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Patil PJ, Usman M, Zhang C, Mehmood A, Zhou M, Teng C, Li X. An updated review on food-derived bioactive peptides: Focus on the regulatory requirements, safety, and bioavailability. Compr Rev Food Sci Food Saf 2022; 21:1732-1776. [PMID: 35142435 DOI: 10.1111/1541-4337.12911] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/07/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023]
Abstract
Food-derived bioactive peptides (BAPs) are recently utilized as functional food raw materials owing to their potential health benefits. Although there is a huge amount of scientific research about BAPs' identification, purification, characterization, and physiological functions, and subsequently, many BAPs have been marketed, there is a paucity of review on the regulatory requirements, bioavailability, and safety of BAPs. Thus, this review focuses on the toxic peptides that could arise from their primary proteins throughout protein extraction, protein pretreatment, and BAPs' formulation. Also, the influences of BAPs' length and administration dosage on safety are summarized. Lastly, the challenges and possibilities in BAPs' bioavailability and regulatory requirements in different countries were also presented. Results revealed that the human studies of BAPs are essential for approvals as healthy food and to prevent the consumers from misinformation and false promises. The BAPs that escape the gastrointestinal tract epithelium and move to the stomach are considered good peptides and get circulated into the blood using different pathways. In addition, the hydrophobicity, net charge, molecular size, length, amino acids composition/sequences, and structural characteristics of BAPs are critical for bioavailability, and appropriate food-grade carriers can enhance it. The abovementioned features are also vital to optimize the solubility, water holding capacity, emulsifying ability, and foaming property of BAPs in food products. In the case of safety, the possible allergenic and toxic peptides often exhibit physiological functions and could be produced during the hydrolysis of food proteins. It was also noted that the production of iso-peptides bonds and undesirable Maillard reaction might occur during protein extraction, sample pretreatments, and peptide synthesis.
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Affiliation(s)
- Prasanna J Patil
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Muhammad Usman
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chengnan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Arshad Mehmood
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Mingchun Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chao Teng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China.,School of Food and Health, Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing, China
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Chaudhary N, Mohan B, Mavuduru RS, Kumar Y, Taneja N. Characterization, genome analysis and in vitro activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant and extensively drug-resistant biofilm-forming uropathogenic Escherichia coli isolates, India. J Appl Microbiol 2022; 132:3387-3404. [PMID: 34989075 DOI: 10.1111/jam.15439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/23/2022]
Abstract
AIM We aimed to study host range, stability, genome and antibiofilm activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant (MDR) and extensively drug-resistant (XDR) biofilm-forming uropathogenic Escherichia coli isolates. METHODS AND RESULTS A novel lytic phage vB_EcoA_RDN8.1 active against UPEC strains resistant to third-generation cephalosporins, fluoroquinolones, aminoglycosides, imipenem, beta-lactamase inhibitor combination and polymyxins was isolated from community raw sewage water of Chandigarh. It exhibited a clear plaque morphology and a burst size of 250. In the time-kill assay, the maximum amount of killing was achieved at MOI 1.0. vB_EcoA_RDN8.1 belongs to the family Autographiviridae, has a genome size of 39.5 kb with a GC content of 51.6%. It was stable over a wide range of temperatures and pH. It was able to inhibit biofilm formation which may be related to an endolysin encoded by ORF 19. CONCLUSIONS The vB_EcoA_RDN8.1 is a novel lytic phage that has the potential for inclusion into phage cocktails being developed for the treatment of urinary tract infections (UTIs) caused by highly drug-resistant UPEC. SIGNIFICANCE AND IMPACT OF THE STUDY We provide a detailed characterization of a novel lytic Escherichia phage with antibiofilm activity having a potential application against MDR and XDR UPEC causing UTIs.
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Affiliation(s)
- Naveen Chaudhary
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ravimohan S Mavuduru
- Department of Urology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yashwant Kumar
- Central Research Institute, National Salmonella and Escherichia Centre, Kasauli, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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53
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Allergic Diseases: A Comprehensive Review on Risk Factors, Immunological Mechanisms, Link with COVID-19, Potential Treatments, and Role of Allergen Bioinformatics. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182212105. [PMID: 34831860 PMCID: PMC8622387 DOI: 10.3390/ijerph182212105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022]
Abstract
The prevalence of allergic diseases is regarded as one of the key challenges in health worldwide. Although the precise mechanisms underlying this rapid increase in prevalence are unknown, emerging evidence suggests that genetic and environmental factors play a significant role. The immune system, microbiota, viruses, and bacteria have all been linked to the onset of allergy disorders in recent years. Avoiding allergen exposure is the best treatment option; however, steroids, antihistamines, and other symptom-relieving drugs are also used. Allergen bioinformatics encompasses both computational tools/methods and allergen-related data resources for managing, archiving, and analyzing allergological data. This study highlights allergy-promoting mechanisms, algorithms, and concepts in allergen bioinformatics, as well as major areas for future research in the field of allergology.
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54
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MacIntosh SC, Shaw M, Connelly M, Yao ZJ. Food and Feed Safety of NS-B5ØØ27-4 Omega-3 Canola ( Brassica napus): A New Source of Long-Chain Omega-3 Fatty Acids. Front Nutr 2021; 8:716659. [PMID: 34660659 PMCID: PMC8514783 DOI: 10.3389/fnut.2021.716659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
DHA canola, a genetically engineered Brassica napus (OECD Unique Identifier NS-B5ØØ27-4), has been developed as one of the first land-based production systems for omega-3 long-chain polyunsaturated fatty acids (LCPUFA), whose health benefits are well-established. Yet, the marine sources of these nutrients are under high pressures due to over-fishing and increasing demand. DHA canola is a plant-based source for these essential fatty acids that produces a high level of docosahexaenoic acid (DHA). This terrestrial system allows for sustainable, scalable and stable production of omega-3 LCPUFA that addresses not only the increasing market demand, but also the complex interplay of agriculture, aquaculture, and human nutrition. The vector used to produce the desired oil profile in DHA canola contains the expression cassettes of seven genes in the DHA biosynthesis pathway and was specifically designed to convert oleic acid to DHA in canola seed. The characterization and safety evaluation of food and feed produced from DHA canola are described and supported by a detailed nutritional analysis of the seed, meal, and oil. Aside from the intended changes of the fatty acid profile, none of the other compositional analytes showed biologically meaningful differences when compared to conventional canola varieties. In addition, the meal from DHA canola is compositionally equivalent to conventional canola meal. Further evidence of nutritional value and safety of DHA canola oil have been confirmed in fish feeding studies. Given that most human populations lack sufficient daily intakes of omega-3 LCPUFA, a dietary exposure assessment is also included. In conclusion, the results from these studies demonstrate it is safe to use products derived from DHA canola in human foods, nutraceuticals, or animal feeds.
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Affiliation(s)
| | - Megan Shaw
- Nuseed Pty Ltd., Laverton North, VIC, Australia
| | | | - Zhuyun June Yao
- Nuseed Nutritional US Inc., West Sacramento, CA, United States
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55
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Mia MM, Hasan M, Hasan MM, Khan SS, Rahman MN, Ahmed S, Basak A, Sakib MN, Banik S. Multi-epitope based subunit vaccine construction against Banna virus targeting on two outer proteins (VP4 and VP9): A computational approach. INFECTION GENETICS AND EVOLUTION 2021; 95:105076. [PMID: 34500093 DOI: 10.1016/j.meegid.2021.105076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/28/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022]
Abstract
Recently, RNA viruses have gained a mammoth concern for causing various outbreaks, and due to pandemics, they are acquiring additional attention throughout the world. An emerging RNA as well as vector-borne Banna Virus (BAV) is a human pathogen resulting in encephalitis, fever, headache, muscle aches, and severe coma. Besides human, pathogenic BAV was also detected from pigs, cattle, ticks, midges, and mosquitoes in Indonesia, China, and Vietnam. Due to high mutation tendency and dearth of a species barrier, this virus will consider as a significant threat in the near future throughout the planet, particularly in Africa. Despite of severe human case fatalities in several countries, there are no specific therapeutics, available vaccines, and other preventive measures against BAV. Thus, to find out the effective therapeutics and preventive strategies are crying exigency. In the present study, a unique multi-epitope-based peptide vaccine candidate is constructed using bioinformatics' tools that efficiently instigate immune cells for generating BAV antibodies. The potential vaccine candidates were developed using both T and B -cell epitopes. UniprotKB database was used to retrieve of two outer proteins (VP9 and VP4), and homologous sequences of BAV taxid: 7763, 649,604, 77,763, and 8453 were searched by NCBI BLAST. These serotypes are the most closely associated with the disease. Then combining the best-selected epitopes in various combinations with different adjuvants, three distinct vaccine candidates were formed. The validity tests were performed for the screened vaccine candidate regarding stability, allergenicity, and antigenicity parameters. Moreover, molecular dynamic simulations of the selected vaccine with TLR-8 immune receptor confirmed the stability of the binding pose and showed a significant response to immune cells. Thus, the results established that the designed chimeric peptide vaccine could enhance the immune response against BAV.
