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Advancing Protein Display on Bacterial Spores through an Extensive Survey of Coat Components

The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 types of proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SPs investigated, 26 formed functional fusions with β-glucuronidase (GUS)─a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed 1) SP promoter activation dynamics, 2) GUS activity on spores, 3) surface availability, and 4) protection from thermal and proteolytic degradation. Multicopy expression and pairwise coexpression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and the difficulty in predicting compatibility between different SP fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface-exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least 4-fold higher than any other SP, including the well-established anchor, CotY. We attribute this to its promoter, which demonstrated early and sustained activation relative to other SPs and its small size (∼3 kDa), which likely minimally interferes with enzyme folding, oligomerization, and activity. Labeling and genetic studies, its hydrophobic nature, and low surface availability suggest that SscA assembles within the inner spore coat, which makes it stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledge base to advance the biotechnological utility of B. subtilis spores.

Bacillus subtilis

Degradable Biocomposite Thermoplastic Polyurethanes

In this project, the team developed tough and degradable biocomposite thermoplastic polyurethanes (TPUs) by incorporating bacterial spores into TPUs as a biofunctional living filler. The team screened various bacteria and selected the Bacillus subtilis ATCC 6633 strain as the final candidate, primarily due to its genomic availability, sporulation ability and TPU assimilation activity. The heat-shock tolerance of ATCC 6633 spores was further improved through evolutionary engineering via Adaptive Laboratory Evolution (ALE), demonstrating a 17.7-fold enhanced germination efficiency post heat-shock treatment compared to the wild-type strain (WT). The team fabricated biocomposite TPUs by incorporating lyophilized powder of heat-shock tolerized (HST) spores during the hot melt extrusion (HME) of TPU at 135 °C. The baseline TPU used in this project is a commercially available soft-grade TPU (BCF45) manufactured by BASF. Colony forming unit (CFU) assays quantified that WT and HST spores in the TPU matrix retained approximately 20% and 100% survivability, respectively, after HME. Tensile testing demonstrated that the spores behaved as a polymer-reinforcing filler, positively affecting the overall tensile properties of the biocomposite TPU. For example, biocomposite TPU with WT and HST spores (BC TPU WT and BC TPU HST , respectively) exhibited up to 25% and 37% improved toughness, respectively, compared to TPU without spores. BC TPU HST showed remarkably improved disintegration in autoclaved compost (92% mass loss in 5 months), which simulated a microbially poor environment for TPU degradation. When compared to TPU without spores (44% mass loss in 5 months) the acceleration of degradation is marked. Respirometry confirmed that 72% of BC TPU HST was biomineralized into CO2 within 6 months, indicating that spores in the biocomposite TPU were germinated by utilizing nutrients in the autoclaved compost, facilitating TPU degradation at the end of the material's life. The team demonstrated the scale-up of biocomposite TPU fabrication using continuous extrusion and injection molding techniques. Processing conditions optimized in a lab-scale microcompounder were successfully transferred to a continuous extruder with a 30-fold increased throughput. Biocomposite TPUs prepared using these industry-relevant processes showed comparable toughness improvements to samples prepared in the lab-scale extruder. Excitingly, following compounding in the pilot-extruder the composite material could be injection molded, while retaining high spore viability and similar toughness improvements. The team also found that spores in biocomposite TPU served as antioxidants, preventing toughness decay during the recycled extrusion of BC TPU HST . Long-term storage tests over one year showed that the addition of spores had no negative effect on the longevity of the TPU. Furthermore, the team demonstrated the fabrication of spore-bearing biocomposite polymers with other polyesters such as PBAT, PLA, and PCL. We obtained promising preliminary data that showed overall toughness improvements for all polymers with spore addition. Finally, life cycle assessment (LCA) and techno-economic analysis (TEA) were carried out, which indicated minimal additional cost of fabrication. Overall, a tough and degradable biocomposite thermoplastic was successfully developed through this project, with all tasks completed successfully, achieving >100% of the objectives.

