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Zhang Y, Bhardwaj SR, Vilches A, Breksa A, Lyu SC, Chinthrajah S, Nadeau KC, Jin T. IgE binding epitope mapping with TL1A tagged peptides. Mol Immunol 2023; 153:194-199. [PMID: 36527758 DOI: 10.1016/j.molimm.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/22/2022]
Abstract
Linear IgE epitopes play essential roles in persistent allergies, including peanut and tree nut allergies. Using chemically synthesized peptides attached to membranes and microarray experiments is one approach for determining predominant epitopes that has seen success. However, the overall expense of this approach and the inherent challenges in scaling up the production and purification of synthetic peptides precludes the general application of this approach. To overcome this problem, we have constructed a plasmid vector for expressing peptides sandwiched between an N-terminal His-tag and a trimeric protein. The vector was used to make overlapping peptides derived from peanut allergens Ara h 2. All the peptides were successfully expressed and purified. The resulting peptides were applied to identify IgE binding epitopes of Ara h 2 using four sera samples from individuals with known peanut allergies. New and previously defined dominant IgE binding epitopes of Ara h 2 were identified. This system may be readily applied to produce agents for component- and epitope-resolved food allergy diagnosis.
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Affiliation(s)
- Yuzhu Zhang
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
| | - Shilpa R Bhardwaj
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Ana Vilches
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Andrew Breksa
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Shu-Chen Lyu
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, 269 Campus Dr, Stanford, CA 94305, USA
| | - Sharon Chinthrajah
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, 269 Campus Dr, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, 269 Campus Dr, Stanford, CA 94305, USA
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027 China.
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2
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Mohanty S, Dabburu GR, Kumar M, Khasa YP. Heterologous expression of novel SUMO proteases from Schizosaccharomyces pombe in E. coli: Catalytic domain identification and optimization of product yields. Int J Biol Macromol 2022; 209:1001-1019. [PMID: 35447271 DOI: 10.1016/j.ijbiomac.2022.04.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Small ubiquitin-related modifier (SUMO) proteins are efficiently used to target the soluble expression of various difficult-to-express proteins in E. coli. However, its utilization in large scale protein production is restricted by the higher cost of Ulp, which is required to cleave SUMO fusion tag from protein-of-interest to generate an authentic N-terminus. This study identified and characterized two novel SUMO proteases i.e., Ulp1 and Ulp2 from Schizosaccharomyces pombe. Codon-optimized gene sequences were cloned and expressed in E. coli. The sequence and structure of SpUlp1 and SpUlp2 catalytic domains were deduced using bioinformatics tools. Protein-protein interaction studies predicted the higher affinity of SpUlp1 towards SUMO compared to its counterpart from Saccharomyces cerevisiae (ScUlp1). The catalytic domain of SpUlp1 was purified using Ni-NTA chromatography with 83.33% recovery yield. Moreover, In vitro activity data further confirmed the fast-acting nature of SpUlp1 catalytic domain, where a 90% cleavage of fusion proteins was obtained within 1 h of incubation, indicating novelty and commercial relevance of S. pombe Ulp1. Biophysical characterization showed 8.8% α-helices, 36.7% β-sheets in SpUlp1SD. From thermal CD and fluorescence data, SpUlp1SD Tm was found to be 45 °C. Further, bioprocess optimization using fed-batch cultivation resulted in 3.5 g/L of SpUlp1SD production with YP/X of 77.26 mg/g DCW and volumetric productivity of 205.88 mg/L/h.
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Affiliation(s)
- Shilpa Mohanty
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Govinda Rao Dabburu
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India
| | - Yogender Pal Khasa
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India.
