101
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Wang H, Lang Q, Li L, Liang B, Tang X, Kong L, Mascini M, Liu A. Yeast Surface Displaying Glucose Oxidase as Whole-Cell Biocatalyst: Construction, Characterization, and Its Electrochemical Glucose Sensing Application. Anal Chem 2013; 85:6107-12. [DOI: 10.1021/ac400979r] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hongwei Wang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
- State Key Laboratory
of Crop
Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai’an, Shandong 271018, People’s
Republic of China
| | - Qiaolin Lang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
| | - Liang Li
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
| | - Bo Liang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
| | - Xiangjiang Tang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
| | - Lingrang Kong
- State Key Laboratory
of Crop
Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai’an, Shandong 271018, People’s
Republic of China
| | - Marco Mascini
- Dipartimento
di Chimica, Universita degli Studi di Firenze, Via della Lastruccia,
3 50019 Sesto Fiorentino, Italy
| | - Aihua Liu
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, People’s Republic of China
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102
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Mann JK, Wood JF, Stephan AF, Tzanakakis ES, Ferkey DM, Park S. Epitope-guided engineering of monobody binders for in vivo inhibition of Erk-2 signaling. ACS Chem Biol 2013; 8:608-16. [PMID: 23227961 PMCID: PMC3600092 DOI: 10.1021/cb300579e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although the affinity optimization of protein binders is straightforward, engineering epitope specificity is more challenging. Targeting a specific surface patch is important because the biological relevance of protein binders depends on how they interact with the target. They are particularly useful to test hypotheses motivated by biochemical and structural studies. We used yeast display to engineer monobodies that bind a defined surface patch on the mitogen activated protein kinase (MAPK) Erk-2. The targeted area ("CD" domain) is known to control the specificity and catalytic efficiency of phosphorylation by the kinase by binding a linear peptide ("D" peptide) on substrates and regulators. An inhibitor of the interaction should thus be useful for regulating Erk-2 signaling in vivo. Although the CD domain constitutes only a small percentage of the surface area of the enzyme (~5%), sorting a yeast displayed monobody library with wild type (wt) Erk-2 and a rationally designed mutant led to isolation of high affinity clones with desired epitope specificity. The engineered binders inhibited the activity of Erk-2 in vitro and in mammalian cells. Furthermore, they specifically inhibited the activity of Erk-2 orthologs in yeast and suppressed a mutant phenotype in round worms caused by overactive MAPK signaling. The study therefore shows that positive and negative screening can be used to bias the evolution of epitope specificity and predictably design inhibitors of biologically relevant protein-protein interaction.
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Affiliation(s)
- Jasdeep K. Mann
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, NY 14260
| | - Jordan F. Wood
- Department of Biological Sciences, University at Buffalo, State University of New York, NY 14260
| | - Anne Fleur Stephan
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, NY 14260
| | - Emmanuel S. Tzanakakis
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, NY 14260
- Department of Biomedical Engineering, University at Buffalo, State University of New York, NY 14260
- Western New York Stem Cell Culture and Analysis Center, University at Buffalo, State University of New York, NY 14260
| | - Denise M. Ferkey
- Department of Biological Sciences, University at Buffalo, State University of New York, NY 14260
| | - Sheldon Park
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, NY 14260
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103
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Surface-associated GroEL facilitates the adhesion of Escherichia coli to macrophages through lectin-like oxidized low-density lipoprotein receptor-1. Microbes Infect 2013; 15:172-80. [DOI: 10.1016/j.micinf.2012.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 09/30/2012] [Accepted: 10/02/2012] [Indexed: 11/18/2022]
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104
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Bentley CA, Bazirgan OA, Graziano JJ, Holmes EM, Smider VV. Arrayed antibody library technology for therapeutic biologic discovery. Methods 2013; 60:91-8. [DOI: 10.1016/j.ymeth.2013.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 01/20/2023] Open
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105
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Tonelli RR, Colli W, Alves MJM. Selection of binding targets in parasites using phage-display and aptamer libraries in vivo and in vitro. Front Immunol 2013; 3:419. [PMID: 23316203 PMCID: PMC3540409 DOI: 10.3389/fimmu.2012.00419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/20/2012] [Indexed: 11/13/2022] Open
Abstract
Parasite infections are largely dependent on interactions between pathogen and different host cell populations to guarantee a successful infectious process. This is particularly true for obligatory intracellular parasites as Plasmodium, Toxoplasma, and Leishmania, to name a few. Adhesion to and entry into the cell are essential steps requiring specific parasite and host cell molecules. The large amount of possible involved molecules poses additional difficulties for their identification by the classical biochemical approaches. In this respect, the search for alternative techniques should be pursued. Among them two powerful methodologies can be employed, both relying upon the construction of highly diverse combinatorial libraries of peptides or oligonucleotides that randomly bind with high affinity to targets on the cell surface and are selectively displaced by putative ligands. These are, respectively, the peptide-based phage display and the oligonucleotide-based aptamer techniques. The phage display technique has been extensively employed for the identification of novel ligands in vitro and in vivo in different areas such as cancer, vaccine development, and epitope mapping. Particularly, phage display has been employed in the investigation of pathogen–host interactions. Although this methodology has been used for some parasites with encouraging results, in trypanosomatids its use is, as yet, scanty. RNA and DNA aptamers, developed by the SELEX process (Systematic Evolution of Ligands by Exponential Enrichment), were described over two decades ago and since then contributed to a large number of structured nucleic acids for diagnostic or therapeutic purposes or for the understanding of the cell biology. Similarly to the phage display technique scarce use of the SELEX process has been used in the probing of parasite–host interaction. In this review, an overall survey on the use of both phage display and aptamer technologies in different pathogenic organisms will be discussed. Using these techniques, recent results on the interaction of Trypanosoma cruzi with the host will be highlighted focusing on members of the 85 kDa protein family, a subset of the gp85/TS superfamily.
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Affiliation(s)
- R R Tonelli
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo São Paulo, Brazil
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106
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Vertès AA. Protein Secretion Systems of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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107
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Nanda V, Hsieh D, Davis A. Prediction and design of outer membrane protein-protein interactions. Methods Mol Biol 2013; 1063:183-96. [PMID: 23975778 DOI: 10.1007/978-1-62703-583-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein-protein interactions (PPI) play central roles in biological processes, motivating us to understand the structural basis underlying affinity and specificity. In this chapter, we focus on biochemical and computational design strategies of assessing and detecting PPIs of β-barrel outer membrane proteins (OMPs). A few case studies are presented highlighting biochemical techniques used to dissect the energetics of oligomerization and determine amino acids forming the key interactions of the PPI sites. Current computational strategies for detecting/predicting PPIs are introduced, and examples of computational and rational engineering strategies applied to OMPs are presented.
