Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917

Contribution of Toxin-Antitoxin Systems to Adherent-Invasive E. coli Pathogenesis

Pathobionts have been implicated in various chronic diseases, including Crohn's disease (CD), a multifactorial chronic inflammatory condition that primarily affects the gastrointestinal tract, causing inflammation and damage to the digestive system. While the exact cause of CD remains unclear, adherent-invasive Escherichia coli (AIEC) strains have emerged as key contributors to its pathogenesis. AIEC are characterized by their ability to adhere to and invade intestinal epithelial cells and survive and replicate inside macrophages. However, the mechanisms underlying the virulence and persistence of AIEC within their host remain the subject of intensive research. Toxin-antitoxin systems (TAs) play a potential role in AIEC pathogenesis and may be therapeutic targets. These systems generally consist of two components: a toxin harmful to the cell and an antitoxin that neutralizes the toxin's effects. They contribute to bacterial survival in adverse conditions and regulate bacterial growth and behavior, affecting various cellular processes in bacterial pathogens. This review focuses on the current information available to determine the roles of TAs in the pathogenicity of AIEC. Their contribution to the AIEC stress response, biofilm formation, phage inhibition, the maintenance of mobile genetic elements, and host lifestyles is discussed.

The biological function of the type II toxin-antitoxin system ccdAB in recurrent urinary tract infections

Urinary tract infections (UTIs) represent a significant challenge in clinical practice, with recurrent forms (rUTIs) posing a continual threat to patient health. Escherichia coli (E. coli) is the primary culprit in a vast majority of UTIs, both community-acquired and hospital-acquired, underscoring its clinical importance. Among different mediators of pathogenesis, toxin-antitoxin (TA) systems are emerging as the most prominent. The type II TA system, prevalent in prokaryotes, emerges as a critical player in stress response, biofilm formation, and cell dormancy. ccdAB, the first identified type II TA module, is renowned for maintaining plasmid stability. This paper aims to unravel the physiological role of the ccdAB in rUTIs caused by E. coli, delving into bacterial characteristics crucial for understanding and managing this disease. We investigated UPEC-induced rUTIs, examining changes in type II TA distribution and number, phylogenetic distribution, and Multi-Locus Sequence Typing (MLST) using polymerase chain reaction (PCR). Furthermore, our findings revealed that the induction of ccdB expression in E. coli BL21 (DE3) inhibited bacterial growth, observed that the expression of both ccdAB and ccdB in E. coli BL21 (DE3) led to an increase in biofilm formation, and confirmed that ccdAB plays a role in the development of persistent bacteria in urinary tract infections. Our findings could pave the way for novel therapeutic approaches targeting these systems, potentially reducing the prevalence of rUTIs. Through this investigation, we hope to contribute significantly to the global effort to combat the persistent challenge of rUTIs.

Minimizing endogenous cryptic plasmids to construct antibiotic-free expression systems for Escherichia coli Nissle 1917

The probiotic bacterium Escherichia coli Nissle 1917 (EcN) holds significant promise for use in clinical and biological industries. However, the reliance on antibiotics to maintain plasmid-borne genes has overshadowed its benefits. In this study, we addressed this issue by engineering the endogenous cryptic plasmids pMUT1 and pMUT2. The non-essential elements were removed to create more stable derivatives pMUT1NR△ and pMUT2HBC△. Synthetic promoters by integrating binding motifs on sigma factors were further constructed and applied for expression of Bacteroides thetaiotaomicron heparinase III and the biosynthesis of ectoine. Compared to traditional antibiotic-dependent expression systems, our newly constructed antibiotic-free expression systems offer considerable advantages for clinical and synthetic biology applications.

