Guanine Limitation Results in CodY-Dependent and -Independent Alteration of Staphylococcus aureus Physiology and Gene Expression

Guanosine enhances the bactericidal effect of ceftiofur sodium on Streptococcus suis by activating bacterial metabolism

The emergence and rapid development of antibiotic resistance poses a serious threat to global public health. Streptococcus suis (S. suis) is an important zoonotic pathogen, and the development of its antibiotic resistance has made the infections difficult to treat. The combination of non-antibiotic compounds with antibiotics is considered a promising strategy against multidrug-resistant bacteria. However, the mechanism by which metabolites act as antibiotic adjuvant remains unclear. Here, we found that guanosine metabolism was repressed in multidrug-resistant S. suis. Exogenous guanosine promoted the antibacterial effects of ceftiofur sodium (CEF) in vitro and in vivo. Furthermore, we demonstrated that exogenous guanosine promoted the biosynthesis of purine pathway, TCA cycle and bacterial respiration, which make bacteria more sensitive to the killing effect of antibacterial. In addition, the function of the cell membrane is affected by guanosine and the accumulation of antimicrobials in the bacteria increased. Bacterial-oxidative stress and DNA damage induced by guanosine is also one of the mechanisms by which the antibacterial effect is enhanced. These results suggest that guanosine is a promising adjuvant for antibacterial drugs and provide new theoretical basis for the clinical treatment of S. suis infection.

Low temperature storage leads to advanced upregulation of typical virulence regulators, pyk and purR of enterotoxigenic Staphylococcus aureus cultured on chicken meat

Staphylococcal enterotoxins have long been studied due to the food-borne illness caused and complex intracellular virulence regulation involved. Along with the popularized application of cold chain production of meat products, there is important significance to explore the influence of low temperature on enterotoxin genes expression correlated to regulators under meat cultivation. In this study, SEA and SEB type Staphylococcus aureus strains (designated Sa08 and Sa13 respectively) were cultivated on chicken meat at 8 and 25 °C, typical virulence regulators (agrA, saeS, srrB, rot, codY and icaA), enterotoxins (sea and seb) and metabolic factors (pyk and pyruvate, purR and xanthosine monophosphate) were monitored. As a result, cell density remained stable (104-105 CFU/g) at 8 °C with slight increase in 6 day, and there were drastic pyruvate accumulation along with storing days. Significant upregulation of typical virulence regulators, pyk, purR and seb occurred in post exponential phase at 25 °C (p < 0.001). Nevertheless, phenotypic indexes failed to correspond to transcriptional changes. Expression of seb depended on the upregulation of typical virulence regulators at 8 and 25 °C, and sea had independent expression profile different from typical virulence regulators at 8 °C. Comparing with 25 °C, consistent advanced upregulation of typical virulence regulators (except codY of Sa08), pyk and purR were observed both for Sa08 and Sa13 at 8 °C, and different strains exhibited varied early metabolic response but similar later metabolic status at 8 °C. These phenomena highlighted a concern that, enterotoxigenic S. aureus colonizing on chicken meat exhibited advanced upregulation of typical virulence regulators and close-related virulence at low temperature.

(p)ppGpp-mediated GTP homeostasis ensures survival and antibiotic tolerance of Staphylococcus aureus

Antibiotic tolerance in non-growing bacterial populations is of major concern regarding antibiotic treatment failures. Whether and how the messenger molecule (p)ppGpp contributes to this phenomenon is controversial. We show for Staphylococcus aureus that (p)ppGpp-dependent restriction of the GTP pool is essential for the culturability of starved cells. Survival was independent of the GTP-responsive regulator CodY. Elevated GTP levels in a starved (p)ppGpp-deficient mutant led to quiescent state characterised by alterations in membrane architecture and a decrease of the proton motive force (PMF). This was accompanied by dysregulation of components involved in electron transport, including qoxABCD, encoding the main terminal oxidase. Increasing qoxABCD transcription by mutation of the transcription start site (iATP to iGTP) partially restored the culturability of the (p)ppGpp-deficient mutant. Thus, regulation of nucleotide-dependent promoters by altered nucleotide levels contribute to starvation adaptability. Loss of PMF under high GTP conditions also renders bacteria susceptible to antibiotics. Thus, targeting the PMF or nucleotide availability may be a valuable strategy to combat antibiotic tolerance.

Cordycepin affects Streptococcus mutans biofilm and interferes with its metabolism

BACKGROUND

Streptococcus mutans (S. mutans) contributes to caries. The biofilm formed by S. mutans exhibits greater resistance to drugs and host immune defenses than the planktonic form of the bacteria. The objective of this study was to evaluate the anti-biofilm effect of cordycepin from the perspective of metabolomics.

