Structural basis of human PRPS2 filaments.

BACKGROUND: PRPP synthase (PRPS) transfers the pyrophosphate groups from ATP to ribose-5-phosphate to produce 5-phosphate ribose-1-pyrophosphate (PRPP), a key intermediate in the biosynthesis of several metabolites including nucleotides, dinucleotides and some amino acids. There are three PRPS isoforms encoded in human genome. While human PRPS1 (hPRPS1) and human PRPS2 (hPRPS2) are expressed in most tissues, human PRPS3 (hPRPS3) is exclusively expressed in testis. Although hPRPS1 and hPRPS2 share 95% sequence identity, hPRPS2 has been shown to be less sensitive to allosteric inhibition and specifically upregulated in certain cancers in the translational level. Recent studies demonstrate that PRPS can form a subcellular compartment termed the cytoophidium in multiple organisms across prokaryotes and eukaryotes. Forming filaments and cytoophidia is considered as a distinctive mechanism involving the polymerization of the protein. Previously we solved the filament structures of Escherichia coli PRPS (ecPRPS) using cryo-electron microscopy (cryo-EM) 1. RESULTS: Order to investigate the function and molecular mechanism of hPRPS2 polymerization, here we solve the polymer structure of hPRPS2 at 3.08 Å resolution. hPRPS2 hexamers stack into polymers in the conditions with the allosteric/competitive inhibitor ADP. The binding modes of ADP at the canonical allosteric site and at the catalytic active site are clearly determined. A point mutation disrupting the inter-hexamer interaction prevents hPRPS2 polymerization and results in significantly reduced catalytic activity. CONCLUSION: Findings suggest that the regulation of hPRPS2 polymer is distinct from ecPRPS polymer and provide new insights to the regulation of hPRPS2 with structural basis.

Filamentation modulates allosteric regulation of PRPS.

Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of E. coli PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.

Structural basis of dynamic P5CS filaments.

The bifunctional enzyme Δ1-pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations in the P5CS gene (ALDH18A1) lead to neurocutaneous syndrome and skin relaxation connective tissue disease in humans, and P5CS deficiency seriously damages the ability to resist adversity in plants. We have recently found that P5CS forms cytoophidia in vivo and filaments in vitro. However, it is difficult to appreciate the function of P5CS filamentation without precise structures. Using cryo-electron microscopy, here we solve the structures of Drosophila full-length P5CS in three states at resolution from 3.1 to 4.3 Å. We observe distinct ligand-binding states and conformational changes for the GK and GPR domains, respectively. Divergent helical filaments are assembled by P5CS tetramers and stabilized by multiple interfaces. Point mutations disturbing those interfaces prevent P5CS filamentation and greatly reduce the enzymatic activity. Our findings reveal that filamentation is crucial for the coordination between the GK and GPR domains, providing a structural basis for the catalytic function of P5CS filaments.

Dietary glycyl-glutamine supplementation ameliorates intestinal integrity, inflammatory response, and oxidative status in association with the gut microbiota in LPS-challenged piglets.

During weaning transition, mammalian newborns suffer severe enteric infections and thus induced gut microbiota dysbiosis, which in turn aggravates enteric disorder. The synthetic dipeptide glycyl-glutamine (GlyGln) has been used as a diet supplement to improve the weaning transition of newborns. However, the effect of dietary GlyGln supplementation on the gut microbiota of piglets with enteric infection remains unclear. Here, weaned piglets received a basal diet or a basal diet supplemented with 0.25% GlyGln for 3 weeks. Five piglets in each group received an intraperitoneal injection of lipopolysaccharide (LPS) (100 µg per kg BW) (LPS and GlyGln + LPS groups) and meanwhile five piglets in a control group received an intraperitoneal injection of saline (Ctrl group). The results showed that dietary GlyGln supplementation improved the LPS induced inflammation response and damage to the ileum morphology by increasing interleukin 10, tight junction proteins, villus height, and the ratio villus height/crypt depth, but decreasing the crypt depth. For the oxidative status, dietary GlyGln supplementation increased the ileal superoxide dismutase and meanwhile reduced the malondialdehyde and nitric oxide synthase activity (NOS) (total NOS and inducible NOS), compared with that in the LPS group. LPS challenge reduced the diversity of gut microbiota and enriched the facultative anaerobic Escherichia coli. The GlyGln restored alpha diversity and the structure of the gut microbiota by enriching obligate anaerobes and short-chain fatty acid (SCFA)-producing bacteria, including Clostridium, Lachnospira, Phascolarctobacterium, Roseburia, Lachnospiraceae, and Synergistetes. GlyGln enriched the gut microbiota function of carbohydrate metabolism and elevated the ileal SCFA concentrations of propionic acid and butyric acid that had been decreased by the LPS challenge. The beneficial effects of dietary GlyGln supplementation are closely associated with its enriched bacteria and SCFAs. Taken together, dietary GlyGln supplementation improved the gut microbiota dysbiosis induced by LPS challenge and enriched obligate anaerobes and SCFA-producing bacteria, which contributed to the amelioration of intestinal integrity, inflammatory responses, and oxidative status.

