Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis.

Commensal bacteria are critically involved in the establishment of tolerance against inflammatory challenges, the molecular mechanisms of which are just being uncovered. All kingdoms of life produce aminoacyl-tRNA synthetases (ARSs). Thus far, the non-translational roles of ARSs have largely been reported in eukaryotes. Here, we report that the threonyl-tRNA synthetase (AmTARS) of the gut-associated bacterium Akkermansia muciniphila is secreted and functions to monitor and modulate immune homeostasis. Secreted AmTARS triggers M2 macrophage polarization and orchestrates the production of anti-inflammatory IL-10 via its unique, evolutionary-acquired regions, which mediates specific interactions with TLR2. This interaction activates the MAPK and PI3K/AKT signaling pathways, which converge on CREB, leading to an efficient production of IL-10 and suppression of the central inflammatory mediator NF-κB. AmTARS restores IL-10-positive macrophages, increases IL-10 levels in the serum, and attenuates the pathological effects in colitis mice. Thus, commensal tRNA synthetases can act as intrinsic mediators that maintain homeostasis.

Two novel genes identified by large-scale transcriptomic analysis are essential for biofilm and rugose colony development of Vibrio vulnificus.

Many pathogenic bacteria form biofilms to survive under environmental stresses and host immune defenses. Differential expression (DE) analysis of the genes in biofilm and planktonic cells under a single condition, however, has limitations to identify the genes essential for biofilm formation. Independent component analysis (ICA), a machine learning algorithm, was adopted to comprehensively identify the biofilm genes of Vibrio vulnificus, a fulminating human pathogen, in this study. ICA analyzed the large-scale transcriptome data of V. vulnificus cells under various biofilm and planktonic conditions and then identified a total of 72 sets of independently co-regulated genes, iModulons. Among the three iModulons specifically activated in biofilm cells, BrpT-iModulon mainly consisted of known genes of the regulon of BrpT, a transcriptional regulator controlling biofilm formation of V. vulnificus. Interestingly, the BrpT-iModulon additionally contained two novel genes, VV1_3061 and VV2_1694, designated as cabH and brpN, respectively. cabH and brpN were shared in other Vibrio species and not yet identified by DE analyses. Genetic and biochemical analyses revealed that cabH and brpN are directly up-regulated by BrpT. The deletion of cabH and brpN impaired the robust biofilm and rugose colony formation. CabH, structurally similar to the previously known calcium-binding matrix protein CabA, was essential for attachment to the surface. BrpN, carrying an acyltransferase-3 domain as observed in BrpL, played an important role in exopolysaccharide production. Altogether, ICA identified two novel genes, cabH and brpN, which are regulated by BrpT and essential for the development of robust biofilms and rugose colonies of V. vulnificus.

A Master Regulator BrpR Coordinates the Expression of Multiple Loci for Robust Biofilm and Rugose Colony Development in Vibrio vulnificus.

Vibrio vulnificus, a fulminating human pathogen, forms biofilms to enhance its survival in nature and pathogenicity during host infection. BrpR is the transcriptional regulator governing robust biofilm and rugose colony formation in V. vulnificus, but little is known about both the direct regulon of BrpR and the role of BrpR in regulation of downstream genes. In this study, transcript analyses revealed that BrpR is highly expressed and thus strongly regulates the downstream gene in the stationary and elevated cyclic di-GMP conditions. Transcriptome analyses discovered the genes, whose expression is affected by BrpR but not by the downstream regulator BrpT. Two unnamed adjacent genes (VV2_1626-1627) were newly identified among the BrpR regulon and designated as brpL and brpG in this study. Genetic analyses showed that the deletion of brpL and brpG impairs the biofilm and rugose colony formation, indicating that brpLG plays a crucial role in the development of BrpR-regulated biofilm phenotypes. Comparison of the colony morphology and exopolysaccharide (EPS) production suggested that although the genetic location and regulation of brpLG are distinct from the brp locus, brpABCDFHIJK (VV2_1574-1582), brpLG is also responsible for the robust EPS production together with the brp locus genes. Electrophoretic mobility shift assays and DNase I protection assays demonstrated that BrpR regulates the expression of downstream genes in distinct loci by directly binding to their upstream regions, revealing a palindromic binding sequence. Altogether, this study suggests that BrpR is a master regulator coordinating the expression of multiple loci responsible for EPS production and thus, contributing to the robust biofilm and rugose colony formation of V. vulnificus.

Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model.

