CsrA and TnaB coregulate tryptophanase activity to promote exotoxin-induced killing of Caenorhabditis elegans by enteropathogenic Escherichia coli

Biological studies reveal the role of trpA gene in biofilm formation, motility, hemolysis and virulence in Vibrio anguillarum

Vibrio anguillarum is a pathogen responsible for vibriosis in aquaculture animals. The formation of bacterial biofilm contributes to infections and increases resistance to antibiotics. Tryptophanase and its substrate tryptophan have been recognized as signal molecules regulating bacterial biofilm formation. This study aimed to investigate the role of the trpA gene encoding tryptophan synthase in V. anguillarum through constructing a trpA mutant (ΔtrpA) and its complemented strain (CΔtrpA). The ΔtrpA produced less tryptophan compared to the WT and ΔtrpA strains, with almost no detectable indole synthesis in the ΔtrpA mutant. RNAseq analysis showed that 152 genes were differentially expressed in the ΔtrpA mutant, including 64 upregulated and 88 downregulated genes. KEGG enrichment analysis and qRT-PCR validation indicated that genes associated with bacterial chemotaxis, two component system, quorum sensing and biofilm formation were downregulated. Crystal violet staining confirmed that the ΔtrpA mutant decreased biofilm formation due to the reduced tryptophan and indole. Our studies also showed that TrpA plays an important role in the motility and hemolytic ability of V. anguillarum. Finally, the virulence of the ΔtrpA mutant was evaluated using a Tetrahymena infection model, which demonstrated that the virulence of ΔtrpA mutant was significantly attenuated. These findings provide insight into the role of trpA gene in biofilm formation, motility, hemolysis, and virulence in V. anguillarum.

The RNA chaperone protein ProQ is a pleiotropic regulator in enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli (EPEC) is a gastrointestinal pathogen that affects individuals of all age groups, with infections ranging from subclinical colonization to acute or persistent diarrhea. The bacterium's ability to cause diarrhea depends on the locus of enterocyte effacement (LEE) pathogenicity island. Although regulation of the LEE has been systematically characterized, until the last decade, studies mainly focused on its transcriptional control. Posttranscriptional regulation of the LEE continues to be an underappreciated and understudied area of gene regulation. In the past few years, multiple reports have shed light on the roles of RNA-binding proteins, such as Hfq and CsrA, that modulate virulence in EPEC. This study was undertaken to explore the role of another RNA chaperone protein, ProQ, in the pathophysiology of EPEC. Our results suggest that deletion of proQ globally derepresses gene expression from the LEE in lysogeny broth (LB) suggesting that ProQ is a negative regulator of the LEE. Further interrogation revealed that ProQ exerts its effect by downregulating the expression of PerC - a prominent transcriptional activator of the LEE-encoded master regulator ler, which, in turn leads to the observed repression from the other LEE operons. Furthermore, ProQ appears to moonlight as it affects other physiological processes including type IV pili biogenesis, flagellar-dependent motility, biofilm formation, tryptophan metabolism, and antibiotic resistance. Our study provides the very first evidence to implicate ProQ as a pleiotropic regulator in EPEC.

Discovery of New Fusobacterium nucleatum Inhibitors to Attenuate Migratory Capability of Colon Cancer Cells by the Drug Repositioning Strategy

Recent studies revealed that intestinal microbiota played important roles in colorectal cancer (CRC) carcinogenesis. Particularly, Fusobacterium nucleatum was confirmed to promote the proliferation and metastasis of CRC. Therefore, targeting F. nucleatum may be a potential preventive and therapeutic approach for CRC. Herein, 2,272 off-patent drugs were screened inhibitory activity against F. nucleatum. Among the hits, nitisinone was identified as a promising anti-F. nucleatum lead compound. Further optimization of nitisinone led to the discovery of more potent derivatives. Particularly, compounds 19q and 22c showed potent anti-F. nucleatum activity (MIC50 = 1 and 2 μg/mL, respectively) with low cytotoxicity. Among them, compound 19q effectively attenuated the migratory ability of MC-38 cells induced by F. nucleatum. Preliminary mechanism studies suggested that nitisinone and its derivatives might act by downregulating nitroreductase and tryptophanase. Thus, the development of small molecule F. nucleatum inhibitors represents an effective strategy to treat CRC.