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Krajewska M, Koprowski P. Solubilization, purification, and functional reconstitution of human ROMK potassium channel in copolymer styrene-maleic acid (SMA) nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183555. [PMID: 33444624 DOI: 10.1016/j.bbamem.2021.183555] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/13/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Expression, purification, and functional reconstitution of mammalian ion channels are often challenging. Heterologous expression of mammalian channels in bacteria can be advantageous due to unrelated protein environment and the lack of risk of copurification of endogenous proteins, e.g., accessory channel subunits that can influence the channel activity. Also, direct recording of channel activity could be challenging due to their intracellular localization like in the case of mitochondrial channels. The activity of purified channels can be characterized at the single-molecule level by electrophysiological techniques, such as planar lipid bilayers (PLB). In this work, we describe a simple approach to accomplish PLB recording of the activity of single renal outer medullary potassium channels ROMK expressed in E. coli. We focused on the ROMK2 isoform that is present at low levels in the mitochondria and can be responsible for mitoKATP activity. We screened for the best construct to express the codon-optimized ROMK proteins with a 6xHis tag for protein purification. The strategy involved the use of optimal styrene-maleic acid (SMA) copolymer, which forms so-called polymer nanodiscs, to solubilize and purify ROMK-containing SMA lipid particles (SMALPs), which were amenable for fusion with PLB. Reconstituted ROMK channels exhibited ion selectivity, rectification, and pharmacological properties, which are in agreement with previous work on ROMK channels.
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Affiliation(s)
- Milena Krajewska
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, Pasteur str. 3, Warsaw 02-093, Poland
| | - Piotr Koprowski
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology PAS, Pasteur str. 3, Warsaw 02-093, Poland.
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Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M, Sinnreich M, Aihara H, Kinter J. DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. FASEB J 2020; 34:4573-4590. [PMID: 32020675 PMCID: PMC7079142 DOI: 10.1096/fj.201902696] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/17/2020] [Indexed: 01/13/2023]
Abstract
Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio‐scapulo‐humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.
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Affiliation(s)
- Christian Klingler
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Jon Ashley
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Department of Health Technology, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adeline Stiefvater
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.,Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Michael Sinnreich
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jochen Kinter
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
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Lin L, Moran TP, Peng B, Yang J, Culton DA, Che H, Jiang S, Liu Z, Geng S, Zhang Y, Diaz LA, Qian Y. Walnut antigens can trigger autoantibody development in patients with pemphigus vulgaris through a "hit-and-run" mechanism. J Allergy Clin Immunol 2019; 144:720-728.e4. [PMID: 31071340 PMCID: PMC6742533 DOI: 10.1016/j.jaci.2019.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Environmental factors, as well as genetic predisposition, are known to be critical for the development of autoimmunity. However, the environmental agents that trigger autoimmune responses have remained elusive. One possible explanation is the "hit-and-run" mechanism in which the inciting antigens that initiate autoimmune responses are not present at the time of overt autoimmune disease. OBJECTIVE After our previous findings that some allergens can incite autoimmune responses, we investigated the potential role of environmental allergens in triggering autoantibody development in patients with an autoimmune skin disease, pemphigus vulgaris (PV). METHODS Revertant/germline mAbs (with mutations on variable regions of heavy and light chains reverted to germline forms) of 8 anti-desmoglein (Dsg) 3 pathogenic mAbs from patients with PV were tested for reactivity against a panel of possible allergens, including insects, pollens, epithelia, fungi, and food antigens. RESULTS All the PV germline mAbs were reactive to antigens from walnut, including the well-known allergen Jug r 2 and an uncharacterized 85-kDa protein component. Sera from patients with PV contained significantly greater levels of anti-Dsg3 autoantibodies than walnut-specific antibodies, suggesting that the autoreactive B-cell response in patients with PV might be initially triggered by walnut antigens but is subsequently driven by Dsg3. CONCLUSION Our findings suggest that walnut antigens/allergens can initiate autoantibody development in patients with PV through a "hit-and-run" mechanism. The revertant/germline mAb approach might provide a paradigm for the etiological study of other allergic and autoimmune diseases.
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Affiliation(s)
- Lan Lin
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Timothy P Moran
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bin Peng
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Dermatology, Northwest Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Jinsheng Yang
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Donna A Culton
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Huilian Che
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Western Regional Research Center, US Department of Agriculture, Albany, Calif
| | - Songsong Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Western Regional Research Center, US Department of Agriculture, Albany, Calif
| | - Zhi Liu
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Songmei Geng
- Department of Dermatology, Northwest Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yuzhu Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Luis A Diaz
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ye Qian
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC.