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Affiliation(s)
- Md Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh..
| | - Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh..
| | - Md Mahadi Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Sumaya Shargin Khan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Nahian Rahman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shakil Ahmed
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Ankita Basak
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmuj Sakib
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shrabonti Banik
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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56
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Immunoinformatics aided design of peptide-based vaccines against ebolaviruses. VITAMINS AND HORMONES 2021; 117:157-187. [PMID: 34420579 DOI: 10.1016/bs.vh.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ebolaviruses are at the forefront of emerging viruses and present a very perceptible threat to global peace and harmony. In the last decade, Ebola virus disease has claimed more than 90% of total lives since its inception in 1976. Owing to multiple host immune evasion methods employed by the virus and the limitations of traditional vaccine development approaches, finding a globally effective and reliable counter measure against Ebola virus remains a challenge. Highly conserved peptide fragments belonging to critical viral proteins and containing multiple epitopes which have the capacity to interact with a wide array of HLA molecules present a viable solution. Immunoinformatics or computational immunology enables rapid screening and shortlisting of plausible epitopes with a high immunogenic potential, thus, supporting expeditious elucidation of efficacious vaccine candidates. In light of above facts, we describe a computational methodology in this chapter for identification of potent peptide vaccine candidates against human infecting viruses. By applying this stringent methodology, we were able to identify multiple, immunogenic ebolavirus peptide fragments which, after verification in animal models, might be considered as part of future synthetic Ebola vaccine.
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57
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van Ree R, Sapiter Ballerda D, Berin MC, Beuf L, Chang A, Gadermaier G, Guevera PA, Hoffmann-Sommergruber K, Islamovic E, Koski L, Kough J, Ladics GS, McClain S, McKillop KA, Mitchell-Ryan S, Narrod CA, Pereira Mouriès L, Pettit S, Poulsen LK, Silvanovich A, Song P, Teuber SS, Bowman C. The COMPARE Database: A Public Resource for Allergen Identification, Adapted for Continuous Improvement. FRONTIERS IN ALLERGY 2021; 2:700533. [PMID: 35386979 PMCID: PMC8974746 DOI: 10.3389/falgy.2021.700533] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
Motivation: The availability of databases identifying allergenic proteins via a transparent and consensus-based scientific approach is of prime importance to support the safety review of genetically-modified foods and feeds, and public safety in general. Over recent years, screening for potential new allergens sequences has become more complex due to the exponential increase of genomic sequence information. To address these challenges, an international collaborative scientific group coordinated by the Health and Environmental Sciences Institute (HESI), was tasked to develop a contemporary, adaptable, high-throughput process to build the COMprehensive Protein Allergen REsource (COMPARE) database, a publicly accessible allergen sequence data resource along with bioinformatics analytical tools following guidelines of FAO/WHO and CODEX Alimentarius Commission. Results: The COMPARE process is novel in that it involves the identification of candidate sequences via automated keyword-based sorting algorithm and manual curation of the annotated sequence entries retrieved from public protein sequence databases on a yearly basis; its process is meant for continuous improvement, with updates being transparently documented with each version; as a complementary approach, a yearly key-word based search of literature databases is added to identify new allergen sequences that were not (yet) submitted to protein databases; in addition, comments from the independent peer-review panel are posted on the website to increase transparency of decision making; finally, sequence comparison capabilities associated with the COMPARE database was developed to evaluate the potential allergenicity of proteins, based on internationally recognized guidelines, FAO/WHO and CODEX Alimentarius Commission
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Affiliation(s)
- Ronald van Ree
- Departments of Experimental Immunology and of Otorhinolaryngology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Dexter Sapiter Ballerda
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States
| | - M. Cecilia Berin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Laurent Beuf
- Limagrain Field Seeds, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Alexander Chang
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States
| | - Gabriele Gadermaier
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Paul A. Guevera
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States
| | | | - Emir Islamovic
- Regulatory Science Seeds and Traits, BASF Corporation, Morrisville, NC, United States
| | - Liisa Koski
- Health and Environmental Sciences Institute (HESI), Washington, DC, United States
| | - John Kough
- Office of Pesticide Programs, Microbial Pesticides Branch, US Environmental Protection Agency, Washington, DC, United States
| | | | - Scott McClain
- Syngenta Crop Protection LLC, Research Triangle Park, NC, United States
| | - Kyle A. McKillop
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States
| | | | - Clare A. Narrod
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States
| | - Lucilia Pereira Mouriès
- Health and Environmental Sciences Institute (HESI), Washington, DC, United States
- *Correspondence: Lucilia Pereira Mouriès
| | - Syril Pettit
- Health and Environmental Sciences Institute (HESI), Washington, DC, United States
| | - Lars K. Poulsen
- Allergy Clinic, Department of Dermatology and Allergy, Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Andre Silvanovich
- Bayer U.S., Crop Science Regulatory Science Building FF4, Chesterfield, MO, United States
| | - Ping Song
- Seeds Regulatory Science, Corteva Agriscience LLC, Indianapolis, IN, United States
| | - Suzanne S. Teuber
- Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
- Division of Rheumatology, Allergy, and Clinical Immunology, Davis, CA, United States
- Veterans Affairs Northern California Healthcare System, Mather, CA, United States
| | - Christal Bowman
- Formerly: Human Safety Regulatory Toxicology, Bayer CropScience LP, Research Triangle Park, NC, United States
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58
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Mishra A, Kumar A. Mapping B-Cell Epitopes for Nonspecific Lipid Transfer Proteins of Legumes Consumed in India and Identification of Critical Residues Responsible for IgE Binding. Foods 2021; 10:foods10061269. [PMID: 34199581 PMCID: PMC8227083 DOI: 10.3390/foods10061269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/26/2022] Open
Abstract
Nonspecific lipid transfer proteins (nsLTPs) have been categorized as panallergens and display widespread occurrence across plant-kingdom. Present study, investigated B-cell epitopes for LTPs from chickpea, mung-bean, cowpea, pigeon-pea, and soybean via in silico methods. In-silico predicted regions were evaluated for epitope-conservancy and property-based peptide similarity search by different allergen databases. Additionally, the in-silico predicted regions were compared with the experimentally validated epitopes of peach-LTP. Sequence-homology studies showed that chickpea and mung-bean LTPs shared significant homology, i.e., >70% and >60%, respectively, with other LTP allergens from lentil, garden-pea, peanut, etc. Phylogenetic-analysis also showed chickpea and mung-bean LTPs to be closely related to allergenic LTPs from lentil and peanut, respectively. Epitope-conservation analysis showed that two of the predicted B-cell epitopic regions in chickpea and mung-bean LTPs were also conserved in other allergenic LTPs from peach, peanut, garden-pea, lentil, and green-bean, and might serve as conserved B-cell epitopes of the LTP protein family. Property-distance index values for chickpea and mung-bean LTPs also showed that most of the epitopes shared similarity with the reported allergens like-lentil, peanut, apple, plum, tomato, etc. Present findings, may be explored for identification of probable allergenicity of novel LTPs, on the basis of the reported conserved B-cell epitopes, responsible for potential cross-reactivity.
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Affiliation(s)
- Ankita Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India;
- Correspondence:
| | - Ashok Kumar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India;
- Centre for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
- Centre for Nanosciences, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
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59
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Benedé S, Lozano-Ojalvo D, Cristobal S, Costa J, D'Auria E, Velickovic TC, Garrido-Arandia M, Karakaya S, Mafra I, Mazzucchelli G, Picariello G, Romero-Sahagun A, Villa C, Roncada P, Molina E. New applications of advanced instrumental techniques for the characterization of food allergenic proteins. Crit Rev Food Sci Nutr 2021; 62:8686-8702. [PMID: 34060381 DOI: 10.1080/10408398.2021.1931806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.
