以分枝杆菌噬菌体为例探索生命科学研究型教学

综合多学科技术手段研究生物体系复杂问题,是目前生物医学研究的显著特征之一,这为本科生教学改革提出了新的更高的要求。噬菌体是开展生命科学研究型教学改革的理想生物材料。文章借鉴美国匹斯堡大学牵头的美国大学生物学教学改革项目“噬菌体猎人”的实践,总结了本课题组近5年来将分枝杆菌噬菌体科研成果转化为本科生命科学研究型教学的经验。     

应用噬菌体肽库筛选能封阻霍乱噬菌体VP1转染菌细胞的寡肽

噬菌体感染细菌首先要吸附于细菌表面受体 ,从目前报道的细菌与噬菌体相互作用的研究中发现 ,这些受体包括细菌细胞外膜上的蛋白、糖脂结构和鞭毛等。霍乱弧菌是霍乱的病原体 ,高守一等 (副霍乱资料汇编 ,1 984,2 37～ 2 4 5 .)从国内分离并选择出 5株噬菌体 (VP1～VP5 ) ,根据霍乱弧菌菌株对噬菌体的敏感性不同 ,将埃尔托型霍乱弧菌分为 32个噬菌体型。结合生物学分型方法 ,可区分埃尔托型霍乱弧菌的两类不同菌株 (流行株和非流行株 )和不同菌型。对各种来源的菌株进行分型 ,可作为一种追溯传染来源、传播途径和分析流行形式的流行病学研…     

噬菌体相互作用与细菌毒力进化

细菌的毒力是细菌的重要生物学特性,在细菌致病过程中起着非常重要的作用。细菌的毒力基因可以编码在质粒、致病岛或噬菌体上。近些年,研究者们发现噬菌体之间的相互作用也是构成细菌毒力的一个重要因素。     

多肽噬菌体展示

噬菌体展示技术已被广泛地应用于生物学研究的各个方面.利用它可融合表达多肽、蛋白质结构域和蛋白质.尤其是多肽噬菌体展示,已被作为一种便利的研究工具去发现和研究那些与受体、酶、凝集素、抗体、核酸以及其他生物分子亲和的多肽配基和酶的底物专一性,该技术在药物的发现,疫苗的设计等医学领域也有着潜在的应用价值.     

一株耐碳青霉烯类鲍曼不动杆菌噬菌体的分离鉴定和临床应用

【背景】耐药菌感染是人类生命健康的重要威胁,寻找抗生素替代或辅助疗法迫在眉睫,噬菌体是细菌的天敌,有很大的开发潜力。【目的】分离针对耐碳青霉烯类鲍曼不动杆菌(carbapenem-resistant Acinetobacter baumannii, CRAB)的烈性噬菌体,治疗患者CRAB肺部感染,为噬菌体疗法的推广积累经验。【方法】用CRAB临床菌株NAB11B做宿主菌,从医院污水中分离新噬菌体,进行生物学特征和基因组特点的表征、分析后制备成高纯度的噬菌体制剂,通过雾化吸入的方式治疗肺部CRAB感染,评估噬菌体疗法的有效性和安全性。【结果】分离到一株新噬菌体,命名为AB＿SZL4,其潜伏期短、增殖速度快、抑菌能力强、生物学稳定性高且不携带有害基因。在临床应用中,噬菌体鸡尾酒联合抗生素疗法能快速清除肺部病原菌,且未见明显噬菌体相关不良反应。【结论】AB＿SZL4是一株有极大临床应用潜力的烈性噬菌体。     

一株类志贺邻单胞菌噬菌体生物学特性及全基因组分析

[目的]多重耐药菌株的出现给食品安全带来严重威胁.噬菌体是不同于抗生素的一类重要杀菌因子,对其生物学特性及基因组的研究和分析可为噬菌体的抗菌应用提供依据.[方法]对噬菌体phiP4-7的生物学特性、基因组学、分类学进行研究.[结果]经透射电子显微镜观察,确定phiP4-7头部直径为(50.59±1.68) nm,尾部长...     

侵染3株模式豆科根瘤菌的噬菌体生物学特性

豆科作物根瘤菌被噬菌体浸染后,在一定程度上会引起根瘤菌数目和结瘤量的降低,进而导致共生固氮作用弱化和作物产量的显著下降.然而,目前关于根瘤菌噬菌体的相关研究报道较少.本研究以3株模式根瘤菌,即慢生型大豆根瘤菌、中华大豆根瘤菌和中华苜蓿根瘤菌为宿主,于黑土农田土壤中采用双层平板培养法从每个宿主细菌分离3株噬菌体,共分离获得9株根瘤菌噬菌体,对其形态结构及生物学特征进行综合分析.结果表明:侵染苜蓿根瘤菌噬菌体(SMM)和慢生型根瘤菌噬菌体(BDM)属于肌尾噬菌体科,而侵染中华根瘤菌噬菌体(SSS)隶属于长尾噬菌体科.9株噬菌体的最佳感染复数均在0.001~1.0的变化范围内.一步生长曲线结果显示,BDM的潜伏期和爆发期明显长于SMM和SSS,但获得的裂解量最小.根瘤菌噬菌体在30~40℃和中性pH条件下侵染活性最大.对比发现,侵染同一宿主的噬菌体生物学特征虽存在一定差异,但分异度远小于不同宿主噬菌体间的差异.     

