Biology subjects

Frees, D.

Publications and source records attributed to Frees, D..

11 recordsLinked to original sources

bioRxiv2025

Activation of the Spx redox sensor counters cysteine-driven Fe(II) depletion under disulfide stress

In many low G+C Gram-positive bacteria, the global regulator Spx helps maintain thiol homeostasis during disulfide stress, when protein thiols form aberrant disulfide bonds that can lead to misfolding and oxidative damage. Spx-dependent gene expression is triggered when an intramolecular disulfide bond forms between two cysteines in its redox switch. Surprisingly, some Spx functions persist even in the absence of an active redox switch, highlighting the need to better understand the physiological significance of maintaining this regulatory feature. Here, we utilize a spxC10A mutant that encodes a redox-insensitive Spx variant to study the role of the Spx redox switch in Staphylococcus aureus. We show that the spxC10A mutant is hypersensitive to diamide-induced disulfide stress and exhibits widespread transcriptional dysregulation of genes that contribute to thiol maintenance and disulfide repair. Remarkably, the spxC10A mutant rapidly adapts to disulfide stress by increasing its intracellular pool of L-cysteine (L-Cys) through enhanced uptake, which helps restore a reduced intracellular environment. However, during this process increased L-Cys inadvertently depletes cytosolic Fe(II), leading to growth inhibition of the spxC10A mutant. Finally, we show that the Spx-dependent control of intracellular L-Cys is critical for S. aureus survival when it encounters human neutrophils. Overall, these findings suggest that staphylococcal adaptation to disulfide stress through intracellular L-Cys accumulation imposes significant fitness costs that S. aureus overcomes by rapid regulatory control of thiol homeostasis through a functional Spx redox switch. SignificanceAll cells have a pool of low molecular weight thiols, such as cysteine, glutathione, bacillithiol, and coenzyme A, to maintain redox balance under oxidative and disulfide stress. Among these, cysteine is a very effective thiol but is highly reactive, and its intracellular concentration must be tightly regulated. In S. aureus, we found that cysteine accumulates intracellularly during disulfide stress and if left unchecked, can inadvertently deplete cytosolic Fe(II), leading to growth inhibition. To prevent cysteine toxicity, S. aureus activates the global regulator Spx, which rapidly induces genes that restore thiol homeostasis and limits cysteine accumulation.

microbiology↗

bioRxiv2025

Unraveling proteomic chaos by independent component analysis - ClpX proficiency promotes the iron and oxygen limitation responses of Staphylococcus aureus and affects the intracellular bacterial behavior

In the opportunistic pathogen Staphylococcus aureus, protein homeostasis is largely mediated by the Caseinolytic protease (Clp) system. The proteases ClpXP and ClpCP are crucial for general and targeted proteolysis, which rely on the unfoldases ClpX and ClpC interacting with specific targets. However, the global effect on the proteome especially under infection-relevant stresses is not well-understood. To assess the effect of ClpX deficiency during infection-related processes, mass spectrometry-based global proteome profiles of S. aureus HG001 wild-type, an isogenic {Delta}clpX mutant, and a clpX complemented strain were recorded under control conditions as well as iron and oxygen limitation. The proteomic profiles revealed specific ClpX- and stress-dependent changes. A set of 24 robust stress-independent ClpX modulated proteins was identified and the stress-dependent influences were unraveled by independent component analysis (using the iModulon approach). These analyses revealed a role of ClpX in e.g., cell division, cell envelope homeostasis, the quinone stress response and prophage activation. Moreover, ClpX-dependent stress-specific effects were observed in the {Delta}clpX mutant, e.g. reduced induction of the heme uptake system under iron limitation and a dampened Rex-controlled oxygen limitation response. This revealed in particular that ClpX is central for heme homeostasis in S. aureus. Furthermore, in a Galleria infection model, the S. aureus {Delta}clpX mutant was attenuated compared to the wild-type HG001. This is consistent with a drastically reduced intracellular replication of the {Delta}clpX-mutant in cell culture-based infection experiments, however, high intracellular persistence of the {Delta}clpX mutant was also observed. This highlights the relevance of ClpX for bacterial fitness and virulence. ImportanceDuring infection processes, pathogens cope with host-mediated stressors. In response to those stressors, bacteria adapt their gene expression as well as their proteome profile. In the pathogen Staphylococcus aureus, protein homeostasis is mainly controlled by the Clp system. In particular, ClpX is the most conserved Clp unfoldase and is involved in overall regulation of virulence and bacterial fitness. However, the majority of ClpX targets remains elusive in S. aureus. With our proteomics approach and in depth data analysis, we provide a resource for global insight into ClpX-dependent adaptation of S. aureus physiology under infection-relevant conditions. Based on this, we uncover ClpXs role as a central player in the iron and oxygen limitation response. In addition, we demonstrate the importance of ClpX in S. aureus bacterial fitness in infection processes. However, reduced levels of ClpX lead to high intracellular persistence, which questions ClpXs suitability as a therapeutical target.