Computational exploration of the genomic assignments, molecular structure, and dynamics of the ccdABXn2 toxin-antitoxin homolog with its bacterial target, the DNA gyrase, in the entomopathogen Xenorhabdus nematophila

Toxin-antitoxin (TA) modules, initially discovered on bacterial plasmids and subsequently identified within chromosomal contexts, hold a pivotal role in the realm of bacterial physiology. Among these, the pioneering TA system, ccd (Control of Cell Death), primarily localized on the F-plasmid, is known for its orchestration of plasmid replication with cellular division. Nonetheless, the precise functions of such systems within bacterial chromosomal settings remain a compelling subject that demands deeper investigation. To bridge this knowledge gap, our study focuses on exploring ccdABXn2, a chromosomally encoded TA module originating from the entomopathogenic bacterium Xenorhabdus nematophila. We meticulously delved into the system's genomic assignments, structural attributes, and functional interplay. Our findings uncovered intriguing patterns-CcdB toxin homologs exhibited higher conservation levels compared to their CcdA antitoxin counterparts. Moreover, we constructed secondary as well as tertiary models for both the CcdB toxin and CcdA antitoxin using threading techniques and subsequently validated their structural integrity. Our exploration extended to the identification of key interactions, including the peptide interaction with gyrase for the CcdB homolog and CcdB toxin interactions for the CcdA homolog, highlighting the intricate TA interaction network. Through docking and simulation analyses, we unequivocally demonstrated the inhibition of replication via binding the CcdB toxin to its target, DNA gyrase. These insights provide valuable knowledge about the metabolic and physiological roles of the chromosomally encoded ccdABXn2 TA module within the context of X. nematophila, significantly enhancing our comprehension of its functional significance within the intricate ecosystem of the bacterial host.Communicated by Ramaswamy H. Sarma.

Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications

Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.

Prospective and challenges of live bacterial therapeutics from a superhero Escherichia coli Nissle 1917

Escherichia coli Nissle 1917 (EcN), the active component of Mutaflor(R), is a notable probiotic from Gram-negative to treat Crohn's disease and irritable bowel syndrome. Therefore, a comprehensive genomic database maximizes the systemic probiotic assessment to discover EcN's role in human health. Recently, advanced synthetic and genetic tools have opened up a rich area to execute EcN as "living medicines" with controllable functions. Incorporating unique biomarkers allows the engineered EcN to switch genes on and off in response to environmental cues. Since EcN holds promise as a safe nature vehicle, more studies are desired to fully realize a wide range of probiotic potential for disease treatment. This review aims to deliver a historical origin of EcN, discuss the recent promising genetic toolbox in the rational design of probiotics, and pinpoint the clinical translation and evaluation of engineered EcN in vitro and in vivo. The summary of safety concerns, strategies of biotherapeutics development, and the challenges and prospects of engineered EcN is also concluded.

Genomic assortment and interactive insights of the chromosomal encoded control of cell death (ccd) toxin-antitoxin (TA) module in Xenorhabdus nematophila

In the present circumstances, toxin-antitoxin (TA) modules have a great consideration due to their elusive role in bacterial physiology. TA modules consist of a toxic part and a counteracting antitoxin part and these are abundant genetic loci harbored on bacterial plasmids and chromosomes. The control of cell death (ccd) TA locus was the first identified TA module and its unitary function (such as plasmid maintenance) has been described, however, the function of its chromosomal counterparts is still ambiguous. Here, we are exploring the genomic assortment, structural and functional association of chromosomally encoded ccdAB TA homolog (ccdABXn1) in the genome of an entomopathogenic bacterium Xenorhabdus nematophila. This bacterium is a symbiotic model with the nematode Steinernema carpocapsae that infects and kills the host insect. By genomic assortment analysis, our observations suggested that CcdA antitoxin homologs are not more closely related than CcdB toxin homologs. Further results suggest that the ccdABXn1 TA homolog has sulphonamide (such as 4C6, for CcdA homolog) and peptide (such as gyrase, for CcdB homolog) ligand partners with a typical TA interaction network that may affect essential cellular metabolism of the X. nematophila. Collectively, our results improve the knowledge and conception of the metabolic interactive role of ccdAB TA homologs in X. nematophila physiology.Communicated by Ramaswamy H. Sarma.

Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment

AIMS

Bacterial persisters are rare phenotypic variants in clonal bacterial cultures that can endure antimicrobial therapy and potentially contribute to infection relapse. Here, we investigate the potential of leveraging microbial interactions to disrupt persisters as they resuscitate during the post-antibiotic treatment recovery period.

