Structural biology of the purine biosynthetic pathway

Cellular metabolomics study in colorectal cancer cells and media following treatment with 5-fluorouracil by gas chromatography-tandem mass spectrometry

BACKGROUND

Metabolic reprogramming is a distinctive characteristic of colorectal cancer (CRC) which provides energy and nutrients for rapid proliferation. Although numerous studies have explored the rewired metabolism of CRC, the metabolic alterations occurring in CRC when the cell cycle is arrested by treatment with 5-fluorouracil (5-FU), an anticancer drug that arrests the S phase, remain unclear.

METHODS

A systematic profiling analysis was conducted as ethoxycarbonyl/methoxime/tert-butyldimethylsilyl derivatives using gas chromatography-tandem mass spectrometry in HT29 cells and media following 5-FU treatment in a concentration- and time-dependent manner.

RESULTS

In HT29 cells of 24 h after 5-FU treatment (3-100 μM) and 48 h after 5-FU treatment (1-10 μM), six amino acids, including valine, leucine, isoleucine, serine, glycine, and alanine and two organic acids, including pyruvic acid and lactic acid, were significantly increased compared to the DMSO-treated group. However, 48 h after 5-FU treatment (30-100 μM) in HT29 cells, the levels of these metabolites decreased along with an approximately 50% reduction in viability, an increase in the level of reactive oxygen species, induction of cycle arrest in the G1 phase, and the induction of apoptosis. On the other hand, the levels of fatty acids showed a continuous increase in HT29 cells 48 h after 5-FU treatment (1-100 μM). In the media, the decreased availabilities in the cellular uptake of nutrient metabolites, including valine, leucine, isoleucine, serine, and glutamine, were observed at 48 h after 5-FU treatment in a dose-dependent manner.

CONCLUSION

It is assumed that there is a possible shift in energy dependence from the tricarboxylic acid cycle to fatty acid metabolism. Thus, metabolic profiling analysis revealed altered energy metabolism in CRC cells following 5-FU treatment.

Purine Metabolism and Dystonia: Perspectives of a Long-Promised Relationship

Dystonia research focuses on the identification of converging biological pathways, allowing to define molecular drivers that serve as treatment targets. We summarize evidence supporting the concept that aberrations in purine metabolism intersect with dystonia pathogenesis. The recent discovery of IMPDH2-related dystonia introduced a gain-of-function paradigm in purinergic system defects, offering new perspectives to understand purine-pool imbalances in brain diseases. We discuss commonalities between known dystonia-linked mechanisms and mechanisms emerging from studies of purine metabolism disorders including Lesch-Nyhan disease. Together, we hypothesize that a greater appreciation of the relevance of purine perturbances in dystonia can offer fresh avenues for therapeutic intervention. ANN NEUROL 2025;97:809-825.

Antibacterial performance and transcriptome analysis of atomically dispersed Ag anchored on C3N4 as an alternative of antibiotics against Escherichia coli under dark condition

Single-atom materials (SA) have been explored as possible candidate as antibacterial agent and existing studies have focused antibacterial ability based on photothermal effect and enzyme-mimic activation of H2O2. However, there is still limited research on the application of SA in dark conditions that are widely present in daily life, such as wound dressing, food active packaging, antimicrobial cotton fabrics, etc. Therefore, within the current study, we synthesized carbon nitride (C3N4) supported silver single-atoms (Ag-C3N4) and evaluated the antibacterial activity of Ag-C3N4 under dark condition. For in-vitro experiment, Ag-C3N4 showed excellent antibacterial ability towards Escherichia coli, with antibacterial rate close to 100 %. Transcriptome analysis revealed that exposure to Ag-C3N4 resulted in 138 differentially expressed genes (DEGs), containing 100 up-regulated gens and 38 down-regulated genes. KEGG enrichment pathway analysis showed that DEGs were mainly associated with metabolic pathways including two component system, quorum sensing, ABC transporter, pyruvate metabolism, oxidative phosphorylation, purine metabolism, and amino acid metabolism, etc. Finally, the mouse wound healing experiment demonstrated wound dressing with Ag-C3N4 significantly accelerated healing. In conclusion, we conducted an in-depth research on the ability of Ag-C3N4 to inhibit Gram-negative bacteria under dark condition, proving that it was a promising bactericide.

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology

The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo-electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.

Purine Chemistry in the Early RNA World at the Origins of Life: From RNA and Nucleobases Lesions to Current Key Metabolic Routes

In early life, RNA probably played the central role and, in the corresponding RNA world, the main produced amino acids and small peptides had to react continuously with RNA, ribonucleos(t)ides and nucleobases, especially with purines. A RNA-peptide world and key metabolic pathways have emerged from the corresponding chemical modifications such as the translation process performed by the ribosome. Some interesting reactions of the purine bicycle and of the corresponding ribonucleos(t)ides are performed under plausible prebiotic conditions and described RNA chemical lesions are reviewed with the prospect to highlight their connection with some major steps of the purine and histidine biosynthetic pathways that are, in an intriguingly way, related through two key metabolites, adenosine 5'-triphosphate and the imidazole ribonucleotide 5-aminoimidazole-4-carboxamide ribonucleotide. Ring-opening reactions of purines stand out as efficient accesses to imidazole ribonucleotides and to formamidopyrimidine (Fapy) ribonucleotides suggesting that biosynthetic pathway' first steps have emerged from RNA and ribonucleos(t)ide damages. Also, are summarized the works on the formation and catalytic properties, under plausible prebiotic conditions, of N6-derivatives of the purine base adenine as potential surrogates of histidine in catalysis accordingly to their structural relationship.

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes

In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.

Chromosomal genes modulating fosfomycin susceptibility in uropathogenic Escherichia coli: a genome-wide analysis

Escherichia coli acquires fosfomycin resistance through chromosomal mutations that reduce drug uptake and by drug-inactivating enzymes. However, the complete resistance mechanisms remain to be elucidated. The aim of this study was to elucidate the genetic mechanisms regulating fosfomycin susceptibility in uropathogenic E. coli (UPEC). We constructed a highly saturated transposon mutant library containing >340,000 unique Tn5 insertions in a clinical UPEC strain. We conducted transposon-directed insertion site sequencing (TraDIS) to screen for chromosomal genes whose mutations are beneficial for bacterial growth and survival in the presence of fosfomycin at 4 and 32 µg/mL. TraDIS analysis identified 67 genes including known resistance determinants (n = 13) as well as a set of novel genes modulating fosfomycin susceptibility (n = 54). These genes are involved in pyruvate metabolism, pentose phosphate pathway, nucleotide biosynthesis, DNA repair, protein translation, cellular iron homeostasis, and biotin biosynthesis. Deletion of 16 selected genes in the wild-type strain resulted in growth advantages and decreased susceptibility when exposed to fosfomycin. Notably, deletion of DNA repair genes (i.e., mutL and mutS) and purine synthesis genes (i.e., purB and its upstream gene hflD) led to the most significant advantages in competitive and non-competitive growth in the presence of fosfomycin, as well as the highest increase of fosfomycin MIC (8- to 16-fold). These findings provide a genome-wide overview of genes required for maintaining fosfomycin susceptibility in E. coli, highlighting new mutations and functional pathways that may be used by UPEC to develop clinical resistance.

Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli

Neonatal bacterial meningitis is associated with substantial mortality and morbidity worldwide. Neonatal meningitis-causing Escherichia coli (NMEC) is the most common gram-negative bacteria responsible for this disease. However, the interactions of NMEC with its environment within the host are poorly understood. Here, we showed that a low level of leucine, a niche-specific signal in the blood, promotes NMEC pathogenicity by enhancing bacterial survival and replication in the blood. A low leucine level downregulates the expression of NsrP, a small RNA (sRNA) identified in this study, in NMEC in an Lrp-dependent manner. NsrP destabilizes the mRNA of the purine biosynthesis-related gene purD by direct base pairing. Decreased NsrP expression in response to low leucine levels in the blood, which is a purine-limiting environment, activates the bacterial de novo purine biosynthesis pathway, thereby enhancing bacterial pathogenicity in the host. Deletion of NsrP or purD significantly increases or decreases the development of E. coli bacteremia and meningitis in animal models, respectively. Furthermore, we showed that intravenous administration of leucine effectively reduces the development of bacteremia and meningitis caused by NMEC by blocking the Lrp-NsrP-PurD signal transduction pathway. This study provides a potential strategy for the prevention and treatment of E. coli-induced meningitis.

[Integrative transcriptomics-metabolomics approach to identify metabolic pathways regulated by glutamine synthetase activity]

Glutamine synthetase (GS), the only enzyme responsible for de novo glutamine synthesis, plays a significant role in cancer progression. As an example of the consequences of GS mutations, the R324C variant causes congenital glutamine deficiency, which results in brain abnormalities and neonatal death. However, the influence of GS-deficient mutations on cancer cells remains relatively unexplored. In this study, we investigated the effects of GS and GS-deficient mutations, including R324C and previously unreported K241R, which serve as models for GS inactivation. This study provided intriguing insights into the intricate relationship between GS mutations and cancer cell metabolism. Our findings strongly support recent studies that suggest GS deletion leads to the suppression of diverse signaling cascades associated with glutamine metabolism under glutamine-stripping conditions. The affected processes include DNA synthesis, the citric acid cycle, and reactive oxygen species (ROS) detoxification. This suppression originates from the inherent inability of cells to autonomously synthesize glutamine under glutamine-depleted conditions. As a key source of reduced nitrogen, glutamine is crucial for the formation of purine and pyrimidine bases, which are essential building blocks for DNA synthesis. Furthermore, the citric acid cycle is inhibited by the absence of negatively charged glutamate within the mitochondrial matrix, particularly when glutamine is scarce. This deficiency decreases the flux of α-ketoglutarate (α-KG), a principal driver of the citric acid cycle. Intermediate metabolites of the citric acid cycle directly or indirectly contribute to the generation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, a core component of redox homeostasis. Using the GS_R324C and GS_K241R mutants, we conducted an integrative transcriptomics and metabolomics analysis. The GS mutants with reduced activity activated multiple amino acid biosynthesis pathways, including arginine-proline, glycine-serine-threonine, and alanine-aspartate-glutamate metabolism. This intriguing behavior led us to hypothesize that despite hindrance of the citric acid cycle, abundant intracellular glutamate is redirected through alternative processes, including transamination. Simultaneously, key metabolic enzymes in the amino acid synthesis pathways, such as glutamic-oxaloacetic transaminase 1 (GOT1), glutamic-pyruvic transaminase 2 (GPT2), pyrroline-5-carboxylate reductase 1 (PYCR1), and phosphoserine aminotransferase 1 (PSAT1), exhibited increased mRNA levels. Additionally, GS deficiency appeared to upregulate the expression of glutamine transporters SLC38A2 and SLC1A5. Thus, restricting extracellular amino acids, such as glutamine, induces a stress response while promoting transcription or translation by a select group of genes, thereby facilitating cellular adaptation. However, similar to GS_WT, both GS_R324C and GS_K241R were modulated by glutamine treatment. Among GS-activity-dependent behaviors, the increased expression of numerous aminoacyl-tRNA synthetases (ARSs), which are critical for aminoacyl-tRNA biosynthesis, remains poorly understood. Most ARS-encoding genes are transcriptionally induced by activating transcription factor 4 (ATF4), the expression of which increases under oxidative stress, endoplasmic reticulum stress, hypoxia, and amino acid limitation. In GS-deficient cells, the increased expression of ATF4 was accompanied by pronounced stress caused by glutamine starvation. Thus, ARS upregulation may predominantly arise from increased ATF4 expression in GS-deficient cells. Additionally, transcriptomic analysis revealed the differential expression of specific genes, regardless of GS activity, suggesting that GS is involved in various processes other than glutamine synthesis, including angiogenesis. Although our omics study was limited to H1299 cells, in subsequent experiments, we validated our findings using additional cell lines, including Hepa1-6 and LN-229. To attain a more comprehensive understanding of the impact of the newly identified GS_K241R mutant, our investigation should be extended to various cell types and mouse models. In summary, we identified and investigated GS-deficient mutations in cancer cells and conducted an integrative transcriptomics-metabolomics analysis with comparisons to wild-type GS. This comprehensive approach provided crucial insights into the intricate pathways modulated by GS activity. Our findings advance the understanding of how GS functions in the context of reprogrammed cellular metabolism, particularly during glutamine deprivation. The altered metabolism triggered by elevated glutamate levels arising from GS mutations highlights the remarkable plasticity of cancer cell metabolism. Notably, considering the increasing research focus on GS as a potential therapeutic target in various cancer types, the findings of this study could provide innovative perspectives for drug development and the formulation of clinical treatment strategies.

A high throughput assay for phosphoribosylformylglycinamidine synthase

Metabolic reprogramming of purine biosynthesis is a hallmark of cancer metabolism and represents a critical vulnerability. The enzyme phosphoribosylformylglycinamidine synthase (PFAS) catalyzes the fourth step in de novo purine biosynthesis and has been demonstrated to be prognostic for survival of liver cancer. Despite the importance of this protein as a drug target, there are no known specific inhibitors of PFAS activity. Here, we describe a new continuous, spectrophotometric assay for the synthase domain of PFAS that is amenable to high-throughput screening (HTS). This mechanism-based fluorescent assay makes use of the acid phosphatase substrate, 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP). PFAS catalyzes the turnover of DiFMUP with a KM of 108 ± 7 µM. After optimization and miniaturization of the assay for 1,536-well format, we conducted a pilot HTS using the LOPAC1280 library. The assay performed extremely well, with an average Z' of 0.94 ± 0.02, average signal to noise of 5.01 ± 0.06, excellent inter plate correlation, and a hit rate of 1.18 %. This assay provides a critically needed tool to advance the study of PFAS enzymology and will be foundational for the discovery of small molecule inhibitors both as functional probes and for the basis of new drug development.