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Affiliation(s)
- Sara Benedé
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
| | - Daniel Lozano-Ojalvo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, NY, USA
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden.,IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Enza D'Auria
- Clinica Pediatrica, Ospedale dei Bambini Vittore Buzzi, Università degli Studi, Milano, Italy
| | - Tanja Cirkovic Velickovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia.,Ghent University Global Campus, Incheon, South Korea.,Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Sibel Karakaya
- Department of Food Engineering, Ege University, Izmir, Turkey
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Alejandro Romero-Sahagun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paola Roncada
- Department of Health Sciences, University Magna Graecia, Catanzaro, Italy
| | - Elena Molina
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
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60
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Azim KF, Lasker T, Akter R, Hia MM, Bhuiyan OF, Hasan M, Hossain MN. Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family. Heliyon 2021; 7:e07022. [PMID: 34041391 PMCID: PMC8144012 DOI: 10.1016/j.heliyon.2021.e07022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/09/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, the study was employed to design a highly immunogenic cross-reactive vaccine against Arenaviridae family using reverse vaccinology approach. The whole proteome of Lassa virus (LASV), Lymphocytic Choriomeningitis virus (LCMV), Lujo virus and Guanarito virus were retrieved and assessed to determine the most antigenic viral proteins. Both T-cell and B-cell epitopes were predicted and screened based on transmembrane topology, antigenicity, allergenicity, toxicity and molecular docking analysis. The final constructs were designed using different adjuvants, top epitopes, PADRE sequence and respective linkers and were assessed for the efficacy, safety, stability and molecular cloning purposes. The proposed epitopes were highly conserved (84%–100%) and showed greater cumulative population coverage. Moreover, T cell epitope GWPYIGSRS was conserved in Junin virus (Argentine mammarenavirus) and Sabia virus (Brazilian mammarenavirus), while B cell epitope NLLYKICLSG was conserved in Machupo virus (Bolivian mammarenavirus) and Sabia virus, indicating the possibility of final vaccine construct to confer a broad range immunity in the host. Docking analysis of the refined vaccine with different MHC molecules and human immune receptors were biologically significant. The vaccine-receptor (V1-TLR3) complex showed minimal deformability at molecular level and was compatible for cloning into pET28a(+) vector of E. coli strain K12. The study could be helpful in developing vaccine to combat arenaviral infections in the future. However, further in vitro and in vivo trials using model animals are highly recommended for the experimental validation of our findings.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tahera Lasker
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Rahima Akter
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mantasha Mahmud Hia
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Omar Faruk Bhuiyan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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Goodman RE, Chapman MD, Slater JE. The Allergen: Sources, Extracts, and Molecules for Diagnosis of Allergic Disease. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 8:2506-2514. [PMID: 32888526 DOI: 10.1016/j.jaip.2020.06.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/10/2020] [Accepted: 06/24/2020] [Indexed: 01/30/2023]
Abstract
Allergenic source materials include pollen, molds, animal dander, and insects; food allergens from nuts, grains, and animals; venoms; and salivary proteins from insects and ticks. Clinical diagnostic tests have used heterogeneous extracts from allergen source materials for skin prick tests (SPTs). In vitro laboratory methods using immunoassays or microarrays can detect serum IgE directed against allergenic proteins where clinical testing may not be suitable. Clinicians rely primarily on licensed commercial extracts of allergens for SPTs. Manufacturers and regulatory agencies have standardized selected extracts for identity, composition, and potency. Allergen sources contain multiple proteins. The IgE antibody responses to these proteins vary between allergic subjects as does the quantity of specific IgE. Component-resolved molecular diagnostics can be used to improve the specificity of allergy testing and resolve clinical cross-reactivities that may affect treatment outcomes. This clinical commentary will review methods for the production, evaluation, and standardization of allergen extracts from the perspective of diagnostic testing that may be useful for allergists in practice.
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Affiliation(s)
- Richard E Goodman
- Food Allergy Research and Resource Program, University of Nebraska, Lincoln, Neb.
| | | | - Jay E Slater
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
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Challenges of automation and scale: Bioinformatics and the evaluation of proteins to support genetically modified product safety assessments. J Invertebr Pathol 2021; 186:107587. [PMID: 33838205 DOI: 10.1016/j.jip.2021.107587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Bioinformatic analyses of protein sequences play an important role in the discovery and subsequent safety assessment of insect control proteins in Genetically Modified (GM) crops. Due to the rapid adoption of high-throughput sequencing methods over the last decade, the number of protein sequences in GenBank and other public databases has increased dramatically. Many of these protein sequences are the product of whole genome sequencing efforts, coupled with automated protein sequence prediction and annotation pipelines. Published genome sequencing studies provide a rich and expanding foundation of new source organisms and proteins for insect control or other desirable traits in GM products. However, data generated by automated pipelines can also confound regulatory safety assessments that employ bioinformatics. Largely this issue does not arise due to underlying sequence, but rather its annotation or associated metadata, and the downstream integration of that data into existing repositories. Observations made during bioinformatic safety assessments are described.
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63
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Assessment of the potential allergenicity and toxicity of Pichia proteins in a novel leghemoglobin preparation. Regul Toxicol Pharmacol 2021; 119:104817. [DOI: 10.1016/j.yrtph.2020.104817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 01/03/2023]
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64
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Abdelmoteleb M, Zhang C, Furey B, Kozubal M, Griffiths H, Champeaud M, Goodman RE. Evaluating potential risks of food allergy of novel food sources based on comparison of proteins predicted from genomes and compared to www.AllergenOnline.org. Food Chem Toxicol 2021; 147:111888. [DOI: 10.1016/j.fct.2020.111888] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/15/2022]
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AllerScreener – A Server for Allergenicity and Cross-Reactivity Prediction. CYBERNETICS AND INFORMATION TECHNOLOGIES 2020. [DOI: 10.2478/cait-2020-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Allergenicity of proteins is a subtle property encoded in their structures. The prediction of allergenicity of novel proteins saves time and resources for subsequent experimental work. In the host antigen-presenting cells, the allergens are processed as antigens by the means of Human Leukocyte Antigens (HLA) class II proteins. Sometimes, people allergic to a given protein show allergic reaction to a different protein, even when the two proteins have different routes of exposure. This phenomenon is termed cross-reactivity. Here, we describe a server for allergenicity and cross-reactivity prediction based on the abilities of allergenic proteins to generate binders to HLA class II proteins. The generated peptides are compared to HLA binders originating from known allergens. As a result, the server returns a list of common binders, origin proteins, and species. Different species generate common HLA binders and this determines their cross-reactivity. The server is named AllerScreener and is freely accessible at:
http://www.ddg-pharmfac.net/AllerScreener
.
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66
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Karnaneedi S, Huerlimann R, Johnston EB, Nugraha R, Ruethers T, Taki AC, Kamath SD, Wade NM, Jerry DR, Lopata AL. Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species. Int J Mol Sci 2020; 22:E32. [PMID: 33375120 PMCID: PMC7792927 DOI: 10.3390/ijms22010032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Accepted: 12/19/2020] [Indexed: 12/19/2022] Open
Abstract
Shellfish allergy affects 2% of the world's population and persists for life in most patients. The diagnosis of shellfish allergy, in particular shrimp, is challenging due to the similarity of allergenic proteins from other invertebrates. Despite the clinical importance of immunological cross-reactivity among shellfish species and between allergenic invertebrates such as dust mites, the underlying molecular basis is not well understood. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo, using Trinity, from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). BLAST searching using the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. The analyses revealed up to 39 unreported allergens in the different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment (Clustal Omega) demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.
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Affiliation(s)
- Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD 4811, Australia; (R.H.); (N.M.W.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Roger Huerlimann
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD 4811, Australia; (R.H.); (N.M.W.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Elecia B. Johnston
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Roni Nugraha
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Department of Aquatic Product Technology, Bogor Agricultural University, Bogor 16680, Indonesia
| | - Thimo Ruethers
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Aya C. Taki
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
| | - Sandip D. Kamath
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
| | - Nicholas M. Wade
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD 4811, Australia; (R.H.); (N.M.W.)
- CSIRO Agriculture and Food, Aquaculture Program, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Dean R. Jerry
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD 4811, Australia; (R.H.); (N.M.W.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Tropical Futures Institute, James Cook University, 149 Sims Drive, Singapore 387380, Singapore
| | - Andreas L. Lopata
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia; (S.K.); (E.B.J.); (R.N.); (T.R.); (A.C.T.); (S.D.K.)
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, The Royal Children’s Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
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Garnham CP, Butler SG, Telmer PG, Black FE, Renaud JB, Sumarah MW. Identification and Characterization of an Aspergillus niger Amine Oxidase that Detoxifies Intact Fumonisins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13779-13790. [PMID: 33174732 DOI: 10.1021/acs.jafc.0c04504] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fumonisin contamination of maize damaged by Fusarium verticillioides and related species is a major problem when it is grown under warm and dry conditions. Consumption of fumonisin contaminated food and feed is harmful to both humans and livestock. Novel tools for reducing or eliminating fumonisin toxicity may be useful to the agri-feed sector to deal with this worldwide problem. Enzymes capable of catabolizing fumonisins have been identified from microorganisms that utilize fumonisins as an energy source. However, fumonisin detoxifying enzymes produced by the very species that biosynthesize the toxin have yet to be reported. Here we describe the identification and characterization of a novel amine oxidase synthesized by the fumonisin-producing fungus Aspergillus niger. We have recombinantly expressed this A. niger enzyme in E. coli and demonstrated its ability to oxidatively deaminate intact fumonisins without requiring exogenous cofactors. This enzyme, termed AnFAO (A. niger fumonisin amine oxidase), displays robust fumonisin deamination activity across a broad range of conditions, has a high native melting temperature, and can be purified to >95% homogeneity at high yield in a one-step enrichment. AnFAO is a promising tool to remediate fumonisin-contaminated feed including maize destined for ethanol production.
