A conserved motif liganding the [4Fe-4S] cluster in [4Fe-4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress

RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification

In this study, we present an extensive analysis of a widespread group of bacterial tRNA de-modifying enzymes, dubbed RudS, which consist of a TudS desulfidase fused to a Domain of Unknown Function 1722 (DUF1722). RudS enzymes exhibit specific de-modification activity towards the 4-thiouridine modification (s4U) in tRNA molecules, as indicated by our experimental findings. The heterologous overexpression of RudS genes in Escherichia coli significantly reduces the tRNA 4-thiouridine content and diminishes UVA-induced growth delay, indicating the enzyme's role in regulating photosensitive tRNA s4U modification. Through a combination of protein modeling, docking studies, and molecular dynamics simulations, we have identified amino acid residues involved in catalysis and tRNA binding. Experimental validation through targeted mutagenesis confirms the TudS domain as the catalytic core of RudS, with the DUF1722 domain facilitating tRNA binding in the anticodon region. Our results suggest that RudS tRNA modification eraser proteins may play a role in regulating tRNA during prokaryotic stress responses.

New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.

Preparation of Iron-Based Sulfides and Their Applications in Biomedical Fields

Recently, iron-based sulfides, including iron sulfide minerals and biological iron sulfide clusters, have attracted widespread interest, owing to their excellent biocompatibility and multi-functionality in biomedical applications. As such, controlled synthesized iron sulfide nanomaterials with elaborate designs, enhanced functionality and unique electronic structures show numerous advantages. Furthermore, iron sulfide clusters produced through biological metabolism are thought to possess magnetic properties and play a crucial role in balancing the concentration of iron in cells, thereby affecting ferroptosis processes. The electrons in the Fenton reaction constantly transfer between Fe²⁺ and Fe³⁺, participating in the production and reaction process of reactive oxygen species (ROS). This mechanism is considered to confer advantages in various biomedical fields such as the antibacterial field, tumor treatment, biosensing and the treatment of neurodegenerative diseases. Thus, we aim to systematically introduce recent advances in common iron-based sulfides.

Bacterial Communication Coordinated Behaviors of Whole Communities to Cope with Environmental Changes

Bacterial communication plays an important role in coordinating microbial behaviors in a community. However, how bacterial communication organizes the entire community for anaerobes to cope with varied anaerobic-aerobic conditions remains unclear. We constructed a local bacterial communication gene (BCG) database comprising 19 BCG subtypes and 20279 protein sequences. BCGs in anammox-partial nitrification consortia coping with intermittent aerobic and anaerobic conditions as well as gene expressions of 19 species were inspected. We found that when suffering oxygen changes, intra- and interspecific communication by a diffusible signal factor (DSF) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) changed first, which in turn induced changes of autoinducer-2 (AI-2)-based interspecific and acyl homoserine lactone (AHLs)-based intraspecific communication. DSF and c-di-GMP-based communication regulated 455 genes, which covered 13.64% of the genomes and were mainly involved in antioxidation and metabolite residue degradation. For anammox bacteria, oxygen influenced DSF and c-di-GMP-based communication through RpfR to upregulate antioxidant proteins, oxidative damage-repairing proteins, peptidases, and carbohydrate-active enzymes, which benefited their adaptation to oxygen changes. Meanwhile, other bacteria also enhanced DSF and c-di-GMP-based communication by synthesizing DSF, which helped anammox bacteria survive at aerobic conditions. This study evidences the role of bacterial communication as an "organizer" within consortia to cope with environmental changes and sheds light on understanding bacterial behaviors from the perspective of sociomicrobiology.

