In silico analyses of structural and allergenicity features of sapodilla (Manilkara zapota) acidic thaumatin-like protein in comparison with allergenic plant TLPs

In silico tools to assess the potential allergenicity of shiitake mushrooms (Lentinula edodes)

BACKGROUND

Computational tools may have an edge over conventional methods for the preliminary evaluation of food allergenicity. In this study, the allergenic potential of Lentinula edodes was evaluated and validated using in silico tools.

RESULTS

The potential cross-reactivity of mushroom proteins with fungal allergens was determined using sequence alignment - the Fast Alignment (FASTA) and Basic Local Alignment Search Tool (BLAST) algorithm. Eight L. edodes proteins were cross-reactive with allergens from fungal origin, showing 52%-89% sequence identity using FASTA algorithm-based alignment. The BLAST data were corroborated by percentage identity and query coverage. Physico-chemical property-based allergenicity was deciphered by AlgPred, Allermatch, and AllergenFP software, which predicted six out of eight proteins as potential allergens. Sequence alignment showed 66%-86% conservancy between mushroom protein and known fungal allergens. Secondary structure and amino acid composition supported structural affinity between query and fungal proteins. Three-dimensional structures of five mushroom proteins were generated, quality assessed, and superimposed with fungal allergens, suggesting possible allergenicity of mushroom proteins. An enzyme-linked immunosorbent assay (ELISA) demonstrated immunoglobulin E (IgE) binding in 13 out of 21 food-hypersensitive patients' sera.

CONCLUSION

In silico tools provide preliminary indications about the potential allergenicity and cross-reactivity of mushroom proteins. This approach may be used for the prelusive allergenicity assessment of allergen sources. © 2022 Society of Chemical Industry.

Plant Thaumatin-like Proteins: Function, Evolution and Biotechnological Applications

Thaumatin-like proteins (TLPs) are a highly complex protein family associated with host defense and developmental processes in plants, animals, and fungi. They are highly diverse in angiosperms, for which they are classified as the PR-5 (Pathogenesis-Related-5) protein family. In plants, TLPs have a variety of properties associated with their structural diversity. They are mostly associated with responses to biotic stresses, in addition to some predicted activities under drought and osmotic stresses. The present review covers aspects related to the structure, evolution, gene expression, and biotechnological potential of TLPs. The efficiency of the discovery of new TLPs is below its potential, considering the availability of omics data. Furthermore, we present an exemplary bioinformatics annotation procedure that was applied to cowpea (Vigna unguiculata) transcriptome, including libraries of two tissues (root and leaf), and two stress types (biotic/abiotic) generated using different sequencing approaches. Even without using genomic sequences, the pipeline uncovered 56 TLP candidates in both tissues and stresses. Interestingly, abiotic stress (root dehydration) was associated with a high number of modulated TLP isoforms. The nomenclature used so far for TLPs was also evaluated, considering TLP structure and possible functions identified to date. It is clear that plant TLPs are promising candidates for breeding purposes and for plant transformation aiming a better performance under biotic and abiotic stresses. The development of new therapeutic drugs against human fungal pathogens also deserves attention. Despite that, applications derived from TLP molecules are still below their potential, as it is evident in our review.

In silico assessment data of allergenicity and cross-reactivity of NP24 epitopes from Solanum lycopersicum (Tomato) fruit

This paper describes data on allergies caused by food (vegetable) and their negative impact on the nutritional balance of the human body. Allergic responses to vegetables such as tomatoes, capsicum and spinach are next to fish, eggs and nuts. Epitopes such as NP24 (allergens) are one of the salt-induced allergenic proteins found in the thaumatin-like protein (TLP) family. The mechanism of allergenicity of TLP found in Solanum lycopersicum (Tomato) fruit is poorly studied. Here we demonstrated allergenicity conferred by the NP24 protein found in Tomato. The data on the cross-reactivity of NP24 protein was generated using Allergen Online and Allermatch tools. Tomato allergenic protein epitope shows a significant identity of with allergens reported in Capsicum, Olive, Kiwi, Tobacco and Banana allergens. Hence, the datasets of sequences, comparative analysis and homology epitope mapping over three dimensional (3D) structures revealed that NP24 has higher cross-reactivity to Capsicum and Tobacco proteins. Thus, this data probably act as limelight for planning wet lab experiments.