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Affiliation(s)
- Christopher P Garnham
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Shane G Butler
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Patrick G Telmer
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Friday E Black
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Justin B Renaud
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Mark W Sumarah
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
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68
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Sharma N, Patiyal S, Dhall A, Pande A, Arora C, Raghava GPS. AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes. Brief Bioinform 2020; 22:5985292. [PMID: 33201237 DOI: 10.1093/bib/bbaa294] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/22/2022] Open
Abstract
AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes were used to identify antigenic regions in a protein. All models were trained on 80% of data called training dataset, and the performance of models was evaluated using 5-fold cross-validation technique. The performance of the final model trained on the training dataset was evaluated on 20% of data called validation dataset; no two proteins in any two sets have more than 40% similarity. First, a Basic Local Alignment Search Tool (BLAST) search has been performed against the dataset, and allergens were predicted based on the level of similarity with known allergens. Second, IgE epitopes obtained from the IEDB database were searched in the dataset to predict allergens based on their presence in a protein. Third, motif-based approaches like multiple EM for motif elicitation/motif alignment and search tool have been used to predict allergens. Fourth, allergen prediction models have been developed using a wide range of machine learning techniques. Finally, the ensemble approach has been used for predicting allergenic protein by combining prediction scores of different approaches. Our best model achieved maximum performance in terms of area under receiver operating characteristic curve 0.98 with Matthew's correlation coefficient 0.85 on the validation dataset. A web server AlgPred 2.0 has been developed that allows the prediction of allergens, mapping of IgE epitope, motif search and BLAST search (https://webs.iiitd.edu.in/raghava/algpred2/).
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Affiliation(s)
- Neelam Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Akshara Pande
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Chakit Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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Abstract
Wheat-based foods have been staple foods since about 10,000 years and constitute a major source of energy, dietary fiber, and micronutrients for the world population. The role of wheat in our diet, however, has recently been scrutinized by pseudoscientific books and media reports promoting the overall impression that wheat consumption makes people sick, stupid, fat, and addicted. Consequently, numerous consumers in Western countries have started to question their dietary habits related to wheat consumption and voluntarily decided to adopt a wheat-free diet without a medical diagnosis of any wheat-related disorder (WRD), such as celiac disease, wheat allergy, or non-celiac gluten sensitivity. The aim of this review is to achieve an objective judgment of the positive aspects of wheat consumption as well as adverse effects for individuals suffering from WRDs. The first part presents wheat constituents and their positive nutritional value, in particular, the consumption of products from whole-grain flours. The second part is focused on WRDs that affect predisposed individuals and can be treated with a gluten-free or -reduced diet. Based on all available scientific knowledge, wheat consumption is safe and healthy for the vast majority of people. There is no scientific evidence to support that the general population would benefit from a wheat-free diet.
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Affiliation(s)
| | | | - Katharina A. Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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70
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Hasan M, Azim KF, Imran MAS, Chowdhury IM, Urme SRA, Parvez MSA, Uddin MB, Ahmed SSU. Comprehensive genome based analysis of Vibrio parahaemolyticus for identifying novel drug and vaccine molecules: Subtractive proteomics and vaccinomics approach. PLoS One 2020; 15:e0237181. [PMID: 32813697 PMCID: PMC7444560 DOI: 10.1371/journal.pone.0237181] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Multidrug-resistant Vibrio parahaemolyticus has become a significant public health concern. The development of effective drugs and vaccines against Vibrio parahaemolyticus is the current research priority. Thus, we aimed to find out effective drug and vaccine targets using a comprehensive genome-based analysis. A total of 4822 proteins were screened from V. parahaemolyticus proteome. Among 16 novel cytoplasmic proteins, 'VIBPA Type II secretion system protein L' and 'VIBPA Putative fimbrial protein Z' were subjected to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules considering free binding energy. On the contrary, 'Sensor histidine protein kinase UhpB' and 'Flagellar hook-associated protein of 25 novel membrane proteins were subjected to T-cell and B-cell epitope prediction, antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking analysis to generate the most immunogenic epitopes. Three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed by their physiochemical properties and molecular docking with MHC molecules- results suggested that the V1 is superior. Besides, the binding affinity of human TLR-1/2 heterodimer and construct V1 could be biologically significant in the development of the vaccine repertoire. The vaccine-receptor complex exhibited deformability at a minimum level that also strengthened our prediction. The optimized codons of the designed construct was cloned into pET28a(+) vector of E. coli strain K12. However, the predicted drug molecules and vaccine constructs could be further studied using model animals to combat V. parahaemolyticus associated infections.
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Affiliation(s)
- Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Kazi Faizul Azim
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Abdus Shukur Imran
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ishtiak Malique Chowdhury
- Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | | | - Md. Sorwer Alam Parvez
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md. Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet, Bangladesh
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71
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Parisi K, Poon S, Renda RF, Sahota G, English J, Yalpani N, Bleackley MR, Anderson MA, van der Weerden NL. Improving the Digestibility of Plant Defensins to Meet Regulatory Requirements for Transgene Products in Crop Protection. FRONTIERS IN PLANT SCIENCE 2020; 11:1227. [PMID: 32922418 PMCID: PMC7456892 DOI: 10.3389/fpls.2020.01227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/27/2020] [Indexed: 06/01/2023]
Abstract
Despite the use of chemical fungicides, fungal diseases have a major impact on the yield and quality of plant produce globally and hence there is a need for new approaches for disease control. Several groups have examined the potential use of antifungal plant defensins for plant protection and have produced transgenic plants expressing plant defensins with enhanced resistance to fungal disease. However, before they can be developed commercially, transgenic plants must pass a series of strict regulations to ensure that they are safe for human and animal consumption as well as the environment. One of the requirements is rapid digestion of the transgene protein in the gastrointestinal tract to minimize the risk of any potential allergic response. Here, we examine the digestibility of two plant defensins, NaD1 from Nicotiana alata and SBI6 from soybean, which have potent antifungal activity against major cereal pathogens. The native defensins were not digestible in simulated gastrointestinal fluid assays. Several modifications to the sequences enhanced the digestibility of the two small proteins without severely impacting their antifungal activity. However, these modified proteins did not accumulate as well as the native proteins when transiently expressed in planta, suggesting that the protease-resistant structure of plant defensins facilitates their stability in planta.
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Affiliation(s)
- Kathy Parisi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Rosemary F. Renda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Gurinder Sahota
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - James English
- Maxygen LLC, Sunnyvale, CA, United States
- Corteva Agriscience, Agriculture Division of DowDuPont, Johnston, IA, United States
| | - Nasser Yalpani
- Corteva Agriscience, Agriculture Division of DowDuPont, Johnston, IA, United States
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Mark R. Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Nicole L. van der Weerden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
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Daly M, Bromilow SN, Nitride C, Shewry PR, Gethings LA, Mills ENC. Mapping Coeliac Toxic Motifs in the Prolamin Seed Storage Proteins of Barley, Rye, and Oats Using a Curated Sequence Database. Front Nutr 2020; 7:87. [PMID: 32766270 PMCID: PMC7379453 DOI: 10.3389/fnut.2020.00087] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Wheat gluten, and related prolamin proteins in rye, barley and oats cause the immune-mediated gluten intolerance syndrome, coeliac disease. Foods labelled as gluten-free which can be safely consumed by coeliac patients, must not contain gluten above a level of 20 mg/Kg. Current immunoassay methods for detection of gluten can give conflicting results and may underestimate levels of gluten in foods. Mass spectrometry methods have great potential as an orthogonal method, but require curated protein sequence databases to support method development. The GluPro database has been updated to include avenin-like sequences from bread wheat (n = 685; GluPro v1.1) and genes from the sequenced wheat genome (n = 699; GluPro v 1.2) and Triticum turgidum ssp durum (n = 210; GluPro v 2.1). Companion databases have been developed for prolamin sequences from barley (n = 64; GluPro v 3.0), rye (n = 41; GluPro v 4.0), and oats (n = 27; GluPro v 5.0) and combined to provide a complete cereal prolamin database, GluPro v 6.1 comprising 1,041 sequences. Analysis of the coeliac toxic motifs in the curated sequences showed that they were absent from the minor avenin-like proteins in bread and durum wheat and barley, unlike the related avenin proteins from oats. A comparison of prolamin proteins from the different cereal species also showed α- and γ-gliadins in bread and durum wheat, and the sulphur poor prolamins in all cereals had the highest density of coeliac toxic motifs. Analysis of ion-mobility mass spectrometry data for bread wheat (cvs Chinese Spring and Hereward) showed an increased number of identifications when using the GluPro v1.0, 1.1 and 1.2 databases compared to the limited number of verified sequences bread wheat sequences in reviewed UniProt. This family of databases will provide a basis for proteomic profiling of gluten proteins from all the gluten containing cereals and support identification of specific peptide markers for use in development of new methods for gluten quantitation based on coeliac toxic motifs found in all relevant cereal species.
