The UvrY response regulator of the BarA-UvrY two-component system contributes to Yersinia ruckeri infection of rainbow trout (Oncorhynchus mykiss)

Pan-genome survey of the fish pathogen Yersinia ruckeri links accessory- and amplified genes to virulence

While both virulent and putatively avirulent Yersinia ruckeri strains exist in aquaculture environments, the relationship between the distribution of virulence-associated factors and de facto pathogenicity in fish remains poorly understood. Pan-genome analysis of 18 complete genomes, representing established virulent and putatively avirulent lineages of Y. ruckeri, revealed the presence of a number of accessory genetic determinants. Further investigation of 68 draft genome assemblies revealed that the distribution of certain putative virulence factors correlated well with virulence and host-specificity. The inverse-autotransporter invasin locus yrIlm was, however, the only gene present in all virulent strains, while absent in lineages regarded as avirulent. Strains known to be associated with significant mortalities in salmonid aquaculture display a combination of serotype O1-LPS and yrIlm, with the well-documented highly virulent lineages, represented by MLVA clonal complexes 1 and 2, displaying duplication of the yrIlm locus. Duplication of the yrIlm locus was further found to have evolved over time in clonal complex 1, where some modern, highly virulent isolates display up to three copies.

Dual RNA-Seq of Trunk Kidneys Extracted From Channel Catfish Infected With Yersinia ruckeri Reveals Novel Insights Into Host-Pathogen Interactions

Host-pathogen intectarions are complex, involving large dynamic changes in gene expression through the process of infection. These interactions are essential for understanding anti-infective immunity as well as pathogenesis. In this study, the host-pathogen interaction was analyzed using a model of acute infection where channel catfish were infected with Yersinia ruckeri. The infected fish showed signs of body surface hyperemia as well as hyperemia and swelling in the trunk kidney. Double RNA sequencing was performed on trunk kidneys extracted from infected channel catfish and transcriptome data was compared with data from uninfected trunk kidneys. Results revealed that the host-pathogen interaction was dynamically regulated and that the host-pathogen transcriptome fluctuated during infection. More specifically, these data revealed that the expression levels of immune genes involved in Cytokine-cytokine receptor interactions, the NF-kappa B signaling pathway, the JAK-STAT signaling pathway, Toll-like receptor signaling and other immune-related pathways were significantly upregulated. Y. ruckeri mainly promote pathogenesis through the flagellum gene fliC in channel catfish. The weighted gene co-expression network analysis (WGCNA) R package was used to reveal that the infection of catfish is closely related to metabolic pathways. This study contributes to the understanding of the host-pathogen interaction between channel catfish and Y. ruckeri, more specifically how catfish respond to infection through a transcriptional perspective and how this infection leads to enteric red mouth disease (ERM) in these fish.

Yersinia ruckeri strain SC09 disrupts proinflammatory activation via Toll/IL-1 receptor-containing protein STIR-3

Virulent pathogenic microorganisms often enhance their infectivity through immune evasion mechanisms. Our research on the integrative and conjugative element (ICE(r2)) of the virulent fish pathogen Yersinia ruckeri SC09 led to the identification of genes related to immune evasion (designated stir-1, stir-2, stir-3 and stir-4), among which stir-1 and stir-2 were determined as the key contributors to bacterial toxicity and immune evasion. Here, we further examined the ability of stir-3 to mediate immune evasion based on detailed bioinformatic analysis of ICE(r2) from Y. ruckeri SC09. Interactions among the translated STIR-1, STIR-2, STIR-3 and STIR-4 proteins in the secretory process were additionally explored. STIR-3 was positively correlated with bacterial toxicity and inhibited host toll-like receptor (TLR) signaling by interacting with MyD88, thereby facilitating bacterial survival in host cells. Importantly, our data showed co-secretion of STIR-1, STIR-2 and STIR-3 as a complex, with secretion failure occurring in the absence of any one of these proteins. While stir-1, stir-2, stir-3 and stir-4 genes werespecific to Y. ruckeri SC09, the ICE(r2) region where these genes were located is a mobile component widely distributed in bacteria. Therefore, the potential transmission risk of these immune evasion genes requires further research attention.