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Affiliation(s)
- Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School-UMDNJ, Piscataway, NJ, USA
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108
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Yamamoto I, Ishihara K, Muramatsu K, Wada Y, Kiwaki M, Kushiro A, Okuda K. Expression of Porphyromonas gingivalis Gingipain Antigen Hgp44 Domain on Surface of Lactococcus lactis. THE BULLETIN OF TOKYO DENTAL COLLEGE 2013; 54:233-41. [DOI: 10.2209/tdcpublication.54.233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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109
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Quantitative evaluation of Candia antarctica lipase B displayed on the cell surface of a Pichia pastoris based on an FS anchor system. Biotechnol Lett 2012; 35:367-74. [DOI: 10.1007/s10529-012-1085-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 11/01/2012] [Indexed: 10/27/2022]
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110
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Paul S, Stang A, Lennartz K, Tenbusch M, Überla K. Selection of a T7 promoter mutant with enhanced in vitro activity by a novel multi-copy bead display approach for in vitro evolution. Nucleic Acids Res 2012; 41:e29. [PMID: 23074193 PMCID: PMC3592457 DOI: 10.1093/nar/gks940] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In vitro evolution of nucleic acids and proteins is a powerful strategy to optimize their biological and physical properties. To select proteins with the desired phenotype from large gene libraries, the proteins need to be linked to the gene they are encoded by. To facilitate selection of the desired phenotype and isolation of the encoding DNA, a novel bead display approach was developed, in which each member of a library of beads is first linked to multiple copies of a clonal gene variant by emulsion polymerase chain reaction. Beads are transferred to a second emulsion for an in vitro transcription-translation reaction, in which the protein encoded by each bead's amplicon covalently binds to the bead present in the same picoliter reactor. The beads then contain multiple copies of a clonal gene variant and multiple molecules of the protein encoded by the bead's gene variant and serve as the unit of selection. As a proof of concept, we screened a randomized library of the T7 promoter for high expression levels by flow cytometry and identified a T7 promoter variant with an ~10-fold higher in vitro transcriptional activity, confirming that the multi-copy bead display approach can be efficiently applied to in vitro evolution.
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Affiliation(s)
- Siddhartha Paul
- Department of Molecular and Medical Virology, Ruhr-University Bochum, D-44780 Bochum, Germany
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111
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Jarmander J, Gustavsson M, Do TH, Samuelson P, Larsson G. A dual tag system for facilitated detection of surface expressed proteins in Escherichia coli. Microb Cell Fact 2012; 11:118. [PMID: 22943700 PMCID: PMC3511212 DOI: 10.1186/1475-2859-11-118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/18/2012] [Indexed: 11/17/2022] Open
Abstract
Background The discovery of the autotransporter family has provided a mechanism for surface expression of proteins in laboratory strains of Escherichia coli. We have previously reported the use of the AIDA-I autotransport system to express the Salmonella enterica serovar Enteritidis proteins SefA and H:gm. The SefA protein was successfully exposed to the medium, but the orientation of H:gm in the outer membrane could not be determined due to proteolytic cleavage of the N-terminal detection-tag. The goal of the present work was therefore to construct a vector containing elements that facilitates analysis of surface expression, especially for proteins that are sensitive to proteolysis or otherwise difficult to express. Results The surface expression system pAIDA1 was created with two detection tags flanking the passenger protein. Successful expression of SefA and H:gm on the surface of E. coli was confirmed with fluorescently labeled antibodies specific for the N-terminal His6-tag and the C-terminal Myc-tag. While both tags were detected during SefA expression, only the Myc-tag could be detected for H:gm. The negative signal indicates a proteolytic cleavage of this protein that removes the His6-tag facing the medium. Conclusions Expression levels from pAIDA1 were comparable to or higher than those achieved with the formerly used vector. The presence of the Myc- but not of the His6-tag on the cell surface during H:gm expression allowed us to confirm the hypothesis that this fusion protein was present on the surface and oriented towards the cell exterior. Western blot analysis revealed degradation products of the same molecular weight for SefA and H:gm. The size of these fragments suggests that both fusion proteins have been cleaved at a specific site close to the C-terminal end of the passenger. This proteolysis was concluded to take place either in the outer membrane or in the periplasm. Since H:gm was cleaved to a much greater extent then the three times smaller SefA, it is proposed that the longer translocation time for the larger H:gm makes it more susceptible to proteolysis.
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Affiliation(s)
- Johan Jarmander
- School of Biotechnology, Division of Bioprocess Technology, Royal Institute of Technology, KTH, Stockholm, SE, 106 91, Sweden
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112
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Venet S, Ravn U, Buatois V, Gueneau F, Calloud S, Kosco-Vilbois M, Fischer N. Transferring the characteristics of naturally occurring and biased antibody repertoires to human antibody libraries by trapping CDRH3 sequences. PLoS One 2012; 7:e43471. [PMID: 22937053 PMCID: PMC3427355 DOI: 10.1371/journal.pone.0043471] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/20/2012] [Indexed: 11/18/2022] Open
Abstract
Antibody repertoires are characterized by diversity as they vary not only amongst individuals and post antigen exposure but also differ significantly between vertebrate species. Such plasticity can be exploited to generate human antibody libraries featuring hallmarks of these diverse repertoires. In this study, the focus was to capture CDRH3 sequences, as this region generally accounts for most of the interaction energy with antigen. Sequences from human as well as non-human sources were successfully integrated into human antibody libraries. Next generation sequencing of these libraries proved that the CDRH3 lengths and amino acid composition corresponded to the species of origin. Specific CDRH3 sequences, biased towards the recognition of a model antigen either by immunizing mice or by selecting with phage display, were then integrated into another set of libraries. From these antigen biased libraries, highly potent antibodies were more frequently isolated, indicating that the characteristics of an immune repertoire is transferrable via CDRH3 sequences into a human antibody library. Taken together, these data demonstrate that the properties of naturally or experimentally biased repertoires can be effectively harnessed for the generation of targeted human antibody libraries, substantially increasing the probability of isolating antibodies suitable for therapeutic and diagnostic applications.