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Affiliation(s)
- Matthew Daly
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Sophie N Bromilow
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Chiara Nitride
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Peter R Shewry
- Centre for Crop Genetic Improvement, Rothamsted Research, Harpenden, United Kingdom
| | | | - E N Clare Mills
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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73
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Kochanowski M, Różycki M, Dąbrowska J, Bełcik A, Karamon J, Sroka J, Cencek T. Proteomic and Bioinformatic Investigations of Heat-Treated Anisakis simplex Third-Stage Larvae. Biomolecules 2020; 10:E1066. [PMID: 32708775 PMCID: PMC7407331 DOI: 10.3390/biom10071066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/08/2023] Open
Abstract
Anisakis simplex third-stage larvae are the main source of hidden allergens in marine fish products. Some Anisakis allergens are thermostable and, even highly processed, could cause hypersensitivity reactions. However, Anisakis proteome has not been studied under autoclaving conditions of 121 °C for 60 min, which is an important process in the food industry. The aim of the study was the identification and characterization of allergens, potential allergens, and other proteins of heat-treated A. simplex larvae. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify 470 proteins, including allergens-Ani s 1, Ani s 2, Ani s 3, Ani s 4, Ani s 5-and 13 potential allergens that were mainly homologs of Anisakis spp., Ascaris spp., and Acari allergens. Ani s 2, Ani s 3, Ani s 5, and three possible allergens were found among the top 25 most abundant proteins. The computational analysis allowed us to detect allergen epitopes, assign protein families, and domains as well as to annotate the localization of proteins. The predicted 3D models of proteins revealed similarities between potential allergens and homologous allergens. Despite the partial degradation of heated A. simplex antigens, their immunoreactivity with anti-A. simplex IgG antibodies was confirmed using a Western blot. In conclusion, identified epitopes of allergenic peptides highlighted that the occurrence of Anisakis proteins in thermally processed fish products could be a potential allergic hazard. Further studies are necessary to confirm the IgE immunoreactivity and thermostability of identified proteins.
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Affiliation(s)
- Maciej Kochanowski
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Partyzantów Avenue 57, 24-100 Puławy, Poland; (M.R.); (J.D.); (A.B.); (J.K.); (J.S.); (T.C.)
| | | | | | | | | | | | - Tomasz Cencek
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Partyzantów Avenue 57, 24-100 Puławy, Poland; (M.R.); (J.D.); (A.B.); (J.K.); (J.S.); (T.C.)
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74
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Bastiaan‐Net S, Pina‐Pérez MC, Dekkers BJW, Westphal AH, America AHP, Ariëns RMC, de Jong NW, Wichers HJ, Mes JJ. Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut. Protein Sci 2020; 29:1581-1595. [PMID: 32219913 PMCID: PMC7314402 DOI: 10.1002/pro.3856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Abstract
Proteins from cashew nut can elicit mild to severe allergic reactions. Three allergenic proteins have already been identified, and it is expected that additional allergens are present in cashew nut. pathogenesis-related protein 10 (PR10) allergens from pollen have been found to elicit similar allergic reactions as those from nuts and seeds. Therefore, we investigated the presence of PR10 genes in cashew nut. Using RNA-seq analysis, we were able to identify several PR10-like transcripts in cashew nut and clone six putative PR10 genes. In addition, PR10 protein expression in raw cashew nuts was confirmed by immunoblotting and liquid chromatography-mass spectrometry (LC-MS/MS) analyses. An in silico allergenicity assessment suggested that all identified cashew PR10 proteins are potentially allergenic and may represent three different isoallergens.
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Affiliation(s)
- Shanna Bastiaan‐Net
- Wageningen Food and Biobased ResearchWageningen University and ResearchWageningenThe Netherlands
| | | | - Bas J. W. Dekkers
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Adrie H. Westphal
- BiochemistryWageningen University and ResearchWageningenThe Netherlands
| | - Antoine H. P. America
- Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
| | - Renata M. C. Ariëns
- Wageningen Food and Biobased ResearchWageningen University and ResearchWageningenThe Netherlands
| | | | - Harry J. Wichers
- Wageningen Food and Biobased ResearchWageningen University and ResearchWageningenThe Netherlands
| | - Jurriaan J. Mes
- Wageningen Food and Biobased ResearchWageningen University and ResearchWageningenThe Netherlands
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75
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Maurer-Stroh S, Krutz NL, Kern PS, Gunalan V, Nguyen MN, Limviphuvadh V, Eisenhaber F, Gerberick GF. AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics 2020; 35:3020-3027. [PMID: 30657872 PMCID: PMC6736023 DOI: 10.1093/bioinformatics/btz029] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/18/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
Motivation Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. Results We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. Availability and implementation https://allercatpro.bii.a-star.edu.sg/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Nora L Krutz
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Petra S Kern
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Vithiagaran Gunalan
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Minh N Nguyen
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Frank Eisenhaber
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
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76
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Rost J, Muralidharan S, Lee NA. A label-free shotgun proteomics analysis of macadamia nut. Food Res Int 2020; 129:108838. [DOI: 10.1016/j.foodres.2019.108838] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022]
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77
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Satoh R, Jensen-Jarolim E, Teshima R. Understanding buckwheat allergies for the management of allergic reactions in humans and animals. BREEDING SCIENCE 2020; 70:85-92. [PMID: 32351307 PMCID: PMC7180145 DOI: 10.1270/jsbbs.19051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/14/2019] [Indexed: 05/05/2023]
Abstract
Buckwheat allergy is an immediate hypersensitivity reaction that includes anaphylaxis mediated by specific IgE antibodies. Several IgE-binding proteins in common buckwheat have been reported to be possible clinically relevant buckwheat allergens. Although common buckwheat is popularly consumed in Asia, buckwheat allergy is becoming a serious problem not only in Asia but also in Europe. In addition, common buckwheat has also been found to be a causative agent of allergic symptoms in animals. In recent years, in addition to conventional food allergy testing methods, the development of component-resolved diagnosis (CRD) has improved the diagnostic accuracy of food allergy. The identification of allergens is essential for the construction of CRD. In this review, we introduce the different types of buckwheat allergens and discuss how each buckwheat allergen contributes to the diagnosis of buckwheat allergy. We also present the analysis of buckwheat allergen that will help reduce the allergenicity of common buckwheat and reduce buckwheat allergen molecules. These findings may be beneficial in overcoming buckwheat allergies in humans and animals.
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Affiliation(s)
- Rie Satoh
- Functionality Evaluation Unit, Division of Food Function Research, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
- Corresponding author (e-mail: )
| | - Erika Jensen-Jarolim
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
- The Interuniversity Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Reiko Teshima
- Division of Food Safety, Faculty of Veterinary Medicine, Okayama University of Sciences, 1-3 Ikoinooka, Imabari, Ehime 794-8555, Japan
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78
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Nam UH, Kim JO, Kim JH. De novo transcriptome sequencing and analysis of Anisakis pegreffii (Nematoda: Anisakidae) third-stage and fourth stage larvae. J Nematol 2020; 52:1-16. [PMID: 32298057 PMCID: PMC7266050 DOI: 10.21307/jofnem-2020-041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 01/07/2023] Open
Abstract
Anisakis pegreffii is known as one of the causes of a fish-borne zoonosis, anisakidosis. Despite its significant public health and food hygiene impacts, little is known of the pathogenesis, genetic background of this parasite, at least partly due to the lack of genome and transcriptome information. In this study, RNA-seq and de novo assembly were conducted to obtain transcriptome profiles of the A. pegreffii third and fourth larvae. The third stage larvae (APL3) were collected from chub mackerel and the fourth stage larvae (APL4) were obtained by in vitro culture. In total, 47,243 and 43,660 unigenes were expressed in APL3 and APL4 transcriptomes. Of them, 18,753 were known and 28,490 were novel for APL3, while 18,996 were known and 24,664 were novel for APL4. The most abundantly expressed genes in APL3 were mitochondrial enzymes (COI, COII, COIII) and polyubiquitins (UBB, UBIQP_XENLA). Collagen-related genes (col-145, col-34, col-138, Bm1_54705, col-40) were the most abundantly expressed in APL4. Mitochondrial enzyme genes (COIII, COI) were also highly expressed in APL4. Among the transcripts, 614 were up-regulated in APL3, while 1,309 were up-regulated in APL4. Several protease and protein biosynthesis-related genes were highly expressed in APL3, all of which are thought to be crucial for invading host tissues. Collagen synthesis-related genes were highly expressed in APL4, reflecting active biosynthesis of collagens occurs during moulting process of APL4. Of these differentially expressed genes, several genes (SI, nas-13, EF-TSMT, SFXN2, dhs-27) were validated to highly transcribed in APL3, while other genes (col-40, F09E10.7, pept-1, col-34, VIT) in APL4. The biological roles of these genes in vivo will be deciphered when the reference genome sequences are available, together with in vitro experiments.