Instead of conventional serotyping and virulence gene combination methods, methods have been developed to evaluate the pathogenic potential of newly emerging pathogens. Among them, the machine learning (ML)-based method using whole-genome sequencing (WGS) data are getting attention because of the recent advances in ML algorithms and sequencing technologies. Here, we developed various ML models to predict the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) isolates using their WGS data. The input dataset for the ML models was generated using distinct gene repertoires from positive (pathogenic) and negative (nonpathogenic) control groups in which each STEC isolate was designated based on the source attribution, the relative risk potential of the isolation sources. Among the various ML models examined, a model using the support vector machine (SVM) algorithm, the SVM model, discriminated between the two control groups most accurately. The SVM model successfully predicted the pathogenicity of the isolates from the major sources of STEC outbreaks, the isolates with the history of outbreaks, and the isolates that cannot be assessed by conventional methods. Furthermore, the SVM model effectively differentiated the pathogenic potentials of the isolates at a finer resolution. Permutation importance analyses of the input dataset further revealed the genes important for the estimation, proposing the genes potentially essential for the pathogenicity of STEC. Altogether, these results suggest that the SVM model is a more reliable and broadly applicable method to evaluate the pathogenic potential of STEC isolates compared with conventional methods.

A MARTX Toxin rtxA Gene Is Controlled by Host Environmental Signals through a CRP-Coordinated Regulatory Network in Vibrio vulnificus.

A multifunctional autoprocessing repeats-in-toxin (MARTX) toxin plays an essential role in the virulence of many pathogens, including a fulminating human pathogen Vibrio vulnificus H-NS and HlyU repress and derepress expression of the MARTX toxin gene rtxA in V. vulnificus, respectively. However, little is known about other regulatory proteins and environmental signals involved in rtxA regulation. In this study, we found that a leucine-responsive regulatory protein (Lrp) activates rtxA by binding directly and specifically to the rtxA promoter, P rtxA Phased hypersensitivity resulting from DNase I cleavage of the P rtxA regulatory region suggests that Lrp probably induces DNA bending in P rtxA Lrp activates P rtxA independently of H-NS and HlyU, and leucine inhibits Lrp binding to P rtxA and reduces the Lrp-mediated activation. Furthermore, a cyclic AMP receptor protein (CRP) represses P rtxA , and exogenous glucose relieves the CRP-mediated repression. Biochemical and mutational analyses demonstrated that CRP binds directly and specifically to the upstream region of P rtxA , which presumably alters the DNA conformation in P rtxA and thus represses rtxA Moreover, CRP represses expression of lrp and hlyU by binding directly to their upstream regions, forming coherent feed-forward loops with Lrp and HlyU. In conclusion, expression of rtxA is controlled by a regulatory network comprising CRP, Lrp, H-NS, and HlyU in response to changes in host environmental signals such as leucine and glucose. This collaborative regulation enables the elaborate expression of rtxA, thereby enhancing the fitness and pathogenesis of V. vulnificus during the course of infection.IMPORTANCE A MARTX toxin, RtxA, is an essential virulence factor of many pathogens, including Vibrio species. H-NS and HlyU repress and derepress, respectively, rtxA expression of a life-threatening pathogen, Vibrio vulnificus We found that Lrp directly activates rtxA independently of H-NS and HlyU, and leucine inhibits the Lrp-mediated activation of rtxA Furthermore, we demonstrated that CRP represses rtxA but derepresses in the presence of exogenous glucose. CRP represses rtxA not only directly by binding to upstream of rtxA but also indirectly by repressing lrp and hlyU This is the first report of a regulatory network comprising CRP, Lrp, H-NS, and HlyU, which coordinates the rtxA expression in response to environmental signals such as leucine and glucose during infection. This elaborate regulatory network will enhance the fitness of V. vulnificus and contribute to its successful infection within the host.

A Regulatory Network Controls cabABC Expression Leading to Biofilm and Rugose Colony Development in Vibrio vulnificus.

Biofilms provide bacteria with protection from environmental stresses and host immune defenses. The pathogenic marine bacterium Vibrio vulnificus forms biofilms and colonizes environmental niches such as oysters. The cabABC operon encodes an extracellular matrix protein CabA and the corresponding type I secretion system, which are essential for biofilm and rugose colony development of V. vulnificus. In this study, molecular biological analyses revealed the roles of three transcriptional regulators BrpR, BrpT, and BrpS in the regulatory pathway for the cabABC operon. BrpR induces brpT and BrpT in turn activates the cabABC operon in a sequential cascade, contributing to development of robust biofilm structures. BrpT also activates brpS, but BrpS represses brpT, constituting a negative feedback loop that stabilizes brpT expression. BrpT and BrpS directly bind to specific sequences upstream of cabA, and they constitute a feedforward loop in which BrpT induces brpS and together with BrpS activates cabABC, leading to precise regulation of cabABC expression. Accordingly, BrpS as well as BrpT plays a crucial role in complete development of rugose colonies. This elaborate network of three transcriptional regulators BrpR, BrpT, and BrpS thus tightly controls cabABC regulation, and contributes to successful development of robust biofilms and rugose colonies in V. vulnificus.