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Charlermroj R, Makornwattana M, Phuengwas S, Karoonuthaisiri N. A rapid colorimetric lateral flow test strip for detection of live Salmonella Enteritidis using whole phage as a specific binder. Front Microbiol 2022; 13:1008817. [PMID: 36246228 PMCID: PMC9556839 DOI: 10.3389/fmicb.2022.1008817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Specific antibodies are essential components of immunoassay, which can be applied for the detection of pathogens. However, producing an antibody specific to live bacterial pathogens by the classical method of immunizing animals with live pathogens can be impractical. Phage display technology is an effective alternative method to obtain antibodies with the desired specificity against selected antigenic molecules. In this study, we demonstrated the power of a microarray-based technique for obtaining specific phage-derived antibody fragments against Salmonella, an important foodborne pathogen. The selected phage-displayed antibody fragments were subsequently employed to develop a lateral flow test strip assay for the detection of live Salmonella. The test strips showed specificity to Salmonella Enteritidis without cross-reactivity to eight serovars of Salmonella or other bacteria strains. The test strip assay requires 15 min, whereas the conventional biochemical and serological confirmation test requires at least 24 h. The microarray screening technique for specific phage-based binders and the test strip method can be further applied to other foodborne pathogens.
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Affiliation(s)
- Ratthaphol Charlermroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- *Correspondence: Ratthaphol Charlermroj,
| | - Manlika Makornwattana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sudtida Phuengwas
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- International Joint Research Center on Food Security, Pathum Thani, Thailand
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
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2
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Azouz NP, Klingler AM, Pathre P, Besse JA, Baruch-Morgenstern NB, Ballaban AY, Osswald GA, Brusilovsky M, Habel JE, Caldwell JM, Ynga-Durand MA, Abonia PJ, Hu YC, Wen T, Rothenberg ME. Functional role of kallikrein 5 and proteinase-activated receptor 2 in eosinophilic esophagitis. Sci Transl Med 2021; 12:12/545/eaaz7773. [PMID: 32461336 DOI: 10.1126/scitranslmed.aaz7773] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Eosinophilic esophagitis (EoE) is a chronic, food antigen-driven, inflammatory disease of the esophagus and is associated with impaired barrier function. Evidence is emerging that loss of esophageal expression of the serine peptidase inhibitor, kazal type 7 (SPINK7), is an upstream event in EoE pathogenesis. Here, we provide evidence that loss of SPINK7 mediates its pro-EoE effects via kallikrein 5 (KLK5) and its substrate, protease-activated receptor 2 (PAR2). Overexpression of KLK5 in differentiated esophageal epithelial cells recapitulated the effect of SPINK7 gene silencing, including barrier impairment and loss of desmoglein-1 expression. Conversely, KLK5 deficiency attenuated allergen-induced esophageal protease activity, modified commensal microbiome composition, and attenuated eosinophilia in a murine model of EoE. Inhibition of PAR2 blunted the cytokine production associated with loss of SPINK7 in epithelial cells and attenuated the allergen-induced esophageal eosinophilia in vivo. Clinical samples substantiated dysregulated PAR2 expression in the esophagus of patients with EoE, and delivery of the clinically approved drug α1 antitrypsin (A1AT, a protease inhibitor) inhibited experimental EoE. These findings demonstrate a role for the balance between KLK5 and protease inhibitors in the esophagus and highlight EoE as a protease-mediated disease. We suggest that antagonizing KLK5 and/or PAR2 has potential to be therapeutic for EoE.
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Affiliation(s)
- Nurit P Azouz
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Andrea M Klingler
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Purnima Pathre
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - John A Besse
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Netali Ben Baruch-Morgenstern
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Adina Y Ballaban
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Garrett A Osswald
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Michael Brusilovsky
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Jeff E Habel
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Mario A Ynga-Durand
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA.,Laboratorio de Inmunidad de Mucosas, Sección de Investigación y Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Pablo J Abonia
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229-3026, USA.
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3
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Mkaouar H, Akermi N, Kriaa A, Abraham AL, Jablaoui A, Soussou S, Mokdad-Gargouri R, Maguin E, Rhimi M. Serine protease inhibitors and human wellbeing interplay: new insights for old friends. PeerJ 2019; 7:e7224. [PMID: 31531264 PMCID: PMC6718151 DOI: 10.7717/peerj.7224] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.
