CcpA regulates arginine biosynthesis in Staphylococcus aureus through repression of proline catabolism

Multivariate Modular Metabolic Engineering for the Enhanced Biosynthesis of Cytidine in Bacillus subtilis

As a pyrimidine nucleoside, cytidine is widely used in the medicine and food fields. Therefore, it is important to construct a microbial cell factory for efficient and sustainable cytidine production. Here, we perform modular metabolic engineering modifications on Bacillus subtilis 168 to achieve efficient synthesis of cytidine. First, the cytidine titer reached 0.88 g/L by blocking cytidine degradation and enhancing the cytidine de novo synthesis pathway. Next, the central carbon metabolism was modulated by knocking down CcpA, but the cytidine titer decreased instead. Transcriptome analysis revealed that differential genes were mainly enriched in PTS, glycolysis, TCA cycle, PP pathway, pyrimidine metabolism, aspartate metabolism, and glutamate metabolism. Then, by enhancing the l-aspartate and glutamine synthesis pathways, the cytidine titer was increased to 3.83 g/L. By strengthening the PP pathway to increase PRPP synthesis, the cytidine titer was further increased to 7.03 g/L. Finally, the cytidine titer reached 31.41 g/L by fed-batch fermentation in a 5 L fermenter, which was 4.47-fold that of shake flask fermentation. Overall, the efficient production of cytidine was accomplished through modular metabolic engineering, opening new pathways for the production of cytidine and other nucleosides.

Transcriptional profiling reveals the effect of arginine on Actinobacillus succinogenes growth and fermentation

Actinobacillus succinogenes is considered one of the most promising strains for succinic acid production due to its ability to utilize various carbon sources for high-concentration fermentation. However, limited understanding of genetic and metabolic changes during its growth and fermentation processes hinders further modification of A. succinogenes for application in SA production. In this study, we analyzed transcriptome profiles during A. succinogenes fermentation using high-throughput RNA sequencing. Compared to cells after 8 h of fermentation, cells at 34 h exhibited significant upregulation of genes related to glycerophospholipid metabolism and arginine biosynthesis pathways. We explored the effects of arginine on cell growth and fermentation by overexpressing or knocking down argH encoding argininosuccinate lyase (ArgH), a key enzyme in arginine biosynthesis. The integrity of the arginine metabolic pathway is essential for normal growth, and both exogenous addition of arginine and increased intracellular arginine metabolic flux improved cell growth and SA yield at low pH (5.0 ≤ pH ≤ 6.0). However, at non-low pH (6.0 ≤ pH ≤ 7.0), arginine had no significant effect on cell growth and SA yield. In a 3 L bioreactor under non-low pH conditions, the overexpression strain (::ArgH) produced 73.9 g/L SA with 1.65 g/L/h productivity, similar to the control strain. This implies that arginine metabolism in A. succinogenes is more associated with resistance to acid stress and less closely related to direct SA production. These findings provide insight into the critical physiological and biochemical processes of this non-model microorganism.

ZnO‐CuS/F127 Hydrogels with Multienzyme Properties for Implant‐Related Infection Therapy by Inhibiting Bacterial Arginine Biosynthesis and Promoting Tissue Repair

Implant‐related infections are characterized by the formation of bacterial biofilms. Current treatments have various drawbacks. Nanozymes with enzyme‐like activity can produce highly toxic substances to kill bacteria and remove biofilms without inducing drug resistance. However, it is difficult for current monometallic nanozymes to function well in complex biofilm environments. Therefore, the development of multimetallic nanozymes with efficient multienzyme activities is crucial. In the present study, bimetallic nanozyme, ZnO‐CuS nanoflowers with peroxidase (POD), glutathione oxidase (GSH‐Px), and catalase (CAT) activity are successfully synthesized via calcination and loaded into F127 hydrogels for the treatment of implant‐related infections. The ability of ZnO‐CuS nanoflowers to bind bacteria is key for efficient antimicrobial activity. In addition, ZnO‐CuS nanoflowers with H2O2 disrupt the metabolism of MRSA, including arginine synthesis, nucleotide excision repair, energy metabolism, and protein synthesis. ZnO‐CuS/F127 hydrogel in combination with H2O2 has been demonstrated to be effective in clearing biofilm infection and facilitating the switch of M1 macrophages to M2‐repairative phenotype macrophages for the treatment of implant infections in mice. Furthermore, ZnO‐CuS/F127 hydrogels have favorable biosafety, and their toxicity is negligible. ZnO‐CuS/F127 hydrogel has provided a promising biomedical strategy for the healing of implant‐related infections, highlighting the potential of bimetallic nanozymes for clinical applications.

Regulatory dynamics of arginine metabolism in Staphylococcus aureus

Staphylococcus aureus is a highly significant pathogen with several well studied and defined virulence factors. However, the metabolic pathways that are required to facilitate infection are not well described. Previous data have documented that S. aureus requires glucose catabolism during initial stages of infection. Therefore, certain nutrients whose biosynthetic pathway is under carbon catabolite repression and CcpA, including arginine, must be acquired from the host. However, even though S. aureus encodes pathways to synthesize arginine, biosynthesis of arginine is repressed even in the absence of glucose. Why is S. aureus a functional arginine auxotroph? This review discusses recently described regulatory mechanisms that are linked to repression of arginine biosynthesis using either proline or glutamate as substrates. In addition, recent studies are discussed that shed insight into the ultimate mechanisms linking arginine auxotrophy and infection persistence.

Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus

Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment. Antibiotic tolerance, the ability of bacteria to persist despite normally lethal doses of antibiotics, contributes to antibiotic treatment failure in S. aureus infections. To understand how antibiotic tolerance is induced, S. aureus biofilms exposed to multiple anti-staphylococcal antibiotics are examined using both quantitative proteomics and transposon sequencing. These screens indicate that arginine metabolism is involved in antibiotic tolerance within a biofilm and support the hypothesis that depletion of arginine within S. aureus communities can induce antibiotic tolerance. Consistent with this hypothesis, inactivation of argH, the final gene in the arginine synthesis pathway, induces antibiotic tolerance. Arginine restriction induces antibiotic tolerance via inhibition of protein synthesis. In murine skin and bone infection models, an argH mutant has enhanced ability to survive antibiotic treatment with vancomycin, highlighting the relationship between arginine metabolism and antibiotic tolerance during S. aureus infection. Uncovering this link between arginine metabolism and antibiotic tolerance has the potential to open new therapeutic avenues targeting previously recalcitrant S. aureus infections.

mSphere of Influence: Metabolic redundancies enhance pathogenesis

McKenzie Lehman works in the field of bacterial pathogenesis and metabolism. In this mSphere of Influence article, she reflects on how three papers entitled "Glycolytic dependency of high-level nitric oxide resistance and virulence in Staphylococcus aureus" by N. P. Vitko, N. A. Spahich, and A. R. Richardson (mBio 6:e00045-15, 2015, https://doi.org/10.1128/mbio.00045-15), "The Staphylococcus aureus cystine transporters TcyABC and TcyP facilitate nutrient sulfur acquisition during infection" by J. M. Lensmire, J. P. Dodson, B. Y. Hsueh, M. R. Wischer, et al. (Infect Immun 88:e00690-19, 2020, https://doi.org/10.1128/iai.00690-19), and "The second messenger c-di-AMP inhibits the osmolyte uptake system OpuC in Staphylococcus aureus" by C. F. Schuster, L. E. Bellows, T. Tosi, I. Campeotto, et al. (Sci Signal 16:ra81, 2016, https://doi.org/10.1126/scisignal.aaf7279) impacted her work on bacterial metabolism and pathogenesis.

