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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements

Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A–G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1–OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex

Botulinum neurotoxin serotype A (BoNT/A) is naturally produced by bacteria along with four nontoxic neurotoxin-associated proteins (NTNH, HA70, HA33, and HA17), forming a bimodular large progenitor toxin complex (L-PTC). The BoNT/A–NTNH complex protects the toxin from adverse environment, while the complex consisting of HA proteins facilitates toxin absorption during oral intoxication. How these two independent modules assemble into the L-PTC remains unclear. Here, we report the crystal structure of the BoNT/A–NTNH–HA70 complex at ~2.9-Å resolution. The structure reveals that the BoNT/A–NTNH complex is anchored into a concentric double β-barrel channel of trimeric HA70 through a short β-hairpin of NTNH (termed nLoop), resembling a nut-and-bolt attachment. We find that the nLoop of NTNH is strictly conserved across HA-containing BoNT complexes and that NTNH–HA70 binding is interchangeable among them. Furthermore, we demonstrate that the nLoop functions as a minimal motif enabling attachment of a protein-of-interest to the HA complex, with potential applications in oral biologics delivery.

Science & Technology - Other Topics↗
DOE OSTI2024

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2

Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (H C E) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between H C E and SV2 provide the crucial location and specificity information for H C E to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, H C E exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies

Botulinum neurotoxins (BoNTs) are among the deadliest of bacterial toxins. BoNT serotype A and B in particular pose the most serious threat to humans because of their high potency and persistence. To date, there is no effective treatment for late post-exposure therapy of botulism patients. Here, we aim to develop single-domain variable heavy-chain (VHH) antibodies targeting the protease domains (also known as the light chain, LC) of BoNT/A and BoNT/B as antidotes for post-intoxication treatments. Using a combination of X-ray crystallography and biochemical assays, we investigated the structures and inhibition mechanisms of a dozen unique VHHs that recognize four and three non-overlapping epitopes on the LC of BoNT/A and BoNT/B, respectively. We show that the VHHs that inhibit the LC activity occupy the extended substrate-recognition exosites or the cleavage pocket of LC/A or LC/B and thus block substrate binding. Notably, we identified several VHHs that recognize highly conserved epitopes across BoNT/A or BoNT/B subtypes, suggesting that these VHHs exhibit broad subtype efficacy. Further, we identify two novel conformations of the full-length LC/A, that could aid future development of inhibitors against BoNT/A. Our studies lay the foundation for structure-based engineering of protein- or peptide-based BoNT inhibitors with enhanced potencies and cross-subtypes properties.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

NASA Discipline Exobiology↗
DOE OSTI2024

Chemical Imaging for In Situ Detection and Discrimination of Aquatic Toxins Targeting Voltage Gated Sodium Channels

Biologically derived neurotoxins from cyanobacteria and algae impact environmental resources in addition to being considered a potential biological threat to human and animal health. Activity based assays are essential to detecting and responding to toxic neurotoxin events either naturally occurring or deliberate. Two toxins of interest include saxitoxin and brevetoxin. These toxins bind to and alter the function of voltage-gated sodium channels (NaV channels) which are essential for generating cell membrane action potential. We report the development and refinement of a System for Analysis at Liquid Vacuum Interface (SALVI) to assess the functional activity of saxitoxin and brevetoxin. This approach utilizes a vacuum-compatible microfluidic reactor that permits analysis at the liquid vacuum interface of human derived cells with a neurotoxin of interest in a biologically relevant environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum , Clostridium sporogenes , and Clostridium argentinense

