Identifying New Variables During Infection: Proximity to the Host Epithelium and Epigenetic Programs Alter the Expression of Virulence Factors in Vibrio Cholerae

In the life cycles of facultative pathogens, the ability to transition between the external environment and the host is key to survival. These transitions are accompanied by alterations in transcriptional and proteomic profiles (Merrell et al., 2002; Schild et al., 2007; LaRocque et al., 2008). Numerous studies have investigated the changes in gene expression that occur during these environmental shifts and have identified factors that are important for survival and growth in the two disparate settings. Less is known about the changes in gene expression that result as a pathogen transitions between microenvironments within the host or even the number of such transitions that occur. A single organ or tissue may in fact constitute a wide array of strikingly different environmental conditions for an invading pathogen

The Vibrio cholerae Pst2 Phosphate Transport System Is Upregulated in Biofilms and Contributes to Biofilm-Induced Hyperinfectivity

ABSTRACT Vibrio cholerae is the causative agent of the deadly diarrheal disease cholera. As part of its life cycle, V. cholerae persists in marine environments, where it forms surface-attached communities commonly described as biofilms. Evidence indicates that these biofilms constitute the infectious form of the pathogen during outbreaks. Previous work has shown that biofilm-derived V. cholerae cells, even when fully dispersed from the biofilm matrix, are vastly more infectious than planktonic (free-living) cells. Here, we sought to identify factors that contribute to biofilm-induced hyperinfectivity in V. cholerae , and we present evidence for one aspect of the molecular basis of this phenotype. We identified proteins upregulated during growth in biofilms and determined their contributions to the hyperinfectivity phenotype. We found that PstS2, the periplasmic component of the Pst2 phosphate uptake system, was enriched in biofilms. Another gene in the pst2 locus was transcriptionally upregulated in biofilms. Using the infant mouse model, we found that mutation of two pst2 components resulted in impaired colonization. Importantly, deletion of the Pst2 inner membrane complex caused a greater colonization defect after growth in a biofilm compared to shaking culture. Based on these data, we propose that V. cholerae cells in biofilms upregulate the Pst2 system and therefore gain an advantage upon entry into the host. Further characterization of factors contributing to biofilm-induced hyperinfectivity in V. cholerae will improve our understanding of the transmission of the bacteria from natural aquatic habitats to the human host

On Estimating Recommendation Evaluation Metrics under Sampling

Since the recent study (Krichene and Rendle 2020) done by Krichene and Rendle on the sampling-based top-k evaluation metric for recommendation, there has been a lot of debates on the validity of using sampling to evaluate recommendation algorithms. Though their work and the recent work (Li et al.2020) have proposed some basic approaches for mapping the sampling-based metrics to their global counterparts which rank the entire set of items, there is still a lack of understanding and consensus on how sampling should be used for recommendation evaluation. The proposed approaches either are rather uninformative (linking sampling to metric evaluation) or can only work on simple metrics, such as Recall/Precision (Krichene and Rendle 2020; Li et al. 2020). In this paper, we introduce a new research problem on learning the empirical rank distribution, and a new approach based on the estimated rank distribution, to estimate the top-k metrics. Since this question is closely related to the underlying mechanism of sampling for recommendation, tackling it can help better understand the power of sampling and can help resolve the questions of if and how should we use sampling for evaluating recommendation. We introduce two approaches based on MLE (MaximalLikelihood Estimation) and its weighted variants, and ME(Maximal Entropy) principals to recover the empirical rank distribution, and then utilize them for metrics estimation. The experimental results show the advantages of using the new approaches for evaluating recommendation algorithms based on top-k metrics

A systematic analysis of the in vitro and in vivo functions of the HD-GYP domain proteins of Vibrio cholerae

Abstract Background The second messenger cyclic diguanylate (c-di-GMP) plays a central role in bacterial adaptation to extracellular stimuli, controlling processes such as motility, biofilm development, cell development and, in some pathogens, virulence. The intracellular level of c-di-GMP is controlled by the complementary activities of diguanylate cyclases containing a GGDEF domain and two classes of c-di-GMP phosphodiesterases containing an EAL or HD-GYP hydrolytic domain. Compared to the GGDEF and EAL domains, the functions of HD-GYP domain family proteins are poorly characterized. The human diarrheal pathogen Vibrio cholerae encodes nine putative HD-GYP domain proteins. To determine the contributions of HD-GYP domain proteins to c-di-GMP signaling in V. cholerae, we systematically analyzed the enzymatic functionality of each protein and their involvement in processes known to be regulated by c-di-GMP: motility, biofilm development and virulence. Results Complementary in vitro and in vivo experiments showed that four HD-GYP domain proteins are active c-di-GMP phosphodiesterases: VC1295, VC1348, VCA0210 and VCA0681. Mutation of individual HD-GYP domain genes, as well as combinatorial mutations of multiple HD-GYP domain genes, had no effect on motility or biofilm formation of V. cholerae under the conditions tested. Furthermore, no single HD-GYP domain gene affected intestinal colonization by V. cholerae in an infant mouse model. However, inactivation of multiple HD-GYP domain genes, including the four encoding functional phosphodiesterases, significantly attenuated colonization. Conclusions These results indicate that the HD-GYP family of c-di-GMP phosphodiesterases impacts signaling by this second messenger during infection. Altogether, this work greatly furthers the understanding of this important family of c-di-GMP metabolic enzymes and demonstrates a role for HD-GYP domain proteins in the virulence of V. cholerae