High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes

Virulent genes present in Escherichia coli (E. coli) can cause significant human diseases. These enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) isolates with virulent genes show different expression levels when grown under diverse laboratory conditions. In this research, we have performed differential gene expression analysis using publicly available RNA-seq data on three pathogenic E. coli hybrid isolates in an attempt to characterize the variation in gene interactions that are altered by the presence or absence of virulent factors within the genome. Almost 26.7% of the common genes across these strains were found to be differentially expressed. Out of the 88 differentially expressed genes with virulent factors identified from PATRIC, nine were common in all these strains. A combination of Weighted Gene Co-Expression Network Analysis and Gene Ontology Enrichment Analysis reveals significant differences in gene co-expression involving virulent genes common among the three investigated strains. The co-expression pattern is observed to be especially variable among biological pathways involving metabolism-related genes. This suggests a potential difference in resource allocation or energy generation across the three isolates based on genomic variation.

Atypical Enteropathogenic Escherichia coli: from Kittens to Humans and Beyond!

Atypical enteropathogenic Escherichia coli (aEPEC) are associated with diarrhea worldwide, yet genome-wide investigations to probe their virulome are lacking. In this issue of Infection and Immunity, V. E. Watson, T. H. Hazen, D. A. Rasko, M. E. Jacob, et al. (IAI 89:e00619-20, 2020, https://doi.org/10.1128/IAI.00619-20) sequenced aEPEC isolates from diarrheic and asymptomatic kittens. Using phylogenomics, they demonstrated that these isolates were genetically indistinguishable from human isolates, suggesting that kittens may serve as a reservoir and, perhaps, a much-needed model to interrogate aEPEC virulence. The diarrheic isolates were hypermotile, suggesting that this phenotype may distinguish virulent strains from their innocuous counterparts.

Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli

The carbon storage regulator A (CsrA) is a conserved global regulatory system known to control central carbon pathways, biofilm formation, motility, and pathogenicity. The aim of this study was to characterize changes in major metabolic pathways induced by CsrA in human enteropathogenic Escherichia coli (EPEC) grown under virulence factor-inducing conditions. For this purpose, the metabolomes and transcriptomes of EPEC and an isogenic ∆csrA mutant derivative were analyzed by untargeted mass spectrometry and RNA sequencing, respectively. Of the 159 metabolites identified from untargeted GC/MS and LC/MS data, 97 were significantly (fold change ≥ 1.5; corrected p-value ≤ 0.05) regulated between the knockout and the wildtype strain. A lack of csrA led to an accumulation of fructose-6-phosphate (F6P) and glycogen synthesis pathway products, whereas metabolites in lower glycolysis and the citric acid cycle were downregulated. Associated pathways from the citric acid cycle like aromatic amino acid and siderophore biosynthesis were also negatively influenced. The nucleoside salvage pathways were featured by an accumulation of nucleosides and nucleobases, and a downregulation of nucleotides. In addition, a pronounced downregulation of lyso-lipid metabolites was observed. A drastic change in the morphology in the form of vesicle-like structures of the ∆csrA knockout strain was visible by electron microscopy. Colanic acid synthesis genes were strongly (up to 50 fold) upregulated, and the abundance of colanic acid was 3 fold increased according to a colorimetric assay. The findings expand the scope of pathways affected by the csrA regulon and emphasize its importance as a global regulator.

Environment Controls LEE Regulation in Enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli (EPEC) is a significant cause of infant morbidity and mortality in developing regions of the world. Horizontally acquired genetic elements encode virulence structures, effectors, and regulators that promote bacterial colonization and disease. One such genetic element, the locus of enterocyte effacement (LEE), encodes the type three secretion system (T3SS) which acts as a bridge between bacterial and host cells to pass effector molecules that exert changes on the host. Due to its importance in EPEC virulence, regulation of the LEE has been of high priority and its investigation has elucidated many virulence regulators, including master regulator of the LEE Ler, H-NS, other nucleoid-associated proteins, GrlA, and PerC. Media type, environmental signals, sRNA signaling, metabolic processes, and stress responses have profound, strain-specific effects on regulators and LEE expression, and thus T3SS formation. Here we review virulence gene regulation in EPEC, which includes approaches for lessening disease by exploiting the elucidated regulatory pathways.