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113
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Lee JH, Song C, Kim DH, Park IH, Lee SG, Lee YS, Kim BG. Glutamine (Q)-peptide screening for transglutaminase reaction using mRNA display. Biotechnol Bioeng 2012; 110:353-62. [DOI: 10.1002/bit.24622] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/16/2012] [Accepted: 07/26/2012] [Indexed: 11/06/2022]
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114
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Zheng Y, Xiao Y, Wu H, Wang Q, Xiao J, Zhang Y, Liu Q. Different approaches to expressing Edwardsiella tarda antigen GAPDH in attenuated Vibrio anguillarum for multivalent fish vaccines. JOURNAL OF FISH DISEASES 2012; 35:569-577. [PMID: 22724428 DOI: 10.1111/j.1365-2761.2012.01381.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With the development of gene technology, expressing heterologous antigens in attenuated bacteria has become an important strategy to design multivalent vaccines. In our previous work, an attenuated Vibrio anguillarum named MVAV6203 was developed and proven to be an efficient live vaccine candidate. In this research, we aimed to express protective antigen glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Edwardsiella tarda in attenuated Vibrio anguillarum to establish a multivalent V. anguillarum vector vaccine. Several strategies were compared between low- vs. high-copy plasmid-mediated antigen expression, in vivo-inducible vs. constitutive antigen expression and intracellular vs. surface-displaying antigen expression. Zebrafish, Danio rerio (Hamilton), was applied as the fish model to evaluate the immune protection of the V. anguillarum vector vaccine candidates. Our results demonstrated that V. anguillarum MVAV6203 (pUTatLNG40), which harbours a low-copy plasmid-loaded antigen surface display system under the control of a constitutive promoter, presented the best protective efficacy against the infection of Vibrio anguillarum (relative per cent survival, RPS = 85%) and Edwardsiella tarda (RPS = 70%).
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Affiliation(s)
- Y Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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115
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Kierny MR, Cunningham TD, Kay BK. Detection of biomarkers using recombinant antibodies coupled to nanostructured platforms. NANO REVIEWS 2012; 3:NANO-3-17240. [PMID: 22833780 PMCID: PMC3404449 DOI: 10.3402/nano.v3i0.17240] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/30/2012] [Accepted: 06/09/2012] [Indexed: 12/14/2022]
Abstract
The utility of biomarker detection in tomorrow's personalized health care field will mean early and accurate diagnosis of many types of human physiological conditions and diseases. In the search for biomarkers, recombinant affinity reagents can be generated to candidate proteins or post-translational modifications that differ qualitatively or quantitatively between normal and diseased tissues. The use of display technologies, such as phage-display, allows for manageable selection and optimization of affinity reagents for use in biomarker detection. Here we review the use of recombinant antibody fragments, such as scFvs and Fabs, which can be affinity-selected from phage-display libraries, to bind with both high specificity and affinity to biomarkers of cancer, such as Human Epidermal growth factor Receptor 2 (HER2) and Carcinoembryonic antigen (CEA). We discuss how these recombinant antibodies can be fabricated into nanostructures, such as carbon nanotubes, nanowires, and quantum dots, for the purpose of enhancing detection of biomarkers at low concentrations (pg/mL) within complex mixtures such as serum or tissue extracts. Other sensing technologies, which take advantage of 'Surface Enhanced Raman Scattering' (gold nanoshells), frequency changes in piezoelectric crystals (quartz crystal microbalance), or electrical current generation and sensing during electrochemical reactions (electrochemical detection), can effectively provide multiplexed platforms for detection of cancer and injury biomarkers. Such devices may soon replace the traditional time consuming ELISAs and Western blots, and deliver rapid, point-of-care diagnostics to market.
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Affiliation(s)
- Michael R Kierny
- Department of Biological Sciences, University of Illinois at Chicago (UIC), Chicago, IL, USA
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116
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Gandham L, Nomellini JF, Smit J. Evaluating secretion and surface attachment of SapA, an S-layer-associated metalloprotease of Caulobacter crescentus. Arch Microbiol 2012; 194:865-77. [DOI: 10.1007/s00203-012-0819-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 03/23/2012] [Accepted: 04/23/2012] [Indexed: 11/30/2022]
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117
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Cheng D, Guo Y, Hsing IM. Autoantibody detection by direct counting of antigen-displayed yeast cells. Analyst 2012; 137:999-1004. [PMID: 22193284 DOI: 10.1039/c2an15946e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report a new immunoassay platform based on yeast surface display technology for detection of autoantibodies involved in autoimmune diseases, e.g., systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS). The autoantigens of Ro52/SSA epitope and SmD were chosen to be displayed on the yeast surface with their respective antibodies as the analytes. By using magnetic beads modified with protein G, yeast cells bound with specific target antibody can be captured. The amount of analytes could be determined by counting the number of fluorescent yeast cells captured in a magnetic field. The platform showed promising results in the detection of SLE autoantibodies with high sensitivity and multiplex detection capability over the traditional approaches.
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Affiliation(s)
- Danhui Cheng
- Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
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118
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Yoo TH, Pogson M, Iverson BL, Georgiou G. Directed evolution of highly selective proteases by using a novel FACS-based screen that capitalizes on the p53 regulator MDM2. Chembiochem 2012; 13:649-53. [PMID: 22334509 DOI: 10.1002/cbic.201100718] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Tae Hyeon Yoo
- Department of Molecular Science and Technology, Division of Applied Chemistry and Biological Engineering, Ajou University, Suwon 443-749, South Korea
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119
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Human anti-EGFL7 recombinant full-length antibodies selected from a mammalian cell-based antibody display library. Mol Cell Biochem 2012; 365:77-84. [DOI: 10.1007/s11010-012-1245-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/14/2012] [Indexed: 11/25/2022]
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120
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Mao H, Graziano J, Smider VV. Arrayed protein library technology for therapeutic biologic discovery. Biotechnol Genet Eng Rev 2012; 28:131-45. [DOI: 10.5661/bger-28-131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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121
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122
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Tan JL, Ueda N, Heath D, Mercer AA, Fleming SB. Development of orf virus as a bifunctional recombinant vaccine: Surface display of Echinococcus granulosus antigen EG95 by fusion to membrane structural proteins. Vaccine 2012; 30:398-406. [DOI: 10.1016/j.vaccine.2011.10.079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 09/01/2011] [Accepted: 10/28/2011] [Indexed: 01/24/2023]
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123
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Ilk N, Egelseer EM, Sleytr UB. S-layer fusion proteins--construction principles and applications. Curr Opin Biotechnol 2011; 22:824-31. [PMID: 21696943 PMCID: PMC3271365 DOI: 10.1016/j.copbio.2011.05.510] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 12/04/2022]
Abstract
Crystalline bacterial cell surface layers (S-layers) are the outermost cell envelope component of many bacteria and archaea. S-layers are monomolecular arrays composed of a single protein or glycoprotein species and represent the simplest biological membrane developed during evolution. The wealth of information available on the structure, chemistry, genetics and assembly of S-layers revealed a broad spectrum of applications in nanobiotechnology and biomimetics. By genetic engineering techniques, specific functional domains can be incorporated in S-layer proteins while maintaining the self-assembly capability. These techniques have led to new types of affinity structures, microcarriers, enzyme membranes, diagnostic devices, biosensors, vaccines, as well as targeting, delivery and encapsulation systems.
