 in the genital tract respectively, those in group 3 were intramuscularly injected with 30 μL Vp1, those in the infected group did not receive any intervention, and those in the control group received 30 μL PBS in the genital tract. The vaginal discharge was collected to identify the live chlamydia by cell culture and gene fragment by real time PCR different days after infection. Inhibition rate of 100 μg/m L and 50 μg/m L Vp1 proteins against Ct E strain in the Mc Coy cell cultures was 91% and 79% respectively. The number of intracellular Ct inclusion in the Mc Coy cells co-cultured with vaginal discharge of group 1 and group 2 was less than in the infected group, and that in group 1 was less than in group 2, on the 7th day after Ct inoculation. Real-time PCR showed that chlamydia concentration of the vaginal discharge in group 2 was lower than in the infected group, and that in group 1 was lower than in group 2 on the 10 th day. It was suggested that Vp1 capsid proteins had inhibitory effect on the proliferation of Ct serovar E strain in cell culture and mouse genital tract.

MAPPING EPITOPES OF HUMAN PAPILLOMAVIRUS TYPE 16 L1 PROTEIN WITH A PHAGE DISPLAY EPITOPE LIBRARY

The objective of this study is to map epitopes on HPMAPV16 L1 protein and provide information to the design of HPV16 prophylactic peptide vaccine. The epitopes on L1 protein were screenedby polyclonal and two monoclonal antibodies (BS and F4G3) against RPV16 L1 protin from a 6-merfd phage display epitope library with the method or immuuo-afrinity screening (Biopauuing). Aferthree rounds or Bio-Panning, the Positive phages were detected by L1 antibodies again with ELISA.The positive phages reacted strongly with L1 antibodies were then identified by DNA sequencing.Three mimotopes have been screened by polycloual and two monoclonal antibodies. The mimotope(LSLFSC) reacted with mouoclonal antibody B8 showed 50% pomology with the sequence 270275a. a (DSLFFY) of prototype HPV16 L1. Another mimotope (LTSSYS) reacted with polyclonalantibodies had 66% pomology with the L1 sequence 516~521a. A(TTSSTS), also a mimotope (DRWDRF) was found had the bomologic RF with the known L1 sequence 441 ~446a. a. The mimotopesLSLFSC and DRWDRF were adjacent to the epitopes at 267~269a. a and 422~441 a. a reported byother researchers Previously. Our results suggest that there might be a batch of epitopes on HPV16L1 ppotein, and the predominant epitopes of HPV16 L1 protein are located in the above two domains. These results will be helpful for design or HPV16 prophylactic peatide vaccines and HPVpolyvalent vaccines.

肺癌T7噬菌体文库中MUC1蛋白抗原模拟表位的筛选

目的利用噬菌体表面展示技术,从肺癌T7噬菌体展示文库中筛选MUC1蛋白抗原的模拟表位。方法以MUC1单克隆抗体为靶分子,对肺癌T7噬菌体文库进行淘洗筛选,得到的阳性克隆进行测序并推导其氨基酸序列,对得到的阳性噬菌体克隆进行鉴定。结果经3轮淘选,得到20个阳性克隆。测序获得AAPDFRP、SAPDDRP 2种氨基酸序列,对MUC1单抗的抑制率均在50%以上,与肺癌血清结合特异性较高,此2种蛋白序列可模拟MUC1蛋白抗原表位。结论通过噬菌体展示技术成功筛选到MUC1蛋白的模拟表位序列XAPDXRP(X为任意氨基酸),对肺癌的早期诊断有一定的参考价值。

血清巨噬细胞抑制因子-1在胰腺癌临床检测诊断中的应用价值

目的:探讨MIC-1作为新的肿瘤标志物在胰腺癌临床血清学诊断中的应用价值.方法:采用酶联免疫方法检测101例胰腺癌、10例胰腺良性病变患者及50例正常人血清中的MIC-1表达水平,并与肿瘤标记物CA199进行比较.结果:胰腺癌患者血清中MIC-1表达水平(1427±1056 ng/L)显著高于胰腺良性肿瘤(362±177 ng/L)和正常人血清水平(299±159 ng/L)(P<0.001).MIC-1检测胰腺癌的敏感性、特异性、阳性预测值、阴性预测值和AUC分别为81.2%、94%、96.5%、71.2%和0.92.分别高于CA199的相应对应值72.4%、89.6%、93.4%、61.4%和0.86.与CA199联合检测时,敏感性可提高至91.1%.结论:MIC-1有可能成为用于胰腺癌临床诊断的新肿瘤标记物.

