Characterization of cereulide synthetase, a toxin-producing macromolecular machine

Genomic characterization of Bacillus cereus isolated from food poisoning cases revealed the mechanism of toxin production

Introduction

Bacillus cereus is a ubiquitous opportunistic human pathogen that causes food intoxications worldwide. However, the genomic characteristics and pathogenic mechanisms of B. cereus are still unclear.

Methods

Here, we isolated and purified nine strains of B. cereus (LY01-LY09) that caused vomiting, diarrhea and other symptoms from four foodborne outbreaks happened in Guizhou Province in southwest China from June to September 2021. After colony observation, Gram staining, microscopic examination and biochemical test, they were identified as B. cereus. The genomic characteristics, phylogenetic relationships and virulence factors of the isolated strains were analyzed at the genome level. Genome sequencing, comparative genomic analysis, secondary metabolite analysis and quantitative PCR were utilized to give a thorough exploration of the strains.

Results

We obtained the genome maps of LY01-LY09 and found that LY01-LY09 had a complex interspecific relationship with B. anthracis and B. thuringiensis. We also observed a contraction of gene families in LY01-LY09, and the contracted families were mainly associated with prophage, which contributed to the species diversity of B. cereus. The Hsp20 gene family underwent a rapid evolution in LY01-LY09, which facilitated the adaptation of the strains to adverse environmental conditions. Moreover, the LY01-LY09 strains exhibited a higher copy number in the non-ribosomal polypeptide synthetase (NRPS) genes and carried the complete cereulide synthetase (ces) gene cluster sequences. Considering that the NRPS system is a classical regulatory mechanism for emetic toxin synthesis, we hypothesized that LY01-LY09 could synthesize emetic toxins through the regulation of ces gene clusters by the NRPS system.

Discussion

These findings are important for further investigation into the evolutionary relationship between B. cereus and their related species, as well as the underlying mechanisms governing the synthesis and secretion of bacterial toxins.

Cereulide and Emetic Bacillus cereus: Characterizations, Impacts and Public Precautions

Cereulide, which can be produced by Bacillus cereus, is strongly associated with emetic-type food poisoning outbreaks. It is an extremely stable emetic toxin, which is unlikely to be inactivated by food processing. Considering the high toxicity of cereulide, its related hazards raise public concerns. A better understanding of the impact of B. cereus and cereulide is urgently needed to prevent contamination and toxin production, thereby protecting public health. Over the last decade, a wide range of research has been conducted regarding B. cereus and cereulide. Despite this, summarized information highlighting precautions at the public level involving the food industry, consumers and regulators is lacking. Therefore, the aim of the current review is to summarize the available data describing the characterizations and impacts of emetic B. cereus and cereulide; based on this information, precautions at the public level are proposed.

Intraspecific Diversity and Pathogenicity of Bacillus thuringiensis Isolates from an Emetic Illness

This study describes an emetic food-borne intoxication associated with a Bacillus cereus group species and the characterization of the bacterial isolates from the incident in aspects of molecular tying, genetic factors, cytotoxicity, and pathogenic mechanisms relating to emetic illness. Through the polyphasic identification approach, all seven isolates obtained from food and clinical samples were identified as Bacillus thuringiensis. According to multilocus sequence typing (MLST) analysis, intraspecific diversity was found within the B. thuringiensis isolates. Four allelic profiles were found, including two previously known STs (ST8 and ST15) and two new STs (ST2804 and ST2805). All isolates harbored gene fragments located in the cereulide synthetase (ces) gene cluster. The heat-treated culture supernatants of three emetic B. thuringiensis isolates, FC2, FC7, and FC8, caused vacuolation and exhibited toxicity to Caco-2 cells, with CC₅₀ values of 56.57, 72.17, and 79.94 µg/mL, respectively. The flow cytometry with the Annexin V/PI assay revealed both apoptosis and necrosis mechanisms, but necrosis was the prominent mechanism that caused Caco-2 cell destruction by FC2, the most toxic isolate.