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Affiliation(s)
- U-Hwa Nam
- Department of Marine Bioscience, College of Life Science, Gangneung-Wonju National University , Gangneung, 25457, Korea
| | - Jong-Oh Kim
- Institute of Marine Biotechnology, Pukyong National University , Busan, 48513, Korea
| | - Jeong-Ho Kim
- Department of Marine Bioscience, College of Life Science, Gangneung-Wonju National University , Gangneung, 25457, Korea
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79
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Manufacturing and quality assessment of allergenic extracts for immunotherapy: state of the art. Curr Opin Allergy Clin Immunol 2019; 19:640-645. [DOI: 10.1097/aci.0000000000000579] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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80
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Radauer C, Breiteneder H. Allergen databases-A critical evaluation. Allergy 2019; 74:2057-2060. [PMID: 31020992 DOI: 10.1111/all.13841] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Christian Radauer
- Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - Heimo Breiteneder
- Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
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81
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Detection and identification of allergens from Canadian mustard varieties of Sinapis alba and Brassica juncea. Biomolecules 2019; 9:biom9090489. [PMID: 31540036 PMCID: PMC6770452 DOI: 10.3390/biom9090489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Currently, information on the allergens profiles of different mustard varieties is rather scarce. Therefore, the objective of this study was to assess protein profiles and immunoglobulin E (IgE)-binding patterns of selected Canadian mustard varieties. Optimization of a non-denaturing protein extraction from the seeds of selected mustard varieties was first undertaken, and the various extracts were quantitatively and qualitatively analyzed by means of protein recovery determination and protein profiling. The IgE-binding patterns of selected mustard seeds extracts were assessed by immunoblotting using sera from mustard sensitized and allergic individuals. In addition to the known mustard allergens—Sin a 2 (11S globulins), Sin a 1, and Bra j 1 (2S albumins)—the presence of other new IgE-binding protein bands was revealed from both Sinapis alba and Brassica juncea varieties. Mass spectrometry (MS) analysis of the in-gel digested IgE-reactive bands identified the unknown ones as being oleosin, β-glucosidase, enolase, and glutathione-S transferase proteins. A bioinformatic comparison of the amino acid sequence of the new IgE-binding mustard proteins with those of know allergens revealed a number of strong homologies that are highly relevant for potential allergic cross-reactivity. Moreover, it was found that Sin a 1, Bra j 1, and cruciferin polypeptides exhibited a stronger IgE reactivity under non-reducing conditions in comparison to reducing conditions, demonstrating the recognition of conformational epitopes. These results further support the utilization of non-denaturing extraction and analysis conditions, as denaturing conditions may lead to failure in the detection of important immunoreactive epitopes.
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82
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Volpicella M, Leoni C, Dileo MCG, Ceci LR. Progress in the Analysis of Food Allergens through Molecular Biology Approaches. Cells 2019; 8:E1073. [PMID: 31547388 PMCID: PMC6770348 DOI: 10.3390/cells8091073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/04/2019] [Accepted: 09/10/2019] [Indexed: 01/29/2023] Open
Abstract
Food allergies associated with class E immunoglobulins (IgE) are a serious health problem that affects between 1% and 10% of the population of developing countries, with a variability that depends on the geographical area and age range considered. These allergies are caused by a cross-link reaction between a specific food protein (the allergen) and the host IgE. Allergic reactions can range from mild itching to anaphylactic shock and there are no clues to predict the effects of an allergen. Strict avoidance of allergenic food is the only way to avoid possible serious allergic reactions. In the last 30 years a growing number of molecular studies have been conducted to obtain information on the diffusion of food allergens and to establish the structural basis of their allergenicity. At the same time, these studies have also allowed the development of molecular tools (mainly based on synthetic peptides and recombinant allergens) that can be of great help for diagnostic and therapeutic approaches of food allergies. Accordingly, this review focuses on advances in the study of food allergens made possible by molecular technologies and how results and technologies can be integrated for the development of a systematic food molecular allergology. The review may be of interest both to scientists approaching this field of investigation and to physicians who wish to have an update on the progress of research in diagnosis and therapy of food allergies.
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Affiliation(s)
- Mariateresa Volpicella
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Amendola 165/a, 70126 Bari, Italy.
- Institute of Bioenergetics, Biomembranes and Molecular Biotechnologies, Italian National Research Council, Via Amendola 165/a, 70126 Bari, Italy.
| | - Claudia Leoni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Amendola 165/a, 70126 Bari, Italy.
| | - Maria C G Dileo
- Department of Biology, University of Bari, Via Amendola 165/a, 70126 Bari, Italy.
| | - Luigi R Ceci
- Institute of Bioenergetics, Biomembranes and Molecular Biotechnologies, Italian National Research Council, Via Amendola 165/a, 70126 Bari, Italy.
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83
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Herman RA, Song P. Validation of bioinformatic approaches for predicting allergen cross reactivity. Food Chem Toxicol 2019; 132:110656. [PMID: 31279045 DOI: 10.1016/j.fct.2019.110656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 01/26/2023]
Abstract
Part of the allergenicity assessment of newly expressed proteins in genetically engineered food crops involves an assessment of potential cross-reactivity with known allergens. Bioinformatic approaches are used to evaluate the amino acid sequence identity or similarity between newly expressed proteins and the sequences of known allergens. To be useful, such approaches must be sensitive to detecting cross-reactive potential, but also capable of excluding low-risk sequences. One difficulty in comparing the effectiveness of different bioinformatic approaches has been the lack of a standardized validation and evaluation method. Here, we propose a standardized method for evaluating the sensitivity of different bioinformatic algorithms using a comprehensive database of known allergen sequences. We combine this with a previously described method for evaluating selectivity using sequences from a crop not known to commonly cause food allergy (e.g. maize) to compare the standard ">35% identity-criterion over sliding-window of ≥80 amino acids" bioinformatic approach with the previously described "one-to-one (1:1) FASTA" similarity approach using an E-value threshold of 1E-9. Results confirm the superiority of the 1:1 FASTA approach for selectively detecting cross-reactive allergens. The validation methods described here can be applied to other algorithms to select even better fit-for-purpose approaches for evaluating cross-reactive risk.