METHODS

The minimum inhibitory concentration (MIC) was determined to evaluate the antimicrobial effect of cordycepin on planktonic S. mutans. The 24-h biofilm was treated with 128 µg/mL of cordycepin for 10 min at the 8- or 20-h time points. Biofilm biomass and metabolism were assessed using crystal violet and MTT assays and cordycepin cytotoxicity was evaluated in human oral keratinocytes (HOK) using CCK-8 assays. The live bacterial rate and the biofilm volume were assessed by confocal laser scanning microscopy. Metabolic changes in the biofilm collected at different times during with cordycepin were analyzed by metabolomics and verified by quantitative real-time PCR.

RESULTS

The results showed that treatment with 128 µg/mL cordycepin reduced both the biomass and metabolic activity of the biofilm without killing the bacteria, and cordycepin at this concentration showed good biocompatibility. Metabolomics analysis showed that differentially abundant metabolites following cordycepin treatment were mainly related to purine and nucleotide metabolism. After immediate treatment with cordycepin, genes related to purine and nucleotide metabolism were downregulated, and the levels of various metabolites changed significantly. However, the effect was reversible. After continuing culture for 4 h, the changes in genes and most metabolites were reversed, although the levels of 2'-deoxyadenosine, 2'-deoxyinosine, and adenine remained significantly different.

CONCLUSIONS

Cordycepin has the effect of anti-biofilm of S. mutans, mainly related to purine and nucleotide metabolism.

DA, Brinsmade SR. CodY controls the SaeR/S two-component system by modulating branched-chain fatty acid synthesis in Staphylococcus aureus

Staphylococcus aureus is a Gram-positive, opportunistic human pathogen that is a leading cause of skin and soft tissue infections and invasive disease worldwide. Virulence in this bacterium is tightly controlled by a network of regulatory factors. One such factor is the global regulatory protein CodY. CodY links branched-chain amino acid sufficiency to the production of surface-associated and secreted factors that facilitate immune evasion and subversion. Our previous work revealed that CodY regulates virulence factor gene expression indirectly in part by controlling the activity of the SaeRS two-component system (TCS). While this is correlated with an increase in membrane anteiso-15:0 and -17:0 branched-chain fatty acids (BCFAs) derived from isoleucine, the true mechanism of control has remained elusive. Herein, we report that CodY-dependent regulation of SaeS sensor kinase activity requires BCFA synthesis. During periods of nutrient sufficiency, BCFA synthesis and Sae TCS activity are kept relatively low by CodY-dependent repression of the ilv-leu operon and the isoleucine-specific permease gene brnQ2. In a codY null mutant, which simulates extreme nutrient limitation, de-repression of ilv-leu and brnQ2 directs the synthesis of enzymes in redundant de novo and import pathways to upregulate production of BCFA precursors. Overexpression of brnQ2, independent of CodY, is sufficient to increase membrane anteiso BCFAs, Sae-dependent promoter activity, and SaeR ~P levels. Our results further clarify the molecular mechanisms by which CodY controls virulence in S. aureus.IMPORTANCEExpression of bacterial virulence genes often correlates with the exhaustion of nutrients, but how the signaling of nutrient availability and the resulting physiological responses are coordinated is unclear. In S. aureus, CodY controls the activity of two major regulators of virulence-the Agr and Sae two-component systems (TCSs)-by unknown mechanisms. This work identifies a mechanism by which CodY controls the activity of the sensor kinase SaeS by modulating the levels of anteiso branched-chain amino acids that are incorporated into the membrane. Understanding the mechanism adds to our understanding of how bacterial physiology and metabolism are linked to virulence and underscores the role virulence in maintaining homeostasis. Understanding the mechanism also opens potential avenues for targeted therapeutic strategies against S. aureus infections.

Dysbiosis and diabetic foot ulcers: A metabolic perspective of Staphylococcus aureus infection

Staphylococcus aureus (S. aureus) infection is the most prevalent and resistant bacterial infection, posing a worldwide health risk. Compared with healthy people, diabetes patients with weak immune function and abnormal metabolism are more vulnerable to bacterial infection, which aggravates the intensity of infection and causes a series of common and dangerous complications, such as diabetes foot ulcer (DFU). Due to metabolic abnormalities of diabetic patients, S. aureus on the skin surface of DFU transitions from a commensal to an invasive infection. During this process, S. aureus resists a series of unfavorable conditions for bacterial growth by altering energy utilization and metabolic patterns, and secretes various virulence factors, causing persistent infection. With the emergence of multiple super-resistant bacteria, antibiotic treatment is no longer the only treatment option, and developing new drugs and therapies is urgent. Regulating the metabolic signaling pathway of S. aureus plays a decisive role in regulating its virulence factors and impacts adjuvant therapy for DFU. This article focuses on studying the impact of regulating metabolic signals on the virulence of S. aureus from a metabolism perspective. It provides an outlook on the future direction of the novel development of antimicrobial therapy.