TcpA, a novel Yersinia ruckeri TIR-containing virulent protein mediates immune evasion by targeting MyD88 adaptors

TIR domain-containing protein is an important member for some bacterial pathogens to subvert host defenses. Here we described a fish virulent Yersinia ruckeri SC09 strain that interfered directly with Toll-like receptor (TLR) function by a TIR-containing protein. Firstly, the novel TIR-containing protein was identified by bioinformatics analysis and named as TcpA. Secondly, the toxic effects of TcpA in fish was demonstrated in vivo challenge experiments through knockout mutant and complement mutant of tcpA gene. Thirdly, The study in vitro revealed that TcpA could down-regulate the expression and secretion of IL-6, IL-1β and TNF-α. Finally, we demonstrated that TcpA could inhibit the TLR signaling pathway through interaction with myeloid differentiation factor 88 (MyD88) in experiments such as NF-κB dependent luciferase reporter system, co-immunoprecipitation, GST pull-down and yeast two-hybrid. The study revealed that TcpA was essential for virulence and was able to interact with the TIR adaptor protein MyD88 and inhibit the pre-inflammatory signal of immune cells and promote the intracellular survival of pathogenic Yersinia ruckeri SC09 strain. In conclusion, our results showed that TcpA acted as a new virulence factor in Y. ruckeri could suppress innate immune response and increase virulence by inhibiting TLR and MyD88-mediated specific signaling, highlighting a novel strategy for innate immune evasion in bacteria.

Overcoming Fish Defences: The Virulence Factors of Yersinia ruckeri

Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the major serotypes of Y. ruckeri but are not effective in all cases. Despite the economic importance of enteric redmouth disease, a detailed molecular understanding of the disease is lacking. A considerable number of mostly omics-based studies have been performed in recent years to identify genes related to Y. ruckeri virulence. This review summarizes the knowledge on Y. ruckeri virulence factors. Understanding the molecular pathogenicity of Y. ruckeri will aid in developing more efficient vaccines and antimicrobial compounds directed against enteric redmouth disease.

A Yersinia ruckeri TIR Domain-Containing Protein (STIR-2) Mediates Immune Evasion by Targeting the MyD88 Adaptor

TIR domain-containing proteins are essential for bacterial pathogens to subvert host defenses. This study describes a fish pathogen, Yersinia ruckeri SC09 strain, with a novel TIR domain-containing protein (STIR-2) that affects Toll-like receptor (TLR) function. STIR-2 was identified in Y. ruckeri by bioinformatics analysis. The toxic effects of this gene on fish were determined by in vivo challenge experiments in knockout mutants and complement mutants of the stir-2 gene. In vitro, STIR-2 downregulated the expression and secretion of IL-6, IL-1β, and TNF-α. Furthermore, the results of NF-κB-dependent luciferase reporter system, co-immunoprecipitation, GST pull-down assays, and yeast two-hybrid assay indicated that STIR-2 inhibited the TLR signaling pathway by interacting with myeloid differentiation factor 88 (MyD88). In addition, STIR-2 promoted the intracellular survival of pathogenic Yersinia ruckeri SC09 strain by binding to the TIR adaptor protein MyD88 and inhibiting the pre-inflammatory signal of immune cells. These results showed that STIR-2 increased virulence in Y. ruckeri and suppressed the innate immune response by inhibiting TLR and MyD88-mediated signaling, serving as a novel strategy for innate immune evasion.

The Infection Process of Yersinia ruckeri: Reviewing the Pieces of the Jigsaw Puzzle

Finding the keys to understanding the infectious process of Yersinia ruckeri was not a priority for many years due to the prompt development of an effective biotype 1 vaccine which was used mainly in Europe and USA. However, the gradual emergence of outbreaks in vaccinated fish, which have been reported since 2003, has awakened interest in the mechanism of virulence in this pathogen. Thus, during the last two decades, a large number of studies have considerably enriched our knowledge of many aspects of the pathogen and its interaction with the host. By means of both conventional and a variety of novel strategies, such as cell GFP tagging, bioluminescence imaging and optical projection tomography, it has been possible to determine three putative Y. ruckeri infection routes, the main point of entry for the bacterium being the gill lamellae. Moreover, a wide range of potential virulence factors have been highlighted by specific gene mutagenesis strategies or genome-wide transposon/plasmid insertion-based screening approaches, such us in vivo expression technology (IVET) and signature tagged mutagenesis (STM). Finally, recent proteomic and whole genomic analyses have allowed many of the genes and systems that are potentially implicated in the organism's pathogenicity and its adaptation to the host environmental conditions to be elucidated. Altogether, these studies contribute to a better understanding of the infectious process of Y. ruckeri in fish, which is crucial for the development of more effective strategies for preventing or treating enteric redmouth disease (ERM).

