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Yadav K, Dwivedi S, Gupta S, Dubey AK, Singh VK, Tanveer A, Yadav S, Yadav D. Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach. 3 Biotech 2022; 12:261. [PMID: 36082361 PMCID: PMC9445148 DOI: 10.1007/s13205-022-03333-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique β-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344-1142 amino acid residues, 35.44-127.41 kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 β-sheets, 1 β-hairpin, 7-12 β bulges, 18-25 strands, 6 -11 helices, 1 helix-helix interaction, 32-49 β turns, 2-6 γ turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03333-w.
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Affiliation(s)
- Kanchan Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Shruti Dwivedi
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Supriya Gupta
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Amit K. Dubey
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Vinay K. Singh
- Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Aiman Tanveer
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Sangeeta Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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Characterization, biological evaluation and molecular docking of mulberry fruit pectin. Sci Rep 2020; 10:21789. [PMID: 33311512 PMCID: PMC7732840 DOI: 10.1038/s41598-020-78086-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/22/2020] [Indexed: 12/23/2022] Open
Abstract
Contemplating the exemplary benefits of pectin on human health, we precisely characterized and evaluated the antibacterial and anticancer activities from purified Mulberry Fruit Pectins (MFP). Here, we tested BR-2 and S-13 varieties of mulberry fruit pectins against six bacterial strains and two human cancer cell lines (HT-29 and Hep G-2), using MIC and an in vitro cell-based assay respectively. The BR-2 mulberry fruit pectin performs superior to S-13 by inhibiting strong bacterial growth (MIC = 500–1000 μg/mL) against tested bacterial strains and cytotoxic activities at the lowest concentration (10 µg/ml) against the Hep G-2 cell line. However, both tested drugs failed to exhibit cytotoxicity on the human colon cancer cell line (HT-29). Based on molecular interaction through docking, pectin binds effectively with the receptors (1e3g, 3t0c, 5czz, 6j7l, 6v40, 5ibs, 5zsy, and 6ggb) and proven to be a promising antimicrobial and anti-cancer agents. The pursuit of unexploited drugs from mulberry fruit pectin will potentially combat against bacterial and cancer diseases. Finally, future perspectives of MFP for the treatment of many chronic diseases will help immensely due to their therapeutic properties.
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Rasheed F, Markgren J, Hedenqvist M, Johansson E. Modeling to Understand Plant Protein Structure-Function Relationships-Implications for Seed Storage Proteins. Molecules 2020; 25:E873. [PMID: 32079172 PMCID: PMC7071054 DOI: 10.3390/molecules25040873] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/30/2022] Open
Abstract
Proteins are among the most important molecules on Earth. Their structure and aggregation behavior are key to their functionality in living organisms and in protein-rich products. Innovations, such as increased computer size and power, together with novel simulation tools have improved our understanding of protein structure-function relationships. This review focuses on various proteins present in plants and modeling tools that can be applied to better understand protein structures and their relationship to functionality, with particular emphasis on plant storage proteins. Modeling of plant proteins is increasing, but less than 9% of deposits in the Research Collaboratory for Structural Bioinformatics Protein Data Bank come from plant proteins. Although, similar tools are applied as in other proteins, modeling of plant proteins is lagging behind and innovative methods are rarely used. Molecular dynamics and molecular docking are commonly used to evaluate differences in forms or mutants, and the impact on functionality. Modeling tools have also been used to describe the photosynthetic machinery and its electron transfer reactions. Storage proteins, especially in large and intrinsically disordered prolamins and glutelins, have been significantly less well-described using modeling. These proteins aggregate during processing and form large polymers that correlate with functionality. The resulting structure-function relationships are important for processed storage proteins, so modeling and simulation studies, using up-to-date models, algorithms, and computer tools are essential for obtaining a better understanding of these relationships.
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Affiliation(s)
- Faiza Rasheed
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Box 101, SE-230 53 Alnarp, Sweden; (F.R.); (J.M.)
- School of Chemical Science and Engineering, Fibre and Polymer Technology, KTH Royal Institute of Technology, SE–100 44 Stockholm, Sweden;
| | - Joel Markgren
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Box 101, SE-230 53 Alnarp, Sweden; (F.R.); (J.M.)
| | - Mikael Hedenqvist
- School of Chemical Science and Engineering, Fibre and Polymer Technology, KTH Royal Institute of Technology, SE–100 44 Stockholm, Sweden;
| | - Eva Johansson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Box 101, SE-230 53 Alnarp, Sweden; (F.R.); (J.M.)