microbiology↗

bioRxiv2025

Cell splitting in Staphylococcus aureus is controlled by an adaptor protein facilitating degradation of a peptidoglycan hydrolase

Regulated protein degradation by Clp proteases is a highly conserved post-translational control mechanism in bacteria. In Staphylococcus aureus, the ClpXP complex targets the peptidoglycan hydrolase Sle1, maintaining a tightly regulated balance between peptidoglycan biosynthesis and hydrolysis, which is required to ensure proper cell splitting without compromising cell integrity. {beta}-lactams antibiotics disturb this balance, leading to their bactericidal effects. The mechanism underlying the specific targeting of Sle1 by the conserved ClpXP complex remains unknown. From a genome-wide screen for determinants of penicillin G susceptibility in S. aureus, we here identify the uncharacterized protein CxaR (for ClpXP-associated autolytic regulator). Growth defects, premature cell splitting, and increased cell lysis were observed in the absence of CxaR. Interestingly, these defects were mitigated by sublethal concentrations of {beta}-lactams. Through sequencing cxaR suppressor mutants, followed by immunoblotting, we show that the cxaR phenotypes are caused by excessive Sle1 accumulation. Indeed, exposure to {beta}-lactams reduces Sle1 levels, thereby rescuing the cells lacking CxaR. Furthermore, in vivo protein-protein interaction assays demonstrated that CxaR directly interacts with both ClpXP and Sle1, whereas no direct interaction was detected between Sle1 and ClpX. In line with this, CxaR was found to co-localize with ClpX adjacent to the septum. Taken together, these findings reveal that CxaR is a new regulatory factor controlling staphylococcal cell splitting by acting as an adaptor protein for controlled ClpXP-mediated degradation of Sle1.

microbiology↗

bioRxiv2025

Temperature-dependent regulation of bacterial cell division hydrolases by the coordinated action of a regulatory RNA and the ClpXP protease

A defining feature of bacteria is the peptidoglycan cell wall which provides structural integrity and prevents osmotic lysis. While peptidoglycan hydrolases are required for daughter cell separation, dysregulated cell wall degradation may result in cell lysis. The mechanisms allowing bacteria to control these deadly enzymes in response to environmental changes remain incompletely understood. Here, we find that in Staphylococcus aureus, temperature-dependent regulation of such hydrolases occurs by the coordinated action of a CHAP domain-specific regulatory RNA and the ClpXP protease. Using a proteomics approach, we identify a hitherto uncharacterized ClpXP controlled autolysin, CxcA, with a catalytic CHAP domain and show that it contributes to separation of daughter cells. CxcA is positively controlled by a non-coding RNA, named Rbc1 (for RNA binding to CHAP domain) transcribed from the antisense strand of cxcA. Notably, Rbc1 is capable of base pairing with RNAs encoding the CHAP domains of numerous cell wall hydrolases and we show that Rbc1 works in trans to upregulate the cell division hydrolase Sle1. Specifically, Rbc1 functions as a thermosensor allowing for upregulation of CxcA and Sle1 at low temperature where daughter cell separation is impeded. Interestingly, the Rbc1-mediated up-regulation of CxcA and Sle1 does not involve mRNA stabilization or increased translation; instead, Rbc1 depletion increases ClpXP-mediated degradation. In conclusion, we identify a novel cell division hydrolase that is highly conserved in Staphylococci and show that it is co-regulated with enzymes containing the catalytic CHAP domain via transcriptional regulation, an RNA-RNA temperature sensory mechanism and the ClpXP protease.