Metabolomic Analysis, Antiproliferative, Anti-Migratory, and Anti-Invasive Potential of Amlodipine in Lung Cancer Cells

Background and Objective

Lung cancer stands as the leading cause of cancer-related fatalities worldwide. While chemotherapy remains a crucial treatment option for managing lung cancer in both early-stage and advanced cases, it is accompanied by significant drawbacks, including severe side effects and the development of chemoresistance. Overcoming chemoresistance represents a considerable challenge in lung cancer treatment. Amlodipine cytotoxicity was previously demonstrated and could make lung cancer cells more susceptible to chemotherapies. This research aims to examine the metabolomics changes that may occur due to amlodipine's anticancer effects on non-small cell lung cancer (NSCLC) cells.

Methods

Amlodipine's effects on A549 and H1299 NSCLC were evaluated using a colorimetric MTT assay, a scratch wound-healing assay and Matrigel invasion chambers to measure cell viability, cell migration and cell invasion. Ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS) was used for the untargeted metabolomics investigation.

Results

Our study revealed that amlodipine significantly reduced proliferation of cancer cells in a dose-dependent fashion with IC50 values of 23 and 25.66 µM in A549 and H1299 cells, respectively. Furthermore, amlodipine reduced the invasiveness and migration of cancer cells. Metabolomics analysis revealed distinct metabolites to be significantly dysregulated (Citramalic acid, L-Proline, dGMP, L-Glutamic acid, Niacinamide, and L-Acetylcarnitine) in amlodipine-treated cells.

Conclusion

The present study illustrates the anticancer effects of amlodipine on lung cancer proliferation, migration, and invasion in vitro and enhance our understanding of how amlodipine exerts its anticancer potential by casting light on these mechanisms.

Bacterial pathogen deploys iminosugar galactosyrin to manipulate plant glycobiology

The extracellular space (apoplast) of plants is an important molecular battleground during infection by many pathogens. We previously found that a plant-secreted β-galactosidase BGAL1 acts in immunity by facilitating the release of immunogenic peptides from bacterial flagellin and that Pseudomonas syringae suppresses this enzyme by producing a small molecule inhibitor called galactosyrin. Here, we elucidated the structure and biosynthesis of galactosyrin and uncovered its multifunctional roles during infection. Structural elucidation by cryo-EM and chemical synthesis revealed that galactosyrin is an iminosugar featuring a unique geminal diol attached to the pyrrolidine moiety that mimics galactose binding to the β-galactosidase active site. Galactosyrin biosynthesis branches off from purine biosynthesis and involves three enzymes of which the first is a reductase that is unique in iminosugar biosynthesis. Besides inhibiting BGAL1 to avoid detection, galactosyrin also changes the glycoproteome and metabolome of the apoplast. The manipulation of host glycobiology may be common to plant-associated bacteria that carry putative iminosugar biosynthesis clusters.

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health

BACKGROUND

Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of penicillin in the early 1940s, has been proposed as a primary contributor to the cumulative alteration of microbiota over generations. However, the mechanistic link between the antibiotics-altered microbiota and chronic conditions remains unclear.

RESULTS

In this study, we discovered that variants of the key beneficial gut microbe, Akkermansia muciniphila, were selected upon exposure to penicillin. These variants had mutations in the promoter of a TEM-type β-lactamase gene or pur genes encoding the de novo purine biosynthesis pathway, and they exhibited compromised abilities to mitigate host obesity in a murine model. Notably, variants of A. muciniphila are prevalent in the human microbiome worldwide.

CONCLUSIONS

These findings highlight a previously unknown mechanism through which antibiotics influence host health by affecting the beneficial capacities of the key gut microbes. Furthermore, the global prevalence of A. muciniphila variants raises the possibility that these variants contribute to global epidemics of chronic conditions, warranting further investigations in human populations. Video Abstract.

Multiplex mapping of protein-protein interaction interfaces

We describe peptide mapping through Sp lit A ntibiotic R esistance C omplementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host, and uses high throughput DNA sequencing results to infer the location of protein-protein interaction (PPI) interfaces. SpARC-map uses only routine microbiology techniques, with no reliance on specialized instrumentation or reconstituting protein complexes in vitro; it can be tuned to detect PPIs over a broad range of affinities; it can be multiplexed to probe multiple PPIs in parallel; its nonspecific background can be precisely measured, enabling the sensitive detection of weak PPIs. Using SpARC-map, we recover the known interface in the (p21-PCNA complex. We also use SpARC-map to probe the purinosome, the weakly bound complex of six purine biosynthetic enzymes, where no PPI interfaces are known. There, we identify interfaces that satisfy structural requirements for substrate channeling; we also identify protein surfaces that participate in multiple distinct interactions, which we validate using site-specific photocrosslinking in live human cells. Finally, we show that SpARC-map results can impose stringent constraints on outputs from machine learning based structure prediction.

Synthesis, evaluation and mechanistic insights of novel IMPDH inhibitors targeting ESKAPEE bacteria

Antimicrobial resistance poses a significant threat to global health, necessitating the development of novel therapeutic agents with unique mechanisms of action. Inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme in guanine nucleotide biosynthesis, is a promising target for the discovery of new antimicrobial agents. High-throughput screening studies have previously identified several urea-based leads as potential inhibitors, although many of these are characterised by reduced chemical stability. In this work, we describe the design and synthesis of a series of heteroaryl-susbtituted analogues and the evaluation of their inhibitory potency against IMPDHs. Our screening targets ESKAPEE pathogens, including Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Several analogues with submicromolar inhibitory potency are identified and show no inhibitory potency on human IMPDH nor cytotoxic effects on human cells. Kinetic studies revealed that these molecules act as noncompetitive inhibitors with respect to the substrates and ligand virtual docking simulations provided insights into the binding interactions at the interface of the NAD+ and IMP binding sites on IMPDH.

Carboxylation in de novo purine biosynthesis

De novo purine biosynthesis is one of two pathways for the synthesis of purine nucleotides that are critical for numerous biological processes, most notably nucleic acid replication. Within the pathway, there is only one carbon-carbon bond formation which is the carboxylation of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). Interestingly, there are two unique pathways within purine biosynthesis to accomplish this transformation and this divergence is species specific. In humans and higher eukaryotes, CAIR is synthesized directly from AIR and carbon dioxide by the enzyme AIR carboxylase. In bacteria, yeast, fungi and plants, CAIR synthesis requires two steps. In the first, AIR is converted into the unstable carbamate, N5-CAIR by the enzyme N5-CAIR synthetase. N5-CAIR is then converted into CAIR by transfer of the CO2 group from N5 to C4. This is catalyzed by the enzyme N5-CAIR mutase. This divergence has provided a biochemical rationale for targeting CAIR synthesis in the development of antimicrobial agents, but recent studies have provided strong evidence that AIR carboxylase plays a critical role in several cancers. Given the significance of these enzymes as drug targets, methods to prepare and evaluate these enzymes is of interest. In this chapter, we have accumulated the most relevant assays and provided methods to synthesize the substrates and purify the enzymes.

Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics

The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. Previous work found that the relationship between [ATP] and growth rate can account for the strength and occurrence of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. Using a combination of flux balance analysis and experimentation, we show that nucleotide synthesis can determine the relationship between [ATP] and growth and thus the strength of inoculum effect in an antibiotic class-dependent manner. If the [ATP]/growth rate is sufficiently high as determined by exogenously supplied nitrogenous bases, the inoculum effect does not occur. This is consistent for both Escherichia coli and Pseudomonas aeruginosa. Interestingly, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect, which may pave the way for intervention strategies to reduce the inoculum effect in the clinic.

IMPORTANCE

If a bacterial population can grow and reach a sufficiently high density, routine doses of antibiotics can be ineffective. This phenomenon, called the inoculum effect, has been observed for nearly all antibiotics and bacterial species. It has also been reported to result in antibiotic failure in the clinic. Understanding how to reduce the inoculum effect can make high-density infections easier to treat. Here, we show that purine and pyrimidine synthesis affect the strength of the inoculum effect; as the transcriptional activity of pyrimidine synthesis increases, the strength of the inoculum effect for aminoglycosides decreases. Conversely, as the transcriptional activity of purine synthesis increases, the strength of the inoculum effect for β-lactam antibiotics decreases. Our work highlights the importance of nucleotide synthesis in determining the strength of the inoculum effect, which may lead to the identification of new ways to treat high-density infections in the clinic.

Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation

ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here, we identify C12orf29 (RLIG1) as an atypical ATP-grasp enzyme that ligates RNA. Human RLIG1 and its homologs autoadenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. RLIG1 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Transcriptomic analyses of Rlig1 knockout mice revealed significant alterations in global tRNA levels in the brains of female mice, but not in those of male mice. Furthermore, crystal structures of a RLIG1 homolog from Yasminevirus bound to nucleotides revealed a minimal and atypical RNA ligase fold with a conserved active site architecture that participates in catalysis. Collectively, our results identify RLIG1 as an RNA ligase and suggest its involvement in tRNA biology.

Salivary Transmembrane Mucins of the MUC1 Family (CA 15-3, CA 27.29, MCA) in Breast Cancer: The Effect of Human Epidermal Growth Factor Receptor 2 (HER2)

The MUC1 family of transmembrane glycoproteins (CA 15-3, CA 27.29, MCA) is aberrantly expressed among patients with breast cancer. Objectives: to measure the level of degradation products of MUC1, including CA 15-3, CA 27.29, and MCA, in the saliva of breast cancer patients and to describe the biochemical processes that influence their expression and the regulation of their biological functions. Methods: The case-control study included three groups (breast cancer, fibroadenomas, and healthy controls). All study participants provided saliva samples strictly before starting treatment. The levels of MUC1, including CA 15-3, CA 27.29, and MCA, free progesterone and estradiol, cytokines (MCP-1, VEGF, TNF-α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-18), and amino acids (Asp, Gln, Gly, His, Leu + Ile, Orn, Phe, Pro, Tyr) were determined. Results: It was shown that the levels of the MUC1 family in the saliva of patients with HER2-positive breast cancer were significantly lower compared to the control group. The level of pro-inflammatory cytokines and the level of free estradiol affected the expression of MUC1. We obtained a reliable relationship between the aggressive nature of tumor growth, an increased level of pro-inflammatory cytokines, a low level of free estradiol, and the suppressed expression of salivary MUC1. Conclusions: Among patients with aggressive breast cancer, a high level of pro-inflammatory cytokines, and a low level of free estradiol, there was an inhibition of the expression of pathologically unchanged glycoprotein MUC1 in saliva.

Altered Metabolites in Hepatocellular Carcinoma (HCC) Paving the Road for Metabolomics Signature and Biomarkers for Early Diagnosis of HCC

Globally, hepatocellular carcinoma (HCC) is one of the most commonly encountered cancers. Because the current early diagnostic tests for HCC are not very sensitive, most cases of the disease are discovered late when it is in its terminal stage. Cellular metabolism changes during carcinogenesis to enable cancer cells to adapt to the hypoxic milieu, boost anabolic synthesis, promote survival, and evade apoptotic death signals. Omic techniques represent a breakthrough in the field of diagnostic technology. For example, Metabolomics analysis could be used to identify these metabolite alterations. Understanding the metabolic alterations linked to HCC is crucial for improving high-risk patients' surveillance and understanding the illness's biology. This review highlights the metabolic alterations linked to energy production in cancer cells, as well as the significantly altered metabolites and pathways associated with hepatocarcinogenesis, including acylcarnitines (ACs), amino acids, proteins, lipids, carbohydrates, glucose, and lactate, which reflect the anabolic and catabolic changes occurring in these cells. Additionally, it discusses the clinical implications of recent metabolomics that may serve as potential biomarkers for early diagnosis and monitoring of the progression of HCC.

A Fragment-Based Screen for Inhibitors of Escherichia coli N5-CAIR Mutase

Although purine biosynthesis is a primary metabolic pathway, there are fundamental differences between how purines are synthesized in microbes versus humans. In humans, the purine intermediate, 4- carboxy-5-aminoimidazole ribonucleotide (CAIR) is directly synthesized from 5-aminoimidazole ribonucleotide (AIR) and carbon dioxide by the enzyme AIR carboxylase. In bacteria, yeast and fungi, CAIR is synthesized from AIR via an intermediate N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) by the enzyme N5-CAIR mutase. The difference in pathways between humans and microbes indicate that N5-CAIR mutase is a potential antimicrobial drug target. To identify inhibitors of E. coli N5-CAIR mutase, a fragment-based screening campaign was conducted using a thermal shift assay and a library of 4,500 fragments. Twenty-eight fragments were initially identified that displayed dose-dependent binding to N5-CAIR mutase with Kd values ranging from 9-309 μM. Of the 28, 14 were obtained from commercial sources for retesting; however, only 5 showed dose-dependent binding to N5-CAIR mutase. The five fragments were assessed for their ability to inhibit enzyme activity. Four out of the 5 showed inhibition with Ki values of 4.8 to 159 μM. All fragments contained nitrogen heterocycles with 3 out of the 4 containing 5-membered heterocycles like those found in the substrate of the enzyme. The identified fragments show similarities to compounds identified from studies on B. anthracis N5-CAIR synthetase and human AIR carboxylase suggesting a common pharmacophore.