CsMYC2 is involved in the regulation of phenylpropanoid biosynthesis induced by trypsin in cucumber (Cucumis sativus) during storage

Trypsin has a new activity of scavenging superoxide anion and generating hydrogen peroxide. Trypsin can significantly improve the storage quality of C. sativus. To illustrate the mechanism of trypsin-induced resistance in fruits and vegetables, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out. Transcriptomic results showed that 1068 genes highly related to phenylpropanoid biosynthesis gathered in the brown module were obtained by WGCNA. In KEGG analysis, differentially expressed genes (DEGs) were also highly enriched in EIP (Environmental Information Processing) pathways "Plant hormone signal transduction (map04075)" and "MAPK signaling pathway-plant (map04016)". Next, 87 genes were identified as the leading edge by GSEA analysis. So far, CsMYC2 was highlighted as a key transcription factor that regulates phenylpropanoid biosynthesis identified by GSEA and WGCNA. Furthermore, the major route of biosynthesis of phenylpropanoid compounds including coumarins, lignins, chlorogenic acid, flavonoids, and derivatives regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Results of O2PLS showed that CsMYC2 was positively correlated with Rosmarinic acid-3-O-glucoside, Epigallocatechin, Quercetin-3-O-sophoroside (Baimaside), and so on. Correlation between CsMYC2, phenylpropanoid related genes, and metabolites in C. sativus was illustrated by co-expression networks. Roles of CsMYC2 were further checked in C. sativus by VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus.

The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H

Ribonucleoside monophosphates are inevitably misincorporated into the DNA genome inside cells, and they need to be excised to avoid chromosome instability. Ribonucleases H (RNases H) are enzymes that specifically hydrolyze the RNA strand of RNA/DNA hybrids or the RNA moiety from DNA containing a stretch of RNA, they therefore are required for DNA integrity. Extensive studies have drawn a mostly clear picture of the mechanisms of RNase H catalysis, but some questions are still lacking definitive answers. This review summarizes three alternative models of RNase H catalysis. The two-metal model is prevalent, but a three-metal model suggests the involvement of a third cation in catalysis. Apparently, the mechanisms underlying metal-dependent hydrolyzation are more complicated than initially thought. We also discuss the metal choices of RNases H and analyze how chemically similar cations function differently. Substrate and cleavage-site specificities vary among RNases H, and this is explicated in detail. An intriguing phenomenon is that organisms have diverse RNase H combinations, which may provide important hints to how rnh genes were transferred during evolution. Whether RNase H is essential for cellular growth, a key question in the study of in vivo functions, is also discussed. This article may aid in understanding the mechanisms underlying RNase H and in developing potentially promising applications of it.

Optimization of a Method for Detecting Intracellular Sulfane Sulfur Levels and Evaluation of Reagents That Affect the Levels in Escherichia coli

Sulfane sulfur is a class of compounds containing zero-valent sulfur. Most sulfane sulfur compounds are reactive and play important signaling roles. Key enzymes involved in the production and metabolism of sulfane sulfur have been characterized; however, little is known about how to change intracellular sulfane sulfur (iSS) levels. To accurately measure iSS, we optimized a previously reported method, in which reactive iSS reacts with sulfite to produce thiosulfate, a stable sulfane sulfur compound, before detection. With the improved method, several factors were tested to influence iSS in Escherichia coli. Temperature, pH, and osmotic pressure showed little effect. At commonly used concentrations, most tested oxidants, including hydrogen peroxide, tert-butyl hydroperoxide, hypochlorous acid, and diamide, did not affect iSS, but carbonyl cyanide m-chlorophenyl hydrazone increased iSS. For reductants, 10 mM dithiothreitol significantly decreased iSS, but tris(2-carboxyethyl)phosphine did not. Among different sulfur-bearing compounds, NaHS, cysteine, S₂O₃²⁻ and diallyl disulfide increased iSS, of which only S₂O₃²⁻ did not inhibit E. coli growth at 10 mM or less. Thus, with the improved method, we have identified reagents that may be used to change iSS in E. coli and other organisms, providing tools to further study the physiological functions of iSS.

