Molecular regulatory mechanisms of Escherichia coli O157:H7 in response to ultrasonic stress revealed by proteomic analysis

Systematic Adaptation of Bacillus licheniformis to 2-Phenylethanol Stress

The compound 2-phenylethanol (2-PE) is a bulk flavor and fragrance with a rose-like aroma that can be produced by microbial cell factories, but its cellular toxicity inhibits cellular growth and limits strain performance. Specifically, the microbe Bacillus licheniformis has shown a strong tolerance to 2-PE. Understanding these tolerance mechanisms is crucial for achieving the hyperproduction of 2-PE. In this report, the mechanisms of B. licheniformis DW2 resistance to 2-PE were studied by multi-omics technology coupled with physiological and molecular biological approaches. 2-PE induced reactive oxygen species formation and affected nucleic acid, ribosome, and cell wall synthesis. To manage 2-PE stress, the antioxidant and global stress response systems were activated; the repair system of proteins and homeostasis of the ion and osmotic were initiated. Furthermore, the tricarboxylic acid cycle and NADPH synthesis pathways were upregulated; correspondingly, scanning electron microscopy revealed that cell morphology was changed. These results provide deeper insights into the adaptive mechanisms of B. licheniformis to 2-PE and highlight the potential targets for genetic manipulation to enhance 2-PE resistance. IMPORTANCE The ability to tolerate organic solvents is essential for bacteria producing these chemicals with high titer, yield, and productivity. As exemplified by 2-PE, bioproduction of 2-PE represents a promising alternative to chemical synthesis and plant extraction approaches, but its toxicity hinders successful large-scale microbial production. Here, a multi-omics approach is employed to systematically study the mechanisms of B. licheniformis DW2 resistance to 2-PE. As a 2-PE-tolerant strain, B. licheniformis displays multifactorial mechanisms of 2-PE tolerance, including activating global stress response and repair systems, increasing NADPH supply, changing cell morphology and membrane composition, and remodeling metabolic pathways. The current work yields novel insights into the mechanisms of B. licheniformis resistance to 2-PE. This knowledge can also be used as a clue for improving bacterial performances to achieve industrial-scale production of 2-PE and potentially applied to the production of other relevant organic solvents, such as tyrosol and hydroxytyrosol.

Quantitative proteomic analysis provides insight into the survival mechanism of Salmonella typhimurium under high-intensity ultrasound treatment

The survival mechanism of Salmonella treated with high-intensity ultrasound (HIU) should be explored to further enhance the bactericidal efficacy of HIU. In this study, culturable Salmonella was reduced by applying HIU. Electron microscope imaging revealed that HIU caused the disintegration of cell structure and leakage of intracellular substances. For the Salmonella after the HIU treatment, key enzymes of the tricarboxylic acid [TCA] cycle were significantly downregulated, which led to a reduced ATP content (45.25%–75.00%), although ATPase activity was augmented by 33.82%–60.64% in the Salmonella. Accordingly, surviving Salmonella could have tolerated the stress of HIU by upregulating their environmental sensing (two-component system), chemotaxis (bacterial chemotaxis), substance uptake (ABC transporter), and ATP production (oxidative phosphorylation). Therefore, synergistically blocking the ATP production, signal transduction, or substance intake of Salmonella offer promising potential strategies to improve the bactericidal effect of HIU in industrial food processing.

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Cell damage and substances leakage were observed in ultrasound treated Salmonella.

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Ultrasonic treatments caused 1017 differentially expressed proteins in Salmonella.

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Ultrasound inhibited tricarboxylic acid cycle and reduced adenosine triphosphate content in Salmonella.

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Salmonella tolerated ultrasound by upregulating two-component system, ABC transport, and bacterial chemotaxis.

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These altered pathways could be potential targets to enhance the lethality of ultrasound.

