1
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Hinmon JA, King JM, Mayo LJ, Faries CR, Lockett YT, Crawford DW, Beardslee PC, Hendricks A, McNaughton BR. Cell surface β-lactamase recruitment: A facile selection to identify protein-protein interactions. Protein Sci 2024; 33:e4919. [PMID: 38501433 PMCID: PMC10949332 DOI: 10.1002/pro.4919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Protein-protein interactions (PPIs) are central to many cellular processes, and the identification of novel PPIs is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved PPIs are therefore valuable research tools. We have developed a facile selection that links PPI-dependent β-lactamase recruitment on the surface of Escherichia coli with resistance to ampicillin. Bacteria displaying a protein that forms a complex with a specific protein-β-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not recruit β-lactamase to the cell surface are killed by ampicillin. Given its simplicity and tunability, we anticipate this selection will be a valuable addition to the palette of methods for illuminating and interrogating PPIs.
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Affiliation(s)
- Jordan A. Hinmon
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Jade M. King
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Latrina J. Mayo
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Cierra R. Faries
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Ya'hnis T. Lockett
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - David W. Crawford
- Department of ChemistryColorado State UniversityFort CollinsColoradoUSA
| | | | | | - Brian R. McNaughton
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
- Department of ChemistryColorado State UniversityFort CollinsColoradoUSA
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2
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Randall JR, Groover KE, O'Donnell AC, Garza JM, Cole TJ, Davies BW. Adapting anti bacterial display to identify serum-active macrocyclic peptide antibiotics. PNAS Nexus 2023; 2:pgad270. [PMID: 37637199 PMCID: PMC10449418 DOI: 10.1093/pnasnexus/pgad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023]
Abstract
The lack of available treatments for many antimicrobial-resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity toward human cells, making in vivo use challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of Gram-negative bacteria without strong inner-membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its function in vivo, suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retain in vivo functionality.
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Affiliation(s)
- Justin R Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kyra E Groover
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Angela C O'Donnell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph M Garza
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - T Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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3
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Shingarova LN, Petrovskaya LE, Kryukova EA, Gapizov SS, Dolgikh DA, Kirpichnikov MP. Display of Oligo-α-1,6-Glycosidase from Exiguobacterium sibiricum on the Surface of Escherichia coli Cells. Biochemistry (Mosc) 2023; 88:716-722. [PMID: 37331717 DOI: 10.1134/s0006297923050140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/20/2023]
Abstract
Cell-surface display using anchor motifs of outer membrane proteins allows exposure of target peptides and proteins on the surface of microbial cells. Previously, we obtained and characterized highly catalytically active recombinant oligo-α-1,6-glycosidase from the psychrotrophic bacterium Exiguobacterium sibiricum (EsOgl). It was also shown that the autotransporter AT877 from Psychrobacter cryohalolentis and its deletion variants efficiently displayed type III fibronectin (10Fn3) domain 10 on the surface of Escherichia coli cells. The aim of the work was to obtain an AT877-based system for displaying EsOgl on the surface of bacterial cells. The genes for the hybrid autotransporter EsOgl877 and its deletion mutants EsOgl877Δ239 and EsOgl877Δ310 were constructed, and the enzymatic activity of EsOgl877 was investigated. Cells expressing this protein retained ~90% of the enzyme maximum activity within a temperature range of 15-35°C. The activity of cells expressing EsOgl877Δ239 and EsOgl877Δ310 was 2.7 and 2.4 times higher, respectively, than of the cells expressing the full-size AT. Treatment of cells expressing EsOgl877 deletion variants with proteinase K showed that the passenger domain localized to the cell surface. These results can be used for further optimization of display systems expressing oligo-α-1,6-glycosidase and other heterologous proteins on the surface of E. coli cells.