A review of chemical signaling mechanisms underlying quorum sensing and its inhibition in Staphylococcus aureus

Staphylococcus aureus is a significant bacterium responsible for multiple infections and is a primary cause of fatalities among patients in hospital environments. The advent of pathogenic bacteria such as methicillin-resistant S. aureus revealed the shortcomings of employing antibiotics to treat bacterial infectious diseases. Quorum sensing enhances S. aureus's survivability through signaling processes. Targeting the key components of quorum sensing has drawn much interest nowadays as a promising strategy for combating infections caused by bacteria. Concentrating on the accessory gene regulator quorum-sensing mechanism is the most commonly suggested anti-virulence approach for S.aureus. Quorum quenching is a common strategy for controlling illnesses triggered by microorganisms since it reduces the pathogenicity of bacteria and improves bacterial biofilm susceptibility to antibiotics, thus providing an intriguing prospect for drug discovery. Quorum sensing inhibition reduces selective stresses and constrains the emergence of antibiotic resistance while limiting bacterial pathogenicity. This review examines the quorum sensing mechanisms involved in S. aureus, quorum sensing targets and gene regulation, environmental factors affecting quorum sensing, quorum sensing inhibition, natural products as quorum sensing inhibitory agents and novel therapeutical strategies to target quorum sensing in S. aureus as drug developing technique to augment conventional antibiotic approaches.

Characteristics of Staphylococcus aureus biofilm matured in tryptic soy broth, low-fat milk, or whole milk samples along with inactivation by 405 nm light combined with folic acid

In the present study, the characteristics of Staphylococcus aureus biofilms matured in tryptic soy broth (TSB), low-fat milk, or whole milk samples were identified along with their resistance to 405 nm light with or without folic acid. Phenotypic properties of carbohydrate and protein contents in extracellular polymeric substance (EPS) of S. aureus biofilms matured in different conditions were identified. The carbohydrate content was higher in the biofilm matured in low-fat milk (1.27) than the samples matured in whole milk (0.58) and TSB (0.10). Protein content in the EPS of biofilm was higher in the sample matured in whole milk (6.59) than the samples matured in low-fat milk (3.24) and TSB (2.08). Moreover, the maturation condition had a significant effect on the membrane lipid composition of the biofilm, producing more unsaturated fatty acids in biofilm matured in milk samples. These changes in biofilm matured in milk samples increased the resistance of S. aureus to 405 nm light in the presence of folic acid (LFA). Additionally, transcriptomic analysis was conducted to identify the response of S. aureus biofilm to LFA treatment. Several genes related to DNA and protein protection from oxidative stress along with biofilm accumulation were overexpressed in the LFA-treated biofilms. These results indicate the maturation of S. aureus biofilm in various samples and the biofilms responses to bactericidal treatments.

CodY is modulated by YycF and affects biofilm formation in Staphylococcus aureus

Background

Staphylococcus aureus (S. aureus) is the leading cause of various infective diseases, including topical soft tissue infections. The goals of this study were to investigate the roles of YycF and CodY in the regulation of biofilm formation and pathogenicity.

Methods

Electrophoretic mobility shift assay (EMSA) was conducted to validate the bound promoter regions of YycF protein. We constructed the codY up-regulated or down-regulated S. aureus mutants. The biofilm biomass was determined by crystal violet microtiter assay and scanning electron microscopy (SEM). Quantitative RT-PCR analysis was used to detect the transcripts of biofilm-related genes. The live and dead cells of S. aureus biofilm were also investigated by confocal laser scanning microscopy (CLSM). We constructed an abscess infection in Sprague Dawley (SD) rat models to determine the effect of CodY on bacterial pathogenicity. We further used the RAW264.7, which were cocultured with S. aureus, to evaluate the effect of CodY on macrophages apoptosis.