用T7噬菌体展示技术筛选乙型肝炎病毒PreS1相互作用蛋白

目的:用T7噬菌体筛选系统筛选乙型肝炎病毒PreS1的相互作用蛋白。方法:应用T7噬菌体展示技术,以通过原核表达的方式得到的乙型肝炎病毒PreS1作为靶分子,对噬菌体人肝细胞cDNA文库进行生物筛选,对筛选到的克隆进行DNA序列分析及同源性搜索。结果:经鉴定得到1个阳性克隆,确定了能与乙型肝炎病毒PreS1相互作用的蛋白可能为:细胞色素C氧化酶1(Cytochrome c Oxidase Subunit I,COX1)。结论:T7噬菌体展示筛选系统是筛选相互作用蛋白的一种简单、快速和有效的手段,筛选到的相互作用蛋白为进一步探讨PreS1的致病机制提供重要依据。

MUC1抗原的表位预测及模拟位的筛选

目的预测MUC1抗原的B细胞表位,从噬菌体随机多肽文库筛选及鉴定MUC1抗原的模拟位。方法联合运用多种方法对MUC1的二级结构和表面特性,如理化性质、亲水性、可塑性、溶剂可及性及免疫原性等方面进行分析,预测MUC1的抗原表位。利用纯化获得的BC2抗体筛选噬菌体随机7肽库,夹心ELISA分析噬菌体克隆,测定阳性克隆DNA序列,竞争性抑制实验鉴定阳性噬菌体克隆。结果MUC1存在有多个潜在的抗原表位位点,可能的蛋白质抗原表位区域:110,2454,6577,8491,108134,140156,159174,179196,199210,220233,237265,270299,316337,351362,369396,411420,445502。经3轮筛选,获得了30个阳性克隆,DNA序列分析并推导出氨基酸序列:TAPDLRP、SAPDLRP、AAPDSRP及LAPDFRP4个噬菌体展示肽克隆抑制率均在50%以上。结论应用多参数预测MUC1抗原的B细胞表位,为进一步研究MUC1结构和功能、选择表达新型MUC1分子奠定了基础。所得序列TAPDLRP、SAPDLRP、AAPDSRP及LAPDFRP模拟MUC1抗原表位。

细胞粘附因子-1与恶性疟原虫感染红细胞结合位点的鉴定

目的 探索恶性疟原虫感染红细胞 (PRBCs)与细胞粘附因子 1 (ICAM 1 )之间的结合位点 ,研制治疗脑型疟的抗粘附药物。 方法 以抗ICAM 1 (I区 )的单抗 1 5 .2为靶 ,采用亲和筛选法对噬菌体随机十二肽库进行 3轮筛选 ,通过ELISA、竞争抑制试验、dot ELISA及Westernblotting鉴定获得的噬菌体短肽与单抗 1 5 .2之间的结合特性。对阳性克隆进行DNA序列测定 ,推导其十二肽的氨基酸序列并与ICAM 1氨基酸全序列进行同源性比较。 结果 经 3轮亲和筛选后 ,结合噬菌体得到良好富集。从第 3轮洗脱液铺制的琼脂板中随机挑取 30个噬菌体单克隆 ,ELISA检测有 2 6个为阳性 ,阳性率达 86 .7%。竞争性ELISA显示多数阳性噬菌体能竞争抑制ICAM 1与 1 5 .2单抗结合。DNA及氨基酸序列分析表明半数以上的噬菌体克隆表达十二肽KLYLIAEGSVAA ,该短肽中K(XX)L(XXX)GSV与ICAM 1的 64～ 73位aa有 50 %的同源性。 结论 阳性噬菌体表达的短肽是 1 5 .2单抗所识别的模拟表位 ,K··L···GSV几个氨基酸可能对ICAM

