Open resource metagenomics: a model for sharing metagenomic libraries

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM²BL [1]). The CM²BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.     

噬菌体表面展示技术

噬菌体表面展示技术是将编码外源肽或抗体的可变区ＤＮＡ 片段插入噬菌体或噬菌粒的基因组中,以融合形式与噬菌体的表面蛋白共同表达于噬菌体表面,经过“吸附———洗脱———扩增”过程筛选并富集外源肽或 特异性抗体。其中噬菌体抗体库技术可以模拟体内抗体产生和成熟过程,不经细胞杂交,甚至不经免疫制备针对任何抗原的单克隆抗体     

应用抗病毒抗体表位筛选的多肽文库的构建

1985年,Sndth在《科学》杂志上提出构建"融合噬菌体",即在这种丝状病毒的包膜蛋白上表达融合蛋白[1]．1990年,Scott和Smith山利用这种表面表达载体建立了随机多肽文库,可以很方便地筛选出抗体及其他功能蛋白的强结合配基[2]．我们建立了十二肽的随机多肽库,将从中筛选出抗HIV-gP160抗体的抗独特型多肽．1材料和方法1．1质粒、菌株和培养墓噬菌粒成h血四、大肠杆菌XLI-Blue和辅助噬菌体VCSM13由军事医学科学院微生物流行病研究所王海涛教授惠赠．SB液体培养基：30gtmptone,20g酵母膏,10gMops溶于IL去离子水中,调pH7．0．枝…     

In vivo versus in vitro screening or selection for catalytic activity in enzymes and abzymes

The recent development of catalytic antibodies and the introduction of new techniques to generate huge libraries of random mutants of existing enzymes have created the need for powerful tools for finding in large populations of cells those producing the catalytically most active proteins. Several approaches have been developed and used to reach this goal. The screening techniques aim at easily detecting the clones producing active enzymes or abzymes; the selection techniques are designed to extract these clones from mixtures. These techniques have been applied both in vivo and in vitro. This review describes the advantages and limitations of the various methods in terms of ease of use, sensitivity, and convenience for handling large libraries. Examples are analyzed and tentative rules proposed. These techniques prove to be quite powerful to study the relationship between structure and function and to alter the properties of enzymes.     

Affinity Selection and Mass Spectrometry-Based Strategies to Identify Lead Compounds in Combinatorial Libraries

The screening of diverse libraries of small molecules created by combinatorial synthetic methods is a recent development which has the potential to accelerate the identification of lead compounds in drug discovery. We have developed a direct and rapid method to identify lead compounds in libraries involving affinity selection and mass spectrometry. In our strategy, the receptor or target molecule of interest is used to isolate the active components from the library physically, followed by direct structural identification of the active compounds bound to the target molecule by mass spectrometry. In a drug design strategy, structurally diverse libraries can be used for the initial identification of lead compounds. Once lead compounds have been identified, libraries containing compounds chemically similar to the lead compound can be generated and used to optimize the binding characteristics. These strategies have also been adopted for more detailed studies of protein–ligand interactions.     

Proligands with protease‐regulated binding activity identified from cell‐displayed prodomain libraries

A general method was developed for the discovery of protease‐activated binding ligands, or proligands, from combinatorial prodomain libraries displayed on the surface of E. coli. Peptide libraries of candidate prodomains were fused with a matrix metalloprotease‐2 substrate linker to a vascular endothelial growth factor‐binding peptide and sorted using a two‐stage flow cytometry screening procedure to isolate proligands that required protease treatment for binding activity. Prodomains that imparted protease‐mediated switching activity were identified after three sorting cycles using two unique library design strategies. The best performing proligand exhibited a 100‐fold improvement in apparent binding affinity after exposure to protease. This method may prove useful for developing therapeutic and diagnostic ligands with improved systemic targeting specificity.     

Novel PARP-1 inhibitors based on a 2-propanoyl-3H-quinazolin-4-one scaffold

Poly(ADP-ribose)polymerase-I (PARP-1) enzyme is involved in maintaining DNA integrity and programmed cell death. A virtual screening of commercial libraries led to the identification of five novel scaffolds with inhibitory profile in the low nanomolar range. A hit-to-lead optimization led to the identification of a group of new potent PARP-1 inhibitors, acyl-piperazinylamides of 3-(4-oxo-3,4-dihydro-quinazolin-2-yl)-propionic acid. Molecular modeling studies highlighted the preponderant role of the propanoyl side chain.