Oxidative stress response system in Escherichia coli arising from diphenyl ditelluride (PhTe)2 exposure

The toxicity of diphenyl ditelluride (PhTe)₂ is associated with its ability to oxidize sulfhydryl groups from biological molecules. Therefore, we evaluated possible molecular mechanisms of toxicity induced by this organochalcogen in Escherichia coli (E. coli) by evaluating oxidative damage markers, relative expression of genes associated with the cellular redox state in bacteria, such as katG, sodA, sodB, soxS, and oxyR, as well as the activity of enzymes responsible for cellular redox balance. After exposure of (PhTe)₂ (6, 12, and 24 μg/mL), there was a decrease in non-protein thiols (NPSH) levels, an increase in protein carbonylation and lipid peroxidation in E. coli. Intra- and extracellular reactive species (RS) was increased at concentrations of 6, 12, and 24 μg/mL. The superoxide dismutase (SOD) activity was increased at the three concentrations tested, while catalase (CAT) activity was higher at 12 and 24 μg/mL. The soxS gene showed lower expression at the three concentrations tested, while the oxyR gene was supressed at 24 μg/mL. The katG antioxidant response gene showed lower expression, and sodA and sodB were positively activated, except for sodB at 6 μg/mL. Our findings demonstrate that exposure to (PhTe)₂ induced RS formation, NPSH depletion and changes in transcriptional factors regulation, characterizing it as a multi-target compound, causing disruption in cellular oxidative state, as well as molecular mechanisms associated in E. coli.

The aerobic electron flux is deficient in fumarate respiration of a strict anaerobe Bacteroides thetaiotaomicron

Why oxygen ceases the growth of strictly anaerobic bacteria is a longstanding question, yet the answer remains unclear. Studies have confirmed that the dehydratase-fumarase containing an iron-sulfur cluster ([4Fe-4S]) is inactivated upon exposure to oxygen in the intestinal obligate anaerobe, Bacteroides thetaiotaomicron (B. thetaiotaomicron); this blocks fumarate respiration, which is the essential energy-producing pathway in anaerobes. Here, we substituted the [4Fe-4S]-dependent fumarase in B. thetaiotaomicron with an iron-free isozyme from E. coli (Ec-FumC). Results show that Ec-FumC successfully performed the catalytic function of fumarase in B. thetaiotaomicron, as the fum-mutant strain that expressed Ec-FumC exhibited succinate-producing ability under anaerobic growth conditions. Ec-FumC is oxygen-resistant and remains active to produce fumarate upon aeration; however, B. thetaiotaomicron mutant that expressed Ec-FumC did not convert fumarate to succinate during air exposure. Biochemical assays of inverted membrane vesicles from wild-type B. thetaiotaomicron confirmed that the electron flux from NADH to fumarate was less efficient in the presence of air as compared to that without oxygen. Our findings suggest that the anaerobic fumarate respiration might be paralyzed due to electron dissipations upon aeration of the obligate anaerobe.

The Fe-S proteome of Escherichia coli: prediction, function and fate

Iron-sulfur (Fe-S) clusters are inorganic ubiquitous and ancient cofactors. Fe-S bound proteins contribute to most cellular processes, including DNA replication and integrity, genetic expression and regulation, metabolism, biosynthesis and most bioenergetics systems. Also, Fe-S proteins hold a great biotechnological potential in metabolite and chemical production, including antibiotics. From classic biophysics and spectroscopy methodologies to recent development in bioinformatics, including structural modeling and chemoproteomics, our capacity to predict and identify Fe-S proteins has spectacularly increased over the recent years. Here, these developments are presented and collectively used to update the composition of Escherichia coli Fe-S proteome, for which we predict 181 occurrences, i.e. 40 more candidates than in our last catalog (Py and Barras, 2010), and equivalent to 4% of its total proteome. Besides, Fe-S clusters can be targeted by redox active compounds or reactive oxygen and nitrosative species, and even be destabilized by contaminant metals. Accordingly, we discuss how cells handle damaged Fe-S proteins, i.e. degradation, recycling or repair.

When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence

The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.