Insight into Ultrasound-Induced Modifications of the Proteome and Flavor-Related Proteins of Unsmoked Bacon by Applying Label-Free Quantitation Technology

The aim of this study was to investigate the modifications of the proteome and flavor-related proteins in unsmoked bacon resulting from ultrasound treatment with the application of label-free quantitation technology together with bioinformatics analysis. Results showed that the expression levels of 137 proteins were markedly affected by ultrasound with most of them being significantly upregulated. The proteins distributed in the cytoplasm and the cytosol, the mitochondrion, and the nucleus were more susceptible to ultrasound treatment. Meanwhile, 20 flavor-related proteins, mostly myofibrillar proteins and metabolic enzymes mainly involved in the metabolic pathways of signaling and cellular processes and environmental information processing, were screened out. In addition, the differential expressions of flavor-related proteins induced by ultrasound were verified by western blotting. This study displayed insightful information from the proteomics perspective for a better understanding of the influential effect of ultrasound treatment on meat flavor.

Phenotyping Bacteria through a Black-Box Approach: Amplifying Surface-Enhanced Raman Spectroscopy Spectral Differences among Bacteria by Inputting Appropriate Environmental Stress

Surface-enhanced Raman spectroscopy (SERS) stands out in the field of microbial analysis due to its rich molecular information, fast analysis speed, and high sensitivity. However, achieving strain-level differentiation is still challenging because numerous bacterial species inevitably have very similar SERS profiles. Here, a method inspired by the black-box theory was proposed to boost the spectral differences, where the undifferentiated bacteria was considered as a type of black-box, external environmental stress was used as the input, and the SERS spectra of bacteria exposed to the same stress was output. For proof of the concept, three types of environmental stress were explored, i.e., ethanol, ultraviolet light (UV), and ultrasound. Enterococcus faecalis (E. faecalis) and three types of Escherichia coli (E. coli) were all subjected to the stimuli (stress) before SERS measurement. Then the collected spectra were processed only by simple principal component analysis (PCA) to achieve differentiation. The results showed that appropriate stress was beneficial to increase the differences in bacterial SERS spectra. When sonication at 490 W for 60 s was used as the input, the optimal differentiation of bacteria at the species (E. faecalis and E. coli) and strain-level (three E. coli) can be achieved.

Bacteriostatic effects of high-intensity ultrasonic treatment on Bacillus subtilis vegetative cells

The bacteriostatic effects of high-intensity ultrasonic treatment (HIU) on Bacillus subtilis vegetative cells were evaluated, and the related mechanisms were explored using quantitative proteomics. The bacteriostatic effect of HIU on B. subtilis was proportional to the ultrasound treatment time and power, and the number of cultivable B. subtilis cells was decreased by approximately one log (at 270 W for 15 min) or half log (at 90 W for 25 min or 360 W for 5 min). Scanning electron microscopy images and gel electrophoresis results showed that HIU caused the destruction of the cell structure and intracellular protein leakage. In addition, HIU treatment at 270 W for 15 min resulted in the greatest decrease (84.22%) in intracellular adenosine triphosphate (ATP) content. The quantitative proteomic analysis showed that B. subtilis resisted the stress of HIU treatment by regulating the key proteins in physiological activities related to membrane transport (ATP-binding cassette [ABC] transporter), signal transduction (the two-component system), and energy metabolism (the tricarboxylic acid [TCA] cycle). HIU-induced physical damage, stress, and metabolic disorders were the main causes of the bacteriostatic effects on B. subtilis. These findings provide a foundation for the subsequent optimization and potential applications of HIU inactivation of B. subtilis.

Transcriptomic analysis reveal differential gene expressions of Escherichia coli O157:H7 under ultrasonic stress

In order to uncover the molecular regulatory mechanisms underlying the phenotypes, the overall regulation of genes at the transcription level in Escherichia coli O157:H7 after ultrasonic stimulation were investigated by RNA-sequencing and real-time quantitative polymerase chain reaction. The results revealed that differential expressions of 1217 genes were significant when exposed at 6.67 W/mL power ultrasonic density for 25 min, including 621 up-regulated and 596 down-regulated genes. Gene transcription related to a series of crucial biomolecular processes were influenced by the ultrasonic stimulation, including carbohydrate metabolism, energy metabolism, membrane transport, signal transduction, transcription and translation. The most enriched pathways were further analyzed in each category. Specifically, genes encoded citrate cycle were down-regulated in E. coli O157:H7, indicating the capacity to decompose carbohydrate and produce energy were decreased under ultrasonic stress. Accompanied with energy loss, the membrane function was affected by the ultrasonic stimulation since the majority of genes encoded ATP-binding cassette transporters were down-regulated. Besides, the autoinducer 2-mediated signal transduction was also inhibited. The interesting thing, however, the protein translation processing was benefited under ultrasonic field. This phenomenon might due to the desperate need of stress response proteins when the bacteria were under stress. We believed that the sonomechanical and sonochemical effects generated by acoustic cavitation were responsible for those gene expression changes.