Result

Quantitative RT-PCR analyses reveled that YycF negatively regulates codY expression. EMSA assays indicated that YycF protein directly binds to the promoter regions of codY gene. Quantitative RT-PCR confirmed the construction of dual- mutant stains codY + ASyycF and codY-ASyycF. The SEM results showed that the biofilm formation in the codY + ASyycF group was sparser than those in the other groups. The crystal violet assays indicated that the codY + ASyycF group formed less biofilms, which was consistent with the immunofluorescence results of the lowest live cell ration in the codY + ASyycF group. The expression levels of biofilm-associated icaA gene were significantly reduced in the codY + strain, indicating codY negatively regulates the biofilm formation. Furthermore, CodY impedes the pathogenicity in a rat-infection model. After cocultured with bacteria or 4-h in vitro, the apoptosis rates of macrophage cells were lowest in the codY + group.

Conclusions

YycF negatively regulate the expression of codY. By interaction with codY, YycF could modulate S. aureus biofilm formation via both eDNA- dependent and PIA- dependent pathways, which can be a significant target for antibiofilm. CodY not only impedes the pathogenicity but also has a role on immunoregulation. Thus, the current evidence may provide a supplementary strategy for managing biofilm infections.

Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response

Staphylococcus aureus infections impose an immense burden on the healthcare system. To establish a successful infection in a hostile host environment, S. aureus must coordinate its gene expression to respond to a wide array of challenges. This balancing act is largely orchestrated by the transcriptional regulatory network. Here, we present a model of 29 independently modulated sets of genes that form the basis for a segment of the transcriptional regulatory network in clinical USA300 strains of S. aureus. Using this model, we demonstrate the concerted role of various cellular systems (e.g., metabolism, virulence, and stress response) underlying key physiological responses, including response during blood infection.

The ability of Staphylococcus aureus to infect many different tissue sites is enabled, in part, by its transcriptional regulatory network (TRN) that coordinates its gene expression to respond to different environments. We elucidated the organization and activity of this TRN by applying independent component analysis to a compendium of 108 RNA-sequencing expression profiles from two S. aureus clinical strains (TCH1516 and LAC). ICA decomposed the S. aureus transcriptome into 29 independently modulated sets of genes (i-modulons) that revealed: 1) High confidence associations between 21 i-modulons and known regulators; 2) an association between an i-modulon and σS, whose regulatory role was previously undefined; 3) the regulatory organization of 65 virulence factors in the form of three i-modulons associated with AgrR, SaeR, and Vim-3; 4) the roles of three key transcription factors (CodY, Fur, and CcpA) in coordinating the metabolic and regulatory networks; and 5) a low-dimensional representation, involving the function of few transcription factors of changes in gene expression between two laboratory media (RPMI, cation adjust Mueller Hinton broth) and two physiological media (blood and serum). This representation of the TRN covers 842 genes representing 76% of the variance in gene expression that provides a quantitative reconstruction of transcriptional modules in S. aureus, and a platform enabling its full elucidation.

Genetic and Biochemical Analysis of CodY-Mediated Cell Aggregation in Staphylococcus aureus Reveals an Interaction between Extracellular DNA and Polysaccharide in the Extracellular Matrix

The global regulator CodY links nutrient availability to the regulation of virulence factor gene expression in Staphylococcus aureus, including many genes whose products affect biofilm formation. Antithetical phenotypes of both biofilm deficiency and accumulation have been reported for codY-null mutants; thus, the role of CodY in biofilm development remains unclear. codY mutant cells of a strain producing a robust biofilm elaborate proaggregation surface-associated features not present on codY mutant cells that do not produce a robust biofilm. Biochemical analysis of the clinical isolate SA564, which aggregates when deficient for CodY, revealed that these features are sensitive to nuclease treatment and are resistant to protease exposure. Genetic analyses revealed that disrupting lgt (the diacylglycerol transferase gene) in codY mutant cells severely weakened aggregation, indicating a role for lipoproteins in the attachment of the biofilm matrix to the cell surface. An additional and critical role of IcaB in producing functional poly-N-acetylglucosamine (PIA) polysaccharide in extracellular DNA (eDNA)-dependent biofilm formation was shown. Moreover, overproducing PIA is sufficient to promote aggregation in a DNA-dependent manner regardless of source of nucleic acids. Taken together, our results point to PIA synthesis as the primary determinant of biofilm formation when CodY activity is reduced and suggest a modified electrostatic net model for matrix attachment whereby PIA associates with eDNA, which interacts with the cell surface via covalently attached membrane lipoproteins. This work counters the prevailing view that polysaccharide- and eDNA/protein-based biofilms are mutually exclusive. Rather, we demonstrate that eDNA and PIA can work synergistically to form a biofilm.IMPORTANCEStaphylococcus aureus remains a global health concern and exemplifies the ability of an opportunistic pathogen to adapt and persist within multiple environments, including host tissue. Not only does biofilm contribute to persistence and immune evasion in the host environment, it also may aid in the transition to invasive disease. Thus, understanding how biofilms form is critical for developing strategies for dispersing biofilms and improving biofilm disease-related outcomes. Using biochemical, genetic, and cell biology approaches, we reveal a synergistic interaction between PIA and eDNA that promotes cell aggregation and biofilm formation in a CodY-dependent manner in S. aureus We also reveal that envelope-associated lipoproteins mediate attachment of the biofilm matrix to the cell surface.