METHODS AND RESULTS

We treated stationary-phase E. coli MG1655 with a DNA-damaging fluoroquinolone and co-cultured the cells with probiotic E. coli Nissle following antibiotic removal. We found that E. coli Nissle reduced the survival of fluoroquinolone persisters and their progeny by over three orders of magnitude within 24 h. Using a bespoke H-diffusion cell apparatus that we developed, we showed that E. coli Nissle antagonized the fluoroquinolone-treated cells in a contact-dependent manner. We further demonstrated that the fluoroquinolone-treated cells can still activate the SOS response as they recover from antibiotic treatment in the presence of E. coli Nissle and that the persisters depend on TolC-associated efflux systems to defend themselves against the action of E. coli Nissle.

CONCLUSION

Our results demonstrate that probiotic bacteria, such as E. coli Nissle, have the potential to inhibit persisters as they resuscitate following antibiotic treatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacterial persisters are thought to underlie chronic infections and they can lead to an increase in antibiotic-resistant mutants in their progenies. Our data suggest that we can leverage the knowledge we gain on the interactions between microbial strains/species that interfere with persister resuscitation, such as those involving probiotic E. coli Nissle and E. coli MG1655 (a K-12 strain), to bolster the activity of our existing antibiotics.

Mechanistic insights into the inhibitory effect of theaflavins on virulence factors production in Streptococcus mutans

Streptococcus mutans is the primary etiological agent associated with cariogenic process. The present study aimed to investigate the antibacterial and anti-virulence activities of theaflavins (TFs) to Streptococcus mutans UA159 as well as the underlying mechanisms. The results showed that TFs were capable of suppressing the acid production, cell adherence, water-insoluble exopolysaccharides production, and biofilm formation by S. mutans UA159 with a dosage-dependent manner while without influencing the cell growth. By a genome-wide transcriptome analysis (RNA-seq), we found that TFs attenuated the biofilm formation of S. mutans UA159 by inhibiting glucosyltransferases activity and the production of glucan-binding proteins (GbpB and GbpC) instead of directly blocking the expression of genes coding for glucosyltransferases. Further, TFs inhibited the expression of genes implicated in peptidoglycan synthesis, glycolysis, lipid synthesis, two-component system, signaling peptide transport (comA), oxidative stress response, and DNA replication and repair, suggesting that TFs suppressed the virulence factors of S. mutans UA159 by affecting the signal transduction and cell envelope stability, and weakening the ability of cells on oxidative stress resistance. In addition, an upregulated expression of the genes involved in protein biosynthesis, amino acid metabolism, and transport system upon TFs treatment indicated that cells increase the protein synthesis and nutrients uptake as one self-protective mechanism to cope with stress caused by TFs. The results of this study increase our current understanding of the anti-virulence activity of TFs on S. mutans and provide clues for the use of TFs in the prevention of dental caries.

Biological Functions of Type II Toxin-Antitoxin Systems in Bacteria

After the first discovery in the 1980s in F-plasmids as a plasmid maintenance system, a myriad of toxin-antitoxin (TA) systems has been identified in bacterial chromosomes and mobile genetic elements (MGEs), including plasmids and bacteriophages. TA systems are small genetic modules that encode a toxin and its antidote and can be divided into seven types based on the nature of the antitoxin molecules and their mechanism of action to neutralise toxins. Among them, type II TA systems are widely distributed in chromosomes and plasmids and the best studied so far. Maintaining genetic material may be the major function of type II TA systems associated with MGEs, but the chromosomal TA systems contribute largely to functions associated with bacterial physiology, including the management of different stresses, virulence and pathogenesis. Due to growing interest in TA research, extensive work has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules. However, there are still controversies about some of the functions associated with different TA systems. This review will discuss the most current findings and the bona fide functions of bacterial type II TA systems.