Genome-wide transcription response of Staphylococcus epidermidis to heat shock and medically relevant glucose levels

Skin serves as both barrier and interface between body and environment. Skin microbes are intermediaries evolved to respond, transduce, or act in response to changing environmental or physiological conditions. We quantified genome-wide changes in gene expression levels for one abundant skin commensal, Staphylococcus epidermidis, in response to an internal physiological signal, glucose levels, and an external environmental signal, temperature. We found 85 of 2,354 genes change up to ~34-fold in response to medically relevant changes in glucose concentration (0-17 mM; adj p ≤0.05). We observed carbon catabolite repression in response to a range of glucose spikes, as well as upregulation of genes involved in glucose utilization in response to persistent glucose. We observed 366 differentially expressed genes in response to a physiologically relevant change in temperature (37-45°C; adj p ≤ 0.05) and an S. epidermidis heat-shock response that mostly resembles the heat-shock response of related staphylococcal species. DNA motif analysis revealed CtsR and CIRCE operator sequences arranged in tandem upstream of dnaK and groESL operons. We identified and curated 38 glucose-responsive genes as candidate ON or OFF switches for use in controlling synthetic genetic systems. Such systems might be used to instrument the in-situ skin microbiome or help control microbes bioengineered to serve as embedded diagnostics, monitoring, or treatment platforms.

Glutamate-dependent arginine biosynthesis requires the inactivation of spoVG, sarA, and ahrC in Staphylococcus aureus

Genome sequencing has demonstrated that Staphylococcus aureus encodes arginine biosynthetic genes argDCJBFGH synthesizing proteins that mediate arginine biosynthesis using glutamate as a substrate. Paradoxically, however, S. aureus does not grow in a defined, glutamate-replete medium lacking arginine and glucose (CDM-R). Studies from our laboratory have found that specific mutations are selected by S. aureus that facilitate growth in CDM-R. However, these selected mutants synthesize arginine utilizing proline as a substrate rather than glutamate. In this study, we demonstrate that the ectopic expression of the argDCJB operon supports the growth of S. aureus in CDM-R, thus documenting the functionality of this pathway. Furthermore, suppressor mutants of S. aureus JE2 putA::Tn, which is defective in synthesizing arginine from proline, were selected on CDM-R agar. Genome sequencing revealed that these mutants had compensatory mutations within both spoVG, encoding an ortholog of the Bacillus subtilis stage V sporulation protein, and sarA, encoding the staphylococcal accessory regulator. Transcriptional studies document that argD expression is significantly increased when JE2 spoVG sarA was grown in CDM-R. Lastly, we found that a mutation in ahrC was required to induce argD expression in JE2 spoVG sarA when grown in an arginine-replete medium (CDM), suggesting that AhrC also functions to repress argDCJB in an arginine-dependent manner. In conclusion, these data indicate that the argDCJB operon is functional when transcribed in vitro and that SNPs within potential putative regulatory proteins are required to alleviate the repression.IMPORTANCEAlthough Staphylococcus aureus has the capability to synthesize all 20 amino acids, it is phenotypically auxotrophic for several amino acids including arginine. This work identifies putative regulatory proteins, including SpoVG, SarA, and AhrC, that function to inhibit the arginine biosynthetic pathways using glutamate as a substrate. Understanding the ultimate mechanisms of why S. aureus is selected to repress arginine biosynthetic pathways even in the absence of arginine will add to the growing body of work assessing the interactions between metabolism and S. aureus pathogenesis.

The neutrophil oxidant hypothiocyanous acid causes a thiol-specific stress response and an oxidative shift of the bacillithiol redox potential in Staphylococcus aureus

IMPORTANCE

Staphylococcus aureus colonizes the skin and the airways but can also lead to life-threatening systemic and chronic infections. During colonization and phagocytosis by immune cells, S. aureus encounters the thiol-reactive oxidant HOSCN. The understanding of the adaptation mechanisms of S. aureus toward HOSCN stress is important to identify novel drug targets to combat multi-resistant S. aureus isolates. As a defense mechanism, S. aureus uses the flavin disulfide reductase MerA, which functions as HOSCN reductase and protects against HOSCN stress. Moreover, MerA homologs have conserved functions in HOSCN detoxification in other bacteria, including intestinal and respiratory pathogens. In this work, we studied the comprehensive thiol-reactive mode of action of HOSCN and its effect on the reversible shift of the E BSH to discover new defense mechanisms against the neutrophil oxidant. These findings provide new leads for future drug design to fight the pathogen at the sites of colonization and infections.

CcpA-Knockout Staphylococcus aureus Induces Abnormal Metabolic Phenotype via the Activation of Hepatic STAT5/PDK4 Signaling in Diabetic Mice

Catabolite control protein A (CcpA), an important global regulatory protein, is extensively found in S. aureus. Many studies have reported that CcpA plays a pivotal role in regulating the tricarboxylic acid cycle and pathogenicity. Moreover, the CcpA-knockout Staphylococcus aureus (S. aureus) in diabetic mice, compared with the wild-type, showed a reduced colonization rate in the tissues and organs and decreased inflammatory factor expression. However, the effect of CcpA-knockout S. aureus on the host's energy metabolism in a high-glucose environment and its mechanism of action remain unclear. S. aureus, a common and major human pathogen, is increasingly found in patients with obesity and diabetes, as recent clinical data reveal. To address this issue, we generated CcpA-knockout S. aureus strains with different genetic backgrounds to conduct in-depth investigations. In vitro experiments with high-glucose-treated cells and an in vivo model study with type 1 diabetic mice were used to evaluate the unknown effect of CcpA-knockout strains on both the glucose and lipid metabolism phenotypes of the host. We found that the strains caused an abnormal metabolic phenotype in type 1 diabetic mice, particularly in reducing random and fasting blood glucose and increasing triglyceride and fatty acid contents in the serum. In a high-glucose environment, CcpA-knockout S. aureus may activate the hepatic STAT5/PDK4 pathway and affect pyruvate utilization. An abnormal metabolic phenotype was thus observed in diabetic mice. Our findings provide a better understanding of the molecular mechanism of glucose and lipid metabolism disorders in diabetic patients infected with S. aureus.

Secretory IgA impacts the microbiota density in the human nose

BACKGROUND

Respiratory mucosal host defense relies on the production of secretory IgA (sIgA) antibodies, but we currently lack a fundamental understanding of how sIgA is induced by contact with microbes and how such immune responses may vary between humans. Defense of the nasal mucosal barrier through sIgA is critical to protect from infection and to maintain homeostasis of the microbiome, which influences respiratory disorders and hosts opportunistic pathogens.

METHODS

We applied IgA-seq analysis to nasal microbiota samples from male and female healthy volunteers, to identify which bacterial genera and species are targeted by sIgA on the level of the individual host. Furthermore, we used nasal sIgA from the same individuals in sIgA deposition experiments to validate the IgA-seq outcomes.