噬菌体展示技术及其在寄生虫研究中的应用

噬菌体展示技术是将外源蛋白或多肽的编码基因或DNA序列插入到噬菌体外壳蛋白结构基因的适当位置,使外源基因随外壳蛋白的表达而表达,并随噬菌体的重新组装而展示到噬菌体表面的生物技术.在研究蛋白质识别或蛋白质与核酸相互作用的生物学过程、蛋白质定向改造、研制新型多肽药物、疫苗和抗体等多领域具有重要作用.就噬菌体展示技术基本原理及特点,以及噬菌体展示技术在寄生虫研究中的应用做一简要综述.     

阪崎肠杆菌噬菌体的分离及其生物学特性

[目的]以阪崎肠杆菌模式菌株及分离菌株为指示菌,从污水中分离出该菌噬菌体,并对其基本生物学特性进行研究.[方法]以双层琼脂法从污水中分离噬菌体,通过同属和同科参考菌株测定噬菌体的特异性和宿主谱;电镜观察噬菌体颗粒形态;随机扩增多态性DNA(RAPD)实验分析噬菌体的分子生物学特性.[结果]从污水中分离得到5株噬菌体,表现出较窄的宿主范围,仅裂解阪崎肠杆菌,以ATCC 51329分离的噬菌体SK2可裂解27株阪崎肠杆菌中的24株(89%),负染经电镜观察,5株噬菌体都是由多面体头部和尾部组成;随机引物(5′-GAAACGGGTG-3′)扩增DNA分析,5株噬菌体DNA明显不同.[结论]分离出的5株噬菌体仅对阪崎肠杆菌敏感,在阪崎肠杆菌的分型、预防、治疗、以及生态环境的净化等方面具有潜在用途.     

噬菌体展示文库筛选技术的研究进展

噬菌体展示技术是将编码外源蛋白或多肽的基因片段定向插入到噬菌体的外壳蛋白基因区,使外源蛋白或多肽通过与噬菌体外壳蛋白融合而表达并展示于噬菌体表面,进而筛选表达特异蛋白或多肽的噬菌体,已发展成为生物学后基因组时代一个强有力的实验技术.噬菌体展示文库的筛选是其关键环节.为了提高筛选效率,许多研究者对传统的筛选技术进行了改进,如选择性感染噬菌体、迟延感染性噬菌体、以DNA为基础的筛选方法、亲合力捕获和反复筛选和封闭筛选法等,用于筛选的靶标也越来越具有多样性,使得这一技术有了更加广阔的发展前景.     

Morphological and genetic analysis of three bacteriophages of Serratia marcescens isolated from environmental water

Increases in multidrug-resistant strains of Serratia marcescens are of great concern in pediatrics, especially in neonatal intensive care units. In the search for bacteriophages to control infectious diseases caused by multidrug-resistant S. marcescens , three phages (KSP20, KSP90, and KSP100) were isolated from environmental water and were characterized morphologically and genetically. KSP20 and KSP90 belonged to morphotype A1 of the family Myoviridae , and KSP100 belonged to morphotype C3 of the family Podoviridae . Analysis of the DNA region coding virion proteins, together with their morphological features, indicated that KSP20, KSP90, and KSP100 were related to the P2-like phage (temperate), T4-type phage (virulent), and phiEco32 phage (virulent), respectively. Based on amino acid sequences of the major capsid protein, KSP90 formed a new branch with a Stenotrophomonas maltophilia phage, Smp14, in the T4-type phage phylogeny. Both Smp14 and phiEco32 have been reported as potential therapeutic phages. These results suggest that KSP90 and KSP100 may be candidate therapeutic phages to control S. marcescens infection.     

Minimal requirements for in vitro reconstitution of the structural subunit of light-harvesting complexes of photosynthetic bacteria