Prevalence and antimicrobial-resistant characterization of Bacillus cereus isolated from ready-to-eat rice products in Eastern China

Bacillus cereus is a major food-borne bacterial pathogen in the world, which can cause diarrhea and emetic syndrome. This study aimed to reveal the quantitative prevalence of B. cereus in ready-to-eat (RTE) rice products in Eastern China and to gain essential information on the characteristics of B. cereus isolates. A total of 91 out of the 1071 samples were positive for B. cereus. The contamination level of B. cereus in 0.5 % of RTE rice product samples outnumbered 10³ CFU/g. The number of B. cereus attained 10⁵−10⁶ CFU/g in one sample. The distribution patterns of virulence genes in B. cereus isolates were identified. 84.6% of the B. cereus isolates had at least one enterotoxin or emetic toxin gene. The predominant pattern was XXV. 9.9% of isolates belonged to it and possessed one enterotoxin gene entFM. The occurrence rate of hblACD and nheABC was 36.3% and 47.3%, respectively. Antimicrobial susceptibility tests revealed a high resistance rate toward penicillin, and 23.1% of the isolates were multi-drug resistant. B. cereus isolates were genotyped by using ERIC-PCR. 89 genotypes were determined. The Hunter Gaston Discriminatory Index (HGDI) attained 0.9995. Relationships analysis revealed that Group A B. cereus isolates tended to carry hblA, hblC, hblD, nheA, nheB, and show resistance to penicillin/trimethoprim/sulfamethoxazole. This study was useful for updating the knowledge of the contamination status of B. cereus in RTE rice products in China.

Structural Organization of Brevilaterin Biosynthesis in Brevibacillus laterosporus S62-9: A Novel MbtH-Independent Cationic Antimicrobial Peptide Synthetase System

Cationic antimicrobial peptides, produced by nonribosomal peptide synthetases (NRPSs), have received great attention in different applications, including as biocontrol and antimicrobial agents against foodborne pathogenic bacteria. Also, Brevibacillus spp. is a competent microorganism to produce cationic antimicrobial peptides yet has received little attention. Herein, Brevibacillus laterosporus S62-9 genome mining revealed an integrated cationic antimicrobial peptide synthetase system that synthesized brevilaterin. Combining biochemical analysis with bioinformatics elucidated that the A domain from this system was the MbtH-independent enzyme and showed activity against the same amino acid in the structure of brevilaterin. Moreover, the creations of the first three and position 12 residues in the sequence were targeted to bre261, bre270, bre2691A, and bre2662, respectively. Further analysis of the specificity-conferring code of the A domain suggested that a tiny difference would make the activity of the A domain very diverse and the range of substrate selection would be enlarged or narrowed by changing some residues in the code. The dissection of this biosynthesis mechanism would contribute to the successful realization of reasonable artificial design and the modification of bioactive peptides, and this capable organism also would be more fully utilized.

Study of the Antibacterial Potency of Electroactivated Solutions of Calcium Lactate and Calcium Ascorbate on Bacillus cereus ATCC 14579 Vegetative Cells

Bacillus cereus is a pathogenic bacterium, Gram-positive, aerobic, and facultative anaerobic that can produce spores and different toxins. It is involved in serious foodborne illnesses such as the diarrheal and emetic syndromes, depending on the ingested toxin. This work is aimed to study the potency of electroactivated solutions (EAS) of calcium lactate, calcium ascorbate, and their mixture as antibacterial agents against B. cereus ATCC 14579 vegetative cells. The solutions used were electroactivated under electric current intensities of 250, 500, and 750 mA for 30 min. The obtained EAS were tested in direct contact with B. cereus (10⁷ CFU/mL) for different durations ranging from 5 s to 2 min. Moreover, standard lactic and ascorbic acids were tested as controls at equivalent titratable acidity as that of the corresponding electroactivated solutions. The obtained results showed that EAS exhibit high antibacterial efficacy against B. cereus vegetative cells. The EAS obtained after electroactivation of calcium lactate and calcium ascorbate were more efficient than those of their corresponding standard acids (lactic and ascorbic). The observed antibacterial effect of the EAS resulted in a reduction of 7 log CFU/mL after 5 s of direct contact in some specific cases. Scanning (SEM) and transmission (TEM) electron microscopic observations provided conclusive evidence of the antibacterial activity of the used EAS. These results outlined the highly antimicrobial potency of EAS against B. cereus vegetative cells and that they can be considered in an eventual strategy to ensure food safety, surface cleaning, as well as replacement of hazardous disinfecting chemicals.