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124
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Kogot JM, Zhang Y, Moore SJ, Pagano P, Stratis-Cullum DN, Chang-Yen D, Turewicz M, Pellegrino PM, de Fusco A, Soh HT, Stagliano NE. Screening of peptide libraries against protective antigen of Bacillus anthracis in a disposable microfluidic cartridge. PLoS One 2011; 6:e26925. [PMID: 22140433 PMCID: PMC3225367 DOI: 10.1371/journal.pone.0026925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/05/2011] [Indexed: 11/21/2022] Open
Abstract
Bacterial surface peptide display has gained popularity as a method of affinity reagent generation for a wide variety of applications ranging from drug discovery to pathogen detection. In order to isolate the bacterial clones that express peptides with high affinities to the target molecule, multiple rounds of manual magnetic activated cell sorting (MACS) followed by multiple rounds of fluorescence activated cell sorting (FACS) are conventionally used. Although such manual methods are effective, alternative means of library screening which improve the reproducibility, reduce the cost, reduce cross contamination, and minimize exposure to hazardous target materials are highly desired for practical application. Toward this end, we report the first semi-automated system demonstrating the potential for screening bacterially displayed peptides using disposable microfluidic cartridges. The Micro-Magnetic Separation platform (MMS) is capable of screening a bacterial library containing 3 × 10¹⁰ members in 15 minutes and requires minimal operator training. Using this system, we report the isolation of twenty-four distinct peptide ligands that bind to the protective antigen (PA) of Bacilus anthracis in three rounds of selection. A consensus motif WXCFTC was found using the MMS and was also found in one of the PA binders isolated by the conventional MACS/FACS approach. We compared MMS and MACS rare cell recovery over cell populations ranging from 0.1% to 0.0000001% and found that both magnetic sorting methods could recover cells down to 0.0000001% initial cell population, with the MMS having overall lower standard deviation of cell recovery. We believe the MMS system offers a compelling approach towards highly efficient, semi-automated screening of molecular libraries that is at least equal to manual magnetic sorting methods and produced, for the first time, 15-mer peptide binders to PA protein that exhibit better affinity and specificity than peptides isolated using conventional MACS/FACS.
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Affiliation(s)
- Joshua M. Kogot
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Yanting Zhang
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Stephen J. Moore
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
| | - Paul Pagano
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Dimitra N. Stratis-Cullum
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - David Chang-Yen
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Marek Turewicz
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Paul M. Pellegrino
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Andre de Fusco
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Nancy E. Stagliano
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
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125
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Altshuler EP, Serebryanaya DV, Katrukha AG. Generation of recombinant antibodies and means for increasing their affinity. BIOCHEMISTRY (MOSCOW) 2011; 75:1584-605. [PMID: 21417996 DOI: 10.1134/s0006297910130067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Highly specific interaction with foreign molecules is a unique feature of antibodies. Since 1975, when Keller and Milstein proposed the method of hybridoma technology and prepared mouse monoclonal antibodies, many antibodies specific to various antigens have been obtained. Recent development of methods for preparation of recombinant DNA libraries and in silico bioinformatics approaches for protein structure analysis makes possible antibody preparation using gene engineering approaches. The development of gene engineering methods allowed creating recombinant antibodies and improving characteristics of existing antibodies; this significantly extends the applicability of antibodies. By modifying biochemical and immunochemical properties of antibodies by changing their amino acid sequences it is possible to create antibodies with properties optimal for certain tasks. For example, application of recombinant technologies resulted in antibody preparation of high affinity significantly exceeding the initial affinity of natural antibodies. In this review we summarize information about the structure, modes of preparation, and application of recombinant antibodies and their fragments and also consider the main approaches used to increase antibody affinity.
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Affiliation(s)
- E P Altshuler
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Russia
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126
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Jiang M, Shao X, Ni H, Yu Z, Li L. In vivo and in vitro surface display of heterologous proteins on Bacillus thuringiensis vegetative cells and spores. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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127
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Rapid probing of biological surfaces with a sparse-matrix peptide library. PLoS One 2011; 6:e23551. [PMID: 21858167 PMCID: PMC3156232 DOI: 10.1371/journal.pone.0023551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 07/20/2011] [Indexed: 02/02/2023] Open
Abstract
Finding unique peptides to target specific biological surfaces is crucial to basic research and technology development, though methods based on biological arrays or large libraries limit the speed and ease with which these necessary compounds can be found. We reasoned that because biological surfaces, such as cell surfaces, mineralized tissues, and various extracellular matrices have unique molecular compositions, they present unique physicochemical signatures to the surrounding medium which could be probed by peptides with appropriately corresponding physicochemical properties. To test this hypothesis, a naïve pilot library of 36 peptides, varying in their hydrophobicity and charge, was arranged in a two-dimensional matrix and screened against various biological surfaces. While the number of peptides in the matrix library was very small, we obtained “hits” against all biological surfaces probed. Sequence refinement of the “hits” led to peptides with markedly higher specificity and binding activity against screened biological surfaces. Genetic studies revealed that peptide binding to bacteria was mediated, at least in some cases, by specific cell-surface molecules, while examination of human tooth sections showed that this method can be used to derive peptides with highly specific binding to human tissue.