Options and Limitations in Clinical Investigation of Bacterial Biofilms

Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.

The Small Regulatory RNA Spot42 Inhibits Indole Biosynthesis to Negatively Regulate the Locus of Enterocyte Effacement of Enteropathogenic Escherichia coli

The locus of enterocyte effacement is necessary for enteropathogenic Escherichia coli (EPEC) to form attaching and effacing (A/E) lesions. A/E lesions are characterized by intimate bacterial adherence to intestinal cells and destruction of microvilli, which leads to diarrhea. Therefore, studies interrogating the regulation of the locus of enterocyte effacement (LEE) are critical for understanding the molecular epidemiology of EPEC infections and developing interventional strategies. Hitherto, most studies have centered on protein-based regulators, whereas the role of small regulatory RNAs remains underappreciated. Previously, we identified the first sRNAs—MgrR, RyhB, and McaS—that regulate the LEE of EPEC. This study was undertaken to identify additional sRNAs that impact the LEE. Our results suggest that the catabolite-responsive sRNA, Spot42, indirectly controls the LEE by inhibiting synthesis of its inducer, indole. Spot42 base-pairs with the tnaCAB mRNA and presumably destabilizes the transcript, thereby preventing expression of the regulatory and structural proteins that are involved in the import and hydrolysis of tryptophan into indole. The absence of intracellular indole leads to reduced transcription of the LEE1-encoded master transcriptional activator Ler, thereby maintaining the LEE in its silenced state and delaying A/E lesion morphogenesis. Our results highlight the importance of riboregulators that synchronize metabolic and virulence pathways in bacterial infection.

Lambda Red-mediated Recombineering in the Attaching and Effacing Pathogen Escherichia albertii

Background

The ability to introduce site-specific mutations in bacterial pathogens is essential towards understanding their molecular mechanisms of pathogenicity. This has been greatly facilitated by the genetic engineering technique of recombineering. In recombineering, linear double- or single-stranded DNA molecules with two terminal homology arms are electroporated into hyperrecombinogenic bacteria that express a phage-encoded recombinase. The recombinase catalyzes the replacement of the endogenous allele with the exogenous allele to generate selectable or screenable recombinants. In particular, lambda red recombinase has been instrumental in engineering mutations to characterize the virulence arsenal of the attaching and effacing (A/E) pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Citrobacter rodentium. Escherichia albertii is another member of this taxon; however, the virulence of E. albertii remains cryptic despite accumulating evidence that E. albertii is an emerging pathogen. Multiple retrospective studies have reported that a substantial number of EPEC and EHEC isolates (~15 %) that were previously incriminated in human outbreaks actually belong to the E. albertii lineage. Thus, there is increased urgency to reliably identify and rapidly engineer mutations in E. albertii to systematically characterize its virulence determinants. To the best of our knowledge not a single chromosomal gene has been altered by targeted mutagenesis in E. albertii since it was first isolated almost 25 years ago. This is disconcerting because an E. albertii outbreak could cause significant morbidity and mortality owing to our inadequate understanding of its virulence program.

Results

In this report we describe a modified lambda red recombineering protocol to mutagenize E. albertii. As proof of principle, we successfully deleted three distinct virulence-associated genetic loci – ler, grlRA, and hfq – and replaced each wild type allele by a mutant allele with an encodable drug resistance cassette bracketed by FRT sites. Subsequently, the FRT-site flanked drug resistance marker was evicted by FLP-dependent site-specific recombination to generate excisants containing a solitary FRT site.

Conclusions

Our protocol will enable researchers to construct marked and unmarked genome-wide mutations in E. albertii, which, in turn, will illuminate its molecular mechanisms of pathogenicity and aid in developing appropriate preventative and therapeutic approaches to combat E. albertii outbreaks.