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Affiliation(s)
- Rod A Herman
- Corteva Agriscience™, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Ping Song
- Corteva Agriscience™, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
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84
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Fiedler KL, Cao W, Zhang L, Naziemiec M, Bedford B, Yin L, Smith N, Arbuckle M, Lopez-Hernandez A, Jackson LS. Detection of gluten in a pilot-scale barley-based beer produced with and without a prolyl endopeptidase enzyme. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1151-1162. [DOI: 10.1080/19440049.2019.1616830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Wanying Cao
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Liyun Zhang
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Magdalena Naziemiec
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Binaifer Bedford
- Center for Food Safety and Applied Nutrition, US FDA, Bedford Park, IL, USA
| | - Lanlan Yin
- Center for Food Safety and Applied Nutrition, US FDA, College Park, MD, USA
| | - Nicholas Smith
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | - Matthew Arbuckle
- Department of Food Science, University of Wisconsin, Madison, WI, USA
| | | | - Lauren S. Jackson
- Center for Food Safety and Applied Nutrition, US FDA, Bedford Park, IL, USA
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85
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Bioinformatic analyses of a potential Salmonella-virus-FelixO1 biocontrol phage BPS15S6 and the characterisation and anti-Enterobacteriaceae-pathogen activity of its endolysin LyS15S6. Antonie van Leeuwenhoek 2019; 112:1577-1592. [DOI: 10.1007/s10482-019-01283-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022]
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86
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Volarath P, Zang Y, Kabadi SV. Application of Computational Methods for the Safety Assessment of Food Ingredients. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-16443-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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87
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Goodman RE, Breiteneder H. The WHO/IUIS Allergen Nomenclature. Allergy 2019; 74:429-431. [PMID: 30515836 DOI: 10.1111/all.13693] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Richard E. Goodman
- Food Allergy Research and Resource Program; University of Nebraska; Lincoln Nebraska
- Chair of the WHO/IUIS Allergen Nomenclature Sub-Committee; Lincoln Nebraska
| | - Heimo Breiteneder
- Institute of Pathophysiology and Allergy Research; Medical University of Vienna; Vienna Austria
- Member of the WHO/IUIS Allergen Nomenclature Sub-Committee; Vienna Austria
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88
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Pilolli R, Gadaleta A, Mamone G, Nigro D, De Angelis E, Montemurro N, Monaci L. Scouting for Naturally Low-Toxicity Wheat Genotypes by a Multidisciplinary Approach. Sci Rep 2019; 9:1646. [PMID: 30733459 PMCID: PMC6367382 DOI: 10.1038/s41598-018-36845-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/29/2018] [Indexed: 12/23/2022] Open
Abstract
Over the last years, great efforts have been devoted to develop effective gluten detoxification strategies with a consequent detrimental alteration of the technological properties as well. Obtaining low-gluten products without affecting the rheological properties of wheat could still be considered a new challenge to face. In this investigation, we presented a comprehensive characterization of durum wheat genotypes aimed at identifying low gluten ones, which combine the potential lower toxicity/immunogenicity with conserved yield and rheological properties to encompass the perspective usability for bread or pasta making. A preliminary profiling of gluten proteins was accomplished by immunoassay-based quantification and liquid chromatography coupled to UV detection, focusing on the gliadin fraction as main responsible for immunoreactivity in celiac disease patients. In addition, data on grain protein content, grain yield per spike, dry gluten and gluten index were collected in order to provide complementary information about productivity-related traits and quali-quantitative characteristics related to wheat nutritional value and its technological properties. The whole pool of data was statistically evaluated driving to the selection of a preferred list of candidate low-toxicity genotypes that were subjected to in-vitro simulated gastroduodenal digestion and untargeted HR-MS/MS peptide identification. Finally, an in-silico risk assessment of potential toxicity for celiac disease patients was performed according to the most recent guidance provided by EFSA.
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Affiliation(s)
- Rosa Pilolli
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), via Giovanni Amendola, 122/O - 70126, Bari, Italy.
| | - Agata Gadaleta
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), via Giovanni Amendola, 122/O - 70126, Bari, Italy
- Department of Agricultural & Environmental Sciences, Università degli Studi di Bari Aldo Moro, via G. Amendola, 165/A - 70126, Bari, Italy
| | - Gianfranco Mamone
- Institute of Food Sciences, National Research Council of Italy (ISA-CNR), via Roma, 64 - 83100, Avellino, Italy
| | - Domenica Nigro
- Department of Soil, Plant & Food Sciences, Università degli Studi di Bari Aldo Moro, via G. Amendola 165/, A - 70126, Bari, Italy
| | - Elisabetta De Angelis
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), via Giovanni Amendola, 122/O - 70126, Bari, Italy
| | - Nicola Montemurro
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), via Giovanni Amendola, 122/O - 70126, Bari, Italy
| | - Linda Monaci
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), via Giovanni Amendola, 122/O - 70126, Bari, Italy
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89
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Scherf KA. Immunoreactive cereal proteins in wheat allergy, non-celiac gluten/wheat sensitivity (NCGS) and celiac disease. Curr Opin Food Sci 2019. [DOI: 10.1016/j.cofs.2019.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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90
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Alves TO, D’Almeida CTS, Scherf KA, Ferreira MSL. Modern Approaches in the Identification and Quantification of Immunogenic Peptides in Cereals by LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2019; 10:1470. [PMID: 31798614 PMCID: PMC6868032 DOI: 10.3389/fpls.2019.01470] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 10/22/2019] [Indexed: 05/17/2023]
Abstract
Celiac disease (CD) is an immunogenic disorder that affects the small intestine. It is caused by the ingestion of gluten, a protein network formed by prolamins and glutelins from cereals such as wheat, barley, rye and, possibly, oats. For predisposed people, gluten presents epitopes able to stimulate T-cells causing symptoms like nausea, vomiting, diarrhea, among others unrelated to the gastrointestinal system. The only treatment for CD is to maintain a gluten-free diet, not exceeding 20 mg/kg of gluten, what is generally considered the safe amount for celiacs. Due to this context, it is very important to identify and quantify the gluten content of food products. ELISA is the most commonly used method to detect gluten traces in food. However, by detecting only prolamins, the results of ELISA tests may be underestimated. For this reason, more reliable and sensitive assays are needed to improve gluten quantification. Because of high sensitivity and the ability to detect even trace amounts of peptides in complex matrices, the most promising approaches to verify the presence of gluten peptides in food are non-immunological techniques, like liquid chromatography coupled to mass spectrometry. Different methodologies using this approach have been developed and described in the last years, ranging from non-targeted and exploratory analysis to targeted and specific methods depending on the purpose of interest. Non-targeted analyses aim to define the proteomic profile of the sample, while targeted analyses allow the search for specific peptides, making it possible to quantify them. This review aims to gather and summarize the main proteomic techniques used in the identification and quantitation of gluten peptides related to CD-activity and gluten-related allergies.
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Affiliation(s)
- Thais O. Alves
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
| | - Carolina T. S. D’Almeida
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
| | - Katharina A. Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Mariana S. L. Ferreira
- Food and Nutrition Graduate Program (PPGAN), Laboratory of Bioactives, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Laboratory of Protein Biochemistry—Center of Innovation in Mass Spectrometry (LBP-IMasS), UNIRIO, Rio de Janeiro, Brazil
- *Correspondence: Mariana S. L. Ferreira,
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91
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Ladics GS. Assessment of the potential allergenicity of genetically-engineered food crops. J Immunotoxicol 2018; 16:43-53. [PMID: 30409058 DOI: 10.1080/1547691x.2018.1533904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An extensive safety assessment process exists for genetically-engineered (GE) crops. The assessment includes an evaluation of the introduced protein as well as the crop containing the protein with the goal of demonstrating the GE crop is "as-safe-as" non-GE crops in the food supply. One of the evaluations for GE crops is to assess the expressed protein for allergenic potential. Currently, no single factor is recognized as a predictor for protein allergenicity. Therefore, a weight-of-the-evidence approach, which accounts for a variety of factors and approaches for an overall assessment of allergenic potential, is conducted. This assessment includes an evaluation of the history of exposure and safety of the gene(s) source; protein structure (e.g. amino acid sequence identity to human allergens); stability of the protein to pepsin digestion in vitro; heat stability of the protein; glycosylation status; and when appropriate, specific IgE binding studies with sera from relevant clinically allergic subjects. Since GE crops were first commercialized over 20 years ago, there is no proof that the introduced novel protein(s) in any commercialized GE food crop has caused food allergy.
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92
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Docking of peptide candidates to HLA-DQ2 and HLA-DQ8 basket as a tool for predicting potential immunotoxic peptides toward celiac diseased people. REVUE FRANCAISE D ALLERGOLOGIE 2018. [DOI: 10.1016/j.reval.2018.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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93
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Are skin sensitisation test methods relevant for proteins? Regul Toxicol Pharmacol 2018; 99:244-248. [DOI: 10.1016/j.yrtph.2018.09.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/21/2022]
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94
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Ladics GS, Sewalt V. Industrial microbial enzyme safety: What does the weight-of-evidence indicate? Regul Toxicol Pharmacol 2018; 98:151-154. [DOI: 10.1016/j.yrtph.2018.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/20/2018] [Accepted: 07/22/2018] [Indexed: 12/20/2022]
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95
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Song P, Podevin N, Mirsky H, Anderson J, Delaney B, Mathesius C, Rowe L, Herman RA. Q-X1-P-X2 motif search for potential celiac disease risk has poor selectivity. Regul Toxicol Pharmacol 2018; 99:233-237. [PMID: 30266240 DOI: 10.1016/j.yrtph.2018.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 11/24/2022]
Abstract
The European Food Safety Authority (EFSA) recently published guidelines for assessment of potential celiac disease risk for newly expressed proteins in genetically modified (GM) crops. This novel step-wise approach prescribes, in part, how to conduct sequence identity searches between a newly expressed protein and known celiac disease peptides including a Q/E-X1-P-X2 amino acid motif. To evaluate the specificity of the recommended sequence identity searches in the context of risk assessment, protein sequences from celiac disease causing crops, as well as from crops not associated with celiac disease, were compared with known HLA-DQ restricted epitopes and searched for the presence of motifs followed by peptide analysis. Searches for the presence of the Q/E-X1-P-X2-motif were found to generate a high proportion of false-positive hits irrelevant to celiac disease risk. Identification of a 9mer exact match between a newly expressed protein and the known celiac disease peptides (recommended by the guideline) along with a supplementary sequence comparisons (suggested by FARRP/AllergenOnline) is considered better suited to more specifically capture the potential risk of a newly expressed protein for celiac disease.