Anti­inflammatory mechanism of berberine on lipopolysaccharide­induced IEC­18 models based on comparative transcriptomics.

Intestinal surface epithelial cells (IECs) have long been considered as an effective barrier for maintaining water and electrolyte balance, and are involved in the mechanism of nutrient absorption. When intestinal inflammation occurs, it is often accompanied by IEC malfunction. Berberine (BBR) is an isoquinoline alkaloid found in numerous types of medicinal plants, which has been clinically used in China to treat symptoms of gastrointestinal pathogenic bacterial infection, especially bacteria­induced diarrhea and inflammation. In the present study, IEC­18 rat intestinal epithelial cells were treated with lipopolysaccharide (LPS) to establish an in vitro model of epithelial cell inflammation, and the cells were subsequently treated with BBR in order to elucidate the anti­inflammatory mechanism. Transcriptome data were then searched to find the differentially expressed genes (DEGs) compared between two of the treatment groups (namely, the LPS and LPS+BBR groups), and DEGs were analyzed using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Weighted Gene Correlation Network Analysis and Interactive Pathways Explorer to identify the functions and pathways enriched with DEGs. Finally, reverse transcription­quantitative PCR was used to verify the transcriptome data. These experiments revealed that, comparing between the LPS and LPS+BBR groups, the functions and pathways enriched in DEGs were 'DNA replication', 'cell cycle', 'apoptosis', 'leukocyte migration' and the 'NF­κB and AP­1 pathways'. The results revealed that BBR is able to restrict DNA replication, inhibit the cell cycle and promote apoptosis. It can also inhibit the classic inflammatory pathways, such as those mediated by NF­κB and AP­1, and the expression of various chemokines to prevent the migration of leukocytes. According to transcriptomic data, BBR can exert its anti­inflammatory effects by regulating a variety of cellular physiological activities, including cell cycle, apoptosis, inflammatory pathways and leukocyte migration.

Effects of Cortex Phellodendri extract on post-weaning piglets diarrhoea.

The diarrhoea incidence rate is often high among weaning piglets. In light of the fact that Cortex phellodendri has long been used to treat diarrhoea in China, this study aimed to evaluate the effects of Cortex Phellodendri Extract (CPE) on diarrhoea in weaning piglets and the mechanism behind such effects. In the first trial, 36 diarrhoeal weaning piglets were randomly divided into three groups. The control group was injected with 20 mg oxytetracycline/kg BW, while the two treatment groups were orally administered with 10 mg and 20 mg CPE/kg BW respectively. In the second trial, 96 weaning piglets were randomly divided into two groups. The control group was fed basal diet, while 300 mg CPE/kg BW was added to the diet of the treatment group. The pathogenic bacteria were then isolated and identified from the diarrhoeal faecal samples. Cell adhesion and RT-PCR tests were used to investigate the effect of CPE on the adhesion of pathogenic bacteria to IPEC-J2 cells. 16S rDNA-based high-throughput sequencing was used to analyse faecal microflora. The results showed that CPE reduced the diarrhoea incidence rate (p < 0.05) and diarrhoea index (p < 0.05) compared to control group, and increased the richness and evenness of weaning piglets' gut microbiota. Escherichia coli (E. coil) was identified as the causative organism. Cell adhesion and RT-PCR tests suggested that CPE reduced the adhesion of E. coli to IPEC-J2 cells (p < 0.05) and the expression of fae and faeG gene (p < 0.05) responsible for encoding E. coli fimbriae protein.

Cortex Phellodendri extract's anti-diarrhea effect in mice related to its modification of gut microbiota.