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Affiliation(s)
- Héla Mkaouar
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Nizar Akermi
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Aicha Kriaa
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | | | - Amin Jablaoui
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Souha Soussou
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Raja Mokdad-Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Emmanuelle Maguin
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Moez Rhimi
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
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de Souza LR, Scott BM, Bhakta V, Donkor DA, Perruzza DL, Sheffield WP. Serpin Phage Display: The Use of a T7 System to Probe Reactive Center Loop Libraries with Different Serine Proteinases. Methods Mol Biol 2018; 1826:41-64. [PMID: 30194592 DOI: 10.1007/978-1-4939-8645-3_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phage display is a protein engineering approach that involves construction of libraries of variant proteins displayed on the surface of bacteriophage as capsid fusion proteins and their screening for binding and inhibitory function through the use of bait proteins. Recently, we adapted a commercially available T7 phage display system to create phage-displayed serpin libraries hypervariable in up to five positions in their reactive center loop (RCL). The RCL is a key determinant in serpin specificity, the relationship between the structure of a given serpin and which target proteinase(s) it inhibits. In this chapter, we describe protocols to assess the feasibility of this method for different serpin/proteinase combinations and share experience with this technology gathered in the course of studying two serpins and multiple proteinases with this powerful iterative screening approach.
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Affiliation(s)
- Lucas R de Souza
- Centre for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, Brazil
| | - Benjamin M Scott
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Varsha Bhakta
- Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada
| | - David A Donkor
- Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, HSC 4N66, McMaster University, Hamilton, ON, Canada
| | | | - William P Sheffield
- Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada. .,Department of Pathology and Molecular Medicine, HSC 4N66, McMaster University, Hamilton, ON, Canada.
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5
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Fortelny N, Butler GS, Overall CM, Pavlidis P. Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. Mol Cell Proteomics 2017; 16:1038-1051. [PMID: 28385878 PMCID: PMC5461536 DOI: 10.1074/mcp.m116.065706] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/24/2017] [Indexed: 01/18/2023] Open
Abstract
Protein interactions shape proteome function and thus biology. Identification of protein interactions is a major goal in molecular biology, but biochemical methods, although improving, remain limited in coverage and accuracy. Whereas computational predictions can guide biochemical experiments, low validation rates of predictions remain a major limitation. Here, we investigated computational methods in the prediction of a specific type of interaction, the inhibitory interactions between proteases and their inhibitors. Proteases generate thousands of proteoforms that dynamically shape the functional state of proteomes. Despite the important regulatory role of proteases, knowledge of their inhibitors remains largely incomplete with the vast majority of proteases lacking an annotated inhibitor. To link inhibitors to their target proteases on a large scale, we applied computational methods to predict inhibitory interactions between proteases and their inhibitors based on complementary data, including coexpression, phylogenetic similarity, structural information, co-annotation, and colocalization, and also surveyed general protein interaction networks for potential inhibitory interactions. In testing nine predicted interactions biochemically, we validated the inhibition of kallikrein 5 by serpin B12. Despite the use of a wide array of complementary data, we found a high false positive rate of computational predictions in biochemical follow-up. Based on a protease-specific definition of true negatives derived from the biochemical classification of proteases and inhibitors, we analyzed prediction accuracy of individual features, thereby we identified feature-specific limitations, which also affected general protein interaction prediction methods. Interestingly, proteases were often not coexpressed with most of their functional inhibitors, contrary to what is commonly assumed and extrapolated predominantly from cell culture experiments. Predictions of inhibitory interactions were indeed more challenging than predictions of nonproteolytic and noninhibitory interactions. In summary, we describe a novel and well-defined but difficult protein interaction prediction task and thereby highlight limitations of computational interaction prediction methods.