CONCLUSIONS

We observed that the amount of sIgA secreted into the nasal mucosa by the host varied substantially and was negatively correlated with the bacterial density, suggesting that nasal sIgA limits the overall bacterial capacity to colonize. The interaction between mucosal sIgA antibodies and the nasal microbiota was highly individual with no obvious differences between potentially invasive and non-invasive bacterial species. Importantly, we could show that for the clinically relevant opportunistic pathogen and frequent nasal resident Staphylococcus aureus, sIgA reactivity was in part the result of epitope-independent interaction of sIgA with the antibody-binding protein SpA through binding of sIgA Fab regions. This study thereby offers a first comprehensive insight into the targeting of the nasal microbiota by sIgA antibodies. It thereby helps to better understand the shaping and homeostasis of the nasal microbiome by the host and may guide the development of effective mucosal vaccines against bacterial pathogens. Video Abstract.

Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus

Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment, particularly when they are caused by Methicillin-Resistant Staphylococcus aureus (MRSA). Antibiotic tolerance, the ability for bacteria to persist despite normally lethal doses of antibiotics, is responsible for most antibiotic treatment failure in MRSA infections. To understand how antibiotic tolerance is induced, S. aureus biofilms exposed to multiple anti-MRSA antibiotics (vancomycin, ceftaroline, delafloxacin, and linezolid) were examined using both quantitative proteomics and transposon sequencing. These screens indicated that arginine metabolism is involved in antibiotic tolerance within a biofilm and led to the hypothesis that depletion of arginine within S. aureus communities can induce antibiotic tolerance. Consistent with this hypothesis, inactivation of argH, the final gene in the arginine synthesis pathway, induces antibiotic tolerance under conditions in which the parental strain is susceptible to antibiotics. Arginine restriction was found to induce antibiotic tolerance via inhibition of protein synthesis. Finally, although S. aureus fitness in a mouse skin infection model is decreased in an argH mutant, its ability to survive in vivo during antibiotic treatment with vancomycin is enhanced, highlighting the relationship between arginine metabolism and antibiotic tolerance during S. aureus infection. Uncovering this link between arginine metabolism and antibiotic tolerance has the potential to open new therapeutic avenues targeting previously recalcitrant S. aureus infections.

Metabolic reprogramming and altered cell envelope characteristics in a pentose phosphate pathway mutant increases MRSA resistance to β-lactam antibiotics

Central metabolic pathways control virulence and antibiotic resistance, and constitute potential targets for antibacterial drugs. In Staphylococcus aureus the role of the pentose phosphate pathway (PPP) remains largely unexplored. Mutation of the 6-phosphogluconolactonase gene pgl, which encodes the only non-essential enzyme in the oxidative phase of the PPP, significantly increased MRSA resistance to β-lactam antibiotics, particularly in chemically defined media with physiologically-relevant concentrations of glucose, and reduced oxacillin (OX)-induced lysis. Expression of the methicillin-resistance penicillin binding protein 2a and peptidoglycan architecture were unaffected. Carbon tracing and metabolomics revealed extensive metabolic reprogramming in the pgl mutant including increased flux to glycolysis, the TCA cycle, and several cell envelope precursors, which was consistent with increased β-lactam resistance. Morphologically, pgl mutant cells were smaller than wild-type with a thicker cell wall and ruffled surface when grown in OX. The pgl mutation reduced resistance to Congo Red, sulfamethoxazole and oxidative stress, and increased resistance to targocil, fosfomycin and vancomycin. Levels of lipoteichoic acids (LTAs) were significantly reduced in pgl, which may limit cell lysis, while the surface charge of pgl cells was significantly more positive. A vraG mutation in pgl reversed the increased OX resistance phenotype, and partially restored wild-type surface charge, but not LTA levels. Mutations in vraF or graRS from the VraFG/GraRS complex that regulates DltABCD-mediated d-alanylation of teichoic acids (which in turn controls β-lactam resistance and surface charge), also restored wild-type OX susceptibility. Collectively these data show that reduced levels of LTAs and OX-induced lysis combined with a VraFG/GraRS-dependent increase in cell surface positive charge are accompanied by significantly increased OX resistance in an MRSA pgl mutant.

Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects

Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δcas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.

Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects

Group B Streptococcus (GBS; S. agalactiae ) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δ cas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.

Hyperglycemia Increases Severity of Staphylococcus aureus Osteomyelitis and Influences Bacterial Genes Required for Survival in Bone

Hyperglycemia, or elevated blood glucose, renders individuals more prone to developing severe Staphylococcus aureus infections. S. aureus is the most common etiological agent of musculoskeletal infection, which is a common manifestation of disease in hyperglycemic patients. However, the mechanisms by which S. aureus causes severe musculoskeletal infection during hyperglycemia are incompletely characterized. To examine the influence of hyperglycemia on S. aureus virulence during invasive infection, we used a murine model of osteomyelitis and induced hyperglycemia with streptozotocin. We discovered that hyperglycemic mice exhibited increased bacterial burdens in bone and enhanced dissemination compared to control mice. Furthermore, infected hyperglycemic mice sustained increased bone destruction relative to euglycemic controls, suggesting that hyperglycemia exacerbates infection-associated bone loss. To identify genes contributing to S. aureus pathogenesis during osteomyelitis in hyperglycemic animals relative to euglycemic controls, we used transposon sequencing (TnSeq). We identified 71 genes uniquely essential for S. aureus survival in osteomyelitis in hyperglycemic mice and another 61 mutants with compromised fitness. Among the genes essential for S. aureus survival in hyperglycemic mice was the gene encoding superoxide dismutase A (sodA), one of two S. aureus superoxide dismutases involved in detoxifying reactive oxygen species (ROS). We determined that a sodA mutant exhibits attenuated survival in vitro in high glucose and in vivo during osteomyelitis in hyperglycemic mice. SodA therefore plays an important role during growth in high glucose and promotes S. aureus survival in bone. Collectively, these studies demonstrate that hyperglycemia increases the severity of osteomyelitis and identify genes contributing to S. aureus survival during hyperglycemic infection.

Zeolitic Imidazolate Framework-8 Triggers the Inhibition of Arginine Biosynthesis to Combat Methicillin-Resistant Staphylococcus Aureus

The self-preservation and intelligent survival abilities of methicillin-resistant Staphylococcus aureus (MRSA) result in the ineffective treatment of many antibiotics. Nano-drug delivery systems have emerged as a new strategy to overcome MRSA infection. ZIF-8 nanoparticles (ZIF-8 NPs) exhibit good antibacterial activities, while its molecular mechanisms are largely elusive. In this study, the ZIF-8 NPs are prepared using the room temperature solution reaction method. The values of minimum inhibitory concentration of ZIF-8 NPs against Escherichia coli and MRSA isolates are 25 and 12.5 µg mL^-1 , respectively. Transcriptome and metabonomic analyses reveal that ZIF-8 NPs could trigger the inhibition of arginine biosynthesis pathway and the production of ROS, which lead to dysfunctional tricarboxylic acid cycle and disruption of cell membrane integrity, eventually killing MRSA isolates. Moreover, ZIF-8 NPs show desirable treatment and repair effects on mice model of MRSA isolates wound infected-model. The results, for the first time, reveal that the inhibition of arginine biosynthesis mediates the production of ROS and energy metabolism dysfunction contributes to the antibacterial ability of ZIF-8 NPs against MRSA. This study offers a new insight into ZIF-8 NPs combating MRSA isolates.