Analysis of the CodY RNome reveals RsaD as a stress-responsive riboregulator of overflow metabolism in Staphylococcus aureus

In Staphylococcus aureus, the transcription factor CodY modulates the expression of hundreds of genes, including most virulence factors, in response to the availability of key nutrients like GTP and branched-chain amino acids. Despite numerous studies examining how CodY controls gene expression directly or indirectly, virtually nothing is known about the extent to which CodY exerts its effect through small regulatory RNAs (sRNAs). Herein, we report the first set of sRNAs under the control of CodY. We reveal that staphylococcal sRNA RsaD is overexpressed >20-fold in a CodY-deficient strain in three S. aureus clinical isolates and in S. epidermidis. We validated the CodY-dependent regulation of rsaD and demonstrated that CodY directly represses rsaD expression by binding the promoter. Using a combination of molecular techniques, we show that RsaD posttranscriptionally regulates alsS (acetolactate synthase) mRNA and enzyme levels. We further show that RsaD redirects carbon overflow metabolism, contributing to stationary phase cell death during exposure to weak acid stress. Taken together, our data delineate a role for CodY in controlling sRNA expression in a major human pathogen and indicate that RsaD may integrate nutrient depletion and other signals to mount a response to physiological stress experienced by S. aureus in diverse environments.

Noncontiguous operon is a genetic organization for coordinating bacterial gene expression

Bacterial genes are typically grouped into operons defined as clusters of adjacent genes encoding for proteins that fill related roles and are transcribed into a single polycistronic mRNA molecule. This simple organization provides an efficient mechanism to coordinate the expression of neighboring genes and is at the basis of gene regulation in bacteria. Here, we report the existence of a higher level of organization in operon structure that we named noncontiguous operon and consists in an operon containing a gene(s) that is transcribed in the opposite direction to the rest of the operon. This transcriptional architecture is exemplified by the genes menE-menC-MW1733-ytkD-MW1731 involved in menaquinone synthesis in the major human pathogen Staphylococcus aureus We show that menE-menC-ytkD-MW1731 genes are transcribed as a single transcription unit, whereas the MW1733 gene, located between menC and ytkD, is transcribed in the opposite direction. This genomic organization generates overlapping transcripts whose expression is mutually regulated by transcriptional interference and RNase III processing at the overlapping region. In light of our results, the canonical view of operon structure should be revisited by including this operon arrangement in which cotranscription and overlapping transcription are combined to coordinate functionally related gene expression.

MsaB and CodY Interact To Regulate Staphylococcus aureus Capsule in a Nutrient-Dependent Manner

Staphylococcus aureus has a complex regulatory network for controlling the production of capsule polysaccharide. In S. aureus, capsule production is controlled by several regulators in response to various environmental stimuli. Previously, we described MsaB as a new regulator that specifically binds to the cap promoter in a growth phase- or nutrient-dependent manner. In addition to MsaB, several other regulators have also been shown to bind the same region. In this study, we examined the interactions between MsaB and other nutrient-sensing regulators (CodY and CcpE) with respect to binding to the cap promoter in a nutrient-dependent manner. We observed that msaABCR and ccpE interact in a complex fashion to regulate capsule production. However, we confirmed that ccpE does not bind cap directly. We also defined the regulatory relationship between msaABCR and CodY. When nutrients (branched-chain amino acids) are abundant, CodY binds to the promoter region of the cap operon and represses its transcription. However, when nutrient concentrations decrease, MsaB, rather than CodY, binds to the cap promoter. Binding of MsaB to the cap promoter activates transcription of the cap operon. We hypothesize that this same mechanism may be used by S. aureus to regulate other virulence factors.IMPORTANCE Findings from this study define the mechanism of regulation of capsule production in Staphylococcus aureus Specifically, we show that two key regulators, MsaB and CodY, coordinate their functions to control the expression of capsule in response to nutrients. S. aureus fine-tunes the production of capsule by coordinating the activity of several regulators and by sensing nutrient levels. This study demonstrates the importance of incorporating multiple inputs prior to the expression of costly virulence factors, such as capsule.