At least 40 toxin subtypes of botulinum neurotoxins (BoNTs), a heterogenous group of bacterial proteins, are produced by seven different clostridial species. A key factor that drives the diversity of neurotoxigenic clostridia is the association of bont gene clusters with various genomic locations including plasmids, phages and the chromosome. Analysis of Clostridium sporogenes BoNT/B1 strain CDC 1632, C. argentinense BoNT/G strain CDC 2741, and Clostridium parabotulinum BoNT/B1 strain DFPST0006 genomes revealed bont gene clusters within plasmid-like sequences within the chromosome or nested in large contigs, with no evidence of extrachromosomal elements. A nucleotide sequence (255,474 bp) identified in CDC 1632 shared 99.5% identity (88% coverage) with bont/B1-containing plasmid pNPD7 of C. sporogenes CDC 67071; CDC 2741 contig AYSO01000020 (1.1 MB) contained a ~140 kb region which shared 99.99% identity (100% coverage) with plasmid pRSJ17_1 of C. argentinense BoNT/G strain 89G; and DFPST0006 contig JACBDK0100002 (573 kb) contained a region that shared 100% identity (99%) coverage with the bont/B1-containing plasmid pCLD of C. parabotulinum Okra. This is the first report of full-length plasmid DNA-carrying complete neurotoxin gene clusters integrated in three distinct neurotoxigenic species: C. parabotulinum, C. sporogenes and C. argentinense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Integrating Mercury Concentrations in American Alligators ( Alligator mississippiensis ) with Hunter Consumption Surveys to Estimate Exposure Risk

Mercury is a naturally occurring element but is also considered a widespread contaminant due to global anthropogenic activity. Even in moderate amounts, mercury (Hg) is an established neurotoxin and is associated with a range of adverse outcomes both in humans and wildlife. Humans in the United States are most commonly exposed to Hg through contaminated food or drinking water, and the consumption of game species, particularly those occupying higher trophic levels, has the potential to expose hunters to high concentrations of Hg. In the present study, we determined Hg concentrations in tail muscle and blood from American alligators (Alligator mississippiensis) inhabiting a region (Savannah River Site, SC, USA) with known Hg contamination. We then integrated these data with alligator harvest records and previously published surveys of alligator meat consumption patterns to estimate potential exposure risk. We found that the average Hg concentrations in tail muscle (1.34 mg/kg, wet wt) from sampled alligators exceeded the recommended threshold for Hg exposure based on the World Health Organization's guidelines (0.5mg/kg, wet wt). In addition, based on regional consumption patterns reported for both adults and children, we estimated Hg exposures (x¯ Adult = 0.419 μg/kg/day, x¯ Child = 2.24 μg/kg/day) occurring well above the US Environmental Protection Agency methylmercury reference dose of 0.1 μg/kg/day. Although the two reservoirs sampled in the present study are not currently open to alligator hunting, they are connected to waters that are publicly accessible, and the extent of alligator mobility across these sites is not known. Together, the findings reported in the present study further demonstrate the need for active monitoring of Hg concentrations in game species, which can convey substantial exposure risks to the public.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Assessing Microbial Communities Related to Mercury Transformations in Contaminated Streambank Soils

In nature, the bioaccumulative potent neurotoxin methylmercury (MeHg) is produced from inorganic mercury (Hg) predominantly by anaerobic microorganisms. Hg-contaminated soils are a potential source of MeHg due to microbial activity. We examine streambank soils collected from the contaminated East Fork Poplar Creek (EFPC) in Tennessee, USA, where seasonal variations in MeHg levels have been observed throughout the year, suggesting active microbial Hg methylation. In this study, we characterized the microbial community in contaminated bank soil samples collected from two locations over a period of one year and compared the results to soil samples from an uncontaminated reference site with similar geochemistry (n = 12). Microbial community composition and diversity were assessed by 16S rRNA gene amplicon sequencing. Furthermore, to isolate potential methylators from soils, enrichment cultures were prepared using selective media. A set of three clade-specific primers targeting the gene hgcA were used to detect Hg methylators among the δ-Proteobacteria in EFPC bank soils across all seasons. Two families among the δ-Proteobacteria that have been previously associated with Hg methylation, Geobacteraceae and Syntrophobacteraceae, were found to be predominant with relative abundances of 0.13% and 4.0%, respectively. However, in soil enrichment cultures, Firmicutes were predominant among families associated with Hg methylation. Specifically, Clostridiaceae and Peptococcaceae and their genera Clostridium and Desulfosporosinus were among the ten most abundant genera with relative abundances of 2.6% and 1.7%, respectively. These results offer insights into the role of microbial communities on Hg transformation processes in contaminated bank soils in EFPC. Identifying the biogeochemical drivers of MeHg production is critical for future remediation efforts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Contrary effects of phytoplankton Chlorella vulgaris and its exudates on mercury methylation by iron- and sulfate-reducing bacteria