microbiology↗

bioRxiv2024

The Spx stress regulator confers high-level β-lactam resistance and decreases susceptibility to last-line antibiotics in methicillin resistant Staphylococcus aureus

Infections caused by methicillin resistant Staphylococcus aureus (MRSA) are a leading cause of mortality worldwide. MRSA have acquired resistance to next generation {beta}-lactam antibiotics through the horizontal acquisition of the mecA resistance gene. Development of high resistance is, however, often associated with additional mutations in a set of chromosomal core genes, known as potentiators which through poorly described mechanisms enhance resistance. The yjbH gene was recently identified as a hot spot for adaptive mutations during severe infections. Here, we show that inactivation of yjbH increased {beta}-lactam MICs up to 16-folds and transformed MRSA cells with low level of resistance to being homogenously highly resistant to {beta}-lactams. The yjbH gene encodes an adaptor protein that targets the transcriptional stress regulator Spx for degradation by the ClpXP protease. Using CRISPRi to knock down spx transcription, we unambiguously linked hyper-resistance to accumulation of Spx. Spx was previously proposed to be essential, however, our data indicate that Spx is dispensable for growth at 37{degrees}C but becomes essential in the presence of antibiotics with various targets. On the other hand, high Spx levels bypassed the role of PBP4 in {beta}-lactam resistance and broadly decreased MRSA susceptibility to compounds targeting the cell wall or the cell membrane including vancomycin, daptomycin, and nisin. Strikingly, Spx potentiated resistance independently of its redox sensing switch. Collectively, our study identifies a general stress pathway that, in addition to promoting the development of high-level, broad-spectrum {beta}-lactam resistance, also decreases MRSA susceptibility to critical antibiotics of last resort.

microbiology↗

bioRxiv2023

The ClpX chaperone and a hypermorphic FtsA variant with impaired self-interaction are mutually compensatory for coordinating Staphylococcus aureus cell division

Bacterial cell division requires the coordinated assembly and disassembly of a large protein complex called the divisome, however, the exact role of molecular chaperones in this critical process remains unclear. In the important pathogenic bacterium Staphylococcus aureus, the ClpX chaperone is essential for growth at 30{degrees}C and microscopic analyses suggested that ClpX plays a temperature-dependent role in cell division. We here provide genetic evidence that ClpX unfoldase activity is a determinant for proper coordination of cell division by showing that a spontaneous G325V substitution in the ATP-binding domain of the essential FtsA cell division protein rescues growth and septum synthesis in a Staphylococcus aureus clpX mutant. The polymerization state of FtsA is thought to control initiation of bacterial septum synthesis and, while restoring the aberrant FtsA dynamics in clpX cells, the FtsAG325V variant displayed reduced ability to interact with itself and other cell division proteins. In wild-type cells, the ftsAG325V allele shared phenotypes with E. coli superfission ftsA mutants and accelerated the cell cycle, increased the risk of daughter cell lysis, and conferred sensitivity to heat and antibiotics inhibiting cell wall synthesis. Strikingly, lethality was mitigated by spontaneous mutations that inactivate ClpX. Taken together, our results suggest that ClpX promotes septum synthesis by antagonizing FtsA interactions and illuminates the critical role of a protein unfoldase in coordinating bacterial cell division. IMPORTANCEEssential biological processes, such as cell division, are performed by multiple proteins working together in dynamic functional complexes. In eukaryotic cells, the disassembly of such molecular machines is often assisted by molecular chaperones capable of unfolding proteins. The ClpX unfoldase is conserved from bacteria to humans, however, the roles of ClpX in bacterial cell biology remain relatively unexplored. By combining genetic methods with super-resolution microscopy techniques, we show here that ClpX and a mutant variant of the essential cell division protein FtsA mutually compensate for each other in controlling cell division of the pathogenic bacterium Staphylococcus aureus. The selected FtsAG325V variant has diminished self-interactions and restored the aberrant FtsA dynamics in clpX cells suggesting that ClpX promotes cell division by antagonizing FtsA protein interactions. This study, for the first time, illuminates the important role of protein unfoldases in the functioning of the divisome, a multienzyme complex fundamental to bacterial reproduction.