Inhibitory Effects of Surface Pre-Reacted Glass Ionomer Filler Eluate on Streptococcus mutans in the Presence of Sucrose

The surface pre-reacted glass ionomer (S-PRG) filler is a type of bioactive functional glass that releases six different ions. This study examined the effects of the S-PRG filler eluate on Streptococcus mutans in the presence of sucrose. In a solution containing S. mutans, the concentrations of BO33-, Al3+, Sr2+, and F- were significantly higher in the presence of the S-PRG filler eluate than in its absence (p < 0.001). The concentrations of these ions further increased in the presence of sucrose. Additionally, the S-PRG filler eluate significantly reduced glucan formation by S. mutans (p < 0.001) and significantly increased the pH of the bacterial suspension (p < 0.001). Bioinformatic analyses revealed that the S-PRG filler eluate downregulated genes involved in purine biosynthesis (purC, purF, purL, purM, and purN) and upregulated genes involved in osmotic pressure (opuAa and opuAb). At a low pH (5.0), the S-PRG filler eluate completely inhibited the growth of S. mutans in the presence of sucrose and significantly increased the osmotic pressure of the bacterial suspension compared with the control (p < 0.001). These findings suggest that ions released from the S-PRG filler induce gene expression changes and exert an inhibitory effect on S. mutans in the presence of sucrose.

Kinetics of Riboflavin Production by Hyphopichia wangnamkhiaoensis under Varying Nutritional Conditions

Riboflavin, an essential vitamin for humans, is extensively used in various industries, with its global demand being met through fermentative processes. Hyphopichia wangnamkhiaoensis is a novel dimorphic yeast species capable of producing riboflavin. However, the nutritional factors affecting riboflavin production in this yeast species remain unknown. Therefore, we conducted a kinetic study on the effects of various nutritional factors-carbon and energy sources, nitrogen sources, vitamins, and amino acids-on batch riboflavin production by H. wangnamkhiaoensis. Batch experiments were performed in a bubble column bioreactor to evaluate cell growth, substrate consumption, and riboflavin production. The highest riboflavin production was obtained when the yeast growth medium was supplemented with glucose, ammonium sulfate, biotin, and glycine. Using these chemical components, along with the mineral salts from Castañeda-Agullo's culture medium, we formulated a novel, low-cost, and effective culture medium (the RGE medium) for riboflavin production by H. wangnamkhiaoensis. This medium resulted in the highest levels of riboflavin production and volumetric productivity, reaching 16.68 mg/L and 0.713 mg/L·h, respectively, within 21 h of incubation. These findings suggest that H. wangnamkhiaoensis, with its shorter incubation time, could improve the efficiency and cost-effectiveness of industrial riboflavin production, paving the way for more sustainable production methods.

Computational prediction of crucial genes involved in gonorrhea infection and neoplastic cell transformation: A multiomics approach

Neisseria gonorrheae, the causative agent of genitourinary infections, has been associated with asymptomatic or recurrent infections and has the potential to form biofilms and induce inflammation and cell transformation. Herein, we aimed to use computational analysis to predict novel associations between chronic inflammation caused by gonorrhea infection and neoplastic transformation. Prioritization and gene enrichment strategies based on virulence and resistance genes utilizing essential genes from the DEG and PANTHER databases, respectively, were performed. Using the STRING database, protein‒protein interaction networks were constructed with 55 nodes of bacterial proteins and 72 nodes of proteins involved in the host immune response. MCODE and cytoHubba were used to identify 12 bacterial hub proteins (murA, murB, murC, murD, murE, purN, purL, thyA, uvrB, kdsB, lpxC, and ftsH) and 19 human hub proteins, of which TNF, STAT3 and AKT1 had high significance. The PPI networks are based on the connectivity degree (K), betweenness centrality (BC), and closeness centrality (CC) values. Hub genes are vital for cell survival and growth, and their significance as potential drug targets is discussed. This computational study provides a comprehensive understanding of inflammation and carcinogenesis pathways that are activated during gonorrhea infection.

The significant role of amino acid metabolic reprogramming in cancer

Amino acid metabolism plays a pivotal role in tumor microenvironment, influencing various aspects of cancer progression. The metabolic reprogramming of amino acids in tumor cells is intricately linked to protein synthesis, nucleotide synthesis, modulation of signaling pathways, regulation of tumor cell metabolism, maintenance of oxidative stress homeostasis, and epigenetic modifications. Furthermore, the dysregulation of amino acid metabolism also impacts tumor microenvironment and tumor immunity. Amino acids can act as signaling molecules that modulate immune cell function and immune tolerance within the tumor microenvironment, reshaping the anti-tumor immune response and promoting immune evasion by cancer cells. Moreover, amino acid metabolism can influence the behavior of stromal cells, such as cancer-associated fibroblasts, regulate ECM remodeling and promote angiogenesis, thereby facilitating tumor growth and metastasis. Understanding the intricate interplay between amino acid metabolism and the tumor microenvironment is of crucial significance. Expanding our knowledge of the multifaceted roles of amino acid metabolism in tumor microenvironment holds significant promise for the development of more effective cancer therapies aimed at disrupting the metabolic dependencies of cancer cells and modulating the tumor microenvironment to enhance anti-tumor immune responses and inhibit tumor progression.

Metabolic pathways and antimicrobial peptide resistance in bacteria

Antimicrobial resistance is a pressing concern that poses a significant threat to global public health, necessitating the exploration of alternative strategies to combat drug-resistant microbial infections. Recently, antimicrobial peptides (AMPs) have gained substantial attention as possible replacements for conventional antibiotics. Because of their pharmacodynamics and killing mechanisms, AMPs display a lower risk of bacterial resistance evolution compared with most conventional antibiotics. However, bacteria display different mechanisms to resist AMPs, and the role of metabolic pathways in the resistance mechanism is not fully understood. This review examines the intricate relationship between metabolic genes and AMP resistance, focusing on the impact of metabolic pathways on various aspects of resistance. Metabolic pathways related to guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) [collectively (p)ppGpp], the tricarboxylic acid (TCA) cycle, haem biosynthesis, purine and pyrimidine biosynthesis, and amino acid and lipid metabolism influence in different ways metabolic adjustments, biofilm formation and energy production that could be involved in AMP resistance. By targeting metabolic pathways and their associated genes, it could be possible to enhance the efficacy of existing antimicrobial therapies and overcome the challenges exhibited by phenotypic (recalcitrance) and genetic resistance toward AMPs. Further research in this area is needed to provide valuable insights into specific mechanisms, uncover novel therapeutic targets, and aid in the fight against antimicrobial resistance.

Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis

Phosphomethylpyrimidine synthase (ThiC) catalyzes the conversion of AIR to the thiamin pyrimidine HMP-P. This reaction is the most complex enzyme-catalyzed radical cascade identified to date, and the detailed mechanism has remained elusive. In this paper, we describe the trapping of five new intermediates that provide snapshots of the ThiC reaction coordinate and enable the formulation of a revised mechanism for the ThiC-catalyzed reaction.

Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design

Inhibition of hypoxanthine-guanine-xanthine phosphoribosyltransferase activity decreases the pool of 6-oxo and 6-amino purine nucleoside monophosphates required for DNA and RNA synthesis, resulting in a reduction in cell growth. Therefore, inhibitors of this enzyme have potential to control infections, caused by Plasmodium falciparum and Plasmodium vivax, Trypanosoma brucei, Mycobacterium tuberculosis, and Helicobacter pylori. Five compounds synthesized here that contain a purine base covalently linked by a prolinol group to one or two phosphonate groups have Ki values ranging from 3 nM to >10 μM, depending on the structure of the inhibitor and the biological origin of the enzyme. X-ray crystal structures show that, on binding, these prolinol-containing inhibitors stimulated the movement of active site loops in the enzyme. Against TBr in cell culture, a prodrug exhibited an EC50 of 10 μM. Thus, these compounds are excellent candidates for further development as drug leads against infectious diseases as well as being potential anticancer agents.

Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation

ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here we identify C12orf29 as an atypical ATP-grasp enzyme that ligates RNA. Human C12orf29 and its homologs auto-adenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. C12orf29 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Genetic depletion of c12orf29 in female mice alters global tRNA levels in brain. Furthermore, crystal structures of a C12orf29 homolog from Yasminevirus bound to nucleotides reveal a minimal and atypical RNA ligase fold with a unique active site architecture that participates in catalysis. Collectively, our results identify C12orf29 as an RNA ligase and suggest its involvement in tRNA biology.

Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics

The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.

Sulfur (SⅥ)-containing heterocyclic hybrids as antibacterial agents against methicillin-resistant Staphylococcus aureus (MRSA) and its SAR

The discovery of new small molecule-based inhibitors is an attractive field in medicinal chemistry. Structurally diversified heterocyclic derivatives have been investigated to combat multi-drug resistant bacterial infections and they offers several mechanism of action. Methicillin-resistant Staphylococcus aureus (MRSA) is becoming more and more deadly to humans because of its simple method of transmission, quick development of antibiotic resistance, and ability to cause hard-to-treat skin and filmy diseases. The sulfur (SVI) particularly sulfonyl and sulfonamide based heterocyclic moieties, have found to be good anti-MRSA agents. The development of new nontoxic, economical and highly active sulfur (SVI) containing derivatives has become hot research topics in drug discovery research. Presently, more than 150 FDA approved Sulfur (SVI)-based drugs are available in the market, and they are widely used to treat various types of diseases with different therapeutic potential. The present collective data provides the latest advancements in Sulfur (SVI)-hybrid compounds as antibacterial agents against MRSA. It also examines the outcomes of in-vitro and in-vivo investigations, exploring potential mechanisms of action and offering alternative perspectives on the structure-activity relationship (SAR). Sulfur (SVI)-hybrids exhibits synergistic effects with existing drugs to provide antibacterial action against MRSA.

Transposon sequencing reveals metabolic pathways essential for Mycobacterium tuberculosis infection

New drugs are needed to shorten and simplify treatment of tuberculosis caused by Mycobacterium tuberculosis. Metabolic pathways that M. tuberculosis requires for growth or survival during infection represent potential targets for anti-tubercular drug development. Genes and metabolic pathways essential for M. tuberculosis growth in standard laboratory culture conditions have been defined by genome-wide genetic screens. However, whether M. tuberculosis requires these essential genes during infection has not been comprehensively explored because mutant strains cannot be generated using standard methods. Here we show that M. tuberculosis requires the phenylalanine (Phe) and de novo purine and thiamine biosynthetic pathways for mammalian infection. We used a defined collection of M. tuberculosis transposon (Tn) mutants in essential genes, which we generated using a custom nutrient-rich medium, and transposon sequencing (Tn-seq) to identify multiple central metabolic pathways required for fitness in a mouse infection model. We confirmed by individual retesting and complementation that mutations in pheA (Phe biosynthesis) or purF (purine and thiamine biosynthesis) cause death of M. tuberculosis in the absence of nutrient supplementation in vitro and strong attenuation in infected mice. Our findings show that Tn-seq with defined Tn mutant pools can be used to identify M. tuberculosis genes required during mouse lung infection. Our results also demonstrate that M. tuberculosis requires Phe and purine/thiamine biosynthesis for survival in the host, implicating these metabolic pathways as prime targets for the development of new antibiotics to combat tuberculosis.

Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways

Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.

A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis

De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.

Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin

Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.

Amino acid metabolism in tumor biology and therapy

Amino acid metabolism plays important roles in tumor biology and tumor therapy. Accumulating evidence has shown that amino acids contribute to tumorigenesis and tumor immunity by acting as nutrients, signaling molecules, and could also regulate gene transcription and epigenetic modification. Therefore, targeting amino acid metabolism will provide new ideas for tumor treatment and become an important therapeutic approach after surgery, radiotherapy, and chemotherapy. In this review, we systematically summarize the recent progress of amino acid metabolism in malignancy and their interaction with signal pathways as well as their effect on tumor microenvironment and epigenetic modification. Collectively, we also highlight the potential therapeutic application and future expectation.

Assessment of nucleic acid content, amino acid profile, carcass, and meat quality of Thai native chicken

Functional foods are innovative products that hold health-enhancing potential. They are contributing to changing trends in both consumer behavior and the market. This study was conducted to investigate the effects of breed on the nucleic acid content, amino acid profile, carcass, and meat quality of different breeds of chickens. The outcomes of which could lead to the production of functional chicken meat. In this experiment, 4 genotypes of chicken, namely commercial broilers (CBR), Thai native chickens (Mae Hong Son; MHS), Thai native chickens (Pradu Hang Dam; PHD), and male layer chickens (MLC), were fed commercial feed and reared under identical conditions. All chickens were slaughtered at the market age, whereas the breasts and thighs were separated from the carcasses to determine chemical composition and meat quality. The results indicated that carcass and meat quality traits were significantly different (P < 0.05) among chicken breeds and meat parts. Notably, commercial breeds (CBR and MLC) were superior in performance and carcass quality when compared with the Thai native chickens (MHS and PHD). CBR had the highest growth performance and carcass quality traits (P < 0.01), whereas MHS exhibited the lowest weight gain (P < 0.05). However, Thai native chickens were lower in fat, cholesterol, triglycerides, purine, and uric acid (P < 0.05) contents than the commercial breeds. Interestingly, MHS contained the lowest purine and malondialdehyde levels when compared with the other breeds (P < 0.01). Moreover, MHS contained the highest amounts of glutamic acid in both the breasts and thighs (P < 0.05). Therefore, the meat of MHS may be classified as a functional chicken meat, as it was found to have a pleasant meaty taste and hold nutritional value, which positively influences consumers' health.