Unlike the and polypeptides of the core light-harvesting complex (LH1) of Rhodobacter (Rb.) sphaeroides, the and polypeptides of the peripheral light-harvesting complex (LH2) of this organism will not form a subunit complex by in vitro reconstitution with bacteriochlorophyll. Guided by prior experiments with the LH1 polypeptides of Rb. sphaeroides and Rhodospirillum rubrum, which defined a set of interactions required to stabilize the subunit complex, a series of mutations to the Rb. sphaeroides LH2 polypeptide was prepared and studied to determine the minimal changes necessary to enable it to form a subunit-type complex. Three mutants were prepared: Arg at position –10 was changed to Asn (numbering is from the conserved His residue which is known to be coordinated to bacteriochlorophyll); Arg at position –10 and Thr at position +7 were changed to Asn and Arg, respectively; and Arg at position –10 was changed to Trp and the C-terminus from +4 to +10 was replaced with the amino acids found at the corresponding positions in the LH1 polypeptide of Rb. sphaeroides. Only this last multiple mutant polypeptide formed subunit-type complexes in vitro. Thus, the importance of the C-terminal region, which encompasses conserved residues at positions +4, +6 and +7, is confirmed. Two mutants of the LH1 polypeptide of Rb. sphaeroides were also constructed to further evaluate the interactions stabilizing the subunit complex and those necessary for oligomerization of subunits to form LH1 complexes. In one of these mutants, Trp at position –10 was changed to Arg, as found in LH2 at this position, and in the other His at position –18 was changed to Val. The results from these mutants allow us to conclude that the residue at the –10 position is unimportant in subunit formation or oligomerization, while the strictly conserved His at –18 is not required for subunit formation but is very important in oligomerization of subunits to form LH1.     

Genome comparison of Pseudomonas aeruginosa large phages

Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant phiKZ-like Myoviridae. The EL genome sequence comprises 211,215 bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17-55% amino acid identity) with phiKZ proteins. Comparative EL and phiKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and phiKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and phiKZ. Region IV, a 17.7 kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H-N-H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences.     

Unlocking of the filamentous bacteriophage virion during infection is mediated by the C domain of pIII

Protein III (pIII) of filamentous phage is required for both the beginning and the end of the phage life cycle. The infection starts by binding of the N-terminal N2 and N1 domains to the primary and secondary host receptors, F pilus and TolA protein, respectively, whereas the life cycle terminates by the C-terminal domain-mediated release of the membrane-anchored virion from the cell. It has been assumed that the role of the C-terminal domain of pIII in the infection is that of a tether for the receptor-binding domains N1N2 to the main body of the virion. In a poorly understood process that follows receptor binding, the virion disassembles as its protein(s) become integrated into the host inner membrane, resulting in the phage genome entry into the bacterial cytoplasm. To begin revealing the mechanism of this process, we showed that tethering the functional N1N2 receptor-binding domain to the virion via termination-incompetent C domain abolishes infection. This infection defect cannot be complemented by in trans supply of the functional C domain. Therefore, the C domain of pIII acts in concert with the receptor-binding domains to mediate the post receptor binding events in the infection. Based on these findings, we propose a model in which binding of the N1 domain to the periplasmic portion of TolA, the secondary receptor, triggers in cis a conformational change in the C domain, and that this change opens or unlocks the pIII end of the virion, allowing the entry phase of infection to proceed. To our knowledge, this is the first virus that uses the same protein domain both for the insertion into and release from the host membrane.     

Large scale production of phage antibody libraries using a bioreactor

One of the limitations of the use of phage antibody libraries in high throughput selections is the production of sufficient phage antibody library at the appropriate quality. Here, we successfully adapt a bioreactor-based protocol for the production of phage peptide libraries to the production of phage antibody libraries. The titers obtained in the stirred-tank bioreactor are 4 to 5 times higher than in a standard shake flask procedure, and the quality of the phage antibody library produced is indistinguishable to that produced using standard procedures as assessed by Western blotting and functional selections. Availability of this protocol will facilitate the use of phage antibody libraries in high-throughput scale selections.     

Salmonella enterica phage-resistant mutant colonies display an unusual phenotype in the presence of phage Felix 01

AIMS: To investigate irregular colony morphology formation in Salmonella enterica serovar Typhimurium DPC6046 in the presence of a lytic phage, Felix 01. METHODS AND RESULTS: Phage-resistant derivatives of the parent strain DPC6046 were isolated which exhibited an irregular colony morphology. These were subjected to viability studies by using confocal scanning laser microscopy and live/dead BacLight stain to evaluate the cell viability within the colony. The phenomenon was also observed with other S. enterica serotypes tested which were normally sensitive to phage Felix. In the case of strain DPC6046, dead cells were clearly evident at the irregular edges of the phage-resistant colonies in locations where the cell density was lower. This colony morphology was not apparent with two other Salmonella phages tested. CONCLUSIONS: These findings support the hypothesis that the unusual morphology is due to reversion to phage sensitivity and consequent cell death within the colony as it forms. SIGNIFICANCE AND IMPACT OF THE STUDY: The irregular colony morphology observed is peculiar to phage Felix. The confocal scanning laser microscopy methodology allowed the basis for the irregular morphology to be elucidated.     

Large scale production of phage antibody libraries using a bioreactor

One of the limitations of the use of phage antibody libraries in high throughput selections is the production of sufficient phage antibody library at the appropriate quality. Here, we successfully adapt a bioreactor-based protocol for the production of phage peptide libraries to the production of phage antibody libraries. The titers obtained in the stirred-tank bioreactor are 4 to 5 times higher than in a standard shake flask procedure, and the quality of the phage antibody library produced is indistinguishable to that produced using standard procedures as assessed by Western blotting and functional selections. Availability of this protocol will facilitate the use of phage antibody libraries in high-throughput scale selections.