Crystal structure of Sol I 2: a major allergen from fire ant venom

Protein-Ligand Binding and Structural Modelling Studies of Pheromone-Binding Protein-like Sol g 2.1 from Solenopsis geminata Fire Ant Venom

Sol g 2 is the major protein in Solenopsis geminata fire ant venom. It shares the highest sequence identity with Sol i 2 (S. invicta) and shares high structural homology with LmaPBP (pheromone-binding protein (PBP) from the cockroach Leucophaea maderae). We examined the specific Sol g 2 protein ligands from fire ant venom. The results revealed that the protein naturally formed complexes with hydrocarbons, including decane, undecane, dodecane, and tridecane, in aqueous venom solutions. Decane showed the highest affinity binding (Kd) with the recombinant Sol g 2.1 protein (rSol g 2.1). Surprisingly, the mixture of alkanes exhibited a higher binding affinity with the rSol g 2.1 protein compared to a single one, which is related to molecular docking simulations, revealing allosteric binding sites in the Sol g 2.1 protein model. In the trail-following bioassay, we observed that a mixture of the protein sol g 2.1 and hydrocarbons elicited S. geminata worker ants to follow trails for a longer time and distance compared to a mixture containing only hydrocarbons. This suggests that Sol g 2.1 protein may delay the evaporation of the hydrocarbons. Interestingly, the piperidine alkaloids extracted have the highest attraction to the ants. Therefore, the mixture of hydrocarbons and piperidines had a synergistic effect on the trail-following of ants when both were added to the protein.

Characterization and Localization of Sol g 2.1 Protein from Solenopsis geminata Fire Ant Venom in the Central Nervous System of Injected Crickets (Acheta domestica)

Solenopsis geminata is recognized for containing the allergenic proteins Sol g 1, 2, 3, and 4 in its venom. Remarkably, Sol g 2.1 exhibits hydrophobic binding and has a high sequence identity (83.05%) with Sol i 2 from S. invicta. Notably, Sol g 2.1 acts as a mediator, causing paralysis in crickets. Given its structural resemblance and biological function, Sol g 2.1 may play a key role in transporting hydrophobic potent compounds, which induce paralysis by releasing the compounds through the insect's nervous system. To investigate this further, we constructed and characterized the recombinant Sol g 2.1 protein (rSol g 2.1), identified with LC-MS/MS. Circular dichroism spectroscopy was performed to reveal the structural features of the rSol g 2.1 protein. Furthermore, after treating crickets with S. geminata venom, immunofluorescence and immunoblotting results revealed that the Sol g 2.1 protein primarily localizes to the neuronal cell membrane of the brain and thoracic ganglia, with distribution areas related to octopaminergic neuron cell patterns. Based on protein-protein interaction predictions, we found that the Sol g 2.1 protein can interact with octopamine receptors (OctRs) in neuronal cell membranes, potentially mediating Sol g 2.1's localization within cricket central nervous systems. Here, we suggest that Sol g 2.1 may enhance paralysis in crickets by acting as carriers of active molecules and releasing them onto target cells through pH gradients. Future research should explore the binding properties of Sol g 2.1 with ligands, considering its potential as a transporter for active molecules targeting pest nervous systems, offering innovative pest control prospects.

Chemistry and Functions of Imported Fire Ant Venom

In the United States, imported fire ants are often referred to as red imported fire ants, Solenopsis invicta Buren, black imported fire ants, S. richteri Forel, and their hybrid (S. invicta × S. richteri). Due to their aggressive stings and toxic venom, imported fire ants pose a significant threat to public health, agriculture, and ecosystem health. However, venom plays a vital role in the survival of fire ants by serving various crucial functions in defense, foraging, and colony health maintenance. Numerous reviews and book chapters have been published on fire ant venom. Due to its medical importance and the expanding global distribution of these ants, fire ant venom research remains an active and highly productive area, leading to the discovery of new components and functions. This review summarizes the recent advances in our understanding of fire ant venom chemistry and its functions within fire ant colonies.