molecular biology↗

bioRxiv2023

Novel determinant of antibiotic resistance: a clinically selected Staphylococcus aureus clpP mutant survives daptomycin treatment by reducing binding of the antibiotic and adapting a rod-shaped morphology

Daptomycin is a last-resort antibiotic used for treatment of infections caused by Gram-positive antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). Treatment failure is commonly linked to accumulation of point mutations, however, the contribution of single mutations to resistance and the mechanisms underlying resistance remain incompletely understood. Here we show that a single nucleotide polymorphism (SNP) selected during daptomycin therapy inactivates the highly conserved ClpP protease and is causing reduced susceptibility of MRSA to daptomycin, vancomycin, and {beta}-lactam antibiotics as well as decreased expression of virulence factors. Super-resolution microscopy demonstrated that the improved survival of the clpP mutant strain during daptomycin treatment was associated with reduced binding of daptomycin to the septal site and diminished membrane damage. In both the parental strain and the clpP strain, daptomycin inhibited the inward progression of septum synthesis eventually leading to lysis and death of the parental strain while surviving clpP cells were able to continue synthesis of the peripheral cell wall in the presence of 10 x MIC daptomycin resulting in a rod-shaped morphology. To our knowledge, this is the first demonstration that synthesis of the outer cell wall continues in the presence of daptomycin. Collectively, our data provide novel insight into the mechanisms behind bacterial killing and resistance to this important antibiotic. Also, the study emphasizes that treatment with last-line antibiotics is selective for mutations that, like the SNP in clpP, favor antibiotic resistance over virulence gene expression. IMPORTANCEThe bacterium Staphylococcus aureus is a leading cause of life-threatening infections and treatment is challenged by the worldwide dissemination of methicillin-resistant Staphylococcus aureus (MRSA) that are multi-drug resistant. Daptomycin, a cell membrane-targeting cationic lipopeptide, is one of the few antibiotics with activity against MRSA, however, the killing mechanism of daptomycin and the mechanisms leading to resistance are not fully understood. Here we show than an MRSA strain, isolated from the blood of a patient treated with daptomycin, has acquired a mutation that inactivates the ClpXP protease resulting in increased resistance to several antibiotics and diminished expression of virulence genes. Super resolution microscopy showed that the mutant avoids daptomycin-elicited killing by preventing the binding of the antibiotic to the septal site and by growing into a rod-shaped morphology. In summary, this study discloses new perspectives on the mechanism of killing and the mechanism of resistance to an antibiotic of last resort.

microbiology↗

bioRxiv2021

Rapid in vivo development of resistance to daptomycin in vancomycin-resistant Enterococcus faecium due to genomic rearrangements

BackgroundDaptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here we analysed the genomic changes leading to a daptomycin-susceptible VREfm isolate becoming resistant after 40 days of daptomycin and linezolid combination therapy. MethodsThe two isogenic VREfm isolates (daptomycin-susceptible and daptomycin-resistant) were analysed using whole genome sequencing with Illumina and Nanopore. ResultsWhole genome comparative analysis identified the loss of a 46.5 kb fragment and duplication of a 29.7 kb fragment in the daptomycin-resistant isolate, with many implicated genes involved in cell wall synthesis. Two plasmids of the daptomycin-susceptible isolate were also found integrated in the chromosome of the resistant isolate. One nonsynonymous SNP in the rpoC gene was identified in the daptomycin-resistant isolate. ConclusionsDaptomycin resistance developed through chromosomal rearrangements leading to altered cell wall structure. Such novel types of resistance mechanisms can only be identified by comparing closed genomes of isogenic isolates.