Metabolic reprogramming and flux to cell envelope precursors in a pentose phosphate pathway mutant increases MRSA resistance to β-lactam antibiotics

Central metabolic pathways controls virulence and antibiotic resistance, and constitute potential targets for antibacterial drugs. In Staphylococcus aureus the role of the pentose phosphate pathway (PPP) remains largely unexplored. Mutation of the 6-phosphogluconolactonase gene pgl, which encodes the only non-essential enzyme in the oxidative phase of the PPP, significantly increased MRSA resistance to β-lactam antibiotics, particularly in chemically defined media with glucose, and reduced oxacillin (OX)-induced lysis. Expression of the methicillin-resistance penicillin binding protein 2a and peptidoglycan architecture were unaffected. Carbon tracing and metabolomics revealed extensive metabolic reprogramming in the pgl mutant including increased flux to glycolysis, the TCA cycle, and several cell envelope precursors, which was consistent with increased β-lactam resistance. Morphologically, pgl mutant cells were smaller than wild-type with a thicker cell wall and ruffled surface when grown in OX. Further evidence of the pleiotropic effect of the pgl mutation was reduced resistance to Congo Red, sulfamethoxazole and oxidative stress, and increased resistance to targocil, fosfomycin and vancomycin. Reduced binding of wheat germ agglutinin (WGA) to pgl was indicative of lower wall teichoic acid/lipoteichoic acid levels or altered teichoic acid structures. Mutations in the vraFG or graRS loci reversed the increased OX resistance phenotype and restored WGA binding to wild-type levels. VraFG/GraRS was previously implicated in susceptibility to cationic antimicrobial peptides and vancomycin, and these data reveal a broader role for this multienzyme membrane complex in the export of cell envelope precursors or modifying subunits required for resistance to diverse antimicrobial agents. Altogether our study highlights important roles for the PPP and VraFG/GraRS in β-lactam resistance, which will support efforts to identify new drug targets and reintroduce β-lactams in combination with adjuvants or other antibiotics for infections caused by MRSA and other β-lactam resistant pathogens.

Author summary

High-level resistance to penicillin-type (β-lactam) antibiotics significantly limits the therapeutic options for patients with MRSA infections necessitating the use of newer agents, for which reduced susceptibility has already been described. Here we report for the first time that the central metabolism pentose phosphate pathway controls MRSA resistance to penicillin-type antibiotics. We comprehensively demonstrated that mutation of the PPP gene pgl perturbed metabolism in MRSA leading to increased flux to cell envelope precursors to drive increased antibiotic resistance. Moreover, increased resistance was dependent on the VraRG/GraRS multienzyme membrane complex previously implicated in resistance to antimicrobial peptides and vancomycin. Our data thus provide new insights on MRSA mechanisms of β-lactam resistance, which will support efforts to expand the treatment options for infections caused by this and other antimicrobial resistant pathogens.

Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus

Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.

Proline transporters ProT and PutP are required for Staphylococcus aureus infection

Proline acquired via specific transporters can serve as a proteinogenic substrate, carbon and nitrogen source, or osmolyte. Previous reports have documented that Staphylococcus aureus, a major community and nosocomial pathogen, encodes at least four proline transporters, PutP, OpuC, OpuD, and ProP. A combination of genetic approaches and 3H-proline transport assays reveal that a previously unrecognized transporter, ProT, in addition to PutP, are the major proline transporters in S. aureus. Complementation experiments using constitutively expressed non-cognate promoters found that proline transport via OpuD, OpuC, and ProP is minimal. Both proline biosynthesis from arginine and proline transport via ProT are critical for growth when S. aureus is grown under conditions of high salinity. Further, proline transport mediated by ProT or PutP are required for growth in media with and without glucose, indicating both transporters function to acquire proline for proteinogenic purposes in addition to acquisition of proline as a carbon/nitrogen source. Lastly, inactivation of proT and putP resulted in a significant reduction (5 log10) of bacterial burden in murine skin-and-soft tissue infection and bacteremia models, suggesting that proline transport is required to establish a S. aureus infection.

Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains

The complex cross talk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the Staphylococcus aureus USA300 strain by applying independent component analysis (ICA) to 385 RNA sequencing samples. We then combined the modular TRN model with a metabolic model to study the regulation of carbon and amino acid metabolism. Our analysis showed that regulation of central carbon metabolism by CcpA and amino acid biosynthesis by CodY are closely coordinated. In general, S. aureus increases the expression of CodY-regulated genes in the presence of preferred carbon sources such as glucose. This transcriptional coordination was corroborated by metabolic model simulations that also showed increased amino acid biosynthesis in the presence of glucose. Further, we found that CodY and CcpA cooperatively regulate the expression of ribosome hibernation-promoting factor, thus linking metabolic cues with translation. In line with this hypothesis, expression of CodY-regulated genes is tightly correlated with expression of genes encoding ribosomal proteins. Together, we propose a coarse-grained model where expression of S. aureus genes encoding enzymes that control carbon flux and nitrogen flux through the system is coregulated with expression of translation machinery to modularly control protein synthesis. While this work focuses on three key regulators, the full TRN model we present contains 76 total independently modulated sets of genes, each with the potential to uncover other complex regulatory structures and interactions. IMPORTANCE Staphylococcus aureus is a versatile pathogen with an expanding antibiotic resistance profile. The biology underlying its clinical success emerges from an interplay of many systems such as metabolism and gene regulatory networks. This work brings together models for these two systems to establish fundamental principles governing the regulation of S. aureus central metabolism and protein synthesis. Studies of these fundamental biological principles are often confined to model organisms such as Escherichia coli. However, expanding these models to pathogens can provide a framework from which complex and clinically important phenotypes such as virulence and antibiotic resistance can be better understood. Additionally, the expanded gene regulatory network model presented here can deconvolute the biology underlying other important phenotypes in this pathogen.

GltS regulates biofilm formation in methicillin-resistant Staphylococcus aureus

Biofilm-based infection is a major healthcare burden. Methicillin-resistant Staphylococcus aureus (MRSA) is one of major organisms responsible for biofilm infection. Although biofilm is induced by a number of environmental signals, the molecule responsible for environmental sensing is not well delineated. Here we examined the role of ion transporters in biofilm formation and found that the sodium-glutamate transporter gltS played an important role in biofilm formation in MRSA. This was shown by gltS transposon mutant as well as its complementation. The lack of exogenous glutamate also enhanced biofilm formation in JE2 strain. The deficiency of exogenous glutamate intake accelerated endogenous glutamate/glutamine production, which led to the activation of the urea cycle. We also showed that urea cycle activation was critical for biofilm formation. In conclusion, we showed that gltS was a critical regulator of biofilm formation by controlling the intake of exogenous glutamate. An intervention to target glutamate intake may be a potential useful approach against biofilm.

Teg58, a small regulatory RNA, is involved in regulating arginine biosynthesis and biofilm formation in Staphylococcus aureus

Staphylococcus aureus adapts to different environments by sensing and responding to diverse environmental cues. The responses are coordinately regulated by regulatory proteins, and small regulatory RNAs at the transcriptional and translational levels. Here, we characterized teg58, a SarA repressed sRNA, using ChIP-Seq and RNA-Seq analysis of a sarA mutant. Phenotypic and genetic analyses indicated that inactivation of teg58 led to reduced biofilm formation in a process that is independent of SarA, agr, PIA, and PSMs. RNA-Seq analysis of teg58 mutant revealed up-regulation of arginine biosynthesis genes (i.e., argGH) as well as the ability of the mutant to grow in a chemical defined medium (CDM) lacking L-arginine. Exogenous L-arginine or endogenous induction of argGH led to decreased biofilm formation in parental strains. Further analysis in vitro and in vivo demonstrated that the specific interaction between teg58 and the argGH occurred at the post-transcriptional level to repress arginine synthesis. Biochemical and genetic analyses of various arginine catabolic pathway genes demonstrated that the catabolic pathway did not play a significant role in reduced biofilm formation in the teg58 mutant. Overall, results suggest that teg58 is a regulatory sRNA that plays an important role in modulating arginine biosynthesis and biofilm formation in S. aureus.

