Two-component regulatory systems in Helicobacter pylori and Campylobacter jejuni: Attractive targets for novel antibacterial drugs

Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator

Campylobacter jejuni is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, C. jejuni is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant Campylobacter as a serious antibiotic resistance threat in the United States. The C. jejuni CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in C. jejuni that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the cmeABC promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA.

IMPORTANCE

Campylobacter jejuni has emerged as an antibiotic-resistant threat worldwide. CosR is an essential regulator for this bacterium and is important for Campylobacter adaptation to various stresses. Here, we describe the structural basis of CosR binding to target DNA as determined by cryo-electron microscopy and X-ray crystallography. Since CosR is a potential target for intervention, our studies may facilitate the development of novel therapeutics to combat C. jejuni infection.

Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention

Purpose

Polycystic ovary syndrome (PCOS) is a frequent cause of infertility in reproductive-age women. Our work aims to evaluate the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on gut microbiota, with metabolic parameters including body weight and the hormone profile in PCOS.

Patients and Methods

Dehydroepiandrosterone (DHEA)-induced PCOS mice were established and then treated with two GLP-1RAs: liraglutide and novel form semaglutide for four weeks. Changes in body weight and metabolic parameters were measured. Fecal samples were collected and analyzed using metagenomic sequencing.

Results

Liraglutide and semaglutide modulated both alpha and beta diversity of the gut microbiota in PCOS. Liraglutide increased the Bacillota-to-Bacteroidota ratio through up-regulating the abundance of butyrate-producing members of Bacillota like Lachnospiraceae. Moreover, liraglutide showed the ability to reverse the altered microbial composition and the disrupted microbiota functions caused by PCOS. Semaglutide increased the abundance of Helicobacter in PCOS mice (p < 0.01) which was the only bacteria found negatively correlated with body weight. Moreover, pathways involving porphyrin and flavonoids were increased after semaglutide intervention.

Conclusion

Liraglutide and semaglutide improved reproductive and metabolic disorders by modulating the whole structure of gut microbiota in PCOS. The greater efficacy in weight loss compared with liraglutide observed after semaglutide intervention was positively related with Helicobacter. The study may provide new ideas in the treatment and the underlying mechanisms of GLP-1RAs to improve PCOS.

Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts

The perturbations of the gut microbiota and metabolites are closely associated with the progression of inflammatory bowel disease (IBD). However, inconsistent findings across studies impede a comprehensive understanding of their roles in IBD and their potential as reliable diagnostic biomarkers. To address this challenge, here we comprehensively analyze 9 metagenomic and 4 metabolomics cohorts of IBD from different populations. Through cross-cohort integrative analysis (CCIA), we identify a consistent characteristic of commensal gut microbiota. Especially, three bacteria, namely Asaccharobacter celatus, Gemmiger formicilis, and Erysipelatoclostridium ramosum, which are rarely reported in IBD. Metagenomic functional analysis reveals that essential gene of Two-component system pathway, linked to fecal calprotectin, are implicated in IBD. Metabolomics analysis shows 36 identified metabolites with significant differences, while the roles of these metabolites in IBD are still unknown. To further elucidate the relationship between gut microbiota and metabolites, we construct multi-omics biological correlation (MOBC) maps, which highlights gut microbial biotransformation deficiencies and significant alterations in aminoacyl-tRNA synthetases. Finally, we identify multi-omics biomarkers for IBD diagnosis, validated across multiple global cohorts (AUROC values ranging from 0.92 to 0.98). Our results offer valuable insights and a significant resource for developing mechanistic hypotheses on host-microbiome interactions in IBD.