A Deeper Insight into the Tick Salivary Protein Families under the Light of Alphafold2 and Dali: Introducing the TickSialoFam 2.0 Database

Hard ticks feed for several days or weeks on their hosts and their saliva contains thousands of polypeptides belonging to dozens of families, as identified by salivary transcriptomes. Comparison of the coding sequences to protein databases helps to identify putative secreted proteins and their potential functions, directing and focusing future studies, usually done with recombinant proteins that are tested in different bioassays. However, many families of putative secreted peptides have a unique character, not providing significant matches to known sequences. The availability of the Alphafold2 program, which provides in silico predictions of the 3D polypeptide structure, coupled with the Dali program which uses the atomic coordinates of a structural model to search the Protein Data Bank (PDB) allows another layer of investigation to annotate and ascribe a functional role to proteins having so far being characterized as "unique". In this study, we analyzed the classification of tick salivary proteins under the light of the Alphafold2/Dali programs, detecting novel protein families and gaining new insights relating the structure and function of tick salivary proteins.

Odorant-binding protein from the stable fly (Stomoxys calcitrans) has a high-histidine N-terminal extension that binds transition metals

The role of odorant- and pheromone-binding proteins (OBPs) in olfactory function is not fully understood. We found an OBP sequence from the stable fly, Stomoxys calcitrans, ScalOBP60, that has a 25 amino acid N-terminal extension with a high content of histidine and acidic amino acids, suggesting a possible metal binding activity. A search of public databases revealed a large number of other fly OBPs with histidine-rich N-terminal extensions, as well as beetle, wasp and ant OBPs with histidine-rich C-terminal extensions. We recombinantly expressed ScalOBP60, as well as a truncated sequence which lacks the histidine-rich N-terminal region, tScalOBP60. Using fluorescence quenching and electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF), we detected two different types of metal-binding sites. Divalent copper, nickel and zinc bind to the N-terminal histidine-rich region, and divalent copper binds to an internal sequence position. Comparison of the ESI-QTOF spectra of ScalOBP60 and tScalOBP60 showed that the histidine-rich sequence is structurally disordered, but it becomes more ordered in the presence of divalent metal. When copper is bound to the internal site, binding of a hydrophobic ligand to ScalOBP60 is inhibited. The internal and N-terminal metal sites interact allosterically, possibly through a conformational equilibrium, suggesting a mechanism for metal regulation of ligand binding to ScalOBP60. Based on our studies of ScalOBP60, we propose several possible olfactory and non-olfactory functions for this OBP.

Antennal Proteome of the Solenopsis invicta (Hymenoptera: Formicidae): Caste Differences in Olfactory Receptors and Chemosensory Support Proteins

Little is known about the expression pattern of odorant and pheromone transporters, receptors, and deactivation enzymes in the antennae of ants carrying out different tasks. In order to begin filling in this information gap, we compared the proteomes of the antennae of workers and males of the red fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae). Male ants do not perform any colony work, and their only activity is to leave the nest on a mating flight. Previous studies showed that male ants express fewer types of odorant receptors than workers. Thus, we expected to find large differences between male and worker antennae for expression of receptors, transporters, and deactivators of signaling chemicals. We found that the abundance of receptors was consistent with the expected caste-specific signaling complexity, but the numbers of different antenna-specific transporters and deactivating enzymes in males and workers were similar. It is possible that some of these proteins have antenna-specific functions that are unrelated to chemosensory reception. Alternatively, the similar complexity could be a vestige of ant progenitors that had more behaviorally active males. As the reduced behavior of male ants evolved, the selection process may have favored a complex repertoire of transporters and deactivating enzymes alongside a limited repertoire of odorant receptors.

Immunological characterization of the American cockroach allergen Per a 9 expressed in baculovirus-infected insect cells

American cockroach (CR) allergy has been recognized as important IgE-mediated type I hypersensitivity. Per a 9 is an arginine kinase, reacting with IgE in sera of all CR allergic Thai patients. Per a 9 gene was cloned and expressed in eukaryotic systems (baculovirus-infected insect cells). The expressed Per a 9 was purified by Nickel column. The antigenicities were analyzed by ELISA, immunoblot analysis and basophile activation test. The results show that 13 out of 16 (81.3%) sera from American CR patients reacted to Per a 9, confirming that Per a 9 is a major allergen of CR. The IgE reactivity of Per a 9 in the sera from American CR patients was increased 8.3-fold in comparison with the sera from healthy controls. Per a 9 at 1.0 μg/ml induced an approximately up to 5.6-fold increase in CD63 and CCR3 double positive cells when incubating with passively sensitized basophils from by sera from American CR patients.