Gene Cloning, Expression, and Antifungal Activities of Permatin from Naked Oat (Avena nuda)

Thaumatin-like proteins (TLPs) are the products of a large, highly complex gene family involved in host defense. TLPs also belong to the pathogenesis-related family 5 (PR-5) of plant defense proteins. Most TLPs exhibit potential antifungal activities, and their accumulation in the plant is related to many physiological processes. In this study, a gene encoding TLP named permatin with an open reading frame of 678 bp encoding a protein of 225 amino acids with a calculated molecular mass of 23.5 kDa was cloned from naked oat leaves. Phylogenetic analysis revealed that permatin shares high homology with a number of other TLPs among diverse taxa. Model of structure by homology modeling showed that permatin consists of an acidic cleft region consistent with most TLPs. Recombinant NusA-permatin was overexpressed in Escherichia coli strain BL21 and purified by Heparin column combined with Sephacryl S-200 column. The protein exhibited antifungal activity to Fusarium oxysporum (half maximal inhibitory concentration, IC₅₀ = 21.42 μM). Morphological observation showed that NusA-permatin can induce mycelium deformation of F. oxysporum, the cell membrane is blurred, and the diaphragm is not obvious. NusA-permatin also causes membrane permeabilization and reactive oxygen species accumulation in the mycelium of F. oxysporum. Permatin may play an important role in the disease resistance responses of plants against pathogen attacks through its antifungal activity.

Clinical and immuno-proteomic approach on Lantana camara pollen allergy-a major health hazard

BACKGROUND

The incidence of allergic diseases is increasing gradually and is a global burden affecting the socio-economic quality of life. Identification of allergens is the first step towards paving the way for therapeutic interventions against atopic diseases. Our previous investigation figured out that total pollen load correlated significantly with the rise of respiratory allergy in a subtropical city in India. The most dominant pollen responsible for IgE sensitivity in most patients emerged to be from Lantana camara (LC) an obnoxious weed growing in and around suburban areas of West Bengal. In this study, we identified allergenic components from this shrub using an immunoproteomic approach.

METHODS

Determination of dominant pollen species was done using aerobiological sampling during two consecutive years and correlated with hospitalization and skin prick test. Serum was collected from LC positive patients and checked for in vitro allergenicity using ELISA and Histamine assay. Total proteome was profiled in SDS-PAGE, 2D PAGE and immunoblotted to detect IgE binding proteins which were further identified using mass spectrometry.

RESULTS

Lantana camara pollen emerged as a significant contributor from the correlation study with hospital admission of the respiratory allergy sufferers and its extract demonstrated an elevated IgE response in ELISA and histamine release assay tests. Five IgE reactive bands/zones were observed in 1D blot which resolved to 12 allergo-reactive spots in the 2D blot. Mass spectrometric analysis identified nine spots that grouped into four diverse proteins. Pathogenesis-related Thaumatin-like protein was found to be one of the major allergens in Lantana camara.

CONCLUSIONS

This is to our knowledge the first attempt to identify allergens from Lantana camara using a proteomic approach. The allergens identified thereof can be used to prepare hypoallergenic vaccine candidates and design immunotherapy trials against LC pollen and other aeroallergen carriers which are cross-reactive and harbor similar proteins.

In silico allergenicity prediction of several lipid transfer proteins

Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of allergenicity of new molecules based on their homology with known allergens have been released, and guidelines to assess potential allergenicity of proteins through bioinformatics have been established. Even if such tools are only partially reliable yet, they can provide important indications when other kinds of molecular characterization are lacking. The potential allergenicity of 28 amino acid sequences of LTPs homologs, either retrieved from the UniProt database or in silico deduced from the corresponding EST coding sequence, was predicted using 7 publicly available web tools. Moreover, their similarity degree to their closest known LTP allergens was calculated, in order to evaluate their potential cross-reactivity. Finally, all sequences were studied for their identity degree with the peach allergen Pru p 3, considering the regions involved in the formation of its known conformational IgE-binding epitope. Most of the analyzed sequences displayed a high probability to be allergenic according to all the software employed. The analyzed LTPs from bell pepper, cassava, mango, mungbean and soybean showed high homology (>70%) with some known allergenic LTPs, suggesting a potential risk of cross-reactivity for sensitized individuals. Other LTPs, like for example those from canola, cassava, mango, mungbean, papaya or persimmon, displayed a high degree of identity with Pru p 3 within the consensus sequence responsible for the formation, at three-dimensional level, of its major conformational epitope. Since recent studies highlighted how in patients mono-sensitized to peach LTP the levels of IgE seem directly proportional to the chance of developing cross-reactivity to LTPs from non-Rosaceae foods, and these chances increase the more similar the protein is to Pru p 3, these proteins should be taken into special account for future studies aimed at evaluating the risk of cross-allergenicity in highly sensitized individuals.

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17)

FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.