microbiology↗

bioRxiv2019

The Sle1 Cell Wall Amidase Controls Daughter Cell Splitting, Cell Size, and β-Lactam Resistance in Community Acquired Methicillin Resistant Staphylococcus aureus USA300

Most clinically relevant methicillin resistant Staphylococcus aureus (MRSA) strains have become resistant to {beta}-lactams antibiotics through horizontal acquisition of the mecA gene encoding PBP2a, a peptidoglycan transpeptidase with low affinity for {beta}-lactams. The level of resistance conferred by mecA is, however, strain dependent and the mechanisms underlying this phenomenon remain poorly understood. We here show that {beta}-lactam resistance correlates to expression of the Sle1 cell wall amidase in the fast spreading and highly virulent community-acquired MRSA USA300 clone. Sle1 is a substrate of the ClpXP protease, and while the high Sle1 levels in cells lacking ClpXP activity confer {beta}-lactam hyper-resistance, USA300 cells lacking Sle1 are as sensitive to {beta}-lactams as cells lacking mecA. This finding prompted us to assess the cellular roles of Sle1 in more detail, and we demonstrate that high Sle1 levels accelerate the onset of daughter cells splitting and decrease cell size. Vice versa, oxacillin decreases the Sle1 level, and imposes a cell-separation defect that is antagonized by high Sle1 levels, suggesting that high Sle1 levels increase tolerance to oxacillin by promoting cell separation. In contrast, increased oxacillin sensitivity of sle1 cells appears linked to a synthetical lethal effect on septum synthesis. In conclusion, this study demonstrates that Sle1 is a key factor in resistance to {beta}-lactam antibiotics in the JE2 USA300 model strain, and that PBP2a is required for expression of Sle1 in JE2 cells exposed to oxacillin.\n\nImportanceThe bacterium Staphylococcus aureus is a major cause of human disease, and the global spread of S. aureus resistant to {beta}-lactam antibiotics (MRSA) has made treatment increasingly difficult. {beta}-lactams interfere with cross-linking of the bacterial cell wall, however, the killing mechanism of this important class of antibiotics is still not fully understood. Here we provide novel insight into this topic by showing that {beta}-lactam resistance is controlled by the Sle1 cell wall amidase in the fast spreading and highly virulent MRSA USA300 clone. We show that Sle1 high levels accelerate the onset of daughter cells splitting and decrease cell size. Vice versa, oxacillin decreases the Sle1 level, and imposes a cell-separation defect that is antagonized Sle1. The key finding that resistance to {beta}-lactams correlates positively to expression of Sle1 indicates that, in S. aureus, the detrimental effects of {beta}-lactam antibiotics are linked to inhibition of daughter cells splitting.

microbiology↗

bioRxiv2018

SosA inhibits cell division in Staphylococcus aureus in response to DNA damage

Inhibition of cell division is critical for cell viability under DNA damaging conditions. In bacterial cells, DNA damage induces the SOS response, a process that inhibits cell division while repairs are being made. In coccoid bacteria, such as the human pathogen Staphylococcus aureus, the process remains poorly understood. Here we have characterized an SOS-induced cell-division inhibitor, SosA, in S. aureus. We find that in contrast to the wildtype, sosA mutant cells continue division under DNA damaging conditions with decreased viability as a consequence. Conversely, overproduction of SosA leads to cell division inhibition and reduced growth. The SosA protein is localized in the bacterial membrane and mutation of an extracellular amino acid, conserved between homologs of other staphylococcal species, abolished the inhibitory activity as did truncation of the C-terminal 30 amino acids. In contrast, C-terminal truncation of 10 amino acids lead to SosA accumulation and a strong cell division inhibitory activity. A similar phenotype was observed upon expression of wildtype SosA in a mutant lacking the membrane protease, CtpA. Thus, the extracellular C-terminus of SosA is required both for cell-division inhibition and for turnover of the protein. Functional studies showed that SosA is likely to interact with one or more divisome components and, without interfering with early cell-division events, halts cell division at a point where septum formation is initiated yet being unable to progress to septum closure. Our findings provide important insights into cell-division regulation in staphylococci that may foster development of new classes of antibiotics targeting this essential process. ImportanceStaphylococcus aureus is a serious human pathogen and a model organism for cell-division studies in spherical bacteria. We show that SosA is the DNA-damage-inducible cell-division inhibitor in S. aureus that upon expression causes cell swelling and cessation of the cell cycle at a characteristic stage post septum initiation but prior to division plate completion. SosA appears to function via an extracellular activity and is likely to do so by interfering with the essential membrane-associated division proteins, while at the same time being negatively regulated by the membrane protease CtpA. This report represents the first description of the process behind cell-division inhibition in coccoid bacteria. As several pathogens are included in this category, uncovering the molecular details of SosA activity and control can lead to identification of new targets for development of valuable anti-bacterial drugs.