Interplay between reactive oxygen and nitrogen species in living organisms

In living organisms most oxygen consumed is reduced to water via four-electron reduction. However, few percentages of oxygen are reduced by consecutive one electron mechanisms giving rise to superoxide anion radical, (O₂^•-), hydrogen peroxide (H₂O₂) and hydroxyl radical (HO^•) and their derivatives collectively called reactive oxygen species (ROS). Nitric oxide (^•NO) is produced at oxidation of arginine by nitric oxide synthase (NOS) or at reduction of nitrites by diverse reductases. Interaction of ^•NO with O₂^•- results in formation of peroxinitrite (ONOO^-), a powerful oxidant. Additionally, H₂O₂ can interact with ^•NO resulting in HO^• production. Nitric oxide and its derivatives are collectively called reactive nitrogen species (RNS) and together with ROS they form a group of so-called reactive oxygen/nitrogen species (RONS). Nonspecific effects of RONS are related to their interaction with various components of living organisms, whereas specific effects are based mainly on interaction with specific proteins containing [Fe-S]-clusters and thiol groups of cysteine residues. Most early ROS studies were mainly focused on their deleterious effects, whereas now more delicate mechanisms of their involvement in signaling and toxic processes are under inspection. Studies of RNS activities in biological systems started from their vasodilating effects which lead to discovery of activation of soluble guanylate cyclase. Interestingly, at low ROS and RNS concentrations signaling effects prevail, whereas at their high concentrations they affect biological systems inhibiting due to massive oxidation of cellular components.

Sulfur Administration in Fe-S Cluster Homeostasis

Mitochondria are the key organelles of Fe–S cluster synthesis. They contain the enzyme cysteine desulfurase, a scaffold protein, iron and electron donors, and specific chaperons all required for the formation of Fe–S clusters. The newly formed cluster can be utilized by mitochondrial Fe–S protein synthesis or undergo further transformation. Mitochondrial Fe–S cluster biogenesis components are required in the cytosolic iron–sulfur cluster assembly machinery for cytosolic and nuclear cluster supplies. Clusters that are the key components of Fe–S proteins are vulnerable and prone to degradation whenever exposed to oxidative stress. However, once degraded, the Fe–S cluster can be resynthesized or repaired. It has been proposed that sulfurtransferases, rhodanese, and 3-mercaptopyruvate sulfurtransferase, responsible for sulfur transfer from donor to nucleophilic acceptor, are involved in the Fe–S cluster formation, maturation, or reconstitution. In the present paper, we attempt to sum up our knowledge on the involvement of sulfurtransferases not only in sulfur administration but also in the Fe–S cluster formation in mammals and yeasts, and on reconstitution-damaged cluster or restoration of enzyme’s attenuated activity.

LsrB, the hub of ABC transporters involved in the membrane damage mechanisms of heavy ion irradiation in Escherichia coli

BACKGROUND

Ionizing radiation, especially heavy ion (HI) beams, has been widely used in biology and medicine. However, the mechanism of membrane damage by such radiation remains primarily uncharacterized.

PURPOSE

Transcriptomic profiles of Escherichia coli (E. coli) treated with HI illustrated the response mechanisms of the membrane, mainly ABC transporters, related genes regulated by antibiotics treatment through enrichment analyses of GO and KEGG. The networks of protein-protein interactions indicated that LsrB was the crucial one among the ABC transporters specially regulated by HI through the calculation of plugins MCODE and cytoHubba of Cytoscape. Finally, the expression pattern, GO/KEGG enrichment terms, and the interaction between nine LuxS/AI-2 quorum sensing system members were investigated.

CONCLUSIONS

Above all, results suggested that HI might perform membrane damage through regulated material transport, inhibited LuxS/AI-2 system, finally impeded biofilm formation. This work provides further evidence for the role of ABC transporters, especially LsrB, in membrane damage of E. coli to HI. It will provide new strategies for improving the precise application of HI.

