Subtractive screening with the Mycobacterium tuberculosis surface protein phage display library

Liu, Shanshan; Wang, Han; Sun, Changjiang; Lei, Liancheng; Feng, Xin; Yan, Shouqing; Diao, Ying; Gao, Yu; Zhao, Han; Liu, Qianhong; Yao, Cuimei; Li, Minsi

doi:10.1016/j.tube.2011.07.007

Cited by 13 publications

(9 citation statements)

References 28 publications

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“…Here, the selection was based on removal of pIII-deficient phagemid particles which are structurally unstable and easily disassembled by detergent sarkosyl ( Rakonjac and Model, 1998 ; Rakonjac et al, 1999 ). This approach was further used to identify six secretome proteins from Mycobacterium tuberculosis by subtractive panning between the sera of M. tuberculosis patients and BCG-vaccinated healthy subjects ( Liu et al, 2011 ), three of which have not been identified prior to this study and which therefore were novel vaccine candidates. Interestingly, the breakdown of targeting sequences that were able to guide the fusion to the inner E. coli membrane and allow assembly of the virion included not only type I signal sequences, but also type II (lipoprotein) and type IV pre-pilin signal sequences as well as transmembrane helices.…”

Section: Phage Displaymentioning

confidence: 99%

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

et al. 2016

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Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to “bait” of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.

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Section: Phage Displaymentioning

confidence: 99%

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

et al. 2016

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“…Functional annotations of a protein are important and useful to understand the biological properties. Previous studies indicated that surface proteins consisting of secreted and membrane proteins could play a central role in the interaction of the pathogen with its environment, especially in the pathogenicity of MTB [ 55 ], and the term “membrane” was usually used to filter the functional annotation [ 56 - 58 ]. The immune system associated proteins of Homo sapiens would also contribute to the host-pathogen interactions [ 59 ].…”

Section: Resultsmentioning

confidence: 99%

Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs

et al. 2015

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BackgroundEmergence of multiple drug resistant strains of M. tuberculosis (MDR-TB) threatens to derail global efforts aimed at reigning in the pathogen. Co-infections of M. tuberculosis with HIV are difficult to treat. To counter these new challenges, it is essential to study the interactions between M. tuberculosis and the host to learn how these bacteria cause disease.ResultsWe report a systematic flow to predict the host pathogen interactions (HPIs) between M. tuberculosis and Homo sapiens based on sequence motifs. First, protein sequences were used as initial input for identifying the HPIs by ‘interolog’ method. HPIs were further filtered by prediction of domain-domain interactions (DDIs). Functional annotations of protein and publicly available experimental results were applied to filter the remaining HPIs. Using such a strategy, 118 pairs of HPIs were identified, which involve 43 proteins from M. tuberculosis and 48 proteins from Homo sapiens. A biological interaction network between M. tuberculosis and Homo sapiens was then constructed using the predicted inter- and intra-species interactions based on the 118 pairs of HPIs. Finally, a web accessible database named PATH (Protein interactions of M. tuberculosis and Human) was constructed to store these predicted interactions and proteins.ConclusionsThis interaction network will facilitate the research on host-pathogen protein-protein interactions, and may throw light on how M. tuberculosis interacts with its host.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0535-y) contains supplementary material, which is available to authorized users.

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“…When both of these conditions are met, the peptide fused to pIII allows display of the fusion protein on the surface of the virion and complementation of the assembly defect in the gIII -deletion helper phage VCSM13d3, resulting in detergent-resistant virions (phagemid particles). Selection for secretome-encoding inserts is therefore based on treatment of the library, in the form of phagemid particles, that eliminates detergent-sensitive, while preserving the detergent-resistant phagemid particles [40, 41]. A 1 ml aliquot of the overnight culture containing amplified primary library clones was used to inoculate 100 ml of 2 × YT Cm 25 media.…”

Section: Methodsmentioning

confidence: 99%

“…Recently, phage display technology has been adapted for the direct selection and display of secretome proteins, and was applied at a single genome scale to Lactobacillus rhamnosus and Mycobacterium tuberculosis [40, 41]. Sequence analysis and affinity screenings of the resulting phage display secretome libraries allowed characterisation of surface proteins with functions of interest [40–43].…”

Section: Introductionmentioning

confidence: 99%

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

et al. 2014

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BackgroundIn silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects.ResultsBy combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre.ConclusionsAs a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users.

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Subtractive screening with the Mycobacterium tuberculosis surface protein phage display library

Cited by 13 publications

References 28 publications

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

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