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128
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Chen L, Chu CI, Chen KJ, Chen PY, Hu SF, Liu RS. An intelligent approach to the discovery of luminescent materials using a combinatorial approach combined with Taguchi methodology. LUMINESCENCE 2011; 26:229-38. [DOI: 10.1002/bio.1318] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/05/2011] [Accepted: 04/19/2011] [Indexed: 11/11/2022]
Affiliation(s)
| | - Cheng-I Chu
- Department of Chemistry; National Taiwan University; Taipei
| | - Kuo-Ju Chen
- Institute of Electro-optical Science and Technology; National Taiwan Normal University; Taipei; Taiwan
| | - Po-Yuan Chen
- Institute of Electro-optical Science and Technology; National Taiwan Normal University; Taipei; Taiwan
| | - Shu-Fen Hu
- Department of Physics; National Taiwan Normal University; Taipei; Taiwan
| | - Ru-Shi Liu
- Department of Chemistry; National Taiwan University; Taipei
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129
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Chen CL, Wu SC, Tjia WM, Wang CLC, Lohka MJ, Wong SL. Development of a LytE-based high-density surface display system in Bacillus subtilis. Microb Biotechnol 2011; 1:177-90. [PMID: 21261835 PMCID: PMC3864451 DOI: 10.1111/j.1751-7915.2007.00017.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The three N‐terminal, tandemly arranged LysM motifs from a Bacillus subtilis cell wall hydrolase, LytE, formed a cell wall‐binding module. This module, designated CWBMLytE, was demonstrated to have tight cell wall‐binding capability and could recognize two classes of cell wall binding sites with fivefold difference in affinity. The lower‐affinity sites were approximately three times more abundant. Fusion proteins with β‐lactamase attached to either the N‐ or C‐terminal end of CWBMLytE showed lower cell wall‐binding affinity. The number of the wall‐bound fusion proteins was less than that of CWBMLytE. These effects were less dramatic with CWBMLytE at the N‐terminal end of the fusion. Both CWBMLytE and β‐lactamase were essentially functional whether they were at the N‐ or C‐terminal end of the fusion. In the optimal case, 1.2 × 107 molecules could be displayed per cell. As cells overproducing CWBMLytE and its fusions formed filamentous cells (with an average of nine individual cells per filamentous cell), 1.1 × 108β‐lactamase molecules could be displayed per filamentous cell. Overproduced CWBMLytE and its fusions were distributed on the entire cell surface. Surface exposure and accessibility of these proteins were confirmed by immunofluorescence microscopy.
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Affiliation(s)
- Chyi-Liang Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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130
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Quantitative studies of carbohydrate-protein interaction using functionalized bacterial spores in solution and on chips. BIOTECHNOL BIOPROC E 2011. [DOI: 10.1007/s12257-010-0063-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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131
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Nhan NT, Gonzalez de Valdivia E, Gustavsson M, Hai TN, Larsson G. Surface display of Salmonella epitopes in Escherichia coli and Staphylococcus carnosus. Microb Cell Fact 2011; 10:22. [PMID: 21481238 PMCID: PMC3094208 DOI: 10.1186/1475-2859-10-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica serotype Enteritidis (SE) is considered to be one of the most potent pathogenic Salmonella serotypes causing food-borne disease in humans. Since a live bacterial vaccine based on surface display of antigens has many advantages over traditional vaccines, we have studied the surface display of the SE antigenic proteins, H:gm and SefA in Escherichia coli by the β-autotransporter system, AIDA. This procedure was compared to protein translocation in Staphylococcus carnosus, using a staphylococci hybrid vector earlier developed for surface display of other vaccine epitopes. RESULTS Both SefA and H:gm were translocated to the outer membrane in Escherichia coli. SefA was expressed to full length but H:gm was shorter than expected, probably due to a proteolytic cleavage of the N-terminal during passage either through the periplasm or over the membrane. FACS analysis confirmed that SefA was facing the extracellular environment, but this could not be conclusively established for H:gm since the N-terminal detection tag (His6) was cleaved off. Polyclonal salmonella antibodies confirmed the sustained antibody-antigen binding towards both proteins. The surface expression data from Staphylococcus carnosus suggested that the H:gm and SefA proteins were transported to the cell wall since the detection marker was displayed by FACS analysis. CONCLUSION Apart from the accumulated knowledge and the existence of a wealth of equipment and techniques, the results indicate the selection of E. coli for further studies for surface expression of salmonella antigens. Surface expression of the full length protein facing the cell environment was positively proven by standard analysis, and the FACS signal comparison to expression in Staphylococcus carnosus shows that the distribution of the surface protein on each cell was comparatively very narrow in E. coli, the E. coli outer membrane molecules can serve as an adjuvant for the surface antigenic proteins and multimeric forms of the SefA protein were detected which would probably be positive for the realisation of a strong antigenic property. The detection of specific and similar proteolytic cleavage patterns for both the proteins provides a further starting point for the investigation and development of the Escherichia coli AIDA autotransporter efficiency.
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Affiliation(s)
- Nguyen Thanh Nhan
- Vietnam Institute of Biotechnology (IBT), Vietnamese Academy of Science and Technology (VAST), Hanoi, Vietnam
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132
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Production of N-acetyl-D-neuraminic acid by use of an efficient spore surface display system. Appl Environ Microbiol 2011; 77:3197-201. [PMID: 21441321 DOI: 10.1128/aem.00151-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Production of N-acetyl-D-neuraminic acid (Neu5Ac) via biocatalysis is traditionally conducted using isolated enzymes or whole cells. The use of isolated enzymes is restricted by the time-consuming purification process, whereas the application of whole cells is limited by the permeability barrier presented by the microbial cell membrane. In this study, a novel type of biocatalyst, Neu5Ac aldolase presented on the surface of Bacillus subtilis spores, was used for the production of Neu5Ac. Under optimal conditions, Neu5Ac at a high concentration (54.7 g liter⁻¹) and a high yield (90.2%) was obtained under a 5-fold excess of pyruvate over N-acetyl-D-mannosamine. The novel biocatalyst system, which is able to express and immobilize the target enzyme simultaneously on the surface of B. subtilis spores, represents a suitable alternative for value-added chemical production.
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133
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Huang J, Ru B, Dai P. Bioinformatics resources and tools for phage display. Molecules 2011; 16:694-709. [PMID: 21245805 PMCID: PMC6259106 DOI: 10.3390/molecules16010694] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/01/2011] [Accepted: 01/17/2011] [Indexed: 12/22/2022] Open
Abstract
Databases and computational tools for mimotopes have been an important part of phage display study. Five special databases and eighteen algorithms, programs and web servers and their applications are reviewed in this paper. Although these bioinformatics resources have been widely used to exclude target-unrelated peptides, characterize small molecules-protein interactions and map protein-protein interactions, a lot of problems are still waiting to be solved. With the improvement of these tools, they are expected to serve the phage display community better.
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Affiliation(s)
- Jian Huang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China.