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Affiliation(s)
- Lyudmila N Shingarova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sultan S Gapizov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitry A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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4
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Shingarova LN, Petrovskaya LE, Kryukova EA, Gapizov SS, Boldyreva EF, Dolgikh DA, Kirpichnikov MP. Deletion Variants of Autotransporter from Psychrobacter cryohalolentis Increase Efficiency of 10FN3 Exposure on the Surface of Escherichia coli Cells. Biochemistry (Mosc) 2022; 87:932-939. [PMID: 36180989 DOI: 10.1134/s0006297922090061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 06/16/2023]
Abstract
The autotransporter AT877 from Psychrobacter cryohalolentis belongs to the family of outer membrane proteins containing N-terminal passenger and C-terminal translocator domains that form the basis for the design of display systems on the surface of bacterial cells. It was shown in our previous study that the passenger domain of AT877 can be replaced by the cold-active esterase EstPc or the tenth domain of fibronectin type III (10Fn3). In order to increase efficiency of the 10Fn3 surface display in Escherichia coli cells, four deletion variants of the Fn877 hybrid autotransporter were obtained. It was demonstrated that all variants are present in the membrane of bacterial cells and facilitate binding of the antibodies specific against 10Fn3 on the cell surface. The highest level of binding is provided by the variants Δ239 and Δ310, containing four and seven beta-strands out of twelve that comprise the structure of the translocator domain. Using electrophoresis under semi-native conditions, presence of heat modifiability in the full-size Fn877 and its deletion variants was demonstrated, which indicated preservation of beta structure in their molecules. The obtained results could be used to optimize the bacterial display systems of 10Fn3, as well as of other heterologous passenger domains.
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Affiliation(s)
- Lyudmila N Shingarova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sultan S Gapizov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Elena F Boldyreva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Dmitriy A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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5
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Zhao X, Cebrián R, Fu Y, Rink R, Bosma T, Moll GN, Kuipers OP. High-Throughput Screening for Substrate Specificity-Adapted Mutants of the Nisin Dehydratase NisB. ACS Synth Biol 2020; 9:1468-1478. [PMID: 32374981 PMCID: PMC7309312 DOI: 10.1021/acssynbio.0c00130] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Microbial
lanthipeptides are formed by a two-step enzymatic introduction
of (methyl)lanthionine rings. A dehydratase catalyzes the dehydration
of serine and threonine residues, yielding dehydroalanine and dehydrobutyrine,
respectively. Cyclase-catalyzed coupling of the formed dehydroresidues
to cysteines forms (methyl)lanthionine rings in a peptide. Lanthipeptide
biosynthetic systems allow discovery of target-specific, lanthionine-stabilized
therapeutic peptides. However, the substrate specificity of existing
modification enzymes impose limitations on installing lanthionines
in non-natural substrates. The goal of the present study was to obtain
a lanthipeptide dehydratase with the capacity to dehydrate substrates
that are unsuitable for the nisin dehydratase NisB. We report high-throughput
screening for tailored specificity of intracellular, genetically encoded
NisB dehydratases. The principle is based on the screening of bacterially
displayed lanthionine-constrained streptavidin ligands, which have
a much higher affinity for streptavidin than linear ligands. The designed
NisC-cyclizable high-affinity ligands can be formed via mutant NisB-catalyzed
dehydration but less effectively via wild-type NisB activity. In Lactococcus lactis, a cell surface display precursor was
designed comprising DSHPQFC. The Asp residue preceding the serine
in this sequence disfavors its dehydration by wild-type NisB. The
cell surface display vector was coexpressed with a mutant NisB library
and NisTC. Subsequently, mutant NisB-containing bacteria that display
cyclized strep ligands on the cell surface were selected via panning
rounds with streptavidin-coupled magnetic beads. In this way, a NisB
variant with a tailored capacity of dehydration was obtained, which
was further evaluated with respect to its capacity to dehydrate nisin
mutants. These results demonstrate a powerful method for selecting
lanthipeptide modification enzymes with adapted substrate specificity.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Rick Rink
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Tjibbe Bosma
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Gert N. Moll
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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6
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Abstract
Semisynthetic cyclic peptides containing both non-proteinogenic building blocks, as the synthetic part, and a genetically encoded sequence amenable to DNA-based randomization hold great potential to expand the chemical space in the quest for novel bioactive peptides. Key to an efficient selection of novel binders to biomacromolecules is a robust method to link their genotype and phenotype. A novel bacterial cell surface display technology has been developed to present cyclic peptides composed of synthetic and genetically encoded fragments in their backbones. The fragments were combined by protein trans-splicing and intramolecular oxime ligation. To this end, a split intein half and an unnatural amino acid were displayed with the genetically encoded part on the surface of Escherichia coli. Addition of the synthetic fragment equipped with the split intein partner and an aminooxy moiety, as well as the application of a pH-shift protocol, resulted in the onsurface formation of the semisynthetic cyclic peptide. This approach will serve for the generation of cyclic peptide libraries suitable for selection by fluorescence-activated cell sorting, and more generally enables chemical modification of proteins on the bacterial surface.