Staphylococcal saoABC Operon Codes for a DNA-Binding Protein SaoC Implicated in the Response to Nutrient Deficit

Whilst a large number of regulatory mechanisms for gene expression have been characterised to date, transcription regulation in bacteria still remains an open subject. In clinically relevant and opportunistic pathogens, such as Staphylococcus aureus, transcription regulation is of great importance for host-pathogen interactions. In our study we investigated an operon, exclusive to staphylococci, that we name saoABC. We showed that SaoC binds to a conserved sequence motif present upstream of the saoC gene, which likely provides a negative feedback loop. We have also demonstrated that S. aureus ΔsaoB and ΔsaoC mutants display altered growth dynamics in non-optimal media; ΔsaoC exhibits decreased intracellular survival in human dermal fibroblasts, whereas ΔsaoB produces an elevated number of persisters, which is also elicited by inducible production of SaoC in ΔsaoBΔsaoC double mutant. Moreover, we have observed changes in the expression of saoABC operon genes during either depletion of the preferential carbon or the amino acid source as well as during acidification. Comparative RNA-Seq of the wild type and ΔsaoC mutant demonstrated that SaoC influences transcription of genes involved in amino acid transport and metabolism, and notably of those coding for virulence factors. Our results suggest compellingly that saoABC operon codes for a DNA-binding protein SaoC, a novel staphylococcal transcription factor, and its antagonist SaoB. We linked SaoC to the response to nutrient deficiency, a stress that has a great impact on host-pathogen interactions. That impact manifests in SaoC influence on persister formation and survival during internalisation to host cells, as well as on the expression of genes of virulence factors that may potentially result in profound alternations in the pathogenic phenotype. Investigation of such novel regulatory mechanisms is crucial for our understanding of the dynamics of interactions between pathogenic bacteria and host cells, particularly in the case of clinically relevant, opportunistic pathogens such as Staphylococcus aureus.

Staphylococcus aureus Does Not Synthesize Arginine from Proline under Physiological Conditions

The Gram-positive pathogen Staphylococcus aureus is the only bacterium known to synthesize arginine from proline via the arginine-proline interconversion pathway despite having genes for the well-conserved glutamate pathway. Since the proline-arginine interconversion pathway is repressed by CcpA-mediated carbon catabolite repression (CCR), CCR has been attributed to the arginine auxotrophy of S. aureus. Using ribose as a secondary carbon source, here, we demonstrate that S. aureus arginine auxotrophy is not due to CCR but due to the inadequate concentration of proline degradation product. Proline is degraded by proline dehydrogenase (PutA) into pyrroline-5-carboxylate (P5C). Although the PutA expression was fully induced by ribose, the P5C concentration remained insufficient to support arginine synthesis because P5C was constantly consumed by the P5C reductase ProC. When the P5C concentration was artificially increased by either PutA overexpression or proC deletion, S. aureus could synthesize arginine from proline regardless of carbon source. In contrast, when the P5C concentration was reduced by overexpression of proC, it inhibited the growth of the ccpA deletion mutant without arginine. Intriguingly, the ectopic expression of the glutamate pathway enzymes converted S. aureus into arginine prototroph. In an animal experiment, the arginine-proline interconversion pathway was not required for the survival of S. aureus. Based on these results, we concluded that S. aureus does not synthesize arginine from proline under physiological conditions. We also propose that arginine auxotrophy of S. aureus is not due to the CcpA-mediated CCR but due to the inactivity of the conserved glutamate pathway. IMPORTANCE Staphylococcus aureus is a versatile Gram-positive human pathogen infecting various human organs. The bacterium's versatility is partly due to efficient metabolic regulation via the carbon catabolite repression system (CCR). S. aureus is known to interconvert proline and arginine, and CCR represses the synthesis of both amino acids. However, when CCR is released by a nonpreferred carbon source, S. aureus can synthesize proline but not arginine. In this study, we show that, in S. aureus, the intracellular concentration of pyrroline-5-carboxylate (P5C), the degradation product of proline and the substrate of proline synthesis, is too low to synthesize arginine from proline. These results call into question the notion that S. aureus synthesizes arginine from proline.

Catabolic Ornithine Carbamoyltransferase Activity Facilitates Growth of Staphylococcus aureus in Defined Medium Lacking Glucose and Arginine

Previous studies have found that arginine biosynthesis in Staphylococcus aureus is repressed via carbon catabolite repression (CcpA), and proline is used as a precursor. Unexpectedly, however, robust growth of S. aureus is not observed in complete defined medium lacking both glucose and arginine (CDM-R). Mutants able to grow on agar-containing defined medium lacking arginine (CDM-R) were selected and found to contain mutations within ahrC, encoding the canonical arginine biosynthesis pathway repressor (AhrC), or single nucleotide polymorphisms (SNPs) upstream of the native arginine deiminase (ADI) operon arcA1B1D1C1. Reverse transcription-PCR (RT-PCR) studies found that mutations within ccpA or ahrC or SNPs identified upstream of arcA1B1D1C1 increased the transcription of both arcB1 and argGH, encoding ornithine carbamoyltransferase and argininosuccinate synthase/lyase, respectively, facilitating arginine biosynthesis. Furthermore, mutations within the AhrC homologue argR2 facilitated robust growth within CDM-R. Complementation with arcB1 or arcA1B1D1C1, but not argGH, rescued growth in CDM-R. Finally, supplementation of CDM-R with ornithine stimulated growth, as did mutations in genes (proC and rocA) that presumably increased the pyrroline-5-carboxylate and ornithine pools. Collectively, these data suggest that the transcriptional regulation of ornithine carbamoyltransferase and, in addition, the availability of intracellular ornithine pools regulate arginine biosynthesis in S. aureus in the absence of glucose. Surprisingly, ~50% of clinical S. aureus isolates were able to grow in CDM-R. These data suggest that S. aureus is selected to repress arginine biosynthesis in environments with or without glucose; however, mutants may be readily selected that facilitate arginine biosynthesis and growth in specific environments lacking arginine.

Adaptive Metabolism of Staphylococcus aureus Revealed by Untargeted Metabolomics

Staphylococcus aureus (SA) is an opportunistic pathogen that can cause a wide spectrum of infections, from superficial skin inflammation to severe and potentially fatal and invasive diseases. Due to the many potential routes of infection, host-derived environmental signals (oxygen availability, nutrients, etc.) are vital for host colonization and thus contribute to SA's pathogenesis. To uncover the direct effects of environmental factors on SA metabolism, we performed a series of experiments in diverse culture environments and correlated our findings of SA's metabolic adaptation to some of the pathogen's known virulence factors. Untargeted metabolomics was conducted on a Thermo Q-Exactive high-resolution mass spectrometer. We detected 260 intracellular polar metabolites from our bacteria cultured under both aerobic and anaerobic conditions and in glucose- and dextrin-supplemented cultures. These metabolites were mapped to relevant metabolic pathways to elucidate the adaptive metabolic processes of both methicillin-sensitive SA (MSSA) and methicillin-resistant SA (MRSA). We also detected an increased expression of virulence genes agr-I and sea of MRSA supplemented with both glucose and dextrin by qPCR. With the metabolic data collected that may be associated with the adaptive growth and virulence of SA, our study could set up the foundations for future work to identify metabolic inhibitors/modulators to mitigate SA infections in different growth environments.

Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A

Staphylococcus epidermidis is a common commensal of collagen-rich regions of the body, such as the skin, but also represents a threat to patients with medical implants (joints and heart), and to preterm babies. Far less studied than Staphylococcus aureus, the mechanisms behind this increasingly recognised pathogenicity are yet to be fully understood. Improving our knowledge of the metabolic processes that allow S. epidermidis to colonise different body sites is key to defining its pathogenic potential. Thus, we have constructed a fully curated, genome-scale metabolic model for S. epidermidis RP62A, and investigated its metabolic properties with a focus on substrate auxotrophies and its utilisation for energy and biomass production. Our results show that, although glucose is available in the medium, only a small portion of it enters the glycolytic pathways, whils most is utilised for the production of biofilm, storage and the structural components of biomass. Amino acids, proline, valine, alanine, glutamate and arginine, are preferred sources of energy and biomass production. In contrast to previous studies, we have shown that this strain has no real substrate auxotrophies, although removal of proline from the media has the highest impact on the model and the experimental growth characteristics. Further study is needed to determine the significance of proline, an abundant amino acid in collagen, in S. epidermidis colonisation.

Suppression of Thiol-Dependent Antioxidant System and Stress Response in Methicillin-Resistant Staphylococcus aureus by Docosanol: Explication Through Proteome Investigation

The present study was aimed to investigate the effect of docosanol on the protein expression profile of methicillin-resistant Staphylococcus aureus (MRSA). Thus, two-dimensional gel electrophoresis coupled with MALDI-TOF MS technique was utilized to identify the differentially regulated proteins in the presence of docosanol. A total of 947 protein spots were identified from the intracellular proteome of both control and docosanol treated samples among which 40 spots were differentially regulated with a fold change greater than 1.0. Prominently, the thiol-dependent antioxidant system and stress response proteins are downregulated in MRSA, which are critical for survival during oxidative stress. In particular, docosanol downregulated the expression of Tpx, AhpC, BshC, BrxA, and YceI with a fold change of 1.4 (p = 0.02), 1.4 (p = 0.01), 1.6 (p = 0.002), 4.9 (p = 0.02), and 1.4 (p = 0.02), respectively. In addition, docosanol reduced the expression of proteins involved in purine metabolic pathways, biofilm growth cycle, and virulence factor production. Altogether, these findings suggest that docosanol could efficiently target the antioxidant pathway by reducing the expression of bacillithiol and stress-associated proteins.

Proteomics characterization nitrogen fertilizer promotes the starch synthesis and metabolism and amino acid biosynthesis in common buckwheat

Nitrogen (N) affects common buckwheat quality by affecting starch and amino acids (AAs) content, but its molecular mechanism is still unclear. We selected two common buckwheat varieties with high and low starch content, and designed two treatments with 180 and 0 kg N/ha. Application of high-N led to significant increases in starch, amylose and amylopectin content. Of 1337 differentially expressed proteins (DEPs) induced by high-N conditions. 472DEPs were significantly upregulated and 176DEPs downregulated for Xinong9976. 239DEPs were significantly upregulated and 126DEPs downregulated for Beizaosheng. The six alpha-glucan phosphorylases, three alpha-amylases, one granule-bound starch synthase 1 and one sucrose synthase exhibited higher expression at the 180 kg N/ha than at the 0 kg N/ha. In addition, high-N application promoted arginine, leucine, isoleucine and valine biosynthesis. This study revealed the effect of N on the starch and AA content of common buckwheat and its mechanism. The crucial proteins identified may develop the quality of common buckwheat.

Identification and Characterization of Pleiotropic High-Persistence Mutations in the Beta Subunit of the Bacterial RNA Polymerase

Mutations conferring resistance to bactericidal antibiotics reduce the average susceptibility of mutant populations. It is unknown, however, how those mutations affect the survival of individual bacteria. Since surviving bacteria can be a reservoir for recurring infections, it is important to know how survival rates may be affected by resistance mutations and by the choice of antibiotics. Here, we present evidence that (i) Escherichia coli mutants with 100 to 1,000 times increased frequency of survival in ciprofloxacin, an archetypal fluoroquinolone antibiotic, can be readily obtained in a stepwise selection; (ii) the high survival frequency is conferred by mutations in the switch region of the beta subunit of the RNA polymerase; (iii) the switch-region mutations are (p)ppGpp mimics, partially analogous to rpoB stringent mutations; (iv) the stringent and switch region rpoB mutations frequently occur in clinical isolates of E. coli, Acinetobacter baumannii, Mycobacterium tuberculosis, and Staphylococcus aureus, and at least one of them, RpoB S488L, which is a common rifampicin resistance mutations, dramatically increases the survival of a clinical methicillin-resistant S. aureus (MRSA) strain in ampicillin; and (v) the RpoB-associated high-survival phenotype can be reversed by subinhibitory concentrations of chloramphenicol.

The impact of carbon and nitrogen catabolite repression in microorganisms

Organisms have cellular machinery that is focused on optimum utilization of resources to maximize growth and survival depending on various environmental and developmental factors. Catabolite repression is a strategy utilized by various species of bacteria and fungi to accommodate changes in the environment such as the depletion of resources, or an abundance of less-favored nutrient sources. Catabolite repression allows for the rapid use of certain substrates like glucose over other carbon sources. Effective handling of carbon and nitrogen catabolite repression in microorganisms is crucial to outcompete others in nutrient limiting conditions. Investigations into genes and proteins linked to preferential uptake of different nutrients under various environmental conditions can aid in identifying regulatory mechanisms that are crucial for optimum growth and survival of microorganisms. The exact time and way bacteria and fungi switch their utilization of certain nutrients is of great interest for scientific, industrial, and clinical reasons. Catabolite repression is of great significance for industrial applications that rely on microorganisms for the generation of valuable bio-products. The impact catabolite repression has on virulence of pathogenic bacteria and fungi and disease progression in hosts makes it important area of interest in medical research for the prevention of diseases and developing new treatment strategies. Regulatory networks under catabolite repression exemplify the flexibility and the tremendous diversity that is found in microorganisms and provides an impetus for newer insights into these networks.

Diversity, properties and functions of bacterial arginases

The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.

Modeling of stringent-response reflects nutrient stress induced growth impairment and essential amino acids in different Staphylococcus aureus mutants

Stapylococcus aureus colonises the nose of healthy individuals but can also cause a wide range of infections. Amino acid (AA) synthesis and their availability is crucial to adapt to conditions encountered in vivo. Most S. aureus genomes comprise all genes required for AA biosynthesis. Nevertheless, different strains require specific sets of AAs for growth. In this study we show that regulation inactivates pathways under certain conditions which result in these observed auxotrophies. We analyzed in vitro and modeled in silico in a Boolean semiquantitative model (195 nodes, 320 edges) the regulatory impact of stringent response (SR) on AA requirement in S. aureus HG001 (wild-type) and in mutant strains lacking the metabolic regulators RSH, CodY and CcpA, respectively. Growth in medium lacking single AAs was analyzed. Results correlated qualitatively to the in silico predictions of the final model in 92% and quantitatively in 81%. Remaining gaps in our knowledge are evaluated and discussed. This in silico model is made fully available and explains how integration of different inputs is achieved in SR and AA metabolism of S. aureus. The in vitro data and in silico modeling stress the role of SR and central regulators such as CodY for AA metabolisms in S. aureus.

