XRE-Type Regulator BioX Acts as a Negative Transcriptional Factor of Biotin Metabolism in Riemerella anatipestifer

'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

Identification of Critical Immune Regulators and Potential Interactions of IL-26 in Riemerella anatipestifer-Infected Ducks by Transcriptome Analysis and Profiling

Riemerella anatipestifer (RA) is an economically important pathogen in the duck industry worldwide that causes high mortality and morbidity in infected birds. We previously found that upregulated IL-17A expression in ducks infected with RA participates in the pathogenesis of the disease, but this mechanism is not linked to IL-23, which primarily promotes Th17 cell differentiation and proliferation. RNA sequencing analysis was used in this study to investigate other mechanisms of IL-17A upregulation in RA infection. A possible interaction of IL-26 and IL-17 was discovered, highlighting the potential of IL-26 as a novel upstream cytokine that can regulate IL-17A during RA infection. Additionally, this process identified several important pathways and genes related to the complex networks and potential regulation of the host immune response in RA-infected ducks. Collectively, these findings not only serve as a roadmap for our understanding of RA infection and the development of new immunotherapeutic approaches for this disease, but they also provide an opportunity to understand the immune system of ducks.

Transcriptional activation of ompA in Neisseria gonorrhoeae mediated by the XRE family member protein NceR

Increasing antibiotic resistance of Neisseria gonorrhoeae, the causative agent of gonorrhea, is a growing global concern that has renewed vaccine development efforts. The gonococcal OmpA protein was previously identified as a vaccine candidate due to its surface exposure, conservation, stable expression, and involvement in host-cell interactions. We previously demonstrated that the transcription of ompA can be activated by the MisR/MisS two-component system. Interestingly, earlier work suggested that the availability of free iron also influences ompA expression, which we confirmed in this study. In the present study, we found that iron regulation of ompA was independent of MisR and searched for additional regulators. A DNA pull-down assay with the ompA promoter from gonococcal lysates obtained from bacteria grown in the presence or absence of iron identified an XRE (Xenobiotic Response Element) family member protein encoded by NGO1982. We found that an NGO1982 null mutant of N. gonorrhoeae strain FA19 displayed a reduced level of ompA expression compared to the wild-type (WT) parent strain. Given this regulation, and the capacity of this XRE-like protein to regulate a gene involved in peptidoglycan biosynthesis (ltgA), along with its presence in other Neisseria sp., we termed the NGO1982-encoded protein as NceR (Neisseria cell envelope regulator). Critically, results from DNA-binding studies indicated that NceR regulates ompA through a direct mechanism. Thus, ompA expression is subject to both iron-dependent (NceR) and -independent (MisR/MisS) pathways. Hence, levels of the vaccine antigen candidate OmpA in circulating gonococcal strains could be influenced by transcriptional regulatory systems and the availability of iron. IMPORTANCE Herein, we report that the gene encoding a conserved gonococcal surface-exposed vaccine candidate (OmpA) is activated by a heretofore undescribed XRE family transcription factor, which we term NceR. We report that NceR regulation of ompA expression in N. gonorrhoeae is mediated by an iron-dependent mechanism, while the previously described MisR regulatory system is iron-independent. Our study highlights the importance of defining the complexity of coordinated genetic and physiologic systems that regulate genes encoding vaccine candidates to better understand their availability during infection.

Epidemiological investigation and drug resistance characteristics of Riemerella anatipestifer strains from large-scale duck farms in Shandong Province, China from March 2020 to March 2022