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Affiliation(s)
- Shubhendu Palei
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Kira S Becher
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Christian Nienberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
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7
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Andersson KG, Persson J, Ståhl S, Löfblom J. Autotransporter-Mediated Display of a Naïve Affibody Library on the Outer Membrane of Escherichia coli. Biotechnol J 2018; 14:e1800359. [PMID: 30179307 DOI: 10.1002/biot.201800359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/23/2018] [Indexed: 12/14/2022]
Abstract
Development of new affinity proteins using combinatorial protein engineering is today established for generation of monoclonal antibodies and also essential for discovery of binders that are based on non-immunoglobulin proteins. Phage display is most frequently used, but yeast display is becoming increasingly popular, partly due to the option of utilizing fluorescence-activated cell sorting (FACS) for isolation of new candidates. Escherichia coli has several valuable properties for library applications and in particular the high transformation efficiency. The use of various autotransporters and intimins for secretion and anchoring on the outer membrane have shown promising results and particularly for directed evolution of different enzymes. Here, the authors report on display of a large naïve affibody library on the outer membrane of E. coli using the autotransporter Adhesin Involved in Diffuse Adherence (AIDA-I). The expression cassette is first engineered by removing non-essential sequences, followed by introduction of an affibody library, comprising more than 109 variants, into the new display vector. The quality of the library and general performance of the method is assessed by FACS against five different targets, which resulted in a panel of binders with down to nanomolar affinities, suggesting that the method has potential as a complement to phage display for generation of affibody molecules.
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Affiliation(s)
- Ken G Andersson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Jonas Persson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Stefan Ståhl
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - John Löfblom
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
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8
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Jo M, Hwang B, Yoon HW, Jung ST. Escherichia coli inner membrane display system for high-throughput screening of dimeric proteins. Biotechnol Bioeng 2018; 115:2849-2858. [PMID: 30171695 DOI: 10.1002/bit.26826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/23/2018] [Accepted: 08/30/2018] [Indexed: 11/10/2022]
Abstract
Multimer formation is indispensable to the intrinsicbiologicalfunctions of many natural proteins. For example, the human immunoglobulin G (IgG) antibody has two variable regions (heavy chain variable domain [VH] and light chain variable domain [VL]) that must be assembled for specific antigen binding, and homodimerization of the antibody's Fc domain is essential for eliciting therapeutic effector functions. For the more efficient high-throughput directed evolution of multimeric proteins with ease of cultivation and handling, here we report a membrane protein drift and assembly (MPDA) system, in which a multimeric protein is displayed on a bacterial inner membrane by drifting and auto-assembling membrane-anchored subunit polypeptides. This system enabled the auto-assembly of membrane-tethered Fv domains (VH and VL) or the monomeric Fc domain into a functional hetero- or homodimeric protein complex on the bacterial inner membrane. This system could also be used to enrich a desired engineered Fc variant from a mixture containing a million-fold excess of wild-type Fc domain, indicating the applicability of the MPDA system for the high-throughput directed evolution of a variety of multimeric proteins, such as cytokines, enzymes, or structural proteins.
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Affiliation(s)
- Migyeong Jo
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Bora Hwang
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Hyun Woung Yoon
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Sang Taek Jung
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
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9
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Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
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Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
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10
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Salema V, Mañas C, Cerdán L, Piñero-Lambea C, Marín E, Roovers RC, Van Bergen En Henegouwen PMP, Fernández LÁ. High affinity nanobodies against human epidermal growth factor receptor selected on cells by E. coli display. MAbs 2016; 8:1286-1301. [PMID: 27472381 PMCID: PMC5058628 DOI: 10.1080/19420862.2016.1216742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most therapeutic antibodies (Abs) target cell surface proteins on tumor and immune cells. Cloning of Ab gene libraries in E. coli and their display on bacteriophages is commonly used to select novel therapeutic Abs binding target antigens, either purified or expressed on cells. However, the sticky nature of bacteriophages renders phage display selections on cells challenging. We previously reported an E. coli display system for expression of VHHs (i.e., nanobodies, Nbs) on the surface of bacteria and selection of high-affinity clones by magnetic cell sorting (MACS). Here, we demonstrate that E. coli display is also an attractive method for isolation of Nbs against cell surface antigens, such as the epidermal growth factor receptor (EGFR), upon direct selection and screening of Ab libraries on live cells. We employ a whole cell-based strategy using a VHH library obtained by immunization with human tumor cells over-expressing EGFR (i.e., A431), and selection of bacterial clones bound to murine fibroblast NIH-3T3 cells transfected with human EGFR, after depletion of non-specific clones on untransfected cells. This strategy resulted in the isolation of high-affinity Nbs binding distinct epitopes of EGFR, including Nbs competing with the ligand, EGF, as characterized by flow cytometry of bacteria displaying the Nbs and binding assays with purified Nbs using surface plasmon resonance. Hence, our study demonstrates that E. coli display of VHH libraries and selection on cells enables efficient isolation and characterization of high-affinity Nbs against cell surface antigens.