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Lima-Cabello E, Alché JD, Jimenez-Lopez JC. Narrow-Leafed Lupin Main Allergen β-Conglutin (Lup an 1) Detection and Quantification Assessment in Natural and Processed Foods. Foods 2019; 8:foods8100513. [PMID: 31635336 PMCID: PMC6835513 DOI: 10.3390/foods8100513] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/23/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022] Open
Abstract
The increasing prevalence of lupin allergy as a consequence to the functional characteristics of a growing number of sweet lupin-derived foods consumption makes the imperious necessity to develop analytical tools for the detection of allergen proteins in foodstuffs. The current study developed a new highly specific, sensitive and accurate ELISA method to detect, identify and quantify the lupin main allergen β-conglutin (Lup an 1) protein in natural and processed food. The implementation of accurate standards made with recombinant conglutin β1, and an anti-Lup an 1 antibody made from a synthetic peptide commonly shared among β-conglutin isoforms from sweet lupin species was able to detect up to 8.1250 ± 0.1701 ng (0.0406 ± 0.0009 ppm) of Lup an 1. This identified even lupin traces present in food samples which might elicit allergic reactions in sensitized consumers, such as β-conglutin proteins detection and quantification in processed (roasted, fermented, boiled, cooked, pickled, toasted, pasteurized) food, while avoiding cross-reactivity (false positive) with other legumes as peanut, chickpea, lentils, faba bean, and cereals. This study demonstrated that this new ELISA method constitutes a highly sensitive and reliable molecular tool able to detect, identify and quantify Lup an 1. This contributes to a more efficient management of allergens by the food industry, the regulatory agencies and clinicians, thus helping to keep the health safety of the consumers.
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Affiliation(s)
- Elena Lima-Cabello
- Department of Biochemistry, Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Profesor Albareda 1, E-18008 Granada, Spain.
| | - Juan D Alché
- Department of Biochemistry, Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Profesor Albareda 1, E-18008 Granada, Spain.
| | - Jose C Jimenez-Lopez
- Department of Biochemistry, Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Profesor Albareda 1, E-18008 Granada, Spain.
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6019, Australia.
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Li Y, Wang Y, Ran P, Yang P, Liu Z. IgE binding activities and in silico epitope prediction of Der f 32 in Dermatophagoides farinae. Immunol Lett 2019; 213:46-54. [PMID: 31381937 DOI: 10.1016/j.imlet.2019.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/20/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
Abstract
Dermatophagoides farinae is a common indoor allergen source that produces more than 30 allergens, which induces diverse allergic diseases such as allergic rhinitis, allergic asthma and atopic dermatitis. Der f 32 is an inorganic pyrophosphatase and an important allergen from Dermatophagoides farinae. In the present study, Der f 32 was cloned, expressed and purified in order to better understand its structure and immunogenicity. Immunoblotting analysis and ELISA showed 5 of 5 positive reactions to recombinant Der f 32 using serum from house dust mite (HDM)-allergic patients. We constructed homology modeling and predicted epitopes of Der f 32 via bioinformatic tools. The sequence and structural analysis indicated that Der f 32 belonged to the pyrophosphatase family and represented a special structure of external α-helices and internal antiparallel closed β-sheets. In addition, eight B-cell epitopes and four T-cell epitopes were predicted. B-cell epitopes were 24-31, 111-121, 135-140, 168-172, 200-207, 214-220, 237-243, and 268-274 and T-cell epitopes were 47-55, 78-90, 127-135 and 143-151. The B-cell epitopes were distributed completely on the surface of Der f 32 and were located largely in random coils of secondary structures. Hydrophobic and charged amino acids comprised more than 80% of the residues of B-cell epitopes and may participate in IgE binding. The T-cell epitopes were located primarily in the interior of Der f 32 and, to a certain extent avoided degradation by proteases. The structures of T-cell epitopes were surrounded by B-cell epitopes, and this arrangement may have important biological significance for maintaining the immunogenicity of allergens.