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134
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Kuroda K, Ueda M. Molecular design of the microbial cell surface toward the recovery of metal ions. Curr Opin Biotechnol 2011; 22:427-33. [PMID: 21247751 DOI: 10.1016/j.copbio.2010.12.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 12/25/2010] [Accepted: 12/27/2010] [Indexed: 10/18/2022]
Abstract
The genetic engineering of microorganisms to adsorb metal ions is an attractive method to facilitate the environmental cleanup of metal pollution and to enrich the recovery of metal ions such as rare metal ions. For the recovery of metal ions by microorganisms, cell surface design is an effective strategy for the molecular breeding of bioadsorbents as an alternative to intracellular accumulation. The cell surface display of known metal-binding proteins/peptides and the molecular design of novel metal-binding proteins/peptides have been performed using a cell surface engineering approach. The adsorption of specific metal ions is the important challenge for the practical recovery of metal ions. In this paper, we discuss the recent progress in surface-engineered bioadsorbents for the recovery of metal ions.
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Affiliation(s)
- Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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135
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Compton JR, Legler PM, Clingan BV, Olson MA, Millard CB. Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen. Proteins 2011; 79:1048-60. [PMID: 21387408 DOI: 10.1002/prot.22933] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 10/21/2010] [Accepted: 10/24/2010] [Indexed: 11/10/2022]
Abstract
RTA1-33/44-198 is a catalytically inactive, single-domain derivative of the ricin toxin A-chain (RTA) engineered to serve as a stable protein scaffold for presentation of native immunogenic epitopes (Olson et al., Protein Eng Des Sel 2004;17:391-397). To improve the stability and solubility of RTA1-33/44-198 further, we have undertaken the design challenge of introducing a disulfide (SS) bond. Nine pairs of residues were selected for placement of the SS-bond based on molecular dynamics simulation studies of the modeled single-domain chain. Disulfide formation at either of two positions (R48C/T77C or V49C/E99C) involving a specific surface loop (44-55) increased the protein melting temperature by ~5°C compared with RTA1-33/44-198 and by ~13°C compared with RTA. Prolonged stability studies of the R48C/T77C variant (> 60 days at 37°C, pH 7.4) confirmed a > 40% reduction in self-aggregation compared with RTA1-33/44-198 lacking the SS-bond. The R48C/T77C variant retained affinity for anti-RTA antibodies capable of neutralizing ricin toxin, including a monoclonal that recognizes a human B-cell epitope. Introduction of either R48C/T77C or V49C/E99C promoted crystallization of RTA1-33/44-198, and the X-ray structures of the variants were solved to 2.3 A or 2.1 A resolution, respectively. The structures confirm formation of an intramolecular SS-bond, and reveal a single-domain fold that is significantly reduced in volume compared with RTA. Loop 44 to 55 is partly disordered as predicted by simulations, and is positioned to form self-self interactions between symmetry-related molecules. We discuss the importance of RTA loop 34 to 55 as a nucleus for unfolding and aggregation, and draw conclusions for ongoing structure-based minimalist design of RTA-based immunogens.
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Affiliation(s)
- Jaimee R Compton
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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136
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Van Gerven N, Waksman G, Remaut H. Pili and flagella biology, structure, and biotechnological applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:21-72. [PMID: 21999994 DOI: 10.1016/b978-0-12-415906-8.00005-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria and Archaea expose on their outer surfaces a variety of thread-like proteinaceous organelles with which they interact with their environments. These structures are repetitive assemblies of covalently or non-covalently linked protein subunits, organized into filamentous polymers known as pili ("hair"), flagella ("whips") or injectisomes ("needles"). They serve different roles in cell motility, adhesion and host invasion, protein and DNA secretion and uptake, conductance, or cellular encapsulation. Here we describe the functional, morphological and genetic diversity of these bacterial filamentous protein structures. The organized, multi-copy build-up and/or the natural function of pili and flagella have lead to their biotechnological application as display and secretion tools, as therapeutic targets or as molecular motors. We review the documented and potential technological exploitation of bacterial surface filaments in light of their structural and functional traits.
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Affiliation(s)
- Nani Van Gerven
- Structural & Molecular Microbiology, VIB/Vrije Universiteit Brussel, Brussels, Belgium
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137
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Sleytr UB, Schuster B, Egelseer EM, Pum D, Horejs CM, Tscheliessnig R, Ilk N. Nanobiotechnology with S-layer proteins as building blocks. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:277-352. [PMID: 21999999 DOI: 10.1016/b978-0-12-415906-8.00003-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One of the key challenges in nanobiotechnology is the utilization of self- assembly systems, wherein molecules spontaneously associate into reproducible aggregates and supramolecular structures. In this contribution, we describe the basic principles of crystalline bacterial surface layers (S-layers) and their use as patterning elements. The broad application potential of S-layers in nanobiotechnology is based on the specific intrinsic features of the monomolecular arrays composed of identical protein or glycoprotein subunits. Most important, physicochemical properties and functional groups on the protein lattice are arranged in well-defined positions and orientations. Many applications of S-layers depend on the capability of isolated subunits to recrystallize into monomolecular arrays in suspension or on suitable surfaces (e.g., polymers, metals, silicon wafers) or interfaces (e.g., lipid films, liposomes, emulsomes). S-layers also represent a unique structural basis and patterning element for generating more complex supramolecular structures involving all major classes of biological molecules (e.g., proteins, lipids, glycans, nucleic acids, or combinations of these). Thus, S-layers fulfill key requirements as building blocks for the production of new supramolecular materials and nanoscale devices as required in molecular nanotechnology, nanobiotechnology, biomimetics, and synthetic biology.
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Affiliation(s)
- Uwe B Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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138
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Serizawa T, Matsuno H, Sawada T. Specific interfaces between synthetic polymers and biologically identified peptides. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm10602c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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139
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Choi SH, Nam YK, Kim KH. Novel expression system for combined vaccine production in Edwardsiella tarda ghost and cadaver cells. Mol Biotechnol 2010; 46:127-33. [PMID: 20369310 DOI: 10.1007/s12033-010-9277-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To develop combined vaccine systems, we have generated Edwardsiella tarda ghosts (ETG) displaying a foreign protein on the outer membrane and also Ed. tarda cadaver (ETC) expressing a heterologous protein in the cytoplasm. Green fluorescent protein (GFP) was used as a model foreign protein. A constitutive promoter (EtPR C28-1) cloned newly from Ed. tarda was used as a promoter for the expression of foreign protein. Comparison of the strength of the new promoter with a commercially available constitutive promoter (P(HCE)) showed higher expression levels of the novel expression system. The N-terminal domain of ice nucleation protein (InaN), an outer membrane protein of Pseudomonas syringae, was used as an anchor motif for surface display of GFP. By transformation of Ed. tarda with the constructed vectors, GFP was successfully expressed on the surface of ETG and in the cytoplasm of ETC. When compared to P(HCE) driven expression, approximately more than 2 times of GFP was expressed on ETG and in ETC by EtPR C28-1 promoter when judged by fluorescent spectrophotometry. Furthermore, significantly higher expression of GFP on the surface of ETG by EtPR C28-1 than by P(HCE) was demonstrated by serum agglutination assay. These results suggest that the newly cloned Ed. tarda constitutive promoter is capable to express foreign proteins not only on the surface of Ed. tarda ghosts but also in the cytoplasm of Ed. tarda cadavers, and can be used as an efficient promoter for the expression of heterologous antigens of the ETG and ETC-based combined vaccines.