Global proteomic profiling of Yersinia ruckeri strains

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) of salmonids. There is little information regarding the proteomics of Y. ruckeri. Herein, we perform whole protein identification and quantification of biotype 1 and biotype 2 strains of Y. ruckeri grown under standard culture conditions using a shotgun proteomic approach. Proteins were extracted, digested and peptides were separated by a nano liquid chromatography system and analyzed with a high-resolution hybrid triple quadrupole time of flight mass spectrometer coupled via a nano ESI interface. SWATH-MS technology and sophisticated statistical analyses were used to identify proteome differences among virulent and avirulent strains. GO annotation, subcellular localization, virulence proteins and antibiotic resistance ontology were predicted using bioinformatic tools. A total of 1395 proteins were identified in the whole cell of Y. ruckeri. These included proteases, chaperones, cell division proteins, outer membrane proteins, lipoproteins, receptors, ion binding proteins, transporters and catalytic proteins. In virulent strains, a total of 16 proteins were upregulated including anti-sigma regulatory factor, arginine deiminase, phosphate-binding protein PstS and superoxide dismutase Cu-Zu. Additionally, several virulence proteins were predicted such as Clp and Lon pro-teases, TolB, PPIases, PstS, PhoP and LuxR family transcriptional regulators. These putative virulence proteins might be used for development of novel targets for treatment of ERM in fish. Our study represents one of the first global proteomic reference profiles of Y. ruckeri and this data can be accessed via ProteomeXchange with identifier PXD005439. These proteomic profiles elucidate proteomic mechanisms, pathogenicity, host-interactions, antibiotic resistance ontology and localization of Y. ruckeri proteins.

Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism

Yersinia ruckeri is the etiologic agent of enteric red mouth disease (ERM), a severe fish disease prevailing in worldwide aquaculture industries. Here we report for the first time the complete genome of Y. ruckeri (Yersinia ruckeri) SC09, a highly virulent strain isolated from Ictalurus punctatus with severe septicemia. SC09 possesses a single chromosome of 3,923,491 base pairs, which contains 3651 predicted protein coding sequences (CDS), 19 rRNA genes, and 79 tRNA genes. Among the CDS, we have identified a Ysa locus containing genes encoding all the components of a type III secretion system (T3SS). Comparative analysis suggest that SC09-Ysa share extensive similarity in sequence, gene content, and gene arrangement with Salmonella enterica pathogenicity island 1 (SPI1) and chromosome-encoded T3SS from Yersinia enterocolitica biotype 1B. Furthermore, phylogenetic analysis shown that SC09-Ysa and SPI1-T3SS belong on the same branch of the phylogenetic tree. These results suggest that SC09-Ysa and SPI1-T3SS appear to mediate biological function to adapt to specific hosts with a similar niche, and both of them are likely to facilitate the development of an intracellular niche. In addition, our analysis also indicated that a substantial part of the SC09 genome might contribute to adaption in the intestinal microenvironment, including a number of proteins associated with aerobic or anaerobic respiration, signal transduction, and various stress reactions. Genomic analysis of the bacterium offered insights into the pathogenic mechanism associated with intracellular infection and intestinal survivability, which constitutes an important first step in understanding the pathogenesis of Y. ruckeri.

Yersinia ruckeri, the causative agent of enteric redmouth disease in fish

Enteric redmouth disease (ERM) is a serious septicemic bacterial disease of salmonid fish species. It is caused by Yersinia ruckeri, a Gram-negative rod-shaped enterobacterium. It has a wide host range, broad geographical distribution, and causes significant economic losses in the fish aquaculture industry. The disease gets its name from the subcutaneous hemorrhages, it can cause at the corners of the mouth and in gums and tongue. Other clinical signs include exophthalmia, darkening of the skin, splenomegaly and inflammation of the lower intestine with accumulation of thick yellow fluid. The bacterium enters the fish via the secondary gill lamellae and from there it spreads to the blood and internal organs. Y. ruckeri can be detected by conventional biochemical, serological and molecular methods. Its genome is 3.7 Mb with 3406–3530 coding sequences. Several important virulence factors of Y. ruckeri have been discovered, including haemolyin YhlA and metalloprotease Yrp1. Both non-specific and specific immune responses of fish during the course of Y. ruckeri infection have been well characterized. Several methods of vaccination have been developed for controlling both biotype 1 and biotype 2 Y. ruckeri strains in fish. This review summarizes the current state of knowledge regarding enteric redmouth disease and Y. ruckeri: diagnosis, genome, virulence factors, interaction with the host immune responses, and the development of vaccines against this pathogen.

The heat sensitive factor (HSF) of Yersinia ruckeri is produced by an alkyl sulphatase involved in sodium dodecyl sulphate (SDS) degradation but not in virulence

BACKGROUND

The heat sensitive factor (HSF) of the fish pathogen Yersinia ruckeri was previously identified as an unusual band on SDS-PAGE. According to this, Y. ruckeri strains were classified in HSF+ and HSF - in terms of the presence/absence of the factor. Experiments carried out by injection challenge with HSF + strains caused high mortalities in rainbow trout. In contrast, HSF - strains did not cause mortality. In conclusion, HSF appeared to be a relevant virulence factor in Y. ruckeri.