Infectious serositis is a common disease caused by Riemerella anatipestifer (R. anatipestifer) in ducks, characterized by respiratory distress, septicemia, and neurological symptoms. In this study, 1,020 samples (brain and liver) were collected from ducks with suspected R. anatipestifer infection from March 2020 to March 2022 in Shandong Province, of which 171 R. anatipestifer strains were identified by PCR and isolation culture. The serotype of all strains was analyzed, and 74 strains were subjected to drug sensitivity tests and drug resistance genes detection. The results showed that the overall prevalence rate of R. anatipestifer in Shandong Province was 16.7% (171/1,020), with most strains coming from brain samples of ducklings under 3-mo old collected from September to December each year. Histopathological examination showed that heart vessels of the diseased duck were highly dilated and filled with red blood cells, with obvious fibrin exudates outside the pericardium, and fatty degeneration of liver cells. There were 45 strains of serotype 1, 45 strains of serotype 2, 2 strains of serotype 4, 33 strains of serotype 6, 44 strains of serotype 7, and 2 strains of serotype 10. The minimum inhibitory concentration (MIC) of 10 common antibiotics against 74 representative strains was determined by the agar dilution method. It was found that 74 strains had the most severe resistance to gentamicin (77%) and fully susceptible to ceftriaxone, but the 81.1% isolated strains were multidrug resistant. Resistance genes testing of 74 R. anatipestifers showed that tetracycline resistance gene tet X had the highest detection rate of 95.9%, followed by macrolide resistance gene ermF with 77%, and the rate of β-lactam resistance gene blaTEM is the lowest (10.8%). The animal experiment of 4 R. anatipestifer strains with different serotypes showed that they had strong pathogenicity to 7-day-old ducklings, which could cause nervous symptoms, and the mortality rate was 58% to 70%. The autopsy showed obvious pathological changes. These findings of this study on R. anatipestifer will help us to understand the latest prevalence, drug resistance characteristics, and pathogenicity of R. anatipestifer in Shandong, China, and provide a scientific guide for the treatment and control of the disease.

Genome-Wide Analysis and Characterization of the Riemerella anatipestifer Putative T9SS Secretory Proteins with a Conserved C-Terminal Domain

Riemerella anatipestifer is a major pathogenic agent of duck septicemic and exudative diseases. Recent studies have shown that the R. anatipestifer type IX secretion system (T9SS) acts as a crucial virulence factor. We previously identified two T9SS component proteins, GldK and GldM, and one T9SS effector metallophosphoesterase, which play important roles in bacterial virulence. In this study, 19 T9SS-secreted proteins that contained a conserved T9SS C-terminal domain (CTD) were predicted in R. anatipestifer strain Yb2 by searching for CTD-encoding sequences in the whole genome. The proteins were confirmed with a liquid chromatography-tandem mass spectrometry analysis of the bacterial culture supernatant. Nine of them were reported in our previous study. We generated recombinant proteins and mouse antisera for the 19 predicted proteins to confirm their expression in the bacterial culture supernatant and in bacterial cells. Western blotting indicated that the levels of 14 proteins were significantly reduced in the T9SS mutant Yb2ΔgldM culture medium but were increased in the bacterial cells. RT-qPCR indicated that the expression of these genes did not differ between the wild-type strain Yb2 and the T9SS mutant Yb2ΔgldM. Nineteen mutant strains were successfully constructed to determine their virulence and proteolytic activity, which indicated that seven proteins are associated with bacterial virulence, and two proteins, AS87_RS04190 and AS87_RS07295, are protease-activity-associated virulence factors. In summary, we have identified at least 19 genes encoding T9SS-secreted proteins in the R. anatipestifer strain Yb2 genome, which encode multiple functions associated with the bacterium's virulence and proteolytic activity. IMPORTANCE Riemerella anatipestifer T9SS plays an important role in bacterial virulence. We have previously reported nine R. anatipestifer T9SS-secreted proteins and clarified the function of the metallophosphoesterase. In this study, we identified 10 more secreted proteins associated with the R. anatipestifer T9SS, in addition to the nine previously reported. Of these, 14 proteins showed significantly reduced secretion into the bacterial culture medium but increased expression in the bacterial cells of the T9SS mutant Yb2ΔgldM; seven proteins were shown to be associated with bacterial virulence; and two proteins, AS87_RS04190 and AS87_RS07295, were shown to be protease-activity-associated virulence factors. Thus, we have demonstrated that multiple R. anatipestifer T9SS-secreted proteins function in virulence and proteolytic activity.