Impact of the Histidine-Containing Phosphocarrier Protein HPr on Carbon Metabolism and Virulence in Staphylococcus aureus

Carbon catabolite repression (CCR) is a common mechanism pathogenic bacteria use to link central metabolism with virulence factor synthesis. In gram-positive bacteria, catabolite control protein A (CcpA) and the histidine-containing phosphocarrier protein HPr (encoded by ptsH) are the predominant mediators of CCR. In addition to modulating CcpA activity, HPr is essential for glucose import via the phosphotransferase system. While the regulatory functions of CcpA in Staphylococcus aureus are largely known, little is known about the function of HPr in CCR and infectivity. To address this knowledge gap, ptsH mutants were created in S. aureus that either lack the open reading frame or harbor a ptsH variant carrying a thymidine to guanosine mutation at position 136, and the effects of these mutations on growth and metabolism were assessed. Inactivation of ptsH altered bacterial physiology and decreased the ability of S. aureus to form a biofilm and cause infections in mice. These data demonstrate that HPr affects central metabolism and virulence in S. aureus independent of its influence on CcpA regulation.

Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind

Staphylococcus xylosus is found in the microbiota of traditional cheeses, particularly in the rind of soft smeared cheeses. Despite its frequency, the molecular mechanisms allowing the growth and adaptation of S. xylosus in dairy products are still poorly understood. A transcriptomic approach was used to determine how the gene expression profile is modified during the fermentation step in a solid dairy matrix. S. xylosus developed an aerobic metabolism perfectly suited to the cheese rind. It overexpressed genes involved in the aerobic catabolism of two carbon sources in the dairy matrix, lactose and citrate. Interestingly, S. xylosus must cope with nutritional shortage such as amino acids, peptides, and nucleotides, consequently, an extensive up-regulation of genes involved in their biosynthesis was observed. As expected, the gene sigB was overexpressed in relation with general stress and entry into the stationary phase and several genes under its regulation, such as those involved in transport of anions, cations and in pigmentation were up-regulated. Up-regulation of genes encoding antioxidant enzymes and glycine betaine transport and synthesis systems showed that S. xylosus has to cope with oxidative and osmotic stresses. S. xylosus expressed an original system potentially involved in iron acquisition from lactoferrin.

A genomic analysis of osmotolerance in Staphylococcus aureus

A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low a_w environments. A homology transfer based approach, using the well characterised osmotic stress response systems of Bacillus subtilis and Escherichia coli, was used to identify putative osmotolerance loci in Staphylococcus aureus ST772-MRSA-V. A total of 17 distinct putative hyper and hypo-osmotic stress response systems, comprising 78 genes, were identified. The ST772-MRSA-V genome exhibits significant degeneracy in terms of the osmotic stress response; with three copies of opuD, two copies each of nhaK and mrp/mnh, and five copies of opp. Furthermore, regulation of osmotolerance in ST772-MRSA-V appears to be mediated at the transcriptional, translational, and post-translational levels.

Inhibition of Host Arginase Activity Against Staphylococcal Bloodstream Infection by Different Metabolites

Staphylococcus aureus is a notorious bacterial pathogen that often causes soft tissue and bloodstream infections and invariably garners resistance mechanisms against new antibiotics. Modulation of the host immune response by metabolites is a powerful tool against bacterial infections, but has not yet been used against S. aureus infections. In this study, we identified four metabolite biomarkers: L-proline, L-isoleucine, L-leucine, and L-valine (PILV), through a metabolomics study using animal models of S. aureus bloodstream infection. The exogenous administration of each metabolite or of PILV showed anti-infective effects, and a higher protection was achieved with PILV in comparison to individual metabolites. During the staphylococcal infection, the expression of most host arginase and nitric oxide synthase (NOS) isozymes was simultaneously induced in mouse liver, kidney, and blood samples. However, the induction of arginase isozymes was dramatically stronger than that of NOS isozymes. This elevated arginase activity was inhibited by the metabolite biomarkers thus killing S. aureus, and PILV exhibited the strongest inhibition of arginase activity and bacterial inhibition. The suppression of arginase activity also contributed to the metabolite-mediated phagocytic killing of S. aureus in mouse and human blood. Our findings demonstrate the metabolite-mediated arginase inhibition as a therapeutic intervention for S. aureus infection.

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.

Metabolic control of virulence factor production in Staphylococcus aureus

As investigators decipher the underlining mechanisms of Staphylococcus aureus pathogenesis, it is becoming apparent that perturbations in central metabolism alter virulence factor production and infection outcomes. It is also evident that S. aureus has the ability to metabolically adapt to improve colonization and overcome challenges imparted by the immune system. Altered metabolite pools modify virulence factor production suggesting that proper functioning of a core metabolic network is necessary for successful niche colonization and pathogenesis. Herein we discuss four examples of transcriptional regulators that monitor metabolic status. These regulatory systems sense perturbations in the metabolic network and respond by altering the transcription of genes utilized for central metabolism, energy generation and pathogenesis.

Protease-Mediated Growth of Staphylococcus aureus on Host Proteins Is opp3 Dependent

Staphylococcus aureus has the ability to cause infections in a variety of niches, suggesting a robust metabolic capacity facilitating proliferation under various nutrient conditions. The mature skin abscess is glucose depleted, indicating that peptides and free amino acids are important sources of nutrients for S. aureus. Our studies have found that mutations in both pyruvate carboxykinase and glutamate dehydrogenase, enzymes that function in essential gluconeogenesis reactions when amino acids serve as the major carbon source, reduce bacterial burden in a murine skin abscess model. Moreover, peptides liberated from collagen by host protease MMP-9 as well as the staphylococcal protease aureolysin support S. aureus growth in an Opp3-dependent manner under nutrient-limited conditions. Additionally, the presence of peptides induces aureolysin expression. Overall, these studies define one pathway by which S. aureus senses a nutrient-limiting environment and induces factors that function to acquire and utilize carbon from host-derived sources.

Staphylococcus aureus has the ability to cause infections in multiple organ systems, suggesting an ability to rapidly adapt to changing carbon and nitrogen sources. Although there is little information about the nutrients available at specific sites of infection, a mature skin abscess has been characterized as glucose depleted, indicating that peptides and free amino acids are an important source of nutrients for the bacteria. Our studies have found that mutations in enzymes necessary for growth on amino acids, including pyruvate carboxykinase (ΔpckA) and glutamate dehydrogenase (ΔgudB), reduced the ability of the bacteria to proliferate within a skin abscess, suggesting that peptides and free amino acids are important for S. aureus growth. Furthermore, we found that collagen, an abundant host protein that is present throughout a skin abscess, serves as a reservoir of peptides. To liberate peptides from the collagen, we identified that the host protease, MMP-9, as well as the staphylococcal proteases aureolysin and staphopain B function to cleave collagen into peptide fragments that can support S. aureus growth under nutrient-limited conditions. Moreover, the oligopeptide transporter Opp3 is the primary staphylococcal transporter responsible for peptide acquisition. Lastly, we observed that the presence of peptides (3-mer to 7-mer) induces the expression of aureolysin, suggesting that S. aureus has the ability to detect peptides in the environment.