HIV-1 Gag蛋白P2/NC蛋白酶切割位点序列的随机化及噬菌体展示

目的:构建HIV-1 Gag PR蛋白P2/NC切割位点序列随机化的噬菌体展示文库,研究HIV-1蛋白酶(protease PR)耐药性突变对其敏感切割序列的影响。方法:PCR扩增制备重组HIV-1gag基因上的CAP2和NC片段,在CAP2片段5′端引入StuⅠ酶切位点,3′端PR切割位点处的氨基酸序列进行随机化;在NC片段5′端设计重叠区域,3′端引入SalⅠ酶切位点。应用Overlapping PCR将CAP2和NC片段拼接并克隆于噬菌体展示载体LD3-pCANTAB5S上,建立HIV-1PR靶蛋白CAP2和NC之间切割位点随机化的噬菌体展示文库。结果:该噬菌体展示文库库容量为2.1×106,滴度为3.0×1012TU/ml,CAP2/NC片段插入率为52.1%;12个样品的序列分析显示切割位点中随机化的核苷酸与氨基酸均呈随机性分布;10个阳性单克隆噬菌体CAP2/NC-LD3-pCANTAB5S样品中9个与IgG特异结合。结论:成功地对HIV-1PR靶蛋白CAP2和NC之间切割位点进行了随机化并展示于噬菌体表面,构建了其噬菌体展示文库,为筛选耐药性突变的PR敏感切割序列及构建蛋白酶抑制剂噬菌体筛选模型打下基础。

噬菌体展示ICAM-1模拟肽的制备及活性鉴定

目的:获得具有生物学活性的细胞间黏附分子-1(ICAM-1)模拟肽。方法:以噬菌体扩增及PEG沉淀法,大量制备展示十二肽P1、P2的噬菌体。采用ELISA、竞争抑制试验及免疫组化染色法,分别鉴定P1、P2模拟ICAM-1分子的结合特性及生物学活性。结果:噬菌体展示肽P1、P2能与抗ICAM-1单克隆抗体(mAb)15.2特异性结合。该结合作用可被ICAM-1分子竞争性抑制,P1、P2能模拟ICAM-1分子与LFA-1结合的功能。结论:噬菌体展示的短肽P1、P2具有天然ICAM-1的生物学活性。

应用噬菌体展示技术筛选HMGB1启动子结合蛋白

目的:筛选高迁移率族蛋白B1(HMGB1)启动子结合蛋白。方法:应用噬菌体展示技术,以HMGB1启动子DNA作为固相筛选分子,对噬菌体展示环七肽库进行4轮"吸附-洗脱-扩增"生物筛选,从第4轮洗脱物中随机挑选20个单克隆噬菌体扩增后进行ELISA鉴定。对所筛选克隆进行DNA序列测定和生物信息学分析。结果:经过4轮筛选后,对随机选取的20个噬菌体克隆进行鉴定,其中11个可与HMGB1启动子结合。DNA测序后经过同源性搜索,确定了与HMGB1启动子具有结合作用的蛋白,包括激活蛋白-1(activator protein-1,AP-1)等6种已知功能蛋白和2种未知功能蛋白。结论:筛选到HMGB1启动子的结合蛋白,为研究HMGB1基因的转录调控机制奠定基础。