Heat-Labile Enterotoxin: Beyond GM1 Binding

Enterotoxigenic Escherichia coli (ETEC) is a significant source of morbidity and mortality worldwide. One major virulence factor released by ETEC is the heat-labile enterotoxin LT, which is structurally and functionally similar to cholera toxin. LT consists of five B subunits carrying a single catalytically active A subunit. LTB binds the monosialoganglioside GM1, the toxin’s host receptor, but interactions with A-type blood sugars and E. coli lipopolysaccharide have also been identified within the past decade. Here, we review the regulation, assembly, and binding properties of the LT B-subunit pentamer and discuss the possible roles of its numerous molecular interactions

Secretion and Lipopolysaccharide Binding of Heat-Labile Enterotoxin

<p>Enterotoxigenic <italic>Escherichia coli</italic> (ETEC) is a leading cause of morbidity and mortality worldwide. The causative agent of traveler's diarrhea, ETEC is often associated with cholera-like disease, especially in developing countries. One major virulence factor released by ETEC is the heat-labile enterotoxin LT, which upsets the balance of electrolytes in the intestine. LT is highly similar to cholera toxin (CT) produced by <italic>Vibrio cholerae</italic>, both in structure and function. The toxin consists of a single catalytically active A subunit and a ring of five B subunits mediating its binding and secretion. Previous work from our lab has shown that, after export by the type II secretion (T2S) system, LT associates with lipopolysaccharide (LPS) on the bacterial surface. However, little is known about what identifies LT as a T2S substrate, and the portion of the toxin that mediates LPS binding has not previously been defined. Site-directed mutagenesis of residues in a peripheral sugar binding pocket of the toxin was performed, revealing mutations that affect its binding to LPS, as determined by an in vitro cell surface binding assay. One binding mutant, which is expressed and secreted at wild-type levels from ETEC, holds particular promise for further studies of the role of the LT-LPS interaction. Interestingly, some mutations made affected the secretion of the toxin as detected by ganglioside-binding ELISAs of cell-free supernatant, and several mutations affected both secretion and LPS binding. These mutations identify residues of the toxin that are involved in its secretion and association with LPS. In addition, we introduced mutations affecting the secretion of LT into CT, due to the high similarity between the two toxins. While one mutation affects the secretion of each, other mutations affect one toxin but not the other. These results demonstrate that LT and CT are recognized in different ways during T2S. Combined with an analysis of the effects of secretion mutations on the stability of the toxin, the results described here highlight the delicate balance between structure and function of the LT B subunit.</p>Dissertatio

Specificity of the Type II Secretion Systems of Enterotoxigenic Escherichia coli and Vibrio cholerae for Heat-Labile Enterotoxin and Cholera Toxin▿

The Gram-negative type II secretion (T2S) system is a multiprotein complex mediating the release of virulence factors from a number of pathogens. While an understanding of the function of T2S components is emerging, little is known about what identifies substrates for export. To investigate T2S substrate recognition, we compared mutations affecting the secretion of two highly homologous substrates: heat-labile enterotoxin (LT) from enterotoxigenic Escherichia coli (ETEC) and cholera toxin (CT) from Vibrio cholerae. Each toxin consists of one enzymatic A subunit and a ring of five B subunits mediating the toxin's secretion. Here, we report two mutations in LT's B subunit (LTB) that reduce its secretion from ETEC without global effects on the toxin. The Q3K mutation reduced levels of secreted LT by half, and as with CT (T. D. Connell, D. J. Metzger, M. Wang, M. G. Jobling, and R. K. Holmes, Infect. Immun. 63:4091-4098, 1995), the E11K mutation impaired LT secretion. Results in vitro and in vivo show that these mutants are not degraded more readily than wild-type LT. The Q3K mutation did not significantly affect CT B subunit (CTB) secretion from V. cholerae, and the E11A mutation altered LT and CTB secretion to various extents, indicating that these toxins are identified as secretion substrates in different ways. The levels of mutant LTB expressed in V. cholerae were low or undetectable, but each CTB mutant expressed and secreted at wild-type levels in ETEC. Therefore, ETEC's T2S system seems to accommodate mutations in CTB that impair the secretion of LTB. Our results highlight the exquisitely fine-tuned relationship between T2S substrates and their coordinate secretion machineries in different bacterial species