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Affiliation(s)
- Valencio Salema
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Carmen Mañas
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Lidia Cerdán
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Carlos Piñero-Lambea
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Elvira Marín
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Rob C Roovers
- b Cell Biology, Department of Biology, Science Faculty, Utrecht University , Utrecht , The Netherlands
| | | | - Luis Ángel Fernández
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
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11
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Kogot JM, Pennington JM, Sarkes DA, Kingery DA, Pellegrino PM, Stratis-Cullum DN. Screening and characterization of anti-SEB peptides using a bacterial display library and microfluidic magnetic sorting. J Mol Recognit 2015; 27:739-45. [PMID: 25319622 PMCID: PMC4274986 DOI: 10.1002/jmr.2400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 04/22/2014] [Accepted: 05/27/2014] [Indexed: 11/06/2022]
Abstract
Bacterial peptide display libraries enable the rapid and efficient selection of peptides that have high affinity and selectivity toward their targets. Using a 15-mer random library on the outer surface of Escherichia coli (E.coli), high-affinity peptides were selected against a staphylococcal enterotoxin B (SEB) protein after four rounds of biopanning. On-cell screening analysis of affinity and specificity were measured by flow cytometry and directly compared to the synthetic peptide, off-cell, using peptide-ELISA. DNA sequencing of the positive clones after four rounds of microfluidic magnetic sorting (MMS) revealed a common consensus sequence of (S/T)CH(Y/F)W for the SEB-binding peptides R338, R418, and R445. The consensus sequence in these bacterial display peptides has similar amino acid characteristics with SEB peptide sequences isolated from phage display. The Kd measured by peptide-ELISA off-cell was 2.4 nM for R418 and 3.0 nM for R445. The bacterial peptide display methodology using the semiautomated MMS resulted in the discovery of selective peptides with affinity for a food safety and defense threat. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Journal of Molecular Recognition published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Joshua M Kogot
- US Army Research Laboratory; Sensors and Electron Devices, Adelphi, MD, USA
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12
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Sankaran S, Kiren MC, Jonkheijm P. Incorporating Bacteria as a Living Component in Supramolecular Self-Assembled Monolayers through Dynamic Nanoscale Interactions. ACS Nano 2015; 9:3579-86. [PMID: 25738514 DOI: 10.1021/acsnano.5b00694] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Supramolecular assemblies, formed through noncovalent interactions, has become particularly attractive to develop dynamic and responsive architectures to address living systems at the nanoscale. Cucurbit[8]uril (CB[8]), a pumpkin shaped macrocylic host molecule, has been successfully used to construct various self-assembled architectures for biomedical applications since it can simultaneously bind two aromatic guest molecules within its cavity. Such architectures can also be designed to respond to external stimuli. Integrating living organisms as an active component into such supramolecular architectures would add a new dimension to the capabilities of such systems. To achieve this, we have incorporated supramolecular functionality at the bacterial surface by genetically modifying a transmembrane protein to display a CB[8]-binding motif as part of a cystine-stabilized miniprotein. We were able to confirm that this supramolecular motif on the bacterial surface specifically binds CB[8] and forms multiple intercellular ternary complexes leading to aggregation of the bacterial solution. We performed various aggregation experiments to understand how CB[8] interacts with this bacterial strain and also demonstrate that it can be chemically reversed using a competitor. To confirm that this strain can be incorporated with a CB[8] based architecture, we show that the bacterial cells were able to adhere to CB[8] self-assembled monolayers (SAMs) on gold and still retain considerable motility for several hours, indicating that the system can potentially be used to develop supramolecular bacterial biomotors. The bacterial strain also has the potential to be combined with other CB[8] based architectures like nanoparticles, vesicles and hydrogels.