Bottom-Up Proteomic Analysis of Polypeptide Venom Components of the Giant Ant Dinoponera Quadriceps

Ant species have specialized venom systems developed to sting and inoculate a biological cocktail of organic compounds, including peptide and polypeptide toxins, for the purpose of predation and defense. The genus Dinoponera comprises predatory giant ants that inoculate venom capable of causing long-lasting local pain, involuntary shaking, lymphadenopathy, and cardiac arrhythmias, among other symptoms. To deepen our knowledge about venom composition with regard to protein toxins and their roles in the chemical-ecological relationship and human health, we performed a bottom-up proteomics analysis of the crude venom of the giant ant D. quadriceps, popularly known as the "false" tocandiras. For this purpose, we used two different analytical approaches: (i) gel-based proteomics approach, wherein the crude venom was resolved by denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and all protein bands were excised for analysis; (ii) solution-based proteomics approach, wherein the crude venom protein components were directly fragmented into tryptic peptides in solution for analysis. The proteomic data that resulted from these two methodologies were compared against a previously annotated transcriptomic database of D. quadriceps, and subsequently, a homology search was performed for all identified transcript products. The gel-based proteomics approach unequivocally identified nine toxins of high molecular mass in the venom, as for example, enzymes [hyaluronidase, phospholipase A1, dipeptidyl peptidase and glucose dehydrogenase/flavin adenine dinucleotide (FAD) quinone] and diverse venom allergens (homologous of the red fire ant Selenopsis invicta) and venom-related proteins (major royal jelly-like). Moreover, the solution-based proteomics revealed and confirmed the presence of several hydrolases, oxidoreductases, proteases, Kunitz-like polypeptides, and the less abundant inhibitor cysteine knot (ICK)-like (knottin) neurotoxins and insect defensin. Our results showed that the major components of the D. quadriceps venom are toxins that are highly likely to damage cell membranes and tissue, to cause neurotoxicity, and to induce allergic reactions, thus, expanding the knowledge about D. quadriceps venom composition and its potential biological effects on prey and victims.

Identification, expression and characterization of the recombinant Sol g 4.1 protein from the venom of the tropical fire ant Solenopsis geminata

Background

Fire ant venom is a complex mixture consisting of basic piperidine alkaloids, various biologically active peptides and protein components, including a variety of major allergenic proteins. Tropical fire ant Solenopsis geminata is an important stinging ant species that causes anaphylaxis and serious medical problems. Although the biological activities of allergenic venom proteins that are unique to ant venom, particularly Solenopsis 2 and 4, are still unknown, these proteins are believed to play important roles in mediating the effects of the piperidine derivatives in the venom.

Methods

In the present study, the cDNA cloning, sequencing and three-dimensional structure of Sol g 4.1 venom protein are described. The recombinant Sol g 4.1 protein (rSol g 4.1) was produced in E. coli, and its possible function as a hydrophobic binding protein was characterized by paralyzing crickets using the 50% piperidine dose (PD₅₀). Moreover, an antiserum was produced in mice to determine the allergenic properties of Sol g 4.1, and the antiserum was capable of binding to Sol g 4.1, as determined by Western blotting.

Results

The molecular weight of Sol g 4.1 protein is 16 kDa, as determined by SDS-PAGE. The complete cDNA is 414 bp in length and contains a leader sequence of 19 amino acids. The protein consists of six cysteines that presumably form three disulfide bonds, based on a predicted three-dimensional model, creating the interior hydrophobic pocket and stabilizing the structure. The rSol g 4.1 protein was expressed in inclusion bodies, as determined by SDS-PAGE. Dialysis techniques were used to refold the recombinant protein into the native form. Its secondary structure, which primarily consists of α-helices, was confirmed by circular dichroism analysis, and the three-dimensional model was also verified. The results of allergenic analysis performed on mice showed that the obtained protein was predicted to be allergenically active. Moreover, we report on the possible role of the Sol g 4.1 venom protein, which significantly reduced the PD₅₀ from 0.027 to 0.013% in paralyzed crickets via synergistic effects after interactions with piperidine alkaloids.

Conclusions

The primary structure of Sol g 4.1 showed high similarity to that of venom proteins in the Solenopsis 2 and 4 family. Those proteins are life-threatening and produce IgE-mediated anaphylactic reactions in allergic individuals. The possible function of this protein is the binding of the interior hydrophobic pockets with piperidine alkaloids, as determined by the analysis of the structural model and PD₅₀ test.

Electronic supplementary material

The online version of this article (10.1186/s40409-018-0159-6) contains supplementary material, which is available to authorized users.