Investigating the Role of the Host Multidrug Resistance Associated Protein Transporter Family in Burkholderia cepacia Complex Pathogenicity Using a Caenorhabditis elegans Infection Model

This study investigated the relationship between host efflux system of the non-vertebrate nematode Caenorhabditis elegans and Burkholderia cepacia complex (Bcc) strain virulence. This is the first comprehensive effort to profile host-transporters within the context of Bcc infection. With this aim, two different toxicity tests were performed: a slow killing assay that monitors mortality of the host by intestinal colonization and a fast killing assay that assesses production of toxins. A Virulence Ranking scheme was defined, that expressed the toxicity of the Bcc panel members, based on the percentage of surviving worms. According to this ranking the 18 Bcc strains were divided in 4 distinct groups. Only the Cystic Fibrosis isolated strains possessed profound nematode killing ability to accumulate in worms’ intestines. For the transporter analysis a complete set of isogenic nematode single Multidrug Resistance associated Protein (MRP) efflux mutants and a number of efflux inhibitors were interrogated in the host toxicity assays. The Bcc pathogenicity profile of the 7 isogenic C. elegans MRP knock-out strains functionality was classified in two distinct groups. Disabling host transporters enhanced nematode mortality more than 50% in 5 out of 7 mutants when compared to wild type. In particular mrp-2 was the most susceptible phenotype with increased mortality for 13 out 18 Bcc strains, whereas mrp-3 and mrp-4 knock-outs had lower mortality rates, suggesting a different role in toxin-substrate recognition. The use of MRP efflux inhibitors in the assays resulted in substantially increased (>40% on average) mortality of wild-type worms.

Regulation of bacterial virulence by Csr (Rsm) systems

Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5' untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.

Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain

This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.

Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community

BACKGROUND

Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the colicin operon and thus influence antibiotic-mediated community dynamics.

RESULTS

Here, we investigate the community dynamics of colicin-producing, -sensitive, and -resistant/non-producer E. coli strains that colonize a microfabricated spatially-structured habitat. Nutrients are found to strongly influence community dynamics: when growing on amino acids and peptides, colicin-mediated competition is intense and the three strains do not coexist unless spatially separated at large scales (millimeters). Surprisingly, when growing on sugars, colicin-mediated competition is minimal and the three strains coexist at the micrometer scale. Carbon storage regulator A (CsrA) is found to play a key role in translating the type of nutrients into the observed community dynamics by controlling colicin release. We demonstrate that by mitigating lysis, CsrA shapes the community dynamics and determines whether the three strains coexist. Indeed, a mutant producer that is unable to suppress colicin release, causes the collapse of biodiversity in media that would otherwise support co-localized growth of the three strains.

CONCLUSIONS

Our results show how the environmental regulation of an antagonistic trait shapes community dynamics. We demonstrate that nutrient-responsive regulation of colicin release by CsrA, determines whether colicin producer, resistant non-producer, and sensitive strains coexist at small spatial scales, or whether the sensitive strain is eradicated. This study highlights how molecular-level regulatory mechanisms that govern interference competition give rise to community-level biodiversity patterns.

Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan

A transcriptional attenuation mechanism regulates expression of the bacterial tnaCAB operon. This mechanism requires ribosomal arrest induced by the regulatory nascent TnaC peptide in response to free L-tryptophan (L-Trp). In this study we demonstrate, using genetic and biochemical analyses, that in Escherichia coli, TnaC residue I19 and 23S rRNA nucleotide A2058 are essential for the ribosome's ability to sense free L-Trp. We show that the mutational change A2058U in 23S rRNA reduces the concentration dependence of L-Trp-mediated tna operon induction, whereas the TnaC I19L change suppresses this phenotype, restoring the sensitivity of the translating A2058U mutant ribosome to free L-Trp. These findings suggest that interactions between TnaC residue I19 and 23S rRNA nucleotide A2058 contribute to the creation of a regulatory L-Trp binding site within the translating ribosome.

Indole production by the tryptophanase TnaA in Escherichia coli is determined by the amount of exogenous tryptophan

The signalling molecule indole occurs in significant amounts in the mammalian intestinal tract and regulates diverse microbial processes, including bacterial motility, biofilm formation, antibiotic resistance and host cell invasion. In Escherichia coli, the enzyme tryptophanase (TnaA) produces indole from tryptophan, but it is not clear what determines how much indole E. coli can produce and excrete, making it difficult to interpret experiments that investigate the biological effects of indole at high concentrations. Here, we report that the final yield of indole depends directly, and perhaps solely, on the amount of exogenous tryptophan. When supplied with a range of tryptophan concentrations, E. coli converted this amino acid into an equal amount of indole, up to almost 5 mM, an amount well within the range of the highest concentrations so far examined for their physiological effects. Indole production relied heavily on the tryptophan-specific transporter TnaB, even though the alternative transporters AroP and Mtr could import sufficient tryptophan to induce tnaA expression. This TnaB requirement proceeded via tryptophan transport and was not caused by activation of TnaA itself. Bacterial growth was unaffected by the presence of TnaA in the absence of exogenous tryptophan, suggesting that the enzyme does not hydrolyse significant quantities of the internal anabolic amino acid pool. The results imply that E. coli synthesizes TnaA and TnaB mainly, or solely, for the purpose of converting exogenous tryptophan into indole, under conditions and for signalling purposes that remain to be fully elucidated.