Mercury (Hg) is a pervasive environmental pollutant and poses serious health concerns as inorganic Hg(II) can be converted to the neurotoxin methylmercury (MeHg), which bioaccumulates and biomagnifies in food webs. Phytoplankton, representing the base of aquatic food webs, can take up Hg(II) and influence MeHg production, but currently little is known about how and to what extent phytoplankton may impact Hg(II) methylation by itself or by methylating bacteria it harbors. This study investigated whether some species of phytoplankton could produce MeHg and how the live or dead phytoplankton cells and excreted algal organic matter (AOM) impact Hg(II) methylation by several known methylators, including iron-reducing bacteria (FeRB), Geobacter anodireducens SD-1 and Geobacter sulfurreducens PCA, and the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans ND132 (or Pseudodesulfovibrio mercurii). Here our results indicate that, among the 4 phytoplankton species studied, none were capable of methylating Hg(II). However, the presence of phytoplankton cells (either live or dead) from Chlorella vulgaris (CV) generally inhibited Hg(II) methylation by FeRB but substantially enhanced methylation by SRB D. desulfuricans ND132. Enhanced methylation was attributed in part to CV-excreted AOM, which increased Hg(II) complexation and methylation by ND132 cells. In contrast, inhibition of methylation by FeRB was attributed to these bacteria incapable of competing with phytoplankton for Hg(II) binding and uptake. These observations suggest that phytoplankton could play different roles in affecting Hg(II) methylation by the two groups of anaerobic bacteria, FeRB and SRB, and thus shed additional light on how phytoplankton blooms may modulate MeHg production and bioaccumulation in the aquatic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Important Roles of Thiols in Methylmercury Uptake and Translocation by Rice Plants

We report the bioaccumulation of the neurotoxin methylmercury (MeHg) in rice is a significant concern due to its potential risk to humans. Thiols have been known to affect MeHg bioavailability in microorganisms, but how thiols influence MeHg accumulation in rice plants remains unknown. Here, we investigated effects of common low-molecular-weight thiols, including cysteine (Cys), glutathione (GSH), and penicillamine (PEN), on MeHg uptake and translocation by rice plants. Results show that rice roots can rapidly take up MeHg, and this process is influenced by the types and concentrations of thiols in the system. The presence of Cys facilitated MeHg uptake by roots and translocation to shoots, while GSH could only promote MeHg uptake, but not translocation, by roots. Conversely, PEN significantly inhibited MeHg uptake and translocation to shoots. Using labeled 13 Cys assays, we also found that MeHg uptake was coupled with Cys accumulation in rice roots. Moreover, analyses of comparative transcriptomics revealed that key genes associated with metallothionein and SULTR transporter families may be involved in MeHg uptake. These findings provide new insights into the uptake and translocation of MeHg in rice plants and suggest potential roles of thiol attributes in affecting MeHg bioavailability and bioaccumulation in rice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Methylmercury Degradation by Trivalent Manganese