Effect of dietary betaine supplementation on the liver transcriptome profile in broiler chickens under heat stress conditions

OBJECTIVE

The objective of the present study was to investigate the effect of dietary betaine (BT) supplementation on the hepatic transcriptome profiles in broiler chickens raised under heat stress (HS) conditions.

METHODS

A total of 180 (21-d-old) Ross 308 male broiler chicks were allotted to 1 of 3 treatment groups with 6 replicated cages in a completely randomized design. One group was kept under thermoneutral conditions at all times and was fed a basal diet (PC). Other 2 groups were exposed to a cyclic heat stress condition. One of the 2 groups under heat stress conditions was fed the basal diet as a negative control (NC), whereas the other group was fed the basal diet supplemented with 0.2% BT. All chickens were provided with diets and water ad libitum for 21 d. Following the experiment, the liver samples were collected for RNA sequencing analysis.

RESULTS

Broiler chickens in NC and BT group had decreased (p<0.05) growth performance. In the transcriptome analysis, the number of differentially expressed genes were identified in the liver by HS conditions and dietary BT supplementation. In the comparison between NC and PC treatments, genes related to energy and nucleic acid metabolism, amino acid metabolism, and immune system were altered by HS, which support the reason why heat-stressed poultry had decreased growth performance. In the comparison between NC and BT treatments, genes related to lipid metabolism, carbohydrate metabolism, and immune system were differently expressed under HS conditions.

CONCLUSION

HS negatively impacts various physiological processes, including DNA replication, metabolism of amino acids, lipids, and carbohydrates, and cell cycle progression in broiler chickens. Dietary BT supplementation, however, offers potential counteractive effects by modulating liver function, facilitating gluconeogenesis, and enhancing immune systems. These findings provide a basis for understanding molecular responses by HS and the possible benefits of dietary BT supplementation in broiler chickens exposed to HS.

Volatile anesthetic isoflurane exposure facilitates Enterococcus biofilm infection

Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital-acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic-di-AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP-S). With the hypothesis that isoflurane directly bound to PRPP-S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.

The regulation of amino acid metabolism in tumor cell death: from the perspective of physiological functions

Amino acids (AAs) are crucial molecules for the synthesis of mammalian proteins as well as a source of energy and redox equilibrium maintenance. The development of tumors also requires AAs as nutrients. Increased AAs metabolism is frequently seen in tumor cells to produce enough biomass, energy, and reduction agents. However, increased AA demand may result in auxotrophy in some cancer cells, highlighting the vulnerabilities of cancers and exposing the AA metabolism as a potential target for cancer therapy. The dynamic balance of cell survival and death is required for cellular homeostasis, growth, and development. Malignant cells manage to avoid cell death through a range of mechanisms, such as developing an addiction to amino acids through metabolic adaptation. In order to offer some guidance for AA-targeted cancer therapy, we have outlined the function of AA metabolism in tumor progression, the modalities of cell death, and the regulation of AA metabolism on tumor cell death in this review.

New Insights into Radio-Resistance Mechanism Revealed by (Phospho)Proteome Analysis of Deinococcus Radiodurans after Heavy Ion Irradiation

Deinococcus radiodurans (D. radiodurans) can tolerate various extreme environments including radiation. Protein phosphorylation plays an important role in radiation resistance mechanisms; however, there is currently a lack of systematic research on this topic in D. radiodurans. Based on label-free (phospho)proteomics, we explored the dynamic changes of D. radiodurans under various doses of heavy ion irradiation and at different time points. In total, 2359 proteins and 1110 high-confidence phosphosites were identified, of which 66% and 23% showed significant changes, respectively, with the majority being upregulated. The upregulated proteins at different states (different doses or time points) were distinct, indicating that the radio-resistance mechanism is dose- and stage-dependent. The protein phosphorylation level has a much higher upregulation than protein abundance, suggesting phosphorylation is more sensitive to irradiation. There were four distinct dynamic changing patterns of phosphorylation, most of which were inconsistent with protein levels. Further analysis revealed that pathways related to RNA metabolism and antioxidation were activated after irradiation, indicating their importance in radiation response. We also screened some key hub phosphoproteins and radiation-responsive kinases for further study. Overall, this study provides a landscape of the radiation-induced dynamic change of protein expression and phosphorylation, which provides a basis for subsequent functional and applied studies.

Structure-Guided Discovery of N5-CAIR Mutase Inhibitors

Because purine nucleotides are essential for all life, differences between how microbes and humans metabolize purines can be exploited for the development of antimicrobial therapies. While humans biosynthesize purine nucleotides in a 10-step pathway, most microbes utilize an additional 11th enzymatic activity. The human enzyme, aminoimidazole ribonucleotide (AIR) carboxylase generates the product 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) directly. Most microbes, however, require two separate enzymes, a synthetase (PurK) and a mutase (PurE), and proceed through the intermediate, N5-CAIR. Toward the development of therapeutics that target these differences, we have solved crystal structures of the N5-CAIR mutase of the human pathogens Legionella pneumophila (LpPurE) and Burkholderia cenocepacia (BcPurE) and used a structure-guided approach to identify inhibitors. Analysis of the structures reveals a highly conserved fold and active site architecture. Using this data, and three additional structures of PurE enzymes, we screened a library of FDA-approved compounds in silico and identified a set of 25 candidates for further analysis. Among these, we identified several new PurE inhibitors with micromolar IC50 values. Several of these compounds, including the α1-blocker Alfuzosin, inhibit the microbial PurE enzymes much more effectively than the human homologue. These structures and the newly described PurE inhibitors are valuable tools to aid in further studies of this enzyme and provide a foundation for the development of compounds that target differences between human and microbial purine metabolism.

GART Functions as a Novel Methyltransferase in the RUVBL1/β-Catenin Signaling Pathway to Promote Tumor Stemness in Colorectal Cancer

Tumor stemness is associated with the recurrence and incurability of colorectal cancer (CRC), which lacks effective therapeutic targets and drugs. Glycinamide ribonucleotide transformylase (GART) fulfills an important role in numerous types of malignancies. The present study aims to identify the underlying mechanism through which GART may promote CRC stemness, as to developing novel therapeutic methods. An elevated level of GART is associated with poor outcomes in CRC patients and promotes the proliferation and migration of CRC cells. CD133+ cells with increased GART expression possess higher tumorigenic and proliferative capabilities both in vitro and in vivo. GART is identified to have a novel methyltransferase function, whose enzymatic activity center is located at the E948 site. GART also enhances the stability of RuvB-like AAA ATPase 1 (RUVBL1) through methylating its K7 site, which consequently aberrantly activates the Wnt/β-catenin signaling pathway to induce tumor stemness. Pemetrexed (PEM), a compound targeting GART, combined with other chemotherapy drugs greatly suppresses tumor growth both in a PDX model and in CRC patients. The present study demonstrates a novel methyltransferase function of GART and the role of the GART/RUVBL1/β-catenin signaling axis in promoting CRC stemness. PEM may be a promising therapeutic agent for the treatment of CRC.