microbiology↗

bioRxiv2018

The ClpX chaperone controls the Staphylococcus aureus cell cycle but can be bypassed by β-lactam antibiotics

The worldwide spread of Staphylococcus aureus strains resistant to almost all {beta}-lactam antibiotics is of major clinical concern. {beta}-lactams interfere with cross-linking of the bacterial cell wall, but the killing mechanism of this important class of antibiotics is not fully understood. Here we show that sub-lethal doses of {beta}-lactams stimulate the growth of S. aureus mutants lacking the widely conserved chaperone ClpX. S. aureus clpX mutants have a severe growth defect at temperatures below 37{degrees}C, and we reasoned that a better understanding of this growth defect could provide novel insights into how {beta}-lactam antibiotics interfere with growth of S. aureus. We demonstrate that ClpX is important for coordinating the S. aureus cell cycle, and that S. aureus cells devoid of ClpX fail to divide, or lyze spontaneously, at high frequency unless {beta}-lactams are added to the growth medium. Super-resolution imaging revealed that clpX cells display aberrant septum synthesis, and initiate daughter cell separation prior to septum completion at 30{degrees}C, but not at 37{degrees}C. FtsZ localization and dynamics were not affected in the absence of ClpX, suggesting that ClpX affects septum formation and autolytic activation downstream of Z-ring formation. Interestingly, {beta}-lactams restored septum synthesis and prevented premature autolytic splitting of clpX cells. Strikingly, inhibitors of wall teichoic acid (WTA) biosynthesis that work synergistically with {beta}-lactams to kill MRSA synthesis also rescued growth of the clpX mutant, underscoring a functional link between the PBP activity and WTA biosynthesis. The finding that {beta} -lactams can prevent lysis and restore septum synthesis of a mutant with dysregulated cell division lends support to the idea that PBPs function as coordinators of cell division and that {beta} -lactams do not kill S. aureus simply by weakening the cell wall.\n\nAuthor SummaryThe bacterium Staphylococcus aureus is a major cause of human disease, and the rapid spread of S. aureus strains that are resistant to almost all {beta}-lactam antibiotics has made treatment increasingly difficult. {beta}-lactams interfere with cross-linking of the bacterial cell wall but the killing mechanism of this important class of antibiotics is still not fully understood. Here we provide novel insight into this topic by examining a defined S. aureus mutant that has the unusual property of growing markedly better in the presence of {beta}-lactams. Without {beta}-lactams this mutant dies spontaneously at a high frequency due to premature separation of daughter cells during cell division. Cell death of the mutant can, however, be prevented either by exposure to {beta}-lactam antibiotics or by inhibiting synthesis of wall teichoic acid, a major component of the cell wall in Gram-positive bacteria with a conserved role in activation of autolytic splitting of daughter cells. The finding that the detrimental effect of {beta}-lactam antibiotics can be reversed by a mutation that affect the coordination of cell division emphasizes the idea that {beta}-lactams do not kill S. aureus simply by weakening the cell wall but rather by interference with the coordination of cell division.

microbiology↗