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Affiliation(s)
- Yuwei Li
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518060, China; The Third Affiliated Hospital of Shenzhen University, Shenzhen 518020, China; State Key Laboratory of Respiratory Disease, Guangzhou Medical College, Guangzhou, 510006, China
| | - Yuwei Wang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Pixin Ran
- State Key Laboratory of Respiratory Disease, Guangzhou Medical College, Guangzhou, 510006, China
| | - Pingchang Yang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518060, China.
| | - Zhigang Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518060, China; The Third Affiliated Hospital of Shenzhen University, Shenzhen 518020, China.
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Toda K. Relationship between Pectin Methylesterase, Calcium, and the Hardness of Cooked Beans. J JPN SOC FOOD SCI 2018. [DOI: 10.3136/nskkk.65.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Yue X, Lin S, Yu Y, Huang L, Cao J. The putative pectin methylesterase gene, BcMF23a, is required for microspore development and pollen tube growth in Brassica campestris. PLANT CELL REPORTS 2018; 37:1003-1009. [PMID: 29644403 DOI: 10.1007/s00299-018-2285-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 05/24/2023]
Abstract
BcMF23a contributes to pollen wall development via influencing intine construction, which, in turn, influences pollen tube growth. Pollen wall, the morphological out face of pollen, surrounds male gametophyte and plays an important role in plant reproduction. Pectin methylesterases (PMEs) are involved in pollen wall construction by de-esterifying pectin of the intine. In this study, the function of a putative pectin methylesterase gene, Brassica campestris Male Fertility 23a (BcMF23a), was investigated. Knockdown of BcMF23a by artificial microRNA (amiRNA) technology resulted in abnormal pollen intine formation outside of the germinal furrows at the binucleate stage. At the trinucleate stage, 20.69% of pollen possessed the degradation of nuclei, cytoplasm and the intine, resulting in shrunken pollen, whereas the remaining 75.86% were wall-disrupted with degrading cytoplasm and broken exine inside the germinal furrows. In addition, pollen abortion in transgenic plants caused germination percentage reduction by 19% in vitro and pollen tube growth disruption in natural stigma in vivo. Taken together, BcMF23a is involved in pollen development and pollen tube growth, possibly via participating in intine construction. This study may contribute towards understanding the function of pollen-specific PMEs and the molecular regulatory network of pollen wall development.
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Affiliation(s)
- Xiaoyan Yue
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Youjian Yu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, Zhejiang, China
| | - Li Huang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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Patel S, Rani A, Goyal A. Insights into the immune manipulation mechanisms of pollen allergens by protein domain profiling. Comput Biol Chem 2017; 70:31-39. [PMID: 28780227 DOI: 10.1016/j.compbiolchem.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/13/2017] [Accepted: 07/26/2017] [Indexed: 11/25/2022]
Abstract
Plant pollens are airborne allergens, as their inhalation causes immune activation, leading to rhinitis, conjunctivitis, sinusitis and oral allergy syndrome. A myriad of pollen proteins belonging to profilin, expansin, polygalacturonase, glucan endoglucosidase, pectin esterase, and lipid transfer protein class have been identified. In the present in silico study, the protein domains of fifteen pollen sequences were extracted from the UniProt database and submitted to the interactive web tool SMART (Simple Modular Architecture Research Tool), for finding the protein domain profiles. Analysis of the data based on custom-made scripts revealed the conservation of pathogenic domains such as OmpH, PROF, PreSET, Bet_v_1, Cpl-7 and GAS2. Further, the retention of critical domains like CHASE2, Galanin, Dak2, DALR_1, HAMP, PWI, EFh, Excalibur, CT, PbH1, HELICc, and Kelch in pollen proteins, much like cockroach allergens and lethal viruses (such as HIV, HCV, Ebola, Dengue and Zika) was observed. Based on the shared motifs in proteins of taxonomicall-ydispersed organisms, it can be hypothesized that allergens and pathogens manipulate the human immune system in a similar manner. Allergens, being inanimate, cannot replicate in human body, and are neutralized by immune system. But, when the allergens are unremitting, the immune system becomes persistently hyper-sensitized, creating an inflammatory milieu. This study is expected to contribute to the understanding of pollen allergenicity and pathogenicity.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA.