Omics analyses indicate the routes of lignin related metabolites regulated by trypsin during storage of pitaya (Hylocereus undatus)

The storage quality of Hylocereus undatus was significantly improved by trypsin, a novel preservative. The transcriptomic results revealed that antioxidant signal pathways were induced, while lignin catabolic process was impeded by trypsin. In addition, the results of protein-protein interaction (PPI) network networks suggested that flavone 3'-O-methyltransferase 1 (OMT1), ferulic acid 5-hydroxylase 1 (CYP84A1), cellulose synthase isomer (CEV1), and 4-coumarate-CoA ligase 3 (4CL3) act as hubs of peroxidases, lignin related proteins, and proteins involved in the phenylpropanoid metabolism (PLPs) induced by trypsin. Trypsin also regulated the biosynthesis of lignin, chlorogenic acid, and flavonoids. Caffeic acid might be the hub in the metabolic network of the early pathways of phenylpropanoid biosynthesis. It has been hypothesized that trypsin might quickly induce lignin biosynthesis and then up-regulated bioactive metabolites to enhance storage quality of H. undatus.

Catechin gallate acts as a key metabolite induced by trypsin in Hylocereus undatus during storage indicated by omics

Trypsin is a novel superoxide scavenger. The storage quality of H. undatus was significantly improved by trypsin. To investigate the mechanism of flavonoid metabolism regulated by trypsin, combined analysis of widely targeted metabolomic and transcriptome were performed. GO and KEGG enrichment analyses of the transcriptome profiles of H. undatus revealed that some of the flavonoid related biosynthesis pathways were regulated by up or down patterns with the treatment of trypsin. Correlation analysis of flavonoid related genes expression in H. undatus provided a rationale for the functional significance of them. Furthermore, it has been revealed that the most significantly regulated flavonoid was catechin gallate in metabolomic profiles of H. undatus. The major route of flavonoid biosynthesis regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Finally, the results of PPI network revealed that C4H, HCT, and CYP75B1 acted as hub proteins involved in flavonoid metabolism regulated by trypsin.

Mild iron overload induces TRIP12-mediated degradation of YY1 to trigger hepatic inflammation

Increasing populations are found to bear mild hepatic iron overload (HIO) due to unhealthy lifestyles, metabolic diseases, etc., whether this mild but chronic HIO induces hepatic inflammation is unknown. In the present study, mice receiving a 12-months 0.3% dextran-iron diet show mild HIO with no detectable oxidative damages in the liver but have infiltrated macrophages and increased IL-6, TNFα, AST and ALT since 6-months. The HNF4α/miR-122/CCL2 pathway, identified by our previous studies to induce macrophages infiltration, is initiated by chronic mild HIO. After excluding the role of DNA methylation, a modified transcription factor microarray is applied to find that transcription factor YY1 is responsible for HIO-decreased HNF4α expression. Then the E3 ubiquitin ligase TRIP12 is identified by an immunoprecipitation coupled LC-MS/MS and proved to bind and ubiquitinate YY1, leading to its degradation. The overexpression or silence of YY1 in the liver regulates the HNF4α/miR-122/CCL2 pathway. More importantly, YY1 overexpression alleviates chronic mild HIO induced hepatic inflammatory responses. In conclusion, these results elucidate an oxidative-stress-independent, TRIP12/YY1/HNF4α/miR-122/CCL2 pathway of chronic mild HIO inducing hepatic inflammation, implying that effective measures in addition to antioxidants are needed for individuals at the risk of chronic mild HIO.

To resist and persist: Important factors in the pathogenesis of Bacteroides fragilis

Bacteroides fragilis is a most frequent anaerobic pathogen isolated from human infections, particularly found in the abdominal cavity. Different factors contribute to the pathogenesis and persistence of B. fragilis at infection sites. The knowledge of the virulence factors can provide applicable information for finding alternative options for the antibiotic therapy and treatment of B. fragilis caused infections. Herein, a comprehensive review of the important B. fragilis virulence factors was prepared. In addition to B. fragilis toxin (BFT) and its potential role in the diarrhea and cancer development, some other important virulence factors and characteristics of B. fragilis are described including capsular polysaccharides, iron acquisition, resistance to antimicrobial agents, and survival during the prolonged oxidative stress, quorum sensing, and secretion systems.