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.     

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.     

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.     

水蛭素在噬菌体表面的展示

水蛭素是凝血酶强有力的天然抑制剂。通过改造噬菌质粒并构建水蛭素表达载体pCANTAB 5G8Hir,使水蛭素基因通过接头与噬菌体M13的gp3(197～406)基因片段融合。表达产物在gp8信号肽的引导下到达大肠杆菌周质,在辅助噬菌体M13KO7的帮助下组装到丝状噬菌体外壳上。展示在噬菌体表面的水蛭素仍然具有与凝血酶结合并抑制酶活性的作用,说明展示的水蛭素保持了正确的空间构象和生物学活性。水蛭素在噬菌体表面的功成展示为进一步开展其实验定向进化以及结构与功能关系的研究打下基础。     

Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae

Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.     

噬菌体抗体库筛选技术

噬菌体展示技术（Ｐｈａｇｅ Ｄｉｓｐｌａｙ Ｔｅｃｈｎｏｌｏｇｙ）为制备高亲和性抗体提供了有力的工具。噬菌体抗体库的筛选是其中关键的环节,为了提高筛选效率,用包被在固体表面的抗原进行筛选的传统方法不断地被改进,如宿主菌直接洗脱和双层膜筛选系统和抗抗体替代抗原筛选系统。将噬菌体感染宿主菌的过程与筛选过程相关联,产生了选择性感染筛选系统。     

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.     

利用丝状噬菌体展示技术进行抗原决定族图谱及其基因工程的研究

噬茵体展示是90年代初发展起来的一种新型表达技术。其主要特点是得到表达的蛋白或肽段能够被展示在病毒粒子的表面,从而使得大规模的专一性选择成为可能。目前此技术已被广泛用于生命科学研究的不同领域。比较突出的有抗体工程的研究,随机抗原决定族库的研究．以及随机肽在新药开发中的研究。本文将集中回顾一下噬菌体展示技术在抗原决定族定位研究中的应用,及其在新型诊断试剂和疫苗开发中的潜在前景。     

超大容量人源性抗体库的构建

构建大容量抗体库是获得高亲和力抗体的重要基础和保障,如何构建大容量抗体库一直是被关注的热点。本对比分析了天然库、半合成库及全合成库基因多样性的特点,指出获得多样的功能性抗体基因是建库的关键。构建大容量抗体库要从提高连接和转化效率、利用体内重组系统提高抗体基因组合多样性以及提高包装和呈现的效率等多个环节进行条件优化,提高库容量和多样性。     

噬菌体：微小却不简单

噬菌体是专一感染细菌等微生物的病毒,是地球上多样性最高和最丰富的生物体,是生物学研究中重要的模式生物,同时是抗生素耐药菌的天然抗菌剂。噬菌体研究的相关成果极大地推动了生物学各个领域的发展。     

Effects of Polar Organic Solvents on the Biocatalysis of Chlorophyllase in a Biphasic Organic System

The effects of polarity of various organic solvents, including acetone, ethanol, and propanol, used in a biphasic organic system, on the hydrolytic activity of a partially purified chlorophyllase from Phaeodactylum tricornutum were investigated. The different concentrations of each polar organic solvent, from 0 to 40%, were added to a mixture (45:55, v/v) of hexane and a buffer solution of Tris–HCl (20 mm, pH 7.5). The most appropriate concentrations of acetone, ethanol, and propanol for the hydrolytic activity of chlorophyllase were 12.5, 5.0, and 2.5%, respectively. The results indicated that the optimum reaction time for the chlorophyllase activity in the biphasic system decreased from 7.0 h to 3.0, 5.0, and 5.0 h, respectively, upon the addition of an appropriate amount of acetone, ethanol, or propanol. The V_max and K_m as well as the inhibitory effect of phytol on the chlorophyllase activity in the biphasic organic system containing a polar organic solvent were also investigated.     

Functional and molecular characterization of pSE34 encoding a type IV secretion system in Salmonella enterica serotype Enteritidis phage type 34

Salmonella enterica serotype Enteritidis infection remains a serious public health threat to humans. Salmonella Enteritidis phage type 4 (PT4) is a clone that has already caused a global pandemic for years. To investigate why PT34 becomes a subdominantly emerging phage type, molecular characterizations, including serotyping, pulsed-field gel electrophoresis (PFGE), phage typing, and plasmid profiling, were carried out on PT34. The results indicated that relative to PT4, PT34 contained an additional 32-kb DNA segment in PFGE and a 33-kb plasmid pSE34 in plasmid profiling. Southern blot hybridization showed that the DNA segment was the major part of pSE34. All of the S . Enteritidis PT34 clinical isolates possessed pSE34, while PT4 and PT21 did not. Sequencing analysis revealed that pSE34 is 32 950 bp long, with a G+C% content of 41.2%, and contains a total of 53 orf s. Transposon mutagenesis demonstrated that taxB, taxC , and the pilX operon on this plasmid participated in the process of conjugation. In virulence testing, PT34 that harbored pSE34, compared with PT4, showed no increased invasion to tissue culture cells in vitro . The presence of conjugative pSE34 in PT4 caused the conversion of phage type from PT4 to PT34, suggesting that the emergence of PT34 was a result of the introduction of the conjugative pSE34 into its common progenitor PT4.     

Diffusion of bacteriophages through artificial biofilm models

The simple two-chamber diffusion method was improved to study the diffusion properties of bacteriophage (phage) T4 through a model biofilm agarose gel membrane (AGM) embedded with dead host Escherichia coli K12 cells. The apparent diffusion coefficient (D(app) ) of phage T4 was calculated to be 2.4 × 10(-12) m(2) /s in 0.5% AGM, which was lower than the coefficient of 4.2 × 10(-12) m(2) /s in 0.5% AGM without host cells. The phage adsorption process by dead host cells slowed the apparent phage diffusion. The Langmuir adsorption equation was used to simulate phage adsorption under different multiplicity of infections (MOIs); the maximum adsorbed phage MOI was calculated to be 417 PFU/CFU, and the Langmuir adsorption constant K(L) was 6.9 × 10(-4) CFU/PFU. To evaluate the effects of phage proliferation on diffusion, a simple syringe-based biofilm model was developed. The phage was added into this homogenous biofilm model when the host cells were in an exponential growth phase, and the apparent diffusion coefficient was greatly enhanced. We concluded that D(app) of phages through biofilms could be distinctly affected by phage adsorption and proliferation, and that the idea of D(app) and these methods can be used to study diffusion properties through real biofilms.     

噬菌体呈现肽库技术的应用

噬菌体呈现肽库是噬菌体显示技术的一个非常重要的分支。自问世以来,随着分子生物学技术的飞速发展,它已被广泛应用于免疫学、分子生物学、药理学、疫苗学等生命科学领域。简要概述了这一技术的应用。