Major venom proteins of the fire ant Solenopsis invicta: insights into possible pheromone-binding function from mass spectrometric analysis

Proteins in the venom of the fire ant Solenopsis invicta have been suggested to function in pheromone binding. Venom from queens and workers contains different isoforms of these proteins, consistent with the differing pheromones they secrete, but questions remain about the venom protein composition and glandular source. We found that the queen venom contains a previously uncharacterized pheromone-binding protein paralogue known as Sol i 2X1. Using imaging mass spectrometry, we located the main venom proteins in the poison sac, implying that pheromones might have to compete with venom alkaloids for binding. Using the known structure of the worker venom protein Sol i 2w, we generated three-dimensional homology models of the worker venom protein Sol i 4.02, and of the two main venom proteins in queens and female alates, Sol i 2q and Sol i 2X1. Surprisingly, the models show that the proteins have relatively small internal hydrophobic binding pockets that are blocked by about 10 amino acids of the C-terminal region. For these proteins to function as carriers of hydrophobic ligands, a conformational change would be required to displace the C-terminal region, somewhat like the mechanism known to occur in the silk moth pheromone-binding protein.

The Biochemical Toxin Arsenal from Ant Venoms

Ants (Formicidae) represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents.

De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species

BACKGROUND

Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the composition and the potential that these biomolecules could represent. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput approach using Illumina technology has been applied to analyze the genes expressed in active venom glands of this ant species.

RESULTS

A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%), followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue. Finally, about 40% of the generated contigs have no hits in the databases with 25% of the predicted peptides bearing signal peptide emphasizing the potential of the investigation of these sequences as source of new molecules. Among these contigs, six putative novel peptides that show homologies with previously identified antimicrobial peptides were identified.

CONCLUSIONS

To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal. In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.

Structure of allergens and structure based epitope predictions

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

Preparation and identification of Per a 5 as a novel American cockroach allergen

Glutathione S-transferase (GST) from various arthropods can elicit allergic reactions. In the present study, Per a 5, a GST, was cloned from American cockroach (CR) and expressed in both baculovirus-infected insect cell (iPer a 5) and E. coli expression (bPer a 5) systems. The secondary structures were predicted to be 45.93 and 8.69% of α-helix β-sheets in iPer a 5 and 42.54 and 8.49% of α-helix and β-sheets in bPer a 5, respectively. It is found that 4 out of 16 (25%) sera from American CR allergy patients reacted to both bPer a 9 and iPer a 9 as assessed by ELISA and Western blotting analysis, confirming that Per a 5 is not a major allergen of American CR. Induction of upregulated expression of CD63 and CCR3 on passively sensitized human basophils (sera from American CR allergy patients) by approximately up to 4.5- and 3.2-fold indicates that iPer a 5 and bPer a 5 are functionally active. Recombinant Per a 5 (rPer a 5) should be a useful tool for studying and understanding the role of Per a 5 in CR allergy.

In vitro diagnosis of Hymenoptera venom allergy and further development of component resolved diagnostics

For most people Hymenoptera stings result in transient and bothersome local inflammatory responses characterized by pain, itching, redness and swelling. In contrast, for those presenting an IgE-mediated allergic reaction, a re-sting may cause life-threatening reactions. In such patients, correct diagnosis is an absolute prerequisite for effective management, i.e. venom-specific immunotherapy. Generally, identification of the offending insect involves a detailed history along with quantification of venom-specific IgE antibodies and venom skin tests. Unfortunately, due to uncertainties associated with both tests, correct diagnosis is not always straightforward. This review summarizes the potentials and limitations of the various in vitro tests that are currently being used in the diagnosis of Hymenoptera venom allergy. Particular attention is paid to the potential of novel cellular tests such as basophil activation tests and component-resolved diagnosis with recombinant venom allergens in the diagnostic approach of patients with difficult diagnosis, i.e. cases in whom traditional venom specific IgE and skin tests yield equivocal or negative results. Finally, this review also covers the recent discoveries in the field of proteome research of Hymenoptera venoms and the selection of cell types for recombinant allergens production.

SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation package for stochastic simulations and demonstrate its application to protein conformational change, protein-protein association, small-molecule protein docking, and simulation of the growth of nanoscale clusters of organic molecules. Simulation of molecular and nanoscale systems (SIMONA) is easy to use for standard simulations via a graphical user interface and highly parallel both via MPI and the use of graphical processors. It is also extendable to many additional simulations types. Being freely available to academic users, we hope it will enable a large community of researchers in the life- and materials-sciences to use and extend SIMONA in the future. SIMONA is available for download under http://int.kit.edu/nanosim/simona.