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Affiliation(s)
- Seung Hyuk Choi
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, Korea
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140
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Stapleton JA, Swartz JR. Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases. PLoS One 2010; 5:e15275. [PMID: 21151915 PMCID: PMC2997796 DOI: 10.1371/journal.pone.0015275] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 11/03/2010] [Indexed: 01/10/2023] Open
Abstract
Background [FeFe] hydrogenase enzymes catalyze the formation and dissociation of molecular hydrogen with the help of a complex prosthetic group composed of common elements. The development of energy conversion technologies based on these renewable catalysts has been hindered by their extreme oxygen sensitivity. Attempts to improve the enzymes by directed evolution have failed for want of a screening platform capable of throughputs high enough to adequately sample heavily mutated DNA libraries. In vitro compartmentalization (IVC) is a powerful method capable of screening for multiple-turnover enzymatic activity at very high throughputs. Recent advances have allowed [FeFe] hydrogenases to be expressed and activated in the cell-free protein synthesis reactions on which IVC is based; however, IVC is a demanding technique with which many enzymes have proven incompatible. Methodology/Principal Findings Here we describe an extremely high-throughput IVC screen for oxygen-tolerant [FeFe] hydrogenases. We demonstrate that the [FeFe] hydrogenase CpI can be expressed and activated within emulsion droplets, and identify a fluorogenic substrate that links activity after oxygen exposure to the generation of a fluorescent signal. We present a screening protocol in which attachment of mutant genes and the proteins they encode to the surfaces of microbeads is followed by three separate emulsion steps for amplification, expression, and evaluation of hydrogenase mutants. We show that beads displaying active hydrogenase can be isolated by fluorescence-activated cell-sorting, and we use the method to enrich such beads from a mock library. Conclusions/Significance [FeFe] hydrogenases are the most complex enzymes to be produced by cell-free protein synthesis, and the most challenging targets to which IVC has yet been applied. The technique described here is an enabling step towards the development of biocatalysts for a biological hydrogen economy.
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Affiliation(s)
- James A. Stapleton
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- * E-mail:
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141
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Throndset W, Kim S, Bower B, Lantz S, Kelemen B, Pepsin M, Chow N, Mitchinson C, Ward M. Flow cytometric sorting of the filamentous fungus Trichoderma reesei for improved strains. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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142
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Goodin JL, Powell BS, Enama JT, Raab RW, McKown RL, Coffman GL, Andrews GP. Purification and characterization of a recombinant Yersinia pestis V-F1 "Reversed" fusion protein for use as a new subunit vaccine against plague. Protein Expr Purif 2010; 76:136-44. [PMID: 21055471 DOI: 10.1016/j.pep.2010.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 10/22/2010] [Accepted: 10/27/2010] [Indexed: 11/28/2022]
Abstract
We previously developed a unique recombinant protein vaccine against plague composed of a fusion between the Fraction 1 capsular antigen (F1) and the V antigen. To determine if overall expression, solubility, and recovery of the F1-V fusion protein could be enhanced, we modified the original fusion. Standard recombinant DNA techniques were used to reverse the gene order such that the V antigen coding sequence was fused at its C-terminus to the N-terminus of F1. The F1 secretion signal sequence (F1S) was subsequently fused to the N-terminus of V. This new fusion protein, designated F1S-V-F1, was then co-expressed with the Y. pestis Caf1M periplasmic chaperone protein in BL21-Star Escherichia coli. Recombinant strains expressing F1-V, F1S-F1-V, or F1S-V-F1 were compared by cell fractionation, SDS-PAGE, Western blotting, and suspension immunolabelling. F1S-V-F1 exhibited enhanced solubility and secretion when co-expressed with Caf1M resulting in a recombinant protein that is processed in a similar manner to the native F1 protein. Purification of F1S-V-F1 was accomplished by anion-exchange and hydrophobic interaction chromatography. The purification method produced greater than 1mg of purified soluble protein per liter of induced culture. F1S-V-F1 polymerization characteristics were comparable to the native F1. The purified F1S-V-F1 protein appeared equivalent to F1-V in its ability to be recognized by neutralizing antibodies.
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Affiliation(s)
- Jeremy L Goodin
- Bacteriology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
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143
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Engineering of microorganisms towards recovery of rare metal ions. Appl Microbiol Biotechnol 2010; 87:53-60. [PMID: 20393699 DOI: 10.1007/s00253-010-2581-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/16/2010] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved.
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144
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Enrichment of Escherichia coli spheroplasts displaying scFv antibodies specific for antigens expressed on the human cell surface. Appl Microbiol Biotechnol 2010; 88:1385-91. [DOI: 10.1007/s00253-010-2861-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/19/2010] [Accepted: 08/25/2010] [Indexed: 01/22/2023]
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145
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Zhou C, Jacobsen FW, Cai L, Chen Q, Shen WD. Development of a novel mammalian cell surface antibody display platform. MAbs 2010; 2:508-18. [PMID: 20716968 DOI: 10.4161/mabs.2.5.12970] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Antibody display systems have been successfully applied to screen, select and characterize antibody fragments. These systems typically use prokaryotic organisms such as phage and bacteria or lower eukaryotic organisms, such as yeast. These organisms possess either no or different post-translational modification functions from mammalian cells and prefer to display small antibody fragments instead of full-length IgGs. We report here a novel mammalian cell-based antibody display platform that displays full-length functional antibodies on the surface of mammalian cells. Through recombinase-mediated DNA integration, each host cell contains one copy of the gene of interest in the genome. Utilizing a hot-spot integration site, the expression levels of the gene of interest are high and comparable between clones, ensuring a high signal to noise ratio. Coupled with fluorescence-activated cell sorting (FACS) technology, our platform is high throughput and can distinguish antibodies with very high antigen binding affinities directly on the cell surface. Single-round FACS can enrich high affinity antibodies by more than 500 fold. Antibodies with significantly improved neutralizing activity have been identified from a randomly mutagenized library, demonstrating the power of this platform in screening and selecting antibody therapeutics.