| | - Aruna Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Philippe F, Pelloux J, Rayon C. Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. BMC Genomics 2017; 18:456. [PMID: 28595570 PMCID: PMC5465549 DOI: 10.1186/s12864-017-3833-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. Results In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases. An overview of plant PAE proteins, particularly Arabidopsis thaliana PAEs, based on phylogeny analysis, protein motif identification and modeled 3D structure is presented. A phylogenetic tree analysis using protein sequences clustered the plant PAEs into five clades. AtPAEs clustered in four clades in the plant kingdom PAE tree while they formed three clades when a phylogenetic tree was performed only on Arabidopsis proteins, due to isoform AtPAE9. Primitive plants that display a smaller number of PAEs clustered into two clades, while in higher plants, the presence of multiple members of PAE genes indicated a diversification of AtPAEs. 3D homology modeling of AtPAE8 from clade 2 with a human Notum protein showed an α/β hydrolase structure with the hallmark Ser-His-Asp of the active site. A 3D model of AtPAE4 from clade 1 and AtPAE10 from clade 3 showed a similar shape suggesting that the diversification of AtPAEs is unlikely to arise from the shape of the protein. Primary structure prediction analysis of AtPAEs showed a specific motif characteristic of each clade and identified one major group of AtPAEs with a signal peptide and one group without a signal peptide. A multiple sequence alignment of the putative plant PAEs revealed consensus sequences with important putative catalytic residues: Ser, Asp, His and a pectin binding site. Data mining of gene expression profiles of AtPAE revealed that genes from clade 2 including AtPAE7, AtPAE8 and AtPAE11, which are duplicated genes, are highly expressed during plant growth and development while AtPAEs without a signal peptide, including AtPAE2 and AtPAE4, are more regulated in response to plant environmental conditions. Conclusion Bioinformatic analysis of plant, and particularly Arabidopsis, AtPAEs provides novel insights, including new motifs that could play a role in pectin binding and catalytic sites. The diversification of AtPAEs is likely to be related to neofunctionalization of some AtPAE genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3833-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Philippe
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Jérôme Pelloux
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Catherine Rayon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France.
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Jimenez-Lopez JC, Robles-Bolivar P, Lopez-Valverde FJ, Lima-Cabello E, Kotchoni SO, Alché JD. Ole e 13 is the unique food allergen in olive: Structure-functional, substrates docking, and molecular allergenicity comparative analysis. J Mol Graph Model 2016; 66:26-40. [PMID: 27017426 DOI: 10.1016/j.jmgm.2016.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/09/2016] [Accepted: 03/13/2016] [Indexed: 11/25/2022]
Abstract
Thaumatin-like proteins (TLPs) are enzymes with important functions in pathogens defense and in the response to biotic and abiotic stresses. Last identified olive allergen (Ole e 13) is a TLP, which may also importantly contribute to food allergy and cross-allergenicity to pollen allergen proteins. The goals of this study are the characterization of the structural-functionality of Ole e 13 with a focus in its catalytic mechanism, and its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering a) functional-regulatory motifs, b) comparative study of linear sequence, 2-D and 3D structural homology modeling, c) molecular docking with two different β-D-glucans, d) conservational and evolutionary analysis, e) catalytic mechanism modeling, and f) IgE-binding, B- and T-cell epitopes identification and comparison to other allergenic TLPs. Sequence comparison, structure-based features, and phylogenetic analysis identified Ole e 13 as a thaumatin-like protein. 3D structural characterization revealed a conserved overall folding among plants TLPs, with mayor differences in the acidic (catalytic) cleft. Molecular docking analysis using two β-(1,3)-glucans allowed to identify fundamental residues involved in the endo-1,3-β-glucanase activity, and defining E84 as one of the conserved residues of the TLPs responsible of the nucleophilic attack to initiate the enzymatic reaction and D107 as proton donor, thus proposing a catalytic mechanism for Ole e 13. Identification of IgE-binding, B- and T-cell epitopes may help designing strategies to improve diagnosis and immunotherapy to food allergy and cross-allergenic pollen TLPs.