Cortex Phellodendri extract (CPE) has been used in China to treat diarrhea whereas the underlying mechanisms remain poorly understood. Given that dysbiosis of gut microbiota is a potential reason for diarrhea, and that oral CPE has a low absorption rate in intestine, we hypothesized that modification of gut microbiota is an important factor in CPE's anti-diarrhea effect. To test this hypothesis, we established a diarrhea model by challenging post-weaning mice with oral Enterotoxigenic-Escherichia coli (ETEC), and then the mice were treated with two doses of CPE (80 mg/kg bodyweight and 160 mg/kg bodyweight) or the vehicle control (phosphate buffered saline). Diarrhea indices, inflammatory factors, morphology of jejunum, short-chain fatty acids (SCFAs), and serum endocrine were determined. Modification of gut microbiota was analyzed using 16S rDNA high-throughput sequencing. The changes in functional profiles of gut microbiota were predicted using software PICRUSt. We then explored the association between CPE-responding bacteria and the symptoms indices with the spearman's rank correlation coefficient and significance test. Compared with diarrheal mice, CPE decreased Gut/Carcass ratio and water content of stool, increased goblet cell density and villus height/crypt depth of jejunum, as well as decreased inflammatory indices (Tumour Necrosis Factor-α, Myeloperoxidase and Interleukin-1α). CPE shifted the gut microbiota significantly by increasing alpha diversity (observed species, ace, Shannon, and Simpson) and restoring the gut microbiota. CPE increased Firmicutes and decreased Bacteroidetes. The reduced genus Prevotella, Acinetobacter, and Morganella were positively associated with the diarrhea indices, whereas increased genus Odoribacter, Rikenella, and Roseburia were negatively associated with the diarrhea indices. The abundance of carbohydrate metabolism-related gene and SCFAs-producing bacteria were increased, which was evidenced by increased butyric acid and total SCFAs concentration in the caecum. Consequently, endocrine peptides glucagon-like peptide-1, epidermal growth factor, and peptide tyrosine tyrosine in serum were elevated. CONCLUSIONS: CPE shows a shift function on the gut microbiota in alleviating the diarrhea of mice in a dose-dependent manner. In addition, the microbial metabolites SCFAs may mediate CPE's anti-diarrhea effect by enhancing endocrine secretion in mice.

Modulation of Gut Microbial Community and Metabolism by Dietary Glycyl-Glutamine Supplementation May Favor Weaning Transition in Piglets.

Gut microbiota plays a crucial role in diet nutrient metabolism and maintaining host health. The synthetic dipeptides glycyl-glutamine (Gly-Gln) used as diet supplementation to improve the weaning transition of newborns could be metabolized by certain bacteria in vitro. However, the effect of diet Gly-Gln supplementation on gut microbiota in vivo remains largely unknown. 240 piglets at the age of 28 days (day 28) were randomly assigned to two groups that received a basal diet (Ctrl group) or a basal diet supplemented with 0.25% Gly-Gln (Gly-Gln group) for 3 weeks. Five piglets from each group were euthanized for sampling after overnight fasting on day 38 and day 49, respectively. We determined their structure shifts of the gut microbiota using 16S rDNA-based high-throughput sequencing analysis. Microbial metabolites short-chain fatty acids (SCFAs) in the ileum and the colon were determined with high-performance gas chromatography. The concentrations of endocrine peptides including epidermal growth factor, glucagon-like peptide-1, and glucagon-like peptide-2 in ileal mucosa, as well as the serum concentration of interleukin 1 beta, interleukin 6, interleukin 10, and tumor necrosis factor alpha were determined using Enzyme-Linked Immunosorbent Assay. In addition, we also checked the diarrhea ratio, growth performance, and intestinal morphology to assess the favorable effect of dietary Gly-Gln supplementation during the weaning transition. Dietary Gly-Gln supplementation beneficially altered the gut microbiota by increasing bacterial loading, elevating alpha diversity, and increasing the relative abundance of anaerobes and fiber-degrading bacteria (Phylum Fibrobacteres). Accordingly, the microbial metabolites SCFAs in both colon and ileum, as well as the downstream endocrine peptides in the ileum increased. Meanwhile, dietary Gly-Gln's favorable weaning transition was reflected in the increase of growth performance indices and the reduced inflammatory response in a time dependent manner. There were significant correlations among the bacteria which responded to dietary Gly-Gln supplementation and these checked indices. Taken together, dietary Gly-Gln supplementation selectively modulated the gut microbiota, which may favor piglets' weaning-transition. These findings suggest that gut microbiota targeted approaches can be potentially used to improve weaning transition of piglets by dietary functional amino acid.