人源单克隆抗人免疫缺陷病毒1型抗体Fab段基因的获得

应用噬菌体抗体库技术有效地筛选出了多株抗HIV 1人源单克隆抗体。以逆转录聚合酶链反应 (RT PCR)从HIV 1感染者外周血淋巴细胞中扩增抗体轻重链可变区基因 ,插入载体 pCOMB3 ,建立噬菌体抗体库。分别以HIV 1gp41、gp12 0和 gp16 0为固相抗原 ,经过多轮筛选 ,从中获得了多株抗HIV 1gp41、gp12 0和 gp16 0的单克隆抗体Fab段基因。抗HIV特异性噬菌体抗体随抗体库的筛选高度富集 ,抗gp41阳性克隆率由第 2轮的 5 %增加到第6轮的 87%。间接ELISA、竞争抑制ELISA和Dotblot检测结果表明 ,获得的抗HIV 1噬菌体抗体具有较高抗原结合活性和特异性。研究结果显示 :应用该技术获得人源抗病毒基因工程单克隆抗体既省时省力 ,又可获得任意目的单抗基因 ,且易获得高亲和力的抗体。

HIV-1gp41 C-螺旋模拟位的筛选和鉴定

目的 :筛选可作为小分子先导化合物的HIV 1gp4 1C螺旋模拟位 ,为开发抗HIV 1早期感染的小分子药物奠定基础。方法 :以源于HIV 1gp4 1N端的肽N36为靶 ,对噬菌体环七肽库进行亲和筛选。利用ELISA鉴定噬菌体阳性克隆并对其进行DNA序列分析。结果 :3轮筛选后随机挑取 2 6个噬菌体克隆 ,ELISA鉴定表明有 16个克隆可与N36结合 ,将其中 10个克隆DNA测序并推导氨基酸序列 ,每一克隆至少含有 2个疏水氨基酸 ,其中 9个克隆均有WW ,7个克隆有WWH保守序列。挑选阳性噬菌体克隆No 8进一步鉴定 ,游离N36肽阻断No 8克隆与固相化N36结合 ,C34肽竞争抑制N36肽与No 8克隆结合 (IC50 为 12 5 μg ml)。 结论 :表达WW保守序列的肽模拟HIV 1gp4 1C螺旋与N螺旋结合 ,该结果为设计针对HIV介导融膜的抑制剂提供技术支持。

噬菌体随机肽库筛选MUC1抗原模拟表位

目的噬菌体随机多肽文库筛选及鉴定MUC1抗原的模拟表位。方法利用纯化获得的BC2抗体筛选噬菌体随机7肽库,通过夹心ELISA分析噬菌体克隆,测定阳性克隆DNA序列并进行同源性及氨基酸分析,竞争性抑制实验鉴定噬菌体克隆。结果经3轮筛选,获得了30个阳性克隆,DNA序列分析并推导出氨基酸序列:TAPDLRP、SAPDLRP、AAPDSRP及LAPDFRP。鉴定结果表明:4个噬菌体展示肽克隆抑制率均在50%以上。结论所得序列TAPDLRP、SAPDLRPAAPDSRP及LAPDFRP模拟MUC1抗原表位。

噬菌体展示耐药突变HIV-1蛋白酶敏感切割位点六肽随机文库的构建

目的构建耐药性突变HIV-1蛋白酶(protease PR)敏感切割位点序列体外噬菌体筛选模型,研究HIV-1蛋白酶耐药性突变与敏感切割序列的关系。方法用含随机核苷酸序列的引物PCR方法对HIV-1gag基因上的CAP2片段的PR切割位点处的氨基酸序列进行随机化,再将重组CAP2片段和NC片段拼接克隆于噬菌体展示载体LD3-pCANT-AB5S上,建立HIV-1蛋白酶靶蛋白切割位点随机化的噬菌体展示文库。结果该噬菌体展示文库库容量为2.6×106,滴度为4.1×1015TU·L-1,CAP2片段插入率为47.8%;序列分析显示切割位点中随机化的核苷酸与氨基酸均呈随机性分布。结论成功地构建HIV-1蛋白酶的敏感切割序列噬菌体筛选文库,为筛选到突变PR敏感切割序列噬菌体及研究耐药HIV-1蛋白酶抑制剂与突变PR的关系打下基础。