Effect of an Enteroprotective Complementary Feed on Faecal Markers of Inflammation and Intestinal Microbiota Composition in Weaning Puppies

Weaning entails numerous modifications of the intestinal structure and microbiota composition, making puppies at high risk of sickness during this delicate life stage. The aim of this study was to investigate the effects of a four-week administration of a supplement composed of ultramicronised Palmitoylethanolamide, bovine colostrum and Bacillus subtilis (Normalia® Extra, Innovet Italia Srl, Saccolongo, Italy) on markers of gut health and microbiome of weaning puppies. Twenty-nine four-week-old Golden Retriever puppies were randomly assigned to control (CG, n = 13) and treated (TG, n = 16) groups. During the whole experimental time, there were no differences between the groups with regard to average daily gain and faecal score. In TG, faecal calprotectin and zonulin values were statistically significantly decreased compared to CG, especially at week 8 (zonulin: 42.8 ± 1.54 ng/mL and 55.3 ± 42.8 ng/mL, and calprotectin: 2.91 ± 0.38 µg/g and 5.71 ± 0.43 µg/g, in TG and CG, respectively; p < 0.0001 for both comparisons). Bacteria belonging to phylum Campylobacterota decreased (p = 0.04), while those referring to genera Coprococcus and Pseudomonas increased (p = 0.01 and p = 0.04, respectively). The supplementation of the tested complementary feed can promote the intestinal health of puppies and therefore facilitate weaning by lowering gut inflammation.

Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria

In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.

Effect of Cyberlindnera jadinii supplementation on growth performance, serum immunity, antioxidant status, and intestinal health in winter fur-growing raccoon dogs (Nyctereutes procyonoides)

Introduction

This study aimed to investigate the effects of Cyberlindnera jadinii supplementation on the growth performance, nutrient utilization, serum biochemistry, immunity, antioxidant status, and intestinal microbiota of raccoon dogs during the winter fur-growing period.

Methods

Forty-five 135 (±5) day-old male raccoon dogs were randomly assigned to three dietary groups supplemented with 0 (group N), 1 × 10⁹ (group L) and 5 × 10⁹ CFU/g (group H) Cyberlindnera jadinii, with 15 raccoon dogs per group.

Results

The results showed that Cyberlindnera jadinii in groups L and H improved average daily gain (ADG) and decreased feed-to-weight ratio (F/G) (P < 0.05). No significant difference was found in nutrient digestibility and nitrogen metabolism among the three groups (P > 0.05). Compared with group N, serum glucose levels were lower in groups L and H (P < 0.05). The levels of serum immunoglobulins A and G in group L were higher than those in the other two groups (P < 0.05), and the levels of serum immunoglobulins A and M in group H were higher than those in group N (P < 0.05). Supplementation with Cyberlindnera jadinii in groups L and H increased serum superoxide dismutase activity, and the total antioxidant capacity in group H increased compared with group N (P < 0.05). The phyla Bacteroidetes and Firmicutes were dominant in raccoon dogs. The results of principal coordinate analysis (PCoA) showed that the composition of microbiota in the three groups changed significantly (P < 0.05). The relative abundance of Campylobacterota was increased in the H group compared to the N and L groups (P < 0.05). The relative abundance of Sarcina was increased in group L compared with the other two groups (P < 0.05), while the relative abundance of Subdoligranulum and Blautia were decreased in group H compared with the other two groups (P < 0.05). Also, the relative abundance of Prevotella, Sutterella and Catenibacterium was higher in group L (P < 0.05) compared with group H.

Discussion

In conclusion, dietary supplementation with Cyberlindnera jadinii improved growth performance, antioxidant activity, immune status, and improved intestinal microbiota in winter fur-growing raccoon dogs. Among the concentrations tested, 1 × 10⁹ CFU/g was the most effective level of supplementation.

Insights into the Orchestration of Gene Transcription Regulators in Helicobacter pylori

Bacterial pathogens employ a general strategy to overcome host defenses by coordinating the virulence gene expression using dedicated regulatory systems that could raise intricate networks. During the last twenty years, many studies of Helicobacter pylori, a human pathogen responsible for various stomach diseases, have mainly focused on elucidating the mechanisms and functions of virulence factors. In parallel, numerous studies have focused on the molecular mechanisms that regulate gene transcription to attempt to understand the physiological changes of the bacterium during infection and adaptation to the environmental conditions it encounters. The number of regulatory proteins deduced from the genome sequence analyses responsible for the correct orchestration of gene transcription appears limited to 14 regulators and three sigma factors. Furthermore, evidence is accumulating for new and complex circuits regulating gene transcription and H. pylori virulence. Here, we focus on the molecular mechanisms used by H. pylori to control gene transcription as a function of the principal environmental changes.