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Affiliation(s)
- Chen Zhou
- Protein Science, Amgen Inc., Thousand Oaks, CA, USA
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146
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Zarschler K, Janesch B, Kainz B, Ristl R, Messner P, Schäffer C. Cell surface display of chimeric glycoproteins via the S-layer of Paenibacillus alvei. Carbohydr Res 2010; 345:1422-31. [PMID: 20513375 PMCID: PMC4401010 DOI: 10.1016/j.carres.2010.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 04/01/2010] [Accepted: 04/11/2010] [Indexed: 10/19/2022]
Abstract
The Gram-positive, mesophilic bacterium Paenibacillus alvei CCM 2051(T) possesses a two-dimensional crystalline protein surface layer (S-layer) with oblique lattice symmetry composed of a single type of O-glycoprotein species. Herein, we describe a strategy for nanopatterned in vivo cell surface co-display of peptide and glycan epitopes based on this S-layer glycoprotein self-assembly system. The open reading frame of the corresponding structural gene spaA codes for a protein of 983 amino acids, including a signal peptide of 24 amino acids. The mature S-layer protein has a theoretical molecular mass of 105.95kDa and a calculated pI of 5.83. It contains three S-layer homology domains at the N-terminus that are involved in anchoring of the glycoprotein via a non-classical, pyruvylated secondary cell wall polymer to the peptidoglycan layer of the cell wall. For this polymer, several putative biosynthesis enzymes were identified upstream of the spaA gene. For in vivo cell surface display, the hexahistidine tag and the enhanced green fluorescent protein, respectively, were translationally fused to the C-terminus of SpaA. Immunoblot analysis, immunofluorescence staining, and fluorescence microscopy revealed that the fused epitopes were efficiently expressed and successfully displayed via the S-layer glycoprotein matrix on the surface of P. alvei CCM 2051(T) cells. In contrast, exclusively non-glycosylated chimeric SpaA proteins were displayed, when the S-layer of the glycosylation-deficient wsfP mutant was used as a display matrix.
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Affiliation(s)
| | - Bettina Janesch
- Department für NanoBiotechnologie, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Birgit Kainz
- Department für NanoBiotechnologie, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Robin Ristl
- Department für NanoBiotechnologie, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Paul Messner
- Department für NanoBiotechnologie, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Christina Schäffer
- Department für NanoBiotechnologie, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
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147
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Binder U, Matschiner G, Theobald I, Skerra A. High-throughput Sorting of an Anticalin Library via EspP-mediated Functional Display on the Escherichia coli Cell Surface. J Mol Biol 2010; 400:783-802. [DOI: 10.1016/j.jmb.2010.05.049] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/16/2010] [Accepted: 05/20/2010] [Indexed: 01/09/2023]
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148
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Hartmann C, Müller N, Blaukat A, Koch J, Benhar I, Wels WS. Peptide mimotopes recognized by antibodies cetuximab and matuzumab induce a functionally equivalent anti-EGFR immune response. Oncogene 2010; 29:4517-27. [PMID: 20514015 DOI: 10.1038/onc.2010.195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aberrant activation of the epidermal growth factor receptor (EGFR) has been found in human cancers of various origins, and has been implicated in cancer pathogenesis. The therapeutic anti-EGFR antibodies cetuximab and matuzumab inhibit both ligand-induced receptor activation and growth of EGFR-expressing tumor cells. The efficacy of such EGFR-targeted therapies may be further enhanced by induction of functionally equivalent endogenous antibody responses. Here we describe novel peptide sequences selected from random peptide libraries for binding to single-chain antibody fragments of cetuximab or matuzumab. Two of these peptides characterized by KTL and YPLG motifs are recognized equally well by cetuximab and matuzumab, although nonoverlapping epitopes were previously reported for these antibodies. Immunization of experimental animals with synthetic KTL- and YPLG-containing peptides led to induction of antibodies that cross-react with human EGFR, and prevent binding of natural EGFR ligands, ligand-induced receptor activation and tumor cell growth in a manner similar to cetuximab and matuzumab. Our findings show that these peptide mimotopes can induce anti-EGFR antibodies with antitumoral activity, which may have implications for EGFR-specific cancer immunotherapy.
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Affiliation(s)
- C Hartmann
- Chemotherapeutisches Forschungsinstitut, Georg-Speyer-Haus, Frankfurt am Main, Germany
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149
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Tabuchi S, Ito J, Adachi T, Ishida H, Hata Y, Okazaki F, Tanaka T, Ogino C, Kondo A. Display of both N- and C-terminal target fusion proteins on the Aspergillus oryzae cell surface using a chitin-binding module. Appl Microbiol Biotechnol 2010; 87:1783-9. [PMID: 20499230 PMCID: PMC2903697 DOI: 10.1007/s00253-010-2664-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/27/2010] [Accepted: 04/29/2010] [Indexed: 11/28/2022]
Abstract
A novel cell surface display system in Aspergillus oryzae was established by using a chitin-binding module (CBM) from Saccharomyces cerevisiae as an anchor protein. CBM was fused to the N or C terminus of green fluorescent protein (GFP) and the fusion proteins (GFP-CBM and CBM-GFP) were expressed using A. oryzae as a host. Western blotting and fluorescence microscopy analysis showed that both GFP-CBM and CBM-GFP were successfully expressed on the cell surface. In addition, cell surface display of triacylglycerol lipase from A. oryzae (tglA), while retaining its activity, was also successfully demonstrated using CBM as an anchor protein. The activity of tglA was significantly higher when tglA was fused to the C terminus than N terminus of CBM. Together, these results show that CBM used as a first anchor protein enables the fusion of both the N and/or C terminus of a target protein.
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Affiliation(s)
- Soichiro Tabuchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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150
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SAROTUP: scanner and reporter of target-unrelated peptides. J Biomed Biotechnol 2010; 2010:101932. [PMID: 20339521 PMCID: PMC2842971 DOI: 10.1155/2010/101932] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/29/2010] [Indexed: 02/02/2023] Open
Abstract
As epitope mimics, mimotopes have been widely utilized in the study of epitope prediction and the development of new diagnostics, therapeutics, and vaccines. Screening the random peptide libraries constructed with phage display or any other surface display technologies provides an efficient and convenient approach to acquire mimotopes. However, target-unrelated peptides creep into mimotopes from time to time through binding to contaminants or other components of the screening system. In this study, we present SAROTUP, a free web tool for scanning, reporting and excluding possible target-unrelated peptides from real mimotopes. Preliminary tests show that SAROTUP is efficient and capable of improving the accuracy of mimotope-based epitope mapping. It is also helpful for the development of mimotope-based diagnostics, therapeutics, and vaccines.
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