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Affiliation(s)
- Shrikrishnan Sankaran
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
| | - Mustafa Can Kiren
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
| | - Pascal Jonkheijm
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
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Spatola BN, Kaukinen K, Collin P, Mäki M, Kagnoff MF, Daugherty PS. Persistence of elevated deamidated gliadin peptide antibodies on a gluten-free diet indicates nonresponsive coeliac disease. Aliment Pharmacol Ther 2014; 39:407-17. [PMID: 24392888 PMCID: PMC3962785 DOI: 10.1111/apt.12603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/18/2013] [Accepted: 12/11/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Histologically nonresponsive coeliac disease (NRCD) is a potentially serious condition diagnosed during the follow-up of coeliac disease (CD) when patients have persistent villous atrophy despite following a gluten-free diet (GFD). AIM As current assessments of recovery are limited to invasive and costly serial duodenal biopsies, we sought to identify antibody biomarkers for CD patients that do not respond to traditional therapy. METHODS Bacterial display peptide libraries were screened by flow cytometry to identify epitopes specifically recognised by antibodies from patients with NRCD, but not by antibodies from responsive CD patients. Deamidated gliadin was confirmed to be the antigen mimicked by library peptides using ELISA with sera from NRCD (n = 15) and responsive CD (n = 45) patients on a strict GFD for at least 1 year. RESULTS The dominant consensus epitope sequence identified by unbiased library screening QPxx(A/P)FP(E/D) was highly similar to reported deamidated gliadin peptide (dGP) B-cell epitopes. Measurement of anti-dGP IgG titre by ELISA discriminated between NRCD and responsive CD patients with 87% sensitivity and 89% specificity. Importantly, dGP antibody titre correlated with the severity of mucosal damage indicating that IgG dGP titres may be useful to monitor small intestinal mucosal recovery on a GFD. CONCLUSIONS The finding of increased levels of anti-dGP IgG antibodies in CD patients on strict GFDs effectively identifies patients with NRCD. Finally, anti-dGP IgG assays may be useful to monitor mucosal damage and histological improvement in CD patients on a strict GFD.
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Affiliation(s)
- Bradley N. Spatola
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Katri Kaukinen
- School of Medicine, University of Tampere and Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland,Department of Medicine, Seinäjoki Central Hospital, Seinäjoki, Finland
| | - Pekka Collin
- School of Medicine, University of Tampere and Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Markku Mäki
- Center for Child Health Research, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Martin F. Kagnoff
- Laboratory of Mucosal Immunology, Departments of Medicine and Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA,Correspondence ; Postal: Department of Chemical Engineering; Engineering II, Rm 3357; University of California, Santa Barbra; Santa Barbara, CA 93106-5080; Phone: (805) 893-2610
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Sergeeva A, Kolonin MG, Molldrem JJ, Pasqualini R, Arap W. Display technologies: application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev 2006; 58:1622-54. [PMID: 17123658 PMCID: PMC1847402 DOI: 10.1016/j.addr.2006.09.018] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 09/29/2006] [Indexed: 01/17/2023]
Abstract
Recognition of molecular diversity of cell surface proteomes in disease is essential for the development of targeted therapies. Progress in targeted therapeutics requires establishing effective approaches for high-throughput identification of agents specific for clinically relevant cell surface markers. Over the past decade, a number of platform strategies have been developed to screen polypeptide libraries for ligands targeting receptors selectively expressed in the context of various cell surface proteomes. Streamlined procedures for identification of ligand-receptor pairs that could serve as targets in disease diagnosis, profiling, imaging and therapy have relied on the display technologies, in which polypeptides with desired binding profiles can be serially selected, in a process called biopanning, based on their physical linkage with the encoding nucleic acid. These technologies include virus/phage display, cell display, ribosomal display, mRNA display and covalent DNA display (CDT), with phage display being by far the most utilized. The scope of this review is the recent advancements in the display technologies with a particular emphasis on molecular mapping of cell surface proteomes with peptide phage display. Prospective applications of targeted compounds derived from display libraries in the discovery of targeted drugs and gene therapy vectors are discussed.
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Affiliation(s)
- Anna Sergeeva
- Department of Blood and Marrow Transplantation, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Mikhail G. Kolonin
- Department of Genitourinary Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Jeffrey J. Molldrem
- Department of Blood and Marrow Transplantation, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Renata Pasqualini
- Department of Genitourinary Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Wadih Arap
- Department of Genitourinary Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
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