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Affiliation(s)
- Ping Song
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA.
| | - Nancy Podevin
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Henry Mirsky
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Jennifer Anderson
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Bryan Delaney
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Carey Mathesius
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Laura Rowe
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Rod A Herman
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
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96
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Protease resistance of food proteins: a mixed picture for predicting allergenicity but a useful tool for assessing exposure. Clin Transl Allergy 2018; 8:30. [PMID: 30116520 PMCID: PMC6085708 DOI: 10.1186/s13601-018-0216-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/02/2018] [Indexed: 11/10/2022] Open
Abstract
Background Susceptibility to pepsin digestion of candidate transgene products is regarded an important parameter in the weight-of-evidence approach for allergenicity risk assessment of genetically modified crops. It has been argued that protocols used for this assessment should better reflect physiological conditions encountered in representative food consumption scenarios. Aim To evaluate whether inclusion of more physiological conditions, such as sub-optimal and lower pepsin concentrations, in combination with pancreatin digestion, improved the performance of digestibility protocols used in characterization of protein stability. Methods Four pairs of established allergens and their related non/weakly-allergenic counterparts (seed albumins, muscle tropomyosins, plant lipid transfer proteins [LTP] and collagens) plus fish parvalbumin, were subjected to nine combinations of pH (1.2-2.5-4.0) and pepsin-to-protein ratio (PPR: 10-1-0.1 U/µg) for pepsin digestion, followed by pancreatin digestion in the presence of bile salts. Digestion was monitored by SDS-PAGE in conjunction with Coomassie staining and immunoblotting using rabbit antisera and human IgE. Results At pH 4.0 and at PPR 0.1 most proteins, both allergen and non-allergen, were highly resistant to pepsin. Under conditions known to favor pepsin proteolysis, the established major allergens Ara h 2, Pru p 3 and Pen a 1 were highly resistant to proteolysis, while the allergen Cyp c 1 was not. However, this resistance to pepsin digestion only made Ara h 2 and to a lesser extent Pen a 1 and Pru p 3 stand out compared to their non-allergenic counterparts. Largely irrespective of preceding pepsin digestion conditions, pancreatin digestion was very effective for all tested proteins, allergens and non-allergens, except for Cyp c 1 and bovine collagen. Conclusions Sub-optimal pH, low pepsin-to protein ratio, and sequential pepsin and pancreatin digestion protocols do not improve the predictive value in distinguish allergens from non-allergens. Digestion conditions facilitating such distinction differ per protein pair.
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97
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Tiwari V, Mitra D, Tiwari M. Investigation of the interaction of allergens of Glycine max with IgE-antibody for designing of peptidomimetics based anti-allergen. Int Immunopharmacol 2018; 61:394-404. [PMID: 29957496 DOI: 10.1016/j.intimp.2018.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/22/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022]
Abstract
Allergen induced IgE dependent type I hypersensitivity is the main cause of the allergy, which would be a burden on medical setup in coming years. Allergens of Glycine max have been isolated, and their disease relationships are documented. Therefore, it becomes important to investigate the interaction of different allergens of Glycine max with IgE and also screen suitable therapeutics to prevent this interaction. The amino acid sequences of all allergens of Glycine max and their isoallergens have been taken, and 3D structure of allergens (Gly m 3, Gly m 4, Gly m 5, Gly m 6 and Gly m 8) and their isoallergens were generated using Modeller v9.17. The modeled structures were further validated using PSVS, ProSA, RAMPAGE, and PDBsum. HL domain of Fab region of human IgE (PDBID: 2R56) was generated using UCSFchimera. The HL domain was minimized by Schrodinger software using the OPLS_2005 force field. SiteMap identified epitope binding site of the minimized domain. All the predicted epitopes of different allergens were docked to the binding site of HL domain using the Patchdock server. We have also designed a peptidomimetics based inhibitor targeted at interaction interface of Gly m8 and IgE, using in-silico virtual screening, molecular mechanics, and molecular dynamics simulation studies. These studies identified BDE32166344 ((N-(1-{[1-(1-aminocyclopentanecarbonyl)-3-hydroxypyrrolidin-3-yl]methyl}piperidin-4-yl)acetamide) as a peptidomimetics based lead with binding energy of -72.77 kcal/mol. Therefore, the present study investigates the interaction between different Gly m allergens and IgE antibody and identifies peptidomimetics based lead that might be developed as a suitable therapeutics against allergy caused by allergen of Glycine max.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India.
| | - Debarghya Mitra
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
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98
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Kadam K, Karbhal R, Jayaraman VK, Sawant S, Kulkarni-Kale U. AllerBase: a comprehensive allergen knowledgebase. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4157991. [PMID: 29220458 PMCID: PMC5737053 DOI: 10.1093/database/bax066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/08/2017] [Indexed: 12/24/2022]
Abstract
Allergic diseases represent a major health concern worldwide due to steady rise in their prevalence leading to increased disease burden. The field of allergy research has witnessed significant progress and the focus of studies has shifted to molecular level. Vast amounts of data for allergens are archived in allergen databases, which cover diverse aspects of allergens and allergenicity with varying degrees of completeness. Users are required to refer to multiple databases including general purpose immunological databases to obtain relevant data of allergens. AllerBase, a relational database, has been developed with the objective of integrating protein allergens and related data from prevailing bioinformatics resources and published literature. AllerBase is a manually curated comprehensive knowledgebase of experimentally validated allergens where various attributes of allergenicity are made available on a single platform. Links to sequences, structures and immunological data are provided, where available, for all allergens. Data for specific features such as IgE-binding epitopes, IgE cross-reactivity and IgE antibodies are curated and archived. Bibliographic data reporting assays used for experimental characterization of allergens are compiled and processed using text mining approach. AllerBase, thus provides enhanced coverage of data with high granularity. The database can be browsed by category of allergens, epitopes or antibodies. It can also be queried using various attributes such as allergen name, isoallergens/variants, taxonomic level, source organism, sequences, structures, epitopes, antibodies and cross-reactive allergens. AllerBase also provides interface for sequence-based analyses and visualization of structure/epitope which can be used as a framework for translational research. A Completeness Index has been devised to indicate the availability of data on nine attributes for every allergen. This index will also serve as a pointer to identify allergen-specific areas of further research. AllerBase can be used to understand various aspects of allergy and allergenicity at molecular level and to design anti-allergy therapeutics. Database URL:http://bioinfo.net.in/AllerBase/Home.html
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Affiliation(s)
| | | | - V K Jayaraman
- Centre for Modeling and Simulation, Savitribai Phule Pune University, Pune 411007, India.,Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
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Bucholska J, Minkiewicz P, Darewicz M, Iwaniak A. Databases and Associated Bioinformatic Tools in Studies of Food Allergens, Epitopes and Haptens – a Review. POL J FOOD NUTR SCI 2018. [DOI: 10.1515/pjfns-2017-0022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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100
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WHO/IUIS Allergen Nomenclature: Providing a common language. Mol Immunol 2018; 100:3-13. [PMID: 29625844 DOI: 10.1016/j.molimm.2018.03.003] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 03/06/2018] [Indexed: 11/23/2022]
Abstract
A systematic nomenclature for allergens originated in the early 1980s, when few protein allergens had been described. A group of scientists led by Dr. David G. Marsh developed a nomenclature based on the Linnaean taxonomy, and further established the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee in 1986. Its stated aim was to standardize the names given to the antigens (allergens) that caused IgE-mediated allergies in humans. The Sub-Committee first published a revised list of allergen names in 1986, which continued to grow with rare publications until 1994. Between 1994 and 2007 the database was a text table online, then converted to a more readily updated website. The allergen list became the Allergen Nomenclature database (www.allergen.org), which currently includes approximately 880 proteins from a wide variety of sources. The Sub-Committee includes experts on clinical and molecular allergology. They review submissions of allergen candidates, using evidence-based criteria developed by the Sub-Committee. The review process assesses the biochemical analysis and the proof of allergenicity submitted, and aims to assign allergen names prior to publication. The Sub-Committee maintains and revises the database, and addresses continuous challenges as new "omics" technologies provide increasing data about potential new allergens. Most journals publishing information on new allergens require an official allergen name, which involves submission of confidential data to the WHO/IUIS Allergen Nomenclature Sub-Committee, sufficient to demonstrate binding of IgE from allergic subjects to the purified protein.
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