The Many Facets of the Small Non-coding RNA RsaE (RoxS) in Metabolic Niche Adaptation of Gram-Positive Bacteria

Small regulatory RNAs (sRNAs) are increasingly recognized as players in the complex regulatory networks governing bacterial gene expression. RsaE (synonym RoxS) is an sRNA that is highly conserved in bacteria of the Bacillales order. Recent analyses in Bacillus subtilis, Staphylococcus aureus and Staphylococcus epidermidis identified RsaE/RoxS as a potent riboregulator of central carbon metabolism and energy balance with many molecular RsaE/RoxS functions and targets being shared across species. Similarities and species-specific differences in cellular processes modulated by RsaE/RoxS suggest that this sRNA plays a prominent role in the adaptation of Gram-positive bacteria to niches with varying nutrient availabilities and environmental cues. This review summarizes recent findings on the molecular function of RsaE/RoxS and its interaction with mRNA targets. Special emphasis will be on the integration of RsaE/RoxS into metabolic regulatory circuits and, derived from this, the role of RsaE/RoxS as a putative driver to generate phenotypic heterogeneity in bacterial populations. In this respect, we will particularly discuss heterogeneous RsaE expression in S. epidermidis biofilms and its possible contribution to metabolic niche diversification, programmed bacterial lysis and biofilm matrix production.

Virulence and Metabolism

Staphylococcus aureus is clearly the most pathogenic member of the Staphylococcaceae. This is in large part due to the acquisition of an impressive arsenal of virulence factors that are coordinately regulated by a series of dedicated transcription factors. What is becoming more and more appreciated in the field is the influence of the metabolic state of S. aureus on the activity of these virulence regulators and their roles in modulating metabolic gene expression. Here I highlight recent advances in S. aureus metabolism as it pertains to virulence. Specifically, mechanisms of nutrient acquisition are outlined including carbohydrate and non-carbohydrate carbon/energy sources as well as micronutrient (Fe, Mn, Zn and S) acquisition. Additionally, energy producing strategies (respiration versus fermentation) are discussed and put in the context of pathogenesis. Finally, transcriptional regulators that coordinate metabolic gene expression are outlined, particularly those that affect the activities of major virulence factor regulators. This chapter essentially connects many recent observations that link the metabolism of S. aureus to its overall pathogenesis and hints that the mere presence of a plethora of virulence factors may not entirely explain the extraordinary pathogenic potential of S. aureus.

Role of Proline in Pathogen and Host Interactions

SIGNIFICANCE

Proline metabolism has complex roles in a variety of biological processes, including cell signaling, stress protection, and energy production. Proline also contributes to the pathogenesis of various disease-causing organisms. Understanding the mechanisms of how pathogens utilize proline is important for developing new strategies against infectious diseases. Recent Advances: The ability of pathogens to acquire amino acids is critical during infection. Besides protein biosynthesis, some amino acids, such as proline, serve as a carbon, nitrogen, or energy source in bacterial and protozoa pathogens. The role of proline during infection depends on the physiology of the host/pathogen interactions. Some pathogens rely on proline as a critical respiratory substrate, whereas others exploit proline for stress protection.

CRITICAL ISSUES

Disruption of proline metabolism and uptake has been shown to significantly attenuate virulence of certain pathogens, whereas in other pathogens the importance of proline during infection is not known. Inhibiting proline metabolism and transport may be a useful therapeutic strategy against some pathogens. Developing specific inhibitors to avoid off-target effects in the host, however, will be challenging. Also, potential treatments that target proline metabolism should consider the impact on intracellular levels of Δ1-pyrroline-5-carboxylate, a metabolite intermediate that can have opposing effects on pathogenesis.

FUTURE DIRECTIONS

Further characterization of how proline metabolism is regulated during infection would provide new insights into the role of proline in pathogenesis. Biochemical and structural characterization of proline metabolic enzymes from different pathogens could lead to new tools for exploring proline metabolism during infection and possibly new therapeutic compounds.

Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus

The past two decades have witnessed an alarming expansion of staphylococcal disease caused by community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA). The factors underlying the epidemic expansion of CA-MRSA lineages such as USA300, the predominant CA-MRSA clone in the United States, are largely unknown. Previously described virulence and antimicrobial resistance genes that promote the dissemination of CA-MRSA are carried by mobile genetic elements, including phages and plasmids. Here, we used high-resolution genomics and experimental infections to characterize the evolution of a USA300 variant plaguing a patient population at increased risk of infection to understand the mechanisms underlying the emergence of genetic elements that facilitate clonal spread of the pathogen. Genetic analyses provided conclusive evidence that fitness (manifest as emergence of a dominant clone) changed coincidently with the stepwise emergence of (i) a unique prophage and mutation of the regulator of the pyrimidine nucleotide biosynthetic operon that promoted abscess formation and colonization, respectively, thereby priming the clone for success; and (ii) a unique plasmid that conferred resistance to two topical microbiocides, mupirocin and chlorhexidine, frequently used for decolonization and infection prevention. The resistance plasmid evolved through successive incorporation of DNA elements from non-S. aureus spp. into an indigenous cryptic plasmid, suggesting a mechanism for interspecies genetic exchange that promotes antimicrobial resistance. Collectively, the data suggest that clonal spread in a vulnerable population resulted from extensive clinical intervention and intense selection pressure toward a pathogen lifestyle that involved the evolution of consequential mutations and mobile genetic elements.

Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture

BACKGROUND

Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacterial species. Such interactions potentially indirectly impact the human host through virulence, antibiosis and immunomodulation.

RESULTS

Here we explored the responses triggered by the encounter of these two pathogens to identify early processes that are important for survival when facing a potential competitor. Transcriptional profiles of both bacteria were obtained after 3 h co-culture and compared to the respective mono-culture using RNAseq. Global responses in both bacteria included competition for nitrogen sources, amino acids and increased tRNA levels. Both organisms also induced lysogenic mechanisms related to prophage induction (S. aureus) and R- and F- pyocin synthesis (P. aeruginosa), possibly as a response to stress resulting from nutrient limitation or cell damage. Specific responses in S. aureus included increased expression of de novo and salvation pathways for purine and pyrimidine synthesis, a switch to glucose fermentation, and decreased expression of major virulence factors and global regulators.

CONCLUSIONS

Taken together, transcriptomic data indicate that early responses between P. aeruginosa and S. aureus involve competition for resources and metabolic adaptations, rather than the expression of bacteria- or host-directed virulence factors.

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus’ metabolic response to its environment.

Environmental perturbations (e.g., antibiotic stress, nutrient starvation, oxidative stress) induce systems-level perturbations of bacterial cells that vary depending on the growth environment. The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditions. Genome-scale models (GEMs) of metabolism represent a knowledge-based platform for the contextualization and integration of multi-omic measurements and can serve to offer valuable insights of system-level responses. This work provides the most up to date reconstruction effort integrating recent advances in the knowledge of S. aureus molecular biology with previous annotations resulting in the first quantitatively and qualitatively validated S. aureus GEM. GEM guided predictions obtained from model analysis provided insights into the effects of medium composition on metabolic flux distribution and gene essentiality. The model can also serve as a platform to guide network reconstructions for other Staphylococci as well as direct hypothesis generation following the integration of omics data sets, including transcriptomics, proteomics, metabolomics, and multi-strain genomic data.