Impacts of type II toxin-antitoxin systems on cell physiology and environmental behavior in acetic acid bacteria

Acetic acid bacteria (AAB) are a group of Gram-negative and strictly aerobic microorganisms widely used in vinegar industry, especially the species belonging to the genera Acetobacter and Komagataeibacter. The environments inhabited by AAB during the vinegar fermentation, in particular those natural traditional bioprocesses, are complex and dynamically changed, usually accompanied by diverse microorganisms, bacteriophages, and the increasing acetic acid concentration. For this reason, how AAB survive to such harsh niches has always been an interesting research field. Previous omic analyses (e.g., genomics, proteomics, and transcriptomics) have provided abundant clues for the metabolic pathways and bioprocesses indispensable for the acid stress adaptation of AAB. Nevertheless, it is far from fully understanding what factors regulate these modular mechanisms overtly and covertly upon shifting environments. Bacterial toxin-antitoxin systems (TAS), usually consisting of a pair of genes encoding a stable toxin and an unstable antitoxin that is capable of counteracting the toxin, have been uncovered to have a variety of biological functions. Recent studies focusing on the role of TAS in Acetobacter pasteurianus suggest that TAS contribute substantially to the acid stress resistance. In this mini review, we discuss the biological functions of type II TAS in the context of AAB with regard to the acid stress resistance, persister formation and resuscitation, genome stability, and phage immunity. KEY POINTS: • Type II TAS act as regulators in the acid stress resistance of AAB. • Type II TAS are implicated in the formation of acid-tolerant persister cells in AAB. • Type II TAS are potential factors responsible for phage immunity and genome stability.

Tooth brushing using toothpaste containing theaflavins reduces the oral pathogenic bacteria in healthy adults

Theaflavins (TFs) are the main bioactive component in black tea. At present, little effort has been done to evaluate the influence of TFs when included in the toothpaste on the diversity of oral microbiota. In this study, eighty samples collected from the saliva and supragingival plaque of 20 healthy adults using toothpaste with the absence or presence of TFs for a period of 4 weeks were used for the oral microbiome analysis by 16S rRNA gene sequencing. Alpha and beta diversity analysis showed that tooth brushing using the toothpaste with TFs significantly increased the microbial abundance in the saliva samples, and altered the oral microbiota obtained from the saliva and supragingival plaque. The linear discriminant analysis revealed that the use of toothpaste with TFs significantly reduced the abundance of oral pathogens (e.g., Prevotella, Selenomonas, and Atopobium) while increased the abundance of oral-health associated bacteria (e.g., Streptococcus and Rothia). In addition, using toothpaste with TFs reduced the functional pathways abundance relevance to the extracellular polymeric substance (EPS) synthesis while enriched the functions in transporters, ABC transporters, two-component system, and amino acid metabolism. Collectively, our results provide evidence for the application of toothpaste containing TFs as a promising oral care product.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02699-7.

New insights into the antibacterial and quorum sensing inhibition mechanism of Artemisia argyi leaf extracts towards Pseudomonas aeruginosa PAO1

This study aimed to investigate the anti-quorum sensing (QS) activity of Artemisia argyi leaf extracts (AALE) towards Pseudomonas aeruginosa PAO1 as well as the underlying molecular mechanisms. Using a biosensor Chromobacterium violaceum CV026, AALE were found to have anti-QS activity as AALE treatment significantly inhibited the violacein production of C. violaceum CV026 while produced little effect on the cell growth. Beyond that a higher dosage of AALE inhibited cell growth, sub-MIC of AALE significantly reduced the production of QS-regulated virulence factors (pyocyanin, elastase, and rhamnolipid), biofilm formation, and the swarming and swimming motility in P. aeruginosa PAO1 with a dosage-dependent manner. Quantitative real-time PCR (qRT-PCR) analysis did not detect the direct inhibitory effect of AALE on the expression of QS genes (lasI, lasR, rhlI, and rhlR). By iTRAQ-based quantitative proteomic analysis, 129 proteins were found to be differentially expressed upon AALE treatment, with 85 upregulated and 44 downregulated proteins, respectively. Functional enrichment analysis of the differential proteins revealed that AALE exerted anti-QS activity towards P. aeruginosa PAO1 by upregulating the expression of the global regulator CsrA, inducing oxidative stress, and perturbing protein homeostasis. Moreover, the inhibitory effect of AALE on the virulence of P. aeruginosa PAO1 was likely to be achieved by attenuating the expression of QS-regulated genes instead of QS genes. Collectively, the results of this study provide a basis for the future use of AALE as a preservative in controlling food spoilage caused by P. aeruginosa.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02663-5.