RESULTS

We report here the identification and study of the gene coding for the enzyme involved in the production of HSF. Culture medium containing SDS and Coomassie brilliant blue dye was used to screen a mini-Tn5 Km2 mutant library of Y. ruckeri 150. Blue colonies lacking a surrounding creamy deposit, a phenotype described in former studies as HSF - , were identified. DNA sequence analysis of a selected mutant revealed that this had a transposon interruption in a chromosome-located gene which codes for a heat sensitive alkyl sulphatase of 78.7 kDa (YraS; Yersinia ruckeri alkyl sulphatase) which is able to degrade SDS to 1-dodecanol. As it was expected, the introduction of the yraS gene into an HSF - strain turned this into HSF + . Surprisingly, although the protein allows Y. ruckeri to degrade SDS, the bacterium could not use this compound as the sole carbon source. Moreover, the yraS mutant showed a similar level of SDS resistance to the parental strain. It was the interruption of the acrA gene which made Y. ruckeri sensitive to this compound. LD50 experiments showed a similar virulence of the yraS mutant and parental strain.

CONCLUSIONS

The HSF of Y. ruckeri is the product of the alkyl sulphatase YraS, able to degrade SDS to 1-dodecanol. This degradation is not linked to the utilization of SDS as a carbon source and surprisingly, the enzyme is not involved in bacterial virulence or in the high SDS resistance displayed by the bacterium. This role is played by the AcrAB-TolC system.

The yrpAB operon of Yersinia ruckeri encoding two putative U32 peptidases is involved in virulence and induced under microaerobic conditions

In an attempt to dissect the virulence mechanisms of Yersinia ruckeri two adjacent genes, yrpA and yrpB, encoding putative peptidases belonging to the U32 family, were analyzed. Similar genes, with the same genetic organization were identified in genomic analysis of human-pathogenic yersiniae. RT-PCR studies indicated that these genes form an operon in Y. ruckeri. Transcriptional studies using an yrpB::lacZY fusion showed high levels of expression of these genes in the presence of peptone in the culture medium, as well as under oxygen-limited conditions. These two factors had a synergic effect on gene induction when both were present simultaneously during bacterial incubation, which indicates the important role that environmental conditions in the fish gut can play in the regulation of specific genes. LD 50 experiments using an yrpA insertional mutant strain demonstrated the participation of this gene in the virulence of Y. ruckeri.

In vivo monitoring of Yersinia ruckeri in fish tissues: progression and virulence gene expression

In this study, the utilization of bioluminescence imaging (BLI) allowed us to define the progression of Yersinia ruckeri during the infection of rainbow trout. A luminescent Y. ruckeri 150 strain was engineered using the pCS26-Pac plasmid containing the lux operon from Photorhabdus luminescens. Two different models of infection of rainbow trout were defined depending on the route in which bacteria were administered, being the gut the major organ affected following bath immersion. This indicates that this organ is important for bacterial dissemination inside the fish and the establishment of the infection. Moreover, the expression of three previously selected operons by in vivo expression technology (IVET) was analysed, the yhlBA involved in the production of a haemolysin, the cdsAB related to the uptake of cysteine and the yctCBA implicated in citrate uptake. Apart from these factors, the expression of yrp1 encoding a serralysin metalloprotease involved in pathogenesis was also analysed. The results indicated that all of the assayed promoters were expressed during infection of rainbow trout. In addition to these findings, the methodology described in this work constitutes a useful model for studying the infection process in other fish pathogenic bacteria.

Expression of signal transduction system encoding genes of Yersinia pseudotuberculosis IP32953 at 28°C and 3°C

Yersinia pseudotuberculosis is a significant psychrotrophic food pathogen whose cold tolerance mechanisms are poorly understood. Signal transduction systems serve to monitor the environment, but no systematic investigation of their role at cold temperatures in Y. pseudotuberculosis has yet been undertaken. The relative expression levels of 54 genes predicted to encode proteins belonging to signal transduction systems in Y. pseudotuberculosis IP32953 were determined at 28°C and 3°C by quantitative real-time reverse transcription-PCR. The relative expression levels of 44 genes were significantly (p<0.05) higher at 3°C than at 28°C. Genes encoding the two-component system CheA/CheY had the highest relative expression levels at 3°C. Mutational analysis revealed that cheA is important for growth and motility at 3°C. The relative expression level of one gene, rssB, encoding an RpoS regulator, was significantly (p<0.05) lower at 3°C than at 28°C. The results suggest that several signal transduction systems might be used during growth at low temperature, and at least, CheA/CheY two-component system is important for low-temperature growth.

The yctCBA operon of Yersinia ruckeri, involved in in vivo citrate uptake, is not required for virulence

A three-gene operon, named yctCBA (Yersinia citrate transporter), induced by citrate and repressed by glucose was identified from a previously selected in vivo-induced (ivi) clone in the fish pathogen Yersinia ruckeri. Interestingly, despite being an ivi clone, the drastic growth reduction of the yctC mutant in the presence of citrate, and the relatively high content of this compound in rainbow trout serum, the operon was not required for virulence.