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Affiliation(s)
- Nikolaus Fortelny
- From the ‡Department of Biochemistry and Molecular Biology
- §Michael Smith Laboratories
- ¶Centre for Blood Research
| | - Georgina S Butler
- ¶Centre for Blood Research
- ‖Department of Oral Biological and Medical Sciences, Faculty of Dentistry
| | - Christopher M Overall
- From the ‡Department of Biochemistry and Molecular Biology
- ¶Centre for Blood Research
- ‖Department of Oral Biological and Medical Sciences, Faculty of Dentistry
| | - Paul Pavlidis
- §Michael Smith Laboratories;
- **Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
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Proteolytic inactivation of nuclear alarmin high-mobility group box 1 by complement protease C1s during apoptosis. Cell Death Discov 2016; 2:16069. [PMID: 27648302 PMCID: PMC5018544 DOI: 10.1038/cddiscovery.2016.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 02/08/2023] Open
Abstract
Effective clearance of apoptotic cells by phagocytes prevents the release of intracellular alarmins and manifestation of autoimmunity. This prompt efferocytosis is complemented by intracellular proteolytic degradation that occurs within the apoptotic cells and in the efferosome of the phagocytes. Although the role of extracellular proteases in apoptotic cells clearance is unknown, the strong association of congenital C1s deficiency with Systemic Lupus Erythematosus highlights the protective nature that this extracellular protease has against autoimmunity. The archetypical role of serine protease C1s as the catalytic arm of C1 complex (C1qC1r2C1s2) involve in the propagation of the classical complement pathway could not provide the biological basis for this association. However, a recent observation of the ability of C1 complex to cleave a spectrum of intracellular cryptic targets exposed during apoptosis provides a valuable insight to the underlying protective mechanism. High-mobility group box 1 (HMGB1), an intracellular alarmin that is capable of inducing the formation of antinuclear autoantibodies and causes lupus-like conditions in mice, is identified as a novel potential target by bioinformatics analysis. This is verified experimentally with C1s, both in its purified and physiological form as C1 complex, cleaving HMGB1 into defined fragments of 19 and 12 kDa. This cleavage diminishes HMGB1 ability to enhance lipopolysaccharide mediated pro-inflammatory cytokines production from monocytes, macrophages and dendritic cells. Further mass spectrometric analysis of the C1 complex treated apoptotic cellular proteins demonstrated additional C1s substrates and revealed the complementary role of C1s in apoptotic cells clearance through the proteolytic cleavage of intracellular alarmins and autoantigens. C1 complex may have evolved as, besides the bacteriolytic arm of antibodies in which it activates the complement cascade, a tissue renewal mechanism that reduces the immunogenicity of apoptotic tissue debris and decreases the likelihood of autoimmunity.
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A natural genetic variant of granzyme B confers lethality to a common viral infection. PLoS Pathog 2014; 10:e1004526. [PMID: 25502180 PMCID: PMC4263754 DOI: 10.1371/journal.ppat.1004526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/16/2014] [Indexed: 01/02/2023] Open
Abstract
Many immune response genes are highly polymorphic, consistent with the selective pressure imposed by pathogens over evolutionary time, and the need to balance infection control with the risk of auto-immunity. Epidemiological and genomic studies have identified many genetic variants that confer susceptibility or resistance to pathogenic micro-organisms. While extensive polymorphism has been reported for the granzyme B (GzmB) gene, its relevance to pathogen immunity is unexplored. Here, we describe the biochemical and cytotoxic functions of a common allele of GzmB (GzmBW) common in wild mouse. While retaining ‘Asp-ase’ activity, GzmBW has substrate preferences that differ considerably from GzmBP, which is common to all inbred strains. In vitro, GzmBW preferentially cleaves recombinant Bid, whereas GzmBP activates pro-caspases directly. Recombinant GzmBW and GzmBP induced equivalent apoptosis of uninfected targets cells when delivered with perforin in vitro. Nonetheless, mice homozygous for GzmBW were unable to control murine cytomegalovirus (MCMV) infection, and succumbed as a result of excessive liver damage. Although similar numbers of anti-viral CD8 T cells were generated in both mouse strains, GzmBW-expressing CD8 T cells isolated from infected mice were unable to kill MCMV-infected targets in vitro. Our results suggest that known virally-encoded inhibitors of the intrinsic (mitochondrial) apoptotic pathway account for the increased susceptibility of GzmBW mice to MCMV. We conclude that different natural variants of GzmB have a profound impact on the immune response to a common and authentic viral pathogen. Granzymes (Gzm) are serine proteases expressed by cytotoxic T cells and natural killer cells, and are important for the destruction of virally infected cells. To date, the function of these molecules has been assessed exclusively in common laboratory mouse strains that express identical granzyme proteins. In wild mouse populations, variants of granzyme B have been identified, but how these function, especially in the context of infections, is unknown. We have generated a novel mouse strain expressing a granzyme B variant found in wild mice (GzmBW), and exposed these mice to viral infections. The substrates cleaved by GzmBW were found to differ significantly from those cleaved by the GzmBP protein, which is normally expressed by laboratory mice. Alterations in substrate specificity resulted in GzmBW mice being significantly more susceptible to infection with murine cytomegalovirus, a common mouse pathogen. Our findings demonstrate that polymorphisms in granzyme B can profoundly affect the outcome of infections with some viral pathogens.
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