Methylmercury (MeHg) is a potent neurotoxin and has great adverse health impacts on humans. Organisms and sunlight-mediated demethylation are well-known detoxification pathways of MeHg, yet whether abiotic environmental components contribute to MeHg degradation remains poorly known. Here, in this paper, we report that MeHg can be degraded by trivalent manganese (Mn(III)), a naturally occurring and widespread oxidant. We found that 28 ± 4% MeHg could be degraded by Mn(III) located on synthesized Mn dioxide (MnO 2–x ) surfaces during the reaction of 0.91 μg·L –1 MeHg and 5 g·L –1 mineral at an initial pH of 6.0 for 12 h in 10 mM NaNO 3 at 25 °C. The presence of low-molecular-weight organic acids (e.g., oxalate and citrate) substantially enhances MeHg degradation by MnO 2–x via the formation of soluble Mn(III)-ligand complexes, leading to the cleavage of the carbon–Hg bond. MeHg can also be degraded by reactions with Mn(III)-pyrophosphate complexes, with apparent degradation rate constants comparable to those by biotic and photolytic degradation. Thiol ligands (cysteine and glutathione) show negligible effects on MeHg demethylation by Mn(III). This research demonstrates potential roles of Mn(III) in degrading MeHg in natural environments, which may be further explored for remediating heavily polluted soils and engineered systems containing MeHg.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Prediction of Specificity of α-Conotoxins to Subtypes of Human Nicotinic Acetylcholine Receptors with Semi-supervised Machine Learning

Conotoxins are a family of highly toxic neurotoxins composed of cysteine-rich peptides produced by marine cone snails. The most lethal cone snail species to humans is Conus geographus, with fatality rates of up to ∼65% from a single sting, which is caused mostly by the activity of α-conotoxins against human nicotinic acetylcholine receptors (nAChRs). While sequence-based machine learning (ML) classifiers have been trained to identify targets of conotoxins binding voltage-gated ion channels, no ML model has been built to predict the subtype-specific nAChR targets of α-conotoxins. Here, we trained an ML model in a semi-supervised manner to predict the specificity of α-conotoxin binding toward different human nAChR subtypes to overcome the challenge of limited data in subtype-specific nAChR targets of α-conotoxins and the issue that one α-conotoxin can bind multiple nAChR subtypes with high selectivity. We considered additional features of sequences of α-conotoxins in training our ML model, including the secondary structure propensities and electrostatic properties, which resulted in better prediction capability for the ML model. Notably, we identify that most α-conotoxins bind to α3β2, α1γδ, and α7 subtypes of human nAChRs. Our findings from this study provide a framework for predicting targets of various kinds of toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hg Accumulation by Single-Cell Sulfate-Reducing Bacteria Methylating Mercury

Methylmercury (MeHg) is a potent neurotoxin that poses risks to ecosystems and human health. MeHg is produced by microbes following saturating-like kinetics. We hypothesize that this saturation reflects a limited intracellular mercury (Hg) accumulation. Here, in this study, we investigated Hg accumulation in Pseudodesulfovibrio hydrargyri BerOc1, a sulfate-reducing model strain able to methylate Hg. Cells were incubated with 0.5 and 2 μM of mercury (HgCl 2 ), and mercury localization was studied using synchrotron-based nano-X-ray fluorescence and high-resolution analytical electron microscopy. For both concentrations, Hg was detected in the bacterial cytosol, in addition to extracellular (Hg, S)-containing nanoparticles. Intracellular Hg levels were slightly higher at 2 μM than at 0.5 μM (1.61 vs 1.40 pg.mm –2 ), suggesting a regulated accumulation. However, the population exhibited heterogeneity in Hg accumulation, particularly at the highest Hg exposure, with some cells being Hg hyperaccumulators. Correlative imaging between Hg localization and cell viability revealed that these hyperaccumulating cells were non-active. Our results suggest that active cells regulate Hg accumulation. From an analytical perspective, a minor subpopulation of hyperaccumulating cells can bias bulk measurements and should be considered in interpreting Hg accumulation in microorganisms. Environmentally, these cells can impact Hg cycling by acting as a metal sink.

Intracellular accumulation↗