Bacillus cereus Toxin Repertoire: Diversity of (Iso)cereulide(s)

The emetic Bacillus cereus toxin cereulide (1) poses a significant safety risk in the food industry, causing emesis and nausea after consumption of contaminated foods. Analogously to cereulide, the structures of various isocereulides, namely, isocereulides A–G, have been recently reported and could also be identified in B. cereus-contaminated food samples. The HPLC fractionation of B. cereus extracts allows us to isolate additional isocereulides. By applying MSⁿ sequencing, post-hydrolytic dipeptide, amino acid and α-hydroxy acid analyses using UPLC-ESI-TOF-MS to purify the analytes, seven new isocereulides H–N (2–8) could be elucidated in their chemical structures. The structure elucidation was supported by one-dimensional and two-dimensional NMR spectra of the isocereulides H (2), K (5), L and N (6 + 8) and M (7). The toxicity of 2–8 was investigated in a HEp-2 cell assay to determine their respective 50% effective concentration (EC₅₀). Thus, 2–8 exhibited EC₅₀ values ranging from a 0.4- to 1.4-fold value compared to cereulide (1). Missing structure-activity correlations indicate the necessity to determine the toxic potential of all naturally present isocereulides as single compounds to be able to perform a thorough toxicity evaluation of B. cereus-contaminated foods in the future.

Structure Revision of Isocereulide A, an Isoform of the Food Poisoning Emetic Bacillus cereus Toxin Cereulide

The emetic Bacillus cereus toxin cereulide presents an enormous safety hazard in the food industry, inducing emesis and nausea after the consumption of contaminated foods. Additional to cereulide itself, seven structurally related isoforms, namely the isocereulides A–G, have already been elucidated in their chemical structure and could further be identified in B. cereus contaminated food samples. The newly performed isolation of isocereulide A allowed, for the first time, 1D- and 2D-NMR spectroscopy of a biosynthetically produced isocereulide, revealing results that contradict previous assumptions of an l-O-Leu moiety within its chemical structure. By furthermore applying posthydrolytical dipeptide analysis, amino acid and α-hydroxy acid analysis by means of UPLC-ESI-TOF-MS, as well as MSⁿ sequencing, the structure of previously reported isocereulide A could be corrected. Instead of the l-O-Leu as assumed to date, one l-O-Ile unit could be verified in the cyclic dodecadepsipeptide, revising the structure of isocereulide A to [(d-O-Leu-d-Ala-l-O-Val-l-Val)₂(d-O-Leu-d-Ala-l-O-Ile-l-Val)].

Novel Modifications of Nonribosomal Peptides from Brevibacillus laterosporus MG64 and Investigation of Their Mode of Action

Nonribosomal peptides (NRPs) are a class of secondary metabolites usually produced by microorganisms. They are of paramount importance in different applications, including biocontrol and pharmacy. Brevibacillus spp. are a rich source of NRPs yet have received little attention. In this study, we characterize four novel bogorol variants (bogorols I to L, cationic linear lipopeptides) and four succilins (succilins I to L, containing a succinyl group that is attached to the Orn₃/Lys₃ in bogorols I to L) from the biocontrol strain Brevibacillus laterosporus MG64. Further investigation revealed that the bogorol family of peptides employs an adenylation pathway for lipoinitiation, different from the usual pattern, which is based on an external ligase and coenzyme A. Moreover, the formation of valinol was proven to be mediated by a terminal reductase domain and a reductase encoded by the bogI gene. Furthermore, succinylation, which is a novel type of modification in the family of bogorols, was discovered. Its occurrence requires a high concentration of the substrate (bogorols), but its responsible enzyme remains unknown. Bogorols display potent activity against both Gram-positive and Gram-negative bacteria. Investigation of their mode of action reveals that bogorols form pores in the cell membrane of both Gram-positive and Gram-negative bacteria. The combination of bogorols and relacidines, another class of NRPs produced by B. laterosporus MG64, displays a synergistic effect on different pathogens, suggesting the great potential of both peptides as well as their producer B. laterosporus MG64 for broad applications. Our study provides a further understanding of the bogorol family of peptides as well as their applications.IMPORTANCE NRPs form a class of secondary metabolites with biocontrol and pharmaceutical potential. This work describes the identification of novel bogorol variants and succinylated bogorols (namely, succilins) and further investigates their biosynthetic pathway and mode of action. Adenylation domain-mediated lipoinitiation of bogorols represents a novel pathway by which NRPs incorporate fatty acid tails. This pathway provides the possibility to engineer the lipid tail of NRPs without identifying a fatty acid coenzyme ligase, which is usually not present in the biosynthetic gene cluster. The terminal reductase domain (TD) and BogI-mediated valinol formation and their effect on the biological activity of bogorols are revealed. Succinylation, which is rarely reported in NRPs, was discovered in the bogorol family of peptides. We demonstrate that bogorols combat bacterial pathogens by forming pores in the cell membrane. We also report the synergistic effect of two natural products (relacidine B and bogorol K) produced by the same strain, which is relevant for competition for a niche.

Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations

Depsipeptides are compounds that contain both ester bonds and amide bonds. Important natural product depsipeptides include the piscicide antimycin, the K⁺ ionophores cereulide and valinomycin, the anticancer agent cryptophycin, and the antimicrobial kutzneride. Furthermore, database searches return hundreds of uncharacterized systems likely to produce novel depsipeptides. These compounds are made by specialized nonribosomal peptide synthetases (NRPSs). NRPSs are biosynthetic megaenzymes that use a module architecture and multi-step catalytic cycle to assemble monomer substrates into peptides, or in the case of specialized depsipeptide synthetases, depsipeptides. Two NRPS domains, the condensation domain and the thioesterase domain, catalyze ester bond formation, and ester bonds are introduced into depsipeptides in several different ways. The two most common occur during cyclization, in a reaction between a hydroxy-containing side chain and the C-terminal amino acid residue in a peptide intermediate, and during incorporation into the growing peptide chain of an α-hydroxy acyl moiety, recruited either by direct selection of an α-hydroxy acid substrate or by selection of an α-keto acid substrate that is reduced in situ. In this article, we discuss how and when these esters are introduced during depsipeptide synthesis, survey notable depsipeptide synthetases, and review insight into bacterial depsipeptide synthetases recently gained from structural studies.

Bacillus cereus: Epidemiology, Virulence Factors, and Host-Pathogen Interactions

The toxin-producing bacterium Bacillus cereus is an important and neglected human pathogen and a common cause of food poisoning. Several toxins have been implicated in disease, including the pore-forming toxins hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE). Recent work revealed that HBL binds to the mammalian surface receptors LITAF and CDIP1 and that both HBL and NHE induce potassium efflux and activate the NLRP3 inflammasome, leading to pyroptosis. These mammalian receptors, in part, contribute to inflammation and pathology. Other putative virulence factors of B. cereus include cytotoxin K, cereulide, metalloproteases, sphingomyelinase, and phospholipases. In this review, we highlight the latest progress in our understanding of B. cereus biology, epidemiology, and pathogenesis, and discuss potential new directions for research in this field.

Thioesterase from Cereulide Biosynthesis Is Responsible for Oligomerization and Macrocyclization of a Linear Tetradepsipeptide

Cereulide is a toxic cyclic depsidodecapeptide produced in Bacillus cereus by two nonribosomal peptide synthetases, CesA and CesB. While highly similar in structure to valinomycin and with a homologous biosynthetic gene cluster, recent work suggests that cereulide is produced via a different mechanism that relies on a noncanonical coupling of two didepsipeptide-peptidyl carrier protein (PCP) bound intermediates. Ultimately this alternative mechanism generates a tetradepsipeptide-PCP bound intermediate that differs from the tetradepsipeptide-PCP intermediate predicted from canonical activity of CesA and CesB. To differentiate between the mechanisms, both tetradepsipeptides were prepared as N-acetyl cysteamine thioesters (SNAC), and the ability of the purified recombinant terminal CesB thioesterase (CesB TE) to oligomerize and macrocyclize each substrate was probed. Only the canonical substrate is converted to cereulide, ruling out the alternative mechanism. It was demonstrated that CesB TE can use related tetradepsipeptide substrates, such as the valinomycin tetradespipetide and a hybrid cereulide-valinomycin tetradepsipetide in conjunction with its native substrate to generate chimeric natural products. This work clarifies the biosynthetic origins of cereulide and provides a powerful biocatalyst to access analogues of these ionophoric natural products.

Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility

Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes that synthesize natural product therapeutics using a modular synthetic logic, whereby each module adds one aminoacyl substrate to the nascent peptide. We have determined five x-ray crystal structures of large constructs of the NRPS linear gramicidin synthetase, including a structure of a full core dimodule in conformations organized for the condensation reaction and intermodular peptidyl substrate delivery. The structures reveal differences in the relative positions of adjacent modules, which are not strictly coupled to the catalytic cycle and are consistent with small-angle x-ray scattering data. The structures and covariation analysis of homologs allowed us to create mutants that improve the yield of a peptide from a module-swapped dimodular NRPS.

Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis

Nonribosomal depsipeptides are natural products composed of amino and hydroxy acid residues. The hydroxy acid residues often derive from α-keto acids, reduced by ketoreductase domains in the depsipeptide synthetases. Biochemistry and structures reveal the mechanism of discrimination for α-keto acids and a remarkable architecture: flanking intact adenylation and ketoreductase domains are sequences separated by >1,100 residues that form a split 'pseudoA_sub' domain, structurally important for the depsipeptide module's synthetic cycle.

Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin

We report the draft whole-genome sequence of Rothia nasimurium isolated from a porcine tonsil. The genome encodes a nonribosomal peptide synthetase predicted to produce valinomycin, a cyclic dodecadepsipeptide ionophore. Previously, valinomycin was known to be produced only by Streptomyces species and isolates belonging to the Bacillus pumilus group.

Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity

Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes, each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes. This review discusses some of the important insights into the structure, catalytic mechanism, specificity, and gatekeeping functions of C domains revealed since their discovery. In addition, C domains are the archetypal members of the C domain superfamily, which includes several other members that also function as NRPS domains. The other family members can replace the C domain in NRP synthesis, can work in concert with a C domain, or can fulfill diverse and novel functions. These domains include the epimerization (E) domain, the heterocyclization (Cy) domain, the ester-bond forming C domain, the fungal NRPS terminal C domain (C_T), the β-lactam ring forming C domain, and the X domain. We also discuss structural and function insight into C, E, Cy, C_T and X domains, to present a holistic overview of historical and current knowledge of the C domain superfamily. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.

X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture

Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.

Design, synthesis, and biological evaluation of α-hydroxyacyl-AMS inhibitors of amino acid adenylation enzymes

Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate β-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.

Ces locus embedded proteins control the non-ribosomal synthesis of the cereulide toxin in emetic Bacillus cereus on multiple levels

The emetic toxin cereulide produced by Bacillus cereus is synthesized by the modular enzyme complex Ces that is encoded on a pXO1-like megaplasmid. To decipher the role of the genes adjacent to the structural genes cesA/cesB, coding for the non-ribosomal peptide synthetase (NRPS), gene inactivation- and overexpression mutants of the emetic strain F4810/72 were constructed and their impact on cereulide biosynthesis was assessed. The hydrolase CesH turned out to be a part of the complex regulatory network controlling cereulide synthesis on a transcriptional level, while the ABC transporter CesCD was found to be essential for post-translational control of cereulide synthesis. Using a gene inactivation approach, we show that the NRPS activating function of the phosphopantetheinyl transferase (PPtase) embedded in the ces locus was complemented by a chromosomally encoded Sfp-like PPtase, representing an interesting example for the functional interaction between a plasmid encoded NRPS and a chromosomally encoded activation enzyme. In summary, our results highlight the complexity of cereulide biosynthesis and reveal multiple levels of toxin formation control. ces operon internal genes were shown to play a pivotal role by acting at different levels of toxin production, thus complementing the action of the chromosomal key transcriptional regulators AbrB and CodY.