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Affiliation(s)
- J C Jimenez-Lopez
- Plant Reproductive Biology Laboratory; Department of Biochemistry, Cell & Molecular Biology of Plants; Estación Experimental del Zaidín; Spanish National Research Council (CSIC), Granada 18008, Spain; The UWA Institute of Agriculture, The University of Western Australia, Crawley, Perth 6009, Australia.
| | - P Robles-Bolivar
- Plant Reproductive Biology Laboratory; Department of Biochemistry, Cell & Molecular Biology of Plants; Estación Experimental del Zaidín; Spanish National Research Council (CSIC), Granada 18008, Spain
| | - F J Lopez-Valverde
- Plant Reproductive Biology Laboratory; Department of Biochemistry, Cell & Molecular Biology of Plants; Estación Experimental del Zaidín; Spanish National Research Council (CSIC), Granada 18008, Spain
| | - E Lima-Cabello
- Plant Reproductive Biology Laboratory; Department of Biochemistry, Cell & Molecular Biology of Plants; Estación Experimental del Zaidín; Spanish National Research Council (CSIC), Granada 18008, Spain
| | - S O Kotchoni
- Department of Biology; Rutgers, The State University of New Jersey; Camden, NJ 08102, USA; Center for Computational and Integrative Biology; Rutgers, The State University of New Jersey; Camden, NJ 08102, USA
| | - J D Alché
- Plant Reproductive Biology Laboratory; Department of Biochemistry, Cell & Molecular Biology of Plants; Estación Experimental del Zaidín; Spanish National Research Council (CSIC), Granada 18008, Spain
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Jimenez-Lopez JC, Zafra A, Palanco L, Florido JF, Alché JDD. Identification and Assessment of the Potential Allergenicity of 7S Vicilins in Olive (Olea europaea L.) Seeds. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4946872. [PMID: 27034939 PMCID: PMC4789380 DOI: 10.1155/2016/4946872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/25/2016] [Accepted: 02/03/2016] [Indexed: 12/23/2022]
Abstract
Olive seeds, which are a raw material of interest, have been reported to contain 11S seed storage proteins (SSPs). However, the presence of SSPs such as 7S vicilins has not been studied. In this study, following a search in the olive seed transcriptome, 58 sequences corresponding to 7S vicilins were retrieved. A partial sequence was amplified by PCR from olive seed cDNA and subjected to phylogenetic analysis with other sequences. Structural analysis showed that olive 7S vicilin contains 9 α-helixes and 22 β-sheets. Additionally, 3D structural analysis displayed good superimposition with vicilin models generated from Pistacia and Sesamum. In order to assess potential allergenicity, T and B epitopes present in these proteins were identified by bioinformatic approaches. Different motifs were observed among the species, as well as some species-specific motifs. Finally, expression analysis of vicilins was carried out in protein extracts obtained from seeds of different species, including the olive. Noticeable bands were observed for all species in the 15-75 kDa MW interval, which were compatible with vicilins. The reactivity of the extracts to sera from patients allergic to nuts was also analysed. The findings with regard to the potential use of olive seed as food are discussed.
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Affiliation(s)
- Jose C. Jimenez-Lopez
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
- Elayo Group, Castillo de Locubín, 23670 Jaén, Spain
| | - Lucía Palanco
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | | | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
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Kent LM, Loo TS, Melton LD, Mercadante D, Williams MAK, Jameson GB. Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control. J Biol Chem 2015; 291:1289-306. [PMID: 26567911 DOI: 10.1074/jbc.m115.673152] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 12/17/2022] Open
Abstract
Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10⅔-turn parallel β-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged.
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Affiliation(s)
- Lisa M Kent
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Trevor S Loo
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Laurence D Melton
- From Riddet Institute and School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Davide Mercadante
- From Riddet Institute and Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, 69118 Heidelberg, Germany, and
| | - Martin A K Williams
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
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13
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Lupin Allergy: Uncovering Structural Features and Epitopes of β-conglutin Proteins in Lupinus Angustifolius L. with a Focus on Cross-allergenic Reactivity to Peanut and Other Legumes. BIOINFORMATICS AND BIOMEDICAL ENGINEERING 2015. [DOI: 10.1007/978-3-319-16483-0_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Chen H, Yang HW, Wei JF, Tao AL. In silico prediction of the T-cell and IgE-binding epitopes of Per a 6 and Bla g 6 allergens in cockroaches. Mol Med Rep 2014; 10:2130-6. [PMID: 25050891 DOI: 10.3892/mmr.2014.2399] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 04/02/2014] [Indexed: 11/05/2022] Open
Abstract
Per a 6 and Bla g 6 are cockroach allergens found in Periplaneta americana and Blattella germanica, respectively. The objective of the present study was to predict the B‑ and T‑cell epitopes of the Per a 6 and Bla g 6 allergens. Three immunoinformatics tools, the DNAStar Protean system, the Bioinformatics Predicted Antigenic Peptides system and the BepiPred 1.0 server, were used to predict the potential B‑cell epitopes, while Net‑MHCIIpan‑2.0 and NetMHCII‑2.2 were used to predict the T‑cell epitopes of the two allergens. As a result, seven peptides were predicted in the Per a 6 allergen and seven peptides were predicted in the Bla g 6 allergen in the B‑cell epitope predictions. In the T‑cell prediction, the Per a 6 allergen was predicted to have nine strongly binding nonamer core epitope sequences (IC50<50 nm) and 28 weakly binding sequences (50 nm<IC50<500 nm), while the Bla g 6 allergen was predicted to have nine strong binders and 25 weak binders. These results may be useful for peptide‑based vaccine designs.