Protein Profiling of Aedes aegypti Treated with Streptomyces sp. KSF103 Ethyl Acetate Extract Reveals Potential Insecticidal Targets and Metabolic Pathways

The insecticidal activity of Streptomyces sp. KSF103 ethyl acetate (EA) extract against mosquitoes is known; however, the underlying mechanism behind this activity remains elusive. In this study, liquid chromatography with tandem mass spectrometry (LC-MS/MS) was employed to investigate changes in the protein profile of Aedes aegypti larvae and adults treated with lethal concentrations of 50 (LC50) EA extract. By comparing the treated and untreated mosquitoes, this study aimed to identify proteins or pathways that exhibit alterations, potentially serving as targets for future insecticide development. Treatment with a lethal concentration of EA extract upregulated 15 proteins in larvae, while in adults, 16 proteins were upregulated, and two proteins were downregulated. These proteins were associated with metabolism, protein regulation/degradation, energy production, cellular organization and structure, enzyme activity, and catalysis, as well as calcium ion transport and homeostasis. Notably, ATP synthase, fructose-bisphosphate aldolase (FBA), and ATP citrate synthase were significantly expressed in both groups. Gene ontology analysis indicated a focus on energy metabolic processes. Molecular docking revealed a strong interaction between dodemorph, selagine (compounds from the EA extract), and FBA, suggesting FBA as a potential protein target for insecticide development. Further studies such as Western blot and transcriptomic analyses are warranted to validate the findings.

Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide

A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate's prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate's degradation. Cu²⁺-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions.

Purine synthesis suppression reduces the development and progression of pulmonary hypertension in rodent models

AIMS

Proliferation of vascular smooth muscle cells (VSMCs) is a hallmark of pulmonary hypertension (PH). Proliferative cells utilize purine bases from the de novo purine synthesis (DNPS) pathways for nucleotide synthesis; however, it is unclear whether DNPS plays a critical role in VSMC proliferation during development of PH. The last two steps of DNPS are catalysed by the enzyme 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC). This study investigated whether ATIC-driven DNPS affects the proliferation of pulmonary artery smooth muscle cells (PASMCs) and the development of PH.

METHODS AND RESULTS

Metabolites of DNPS in proliferative PASMCs were measured by liquid chromatography-tandem mass spectrometry. ATIC expression was assessed in platelet-derived growth factor-treated PASMCs and in the lungs of PH rodents and patients with pulmonary arterial hypertension. Mice with global and VSMC-specific knockout of Atic were utilized to investigate the role of ATIC in both hypoxia- and lung interleukin-6/hypoxia-induced murine PH. ATIC-mediated DNPS at the mRNA, protein, and enzymatic activity levels were increased in platelet-derived growth factor-treated PASMCs or PASMCs from PH rodents and patients with pulmonary arterial hypertension. In cultured PASMCs, ATIC knockdown decreased DNPS and nucleic acid DNA/RNA synthesis, and reduced cell proliferation. Global or VSMC-specific knockout of Atic attenuated vascular remodelling and inhibited the development and progression of both hypoxia- and lung IL-6/hypoxia-induced PH in mice.

CONCLUSION

Targeting ATIC-mediated DNPS compromises the availability of purine nucleotides for incorporation into DNA/RNA, reducing PASMC proliferation and pulmonary vascular remodelling and ameliorating the development and progression of PH.

Diverse strategies adopted by nature for regulating purine biosynthesis via fine-tuning of purine metabolic enzymes

Purine nucleotides, generated by de novo synthesis and salvage pathways, are essential for metabolism and act as building blocks of genetic material. To avoid an imbalance in the nucleotide pool, nature has devised several strategies to regulate/tune the catalytic performance of key purine metabolic enzymes. Here, we discuss some recent examples, such as stress-regulating alarmones that bind to select pathway enzymes, huge ensembles like dynamic metabolons and self-assembled filaments that highlight the layered fine-control prevalent in the purine metabolic pathway to fulfill requisite purine demands. Examples of enzymes that turn-on only under allosteric control, are regulated via long-distance communication that facilitates transient conduits have additionally been explored.

New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts

The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.

Methionyl-tRNA formyltransferase utilizes 10-formyldihydrofolate as an alternative substrate and impacts antifolate drug action

Methionyl-tRNA formyltransferase (Fmt)-mediated formylation of Met-tRNA^fMet to fMet-tRNA^fMet is crucial for efficient initiation of translation in bacteria and the eukaryotic organelles. Folate dehydrogenase-cyclohydrolase (FolD), a bifunctional enzyme, carries out conversion of 5,10-methylene tetrahydrofolate (5,10-CH₂-THF) to 10-formyl-THF (10-CHO-THF), a metabolite utilized by Fmt as a formyl group donor. In this study, using in vivo and in vitro approaches, we show that 10-CHO-DHF may also be utilized by Fmt as an alternative substrate (formyl group donor) to formylate Met-tRNA^fMet. Dihydrofolate (DHF) formed as a by-product in the in vitro assay was verified by LC-MS/MS analysis. FolD-deficient mutants and Fmt over-expressing strains were more sensitive to trimethoprim (TMP) than the ∆fmt strain, suggesting that the domino effect of TMP leads to inhibition of protein synthesis and strain growth. Antifolate treatment to Escherichia coli showed a decrease in the reduced folate species (THF, 5,10-CH₂-THF, 5-CH₃-THF, 5,10-CH⁺-THF and 5-CHO-THF) and increase in the oxidized folate species (folic acid and DHF). In cells, 10-CHO-DHF and 10-CHO-folic acid were enriched in the stationary phase. This suggests that 10-CHO-DHF is a bioactive metabolite in the folate pathway for generating other folate intermediates and fMet-tRNA^fMet.

Quantitation of Glutamine Synthetase 1 Activity in Drosophila melanogaster

Protocols to assay the activity of glutamine synthetase (GS) are presented as they have been used in our laboratory to correlate the expression levels of the gene encoding Drosophila GS1 gene, the GS1 protein levels, and its activity in extracts of larvae and heads from Drosophila melanogaster. The assays are based on the glutamine synthetase-catalyzed formation of γ-glutamylhydroxylamine in the presence of ATP, L-glutamate, and hydroxylamine, in which hydroxylamine substitutes for ammonia in the reaction. Formation of γ-glutamylhydroxylamine is monitored spectrophotometrically in discontinuous assays upon complex formation with FeCl3. Fixed-time assays and those based on monitoring the time-course of product formation at different reaction times are described. The protocols can be adapted to quantify glutamine synthetase activity on biological materials other than Drosophila.