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Che H, Zhang Y, Jiang S, Jin T, Lyu SC, Nadeau KC, McHugh T. Almond ( Prunus dulcis) Allergen Pru du 8, the First Member of a New Family of Food Allergens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8626-8631. [PMID: 31287307 DOI: 10.1021/acs.jafc.9b02781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An almond allergen with two known short peptide sequences was reported as the almond 2S albumin but was later suspected to be almond vicilin. However, this allergen was not designated by the World Health Organization/International Union of Immunological Societies. This study aimed to determine the true identity of this elusive almond allergen. cDNAs were synthesized from total RNA of the Nonpareil almond. The complete sequence of the previously reported almond allergen was determined from its coding sequence. The deduced protein was produced recombinantly and was confirmed to be a food allergen by testing with 18 almond-allergic sera. The allergen is a potential cysteine-rich antimicrobial protein with characteristic C[X]3C-[X]10-12-C[X]3C motifs of the hairpinin antimicrobial protein. This first member of a novel family of food allergens was named Pru du 8. The signature motif of the hairpinin antimicrobial protein can be found in the N-terminal region of some vicilin allergens (e.g., Ara h 1). It can also be found in the signal peptide of other vicilin allergens (e.g., Car i 2). In many species, however, vicilins do not contain such a motif, indicating that the presence of the signature motifs of the hairpinin antimicrobial protein in vicilins might be a result of translocation during evolution.
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Affiliation(s)
- Huilian Che
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , 17 Qinghua Donglu , Haidian District, Beijing 100038 , People's Republic of China
- Western Regional Research Center, Pacific West Area, Agricultural Research Service , United States Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
| | - Yuzhu Zhang
- Western Regional Research Center, Pacific West Area, Agricultural Research Service , United States Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
| | - Songsong Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , 17 Qinghua Donglu , Haidian District, Beijing 100038 , People's Republic of China
- Western Regional Research Center, Pacific West Area, Agricultural Research Service , United States Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center , University of Science & Technology of China , Hefei , Anhui 230007 , People's Republic of China
| | - Shu-Chen Lyu
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics , Stanford University School of Medicine , 269 Campus Drive , Stanford , California 94305 , United States
| | - Kari C Nadeau
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics , Stanford University School of Medicine , 269 Campus Drive , Stanford , California 94305 , United States
| | - Tara McHugh
- Western Regional Research Center, Pacific West Area, Agricultural Research Service , United States Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
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Che H, Zhang Y, Lyu SC, Nadeau KC, McHugh T. Identification of Almond ( Prunus dulcis) Vicilin As a Food Allergen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:425-432. [PMID: 30512943 DOI: 10.1021/acs.jafc.8b05290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Almond is one of the tree nuts listed by U.S. FDA as a food allergen source. A food allergen identified with patient sera has been debated to be the 2S albumin or the 7S vicilin. However, neither of these proteins has been defined as a food allergen. The purpose of this study was to clone, express, and purify almond vicilin and test whether it is a food allergen. Western blot experiment was performed with 18 individual sera from patients with double-blind, placebo-controlled clinical almond allergy. The results showed that 44% of the sera contained IgE antibodies that recognized the recombinant almond vicilin, indicating that it is an almond allergen. Identifying this and additional almond allergens will facilitate the understanding of the allergenicity of seed proteins in tree nuts and their cross-reactivity.
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Affiliation(s)
- Huilian Che
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , No. 17 Qinghua Donglu, Haidian District , Beijing 100038 , P. R. China
- Agricultural Research Service, Pacific West Area, Western Regional Research Center , U. S. Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
| | - Yuzhu Zhang
- Agricultural Research Service, Pacific West Area, Western Regional Research Center , U. S. Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
| | - Shu-Chen Lyu
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics , Stanford University School of Medicine , 269 Campus Drive , Stanford , California 94305 , United States
| | - Kari C Nadeau
- Division of Pediatric Immunology, Allergy, and Rheumatology, Department of Pediatrics , Stanford University School of Medicine , 269 Campus Drive , Stanford , California 94305 , United States
| | - Tara McHugh
- Agricultural Research Service, Pacific West Area, Western Regional Research Center , U. S. Department of Agriculture , 800 Buchanan Street , Albany , California 94710 , United States
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