In vitro and in vivo model systems for studying enteropathogenic Escherichia coli infections

Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) belong to a group of bacteria known as attaching and effacing (A/E) pathogens that cause disease by adhering to the lumenal surfaces of their host's intestinal epithelium. EPEC and EHEC are major causes of infectious diarrhea that result in significant childhood morbidity and mortality worldwide. Recent advances in in vitro and in vivo modeling of these pathogens have contributed to our knowledge of how EPEC and EHEC attach to host cells and subvert host-cell signaling pathways to promote infection and cause disease. A more detailed understanding of how these pathogenic microbes infect their hosts and how the host responds to infection could ultimately lead to new therapeutic strategies to help control these significant enteric pathogens.

Evaluating the pathogenic potential of environmental Escherichia coli by using the Caenorhabditis elegans infection model

The detection and abundance of Escherichia coli in water is used to monitor and mandate the quality of drinking and recreational water. Distinguishing commensal waterborne E. coli isolates from those that cause diarrhea or extraintestinal disease in humans is important for quantifying human health risk. A DNA microarray was used to evaluate the distribution of virulence genes in 148 E. coli environmental isolates from a watershed in eastern Ontario, Canada, and in eight clinical isolates. Their pathogenic potential was evaluated with Caenorhabditis elegans, and the concordance between the bioassay result and the pathotype deduced by genotyping was explored. Isolates identified as potentially pathogenic on the basis of their complement of virulence genes were significantly more likely to be pathogenic to C. elegans than those determined to be potentially nonpathogenic. A number of isolates that were identified as nonpathogenic on the basis of genotyping were pathogenic in the infection assay, suggesting that genotyping did not capture all potentially pathogenic types. The detection of the adhesin-encoding genes sfaD, focA, and focG, which encode adhesins; of iroN2, which encodes a siderophore receptor; of pic, which encodes an autotransporter protein; and of b1432, which encodes a putative transposase, was significantly associated with pathogenicity in the infection assay. Overall, E. coli isolates predicted to be pathogenic on the basis of genotyping were indeed so in the C. elegans infection assay. Furthermore, the detection of C. elegans-infective environmental isolates predicted to be nonpathogenic on the basis of genotyping suggests that there are hitherto-unrecognized virulence factors or combinations thereof that are important in the establishment of infection.

A family of indoles regulate virulence and Shiga toxin production in pathogenic E. coli

Enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC) and enteroaggregative E. coli (EAEC) are intestinal pathogens that cause food and water-borne disease in humans. Using biochemical methods and NMR-based comparative metabolomics in conjunction with the nematode Caenorhabditis elegans, we developed a bioassay to identify secreted small molecules produced by these pathogens. We identified indole, indole-3-carboxaldehyde (ICA), and indole-3-acetic acid (IAA), as factors that only in combination are sufficient to kill C. elegans. Importantly, although lethal to C. elegans, these molecules downregulate several bacterial processes important for pathogenesis in mammals. These include motility, biofilm formation and production of Shiga toxins. Some pathogenic E. coli strains are known to contain a Locus of Enterocyte Effacement (LEE), which encodes virulence factors that cause “attaching and effacing” (A/E) lesions in mammals, including formation of actin pedestals. We found that these indole derivatives also downregulate production of LEE virulence factors and inhibit pedestal formation on mammalian cells. Finally, upon oral administration, ICA inhibited virulence and promoted survival in a lethal mouse infection model. In summary, the C. elegans model in conjunction with metabolomics has facilitated identification of a family of indole derivatives that broadly regulate physiology in E. coli, and virulence in pathogenic strains. These molecules may enable development of new therapeutics that interfere with bacterial small-molecule signaling.