Ultrasound enhanced production of mycelia and exopolysaccharide by Agaricus bitorquis (Quél.) Sacc. Chaidam

Agaricus bitorquis (Quél.) Sacc. Chaidam (ABSC), is a kind of rare edible macrofungi with a variety of biological ingredients, especially its polysaccharides. However, the low yield limits the popularity and promotion of rare edible macrofungi as well as its macrofungi polysaccharides. Hence, developing a positive and effective cultivation method is of great importance. Herein, an efficient ultrasonic (US) stimulation strategy was developed to improve mycelial growth and exopolysaccharides (EPS) biosynthesis from ABSC in submerged cultivation without light. A time design was employed to illustrate the effect of various process parameters including duration, starting point and times of US irradiation on ABSC productivity. 5 min US treatment for once upon ABSC after fermentation for 48 h could significantly improve EPS production and mycelia growth by above 26% and 15.03%, respectively. Furthermore, six times of 5 min US treatment could make the amount of EPS reach 218.78 ± 17.09 mg/g, which was 2.52-fold higher than that of the control. Moreover, the enhanced effect induced by US was further expounded by fermentation kinetics. Besides, the US treatment could increase mycelia permeability, change structure and reduce mycelial diameter to promote mass transfer, resulting in the improvement of EPS production and mycelia accumulation. The results demonstrated that the present proposed US intensification approach could be useful to boost up the fermentation of ABSC, which possibly applied to yield increase and fermentation product acquisition of macrofungi.

Quorum Sensing System-Regulated Proteins Affect the Spoilage Potential of Co-cultured Acinetobacter johnsonii and Pseudomonas fluorescens From Spoiled Bigeye Tuna (Thunnus obesus) as Determined by Proteomic Analysis

Food spoilage by certain species of bacteria is reported to be regulated by quorum sensing (QS). Acinetobacter johnsonii and Pseudomonas fluorescens, the major specific spoilage organisms, are found to be limited in their QS and co-culture interactions. The aim of this study was to determine how QS-regulated proteins affect the spoilage potential of co-cultured A. johnsonii and P. fluorescens obtained from spoiled bigeye tuna (Thunnus obesus) using a proteomics approach. The A. johnsonii, P. fluorescens, and their co-culture tested the N-acyl-homoserine lactone (AHL) activities using reporter Chromobacterium violaceum CV026 and LC-MS/MS in qualitative and quantitative approaches, respectively. These latter showed that, of the 470 proteins and 444 proteins in A. johnsonii (A) and P. fluorescens (P), respectively, 80 were significantly up-regulated and 97 were significantly down-regulated in A vs. AP, whereas 90 were up-regulated and 65 were down-regulated in P vs. AP. The differentially expressed proteins included the AI-2E family transporter OS, 50S ribosomal protein L3, thioredoxin reductase OS, cysteine synthase CysM OS, DNA-binding response regulator, and amino acid ABC transporter ATPase OS. The cellular process (GO:0009987), metabolic process (GO:0008152), and single-organism process (GO:0044699) were classified into the gene ontology (GO) term. In addition, energy production and conversion, amino acid transport and metabolism, translation, ribosomal structure and biogenesis, post-translational modification, protein turnover, and chaperones were distributed into the clusters of orthologous groups of proteins (COG) terms. The KEGG pathways revealed that 84 and 77 differentially expressed proteins were divided into 20 KEGG pathways in A vs. AP and P vs. AP, respectively, and amino acid metabolism, carbohydrate metabolism, energy metabolism, and translation were significantly enriched. Proteins that correlated with the spoilage-related metabolic pathways, including thioredoxin reductase OS, cysteine synthase OS, and pyridoxal phosphate-dependent enzyme family protein OS, were identified. AI-2E family transporter OS and LuxR family transcriptional regulator OS were identified that related to the QS system. These findings provide a differential proteomic profile of co-culture in A. johnsonii and P. fluorescens, and have potential applications in QS and the regulation of spoilage potential.