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Affiliation(s)
- Hao Chen
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Hai-Wei Yang
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ji-Fu Wei
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Ai-Lin Tao
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
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15
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Li X, Yang HW, Chen H, Wu J, Liu Y, Wei JF. In Silico Prediction of T and B Cell Epitopes of Der f 25 in Dermatophagoides farinae. Int J Genomics 2014; 2014:483905. [PMID: 24895543 PMCID: PMC4033504 DOI: 10.1155/2014/483905] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/28/2014] [Accepted: 03/30/2014] [Indexed: 12/30/2022] Open
Abstract
The house dust mites are major sources of indoor allergens for humans, which induce asthma, rhinitis, dermatitis, and other allergic diseases. Der f 25 is a triosephosphate isomerase, representing the major allergen identified in Dermatophagoides farinae. The objective of this study was to predict the B and T cell epitopes of Der f 25. In the present study, we analyzed the physiochemical properties, function motifs and domains, and structural-based detailed features of Der f 25 and predicted the B cell linear epitopes of Der f 25 by DNAStar protean system, BPAP, and BepiPred 1.0 server and the T cell epitopes by NetMHCIIpan-3.0 and NetMHCII-2.2. As a result, the sequence and structure analysis identified that Der f 25 belongs to the triosephosphate isomerase family and exhibited a triosephosphate isomerase pattern (PS001371). Eight B cell epitopes (11-18, 30-35, 71-77, 99-107, 132-138, 173-187, 193-197, and 211-224) and five T cell epitopes including 26-34, 38-54, 66-74, 142-151, and 239-247 were predicted in this study. These results can be used to benefit allergen immunotherapies and reduce the frequency of mite allergic reactions.
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Affiliation(s)
- Xiaohong Li
- Department of Allergy, First Affiliated Hospital of Anhui Medical University, No. 210, Jixi Road, Anhui Province, Hefei 230022, China
| | - Hai-Wei Yang
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Jiangsu Province, Nanjing 210029, China
| | - Hao Chen
- Research Division of Clinical Pharmacology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Jing Wu
- Department of Allergy, First Affiliated Hospital of Anhui Medical University, No. 210, Jixi Road, Anhui Province, Hefei 230022, China
| | - Yehai Liu
- Department of Allergy, First Affiliated Hospital of Anhui Medical University, No. 210, Jixi Road, Anhui Province, Hefei 230022, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
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16
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Jimenez-Lopez JC, Kotchoni SO, Hernandez-Soriano MC, Gachomo EW, Alché JD. Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen. J Comput Aided Mol Des 2013; 27:873-95. [PMID: 24154826 DOI: 10.1007/s10822-013-9686-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 10/16/2013] [Indexed: 01/22/2023]
Abstract
Isoflavone reductase-like proteins (IRLs) are enzymes with key roles in the metabolism of diverse flavonoids. Last identified olive pollen allergen (Ole e 12) is an IRL relevant for allergy amelioration, since it exhibits high prevalence among atopic patients. The goals of this study are the characterization of (A) the structural-functionality of Ole e 12 with a focus in its catalytic mechanism, and (B) its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering (1) physicochemical properties and functional-regulatory motifs, (2) sequence analysis, 2-D and 3D structural homology modeling comparative study and molecular docking, (3) conservational and evolutionary analysis, (4) catalytic mechanism modeling, and (5) sequence, structure-docking based B-cell epitopes prediction, while T-cell epitopes were predicted by inhibitory concentration and binding score methods. Structural-based detailed features, phylogenetic and sequences analysis have identified Ole e 12 as phenylcoumaran benzylic ether reductase. A catalytic mechanism has been proposed for Ole e 12 which display Lys133 as one of the conserved residues of the IRLs catalytic tetrad (Asn-Ser-Tyr-Lys). Structure characterization revealed a conserved protein folding among plants IRLs. However, sequence polymorphism significantly affected residues involved in the catalytic pocket structure and environment (cofactor and substrate interaction-recognition). It might also be responsible for IRLs isoforms functionality and regulation, since micro-heterogeneities affected physicochemical and posttranslational motifs. This polymorphism might have large implications for molecular differences in B- and T-cells epitopes of Ole e 12, and its identification may help designing strategies to improve the component-resolving diagnosis and immunotherapy of pollen and food allergy through development of molecular tools.