36 MATERIALS SCIENCE

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism

Mechanistic within-host mathematical model of inhalational anthrax

We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is the binding component of the anthrax toxin produced by the bacteria. The model offers a mechanistic description of the early infection dynamics of inhalational anthrax, while its stochastic nature allows us to study the probabilities of different outcomes (for example, how likely it is that the infection will be cleared for a given inhaled dose of spores) in order to explain dose-response data for inhalational anthrax. The model is calibrated via a Bayesian approach, using in vivo data from New Zealand white rabbit and guinea pig infection studies, enabling within-host parameters to be estimated. We also leverage incubation-period data from the Sverdlovsk 1979 anthrax outbreak to show that the model can accurately describe human time-to-symptoms data under reasonable parameter regimes. Finally, we derive a simple approximate formula for the probability of symptom onset before time t, assuming that the number of inhaled spores has a Poisson distribution.

59 BASIC BIOLOGICAL SCIENCES

Evaluation of a high-throughput method for processing sponge-stick samples to detect viable, non-spore-forming biothreat agents

After a bioterrorism incident, surface sampling is often used to determine the extent of contamination and exposure, guiding decontamination efforts and decisions for re-occupancy of affected sites. The sponge-stick (SS) is a preferred and commonly used device for sample collection to detect both spore-forming and non-spore-forming biothreat agents from non-porous surfaces. Here, in this study, a recently developed high-throughput method (HTM) for processing SS samples to detect viable Bacillus anthracis spores was adapted for detection of non-spore-forming biothreat agents, Yersinia pestis and Francisella tularensis. The scalable HTM was used to process up to 20 SS samples simultaneously, compared to the current stomacher-based method which processes one SS at a time. Comparisons of the HTM and the stomacher-based method were statistically indistinguishable for most experiments (P > 0.05) with HTM recoveries of 37–60 % for Y. pestis inoculated at 102–103 cells/SS and held 48 h at 4 °C to mimic sample transport/storage. The HTM was integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis to detect viable Y. pestis in the presence of particulate contamination (Arizona Test Dust, ATD). This approach detected Y. pestis inoculated at 20 cells/SS and ATD did not impact detection (P > 0.05). F. tularensis showed significantly lower recoveries between no-hold time and 48-h hold time (4 °C, P < 0.05) using the HTM, which further testing showed could be due to toxicity of the neutralizing buffer used for SS pre-wetting. With modifications, this method could enhance throughput capacity while maintaining similar recovery efficiencies to current methods for other non-spore-forming bacterial pathogens.

Biological and medical sciences

Molecular and structural characterization of a Bacillus cereus strain producing an anthrax-like capsule

Bacillus cereus is a ubiquitous Gram-positive, spore-forming, rod-shaped saprophytic bacterium, occasionally reported to cause food-borne illnesses. However, instances of B. cereus strains harboring anthrax toxin and capsule genes have elevated certain strains as formidable pathogens and biothreats. This study focuses on the genomic analysis and the structural characterization of capsular material produced by the virulent B. cereus PATH2418 strain, isolated from the wound of a traumatic open fracture patient. The genome was sequenced using Nanopore MinION sequencing, revealing a chromosome of 5,270,283 bp and three plasmids. One plasmid, pATH1, was found to encode an operon for the biosynthesis of a bacterial capsule. This operon had sequence homology to the Bacillus anthracis capBCADE operon, which encodes the poly-γ-D-glutamate (PDGA) capsule. The capsule production in B. cereus PATH2418 was influenced by temperature and CO 2 levels. Structural analysis of the capsular material using a combined approach of nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC) techniques confirmed the presence of a high-molecular-weight poly-γ-glutamate capsule, with an enantiomeric composition of approximately 67% D-glutamic acid and 33% L-glutamic acid, matching that of B. anthracis.

Bacillus cereus