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Affiliation(s)
- Jose C Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008, Granada, Spain,
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17
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Jimenez-Lopez JC, Rodríguez-García MI, Alché JD. Analysis of the effects of polymorphism on pollen profilin structural functionality and the generation of conformational, T- and B-cell epitopes. PLoS One 2013; 8:e76066. [PMID: 24146818 PMCID: PMC3798325 DOI: 10.1371/journal.pone.0076066] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/19/2013] [Indexed: 12/17/2022] Open
Abstract
An extensive polymorphism analysis of pollen profilin, a fundamental regulator of the actin cytoskeleton dynamics, has been performed with a major focus in 3D-folding maintenance, changes in the 2-D structural elements, surface residues involved in ligands-profilin interactions and functionality, and the generation of conformational and lineal B- and T-cell epitopes variability. Our results revealed that while the general fold is conserved among profilins, substantial structural differences were found, particularly affecting the special distribution and length of different 2-D structural elements (i.e. cysteine residues), characteristic loops and coils, and numerous micro-heterogeneities present in fundamental residues directly involved in the interacting motifs, and to some extension these residues nearby to the ligand-interacting areas. Differential changes as result of polymorphism might contribute to generate functional variability among the plethora of profilin isoforms present in the olive pollen from different genetic background (olive cultivars), and between plant species, since biochemical interacting properties and binding affinities to natural ligands may be affected, particularly the interactions with different actin isoforms and phosphoinositides lipids species. Furthermore, conspicuous variability in lineal and conformational epitopes was found between profilins belonging to the same olive cultivar, and among different cultivars as direct implication of sequences polymorphism. The variability of the residues taking part of IgE-binding epitopes might be the final responsible of the differences in cross-reactivity among olive pollen cultivars, among pollen and plant-derived food allergens, as well as between distantly related pollen species, leading to a variable range of allergy reactions among atopic patients. Identification and analysis of commonly shared and specific epitopes in profilin isoforms is essential to gain knowledge about the interacting surface of these epitopes, and for a better understanding of immune responses, helping design and development of rational and effective immunotherapy strategies for the treatment of allergy diseases.
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MESH Headings
- Amino Acid Sequence
- Antigens, Plant/chemistry
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/classification
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/classification
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Food Hypersensitivity/immunology
- Humans
- Models, Molecular
- Molecular Sequence Data
- Olea/chemistry
- Phylogeny
- Plant Proteins/chemistry
- Pollen/chemistry
- Polymorphism, Genetic/immunology
- Profilins/chemistry
- Profilins/classification
- Profilins/genetics
- Profilins/immunology
- Protein Structure, Tertiary
- Sequence Alignment
- Structural Homology, Protein
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Affiliation(s)
- Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of plants, Estación Experimental del Zaidín (EEZ), High Council for Scientific Research (CSIC), Granada, Spain
- * E-mail: (JCJL); (JDA)
| | - María I. Rodríguez-García
- Department of Biochemistry, Cell and Molecular Biology of plants, Estación Experimental del Zaidín (EEZ), High Council for Scientific Research (CSIC), Granada, Spain
| | - Juan D. Alché
- Department of Biochemistry, Cell and Molecular Biology of plants, Estación Experimental del Zaidín (EEZ), High Council for Scientific Research (CSIC), Granada, Spain
- * E-mail: (JCJL); (JDA)
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