ClpC and MecA, components of a proteolytic machine, prevent Spo0A-P-dependent transcription without degradation

MecA: A Multifunctional ClpP-Dependent and Independent Regulator in Gram-Positive Bacteria

MecA is a broadly conserved adaptor protein in Gram-positive bacteria, mediating the recognition and degradation of specific target proteins by ClpCP protease complexes. MecA binds target proteins, often through recognition of degradation tags or motifs, and delivers them to the ClpC ATPase, which unfolds and translocates the substrates into the ClpP protease barrel for degradation. MecA activity is tightly regulated through interactions with ClpC ATPase and other factors, ensuring precise control over protein degradation and cellular homeostasis. Beyond proteolysis, emerging evidence highlights a ClpP-independent role of MecA in modulating the function of its targets, including key enzymes and transcriptional factors involved in biosynthetic and metabolic pathways. However, the full scope and mechanisms of ClpP-independent MecA regulation remain unclear, warranting further investigation.

Developmentally regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation

Bacillus subtilis sporulation entails a dramatic transformation of the two cells required to assemble a dormant spore, with the larger mother cell engulfing the smaller forespore to produce the "cell within a cell" structure that is a hallmark of endospore formation. Sporulation also entails metabolic differentiation, whereby key metabolic enzymes are depleted from the forespore but maintained in the mother cell. This reduces the metabolic potential of the forespore, which becomes dependent on mother cell metabolism and the SpoIIQ-SpoIIIA channel to obtain metabolic building blocks necessary for development. We demonstrate that metabolic differentiation depends on the ClpCP protease and a forespore-produced protein encoded by the yjbA gene, which we have renamed MdfA (metabolic differentiation factor A). MdfA is conserved in aerobic endospore formers and required for spore resistance to hypochlorite. Using mass spectrometry and quantitative fluorescence microscopy, we show that MdfA mediates the depletion of dozens of metabolic enzymes and key transcription factors from the forespore. An accompanying study by Massoni and colleagues demonstrates that MdfA is a ClpC adaptor protein that directly interacts with and stimulates ClpCP activity. Together, these results document a developmentally regulated proteolytic pathway that reshapes forespore metabolism, reinforces differentiation, and enhances spore resistance to the oxidant hypochlorite.

Arginine kinase McsB and ClpC complex impairs the transition to biofilm formation in Bacillus subtilis

Robust biofilm formation on host niches facilitates beneficial Bacillus to promote plant growth and inhibit plant pathogens. Arginine kinase McsB is involved in bacterial development and stress reaction by phosphorylating proteins for degradation through a ClpC/ClpP protease. Conversely, cognate arginine phosphatase YwlE counteracts the process. Regulatory pathways of biofilm formation have been studied in Bacillus subtilis, of which Spo0A∼P is a master transcriptional regulator, which is transcriptionally activated by itself in biofilm formation. Previous studies have shown that Spo0A∼P transcript regulation controls biofilm formation, where MecA binds ClpC to inhibit Spo0A∼P-dependent transcription without triggering degradation. It remains unclear whether McsB and ClpC regulate biofilm formation together and share a similar non-proteolytic mechanism like MecA/ClpC complex. In this study, we characterized McsB and ClpC as negative regulators of biofilm formation and matrix gene eps expression. Our genetic and morphological evidence further indicates that McsB and ClpC inhibit eps expression by decreasing the spo0A and sinI expression, leading to the release of SinR, a known repressor of eps transcription. Given that the spo0A and sinI expression is transcriptionally activated by Spo0A∼P in biofilm formation, we next demonstrate that McsB interacts with Spo0A directly by bacterial two-hybrid system and Glutathione transferase pull-down experiments. Additionally, we present that McsB forms a complex with ClpC to dampen biofilm formation in vivo. Finally, we show that YwlE acts as a positive regulator of biofilm formation, counteracting the function of McsB. These findings suggest that McsB, ClpC, and YwlE play vital roles in the transition to biofilm formation in Bacillus subtilis, providing new insights into the regulatory mechanisms underlying biofilm development and sharing a similar non-proteolytic mechanism in biofilm formation as MecA/ClpC complex.

MecA in Streptococcus mutans is a multi-functional protein

Our recent studies have shown that deficiency of MecA in Streptococcus mutans significantly affects cell division, growth, and biofilm formation. In this study, an in vitro mixed-species model, proteomics, and affinity pull-down assays were used to further characterize the MecA-mediated regulation in S. mutans. The results showed that compared with the wild type, UA159, the mecA mutant significantly reduced its production of glucans and weakened its ability to facilitate mixed-species biofilm formation. Relative to the wild type, the mecA mutant also displayed unique characteristics, including colony morphology, growth rate, and biofilm formation that did not fully resemble any of the clpP, clpX, clpE, clpCE, and clpC individual or combinational mutants. Deletion of mecA was shown to result in alteration of >337 proteins, including down expression of GtfBC&D and adhesin P1. More than 277 proteins were differentially expressed in response to clpP deletion, including increased expression of GtfB. By cross-referencing the two proteomes, a distinctive set of proteins was found to be altered in the mecA mutant, indicating a ClpP-independent role of MecA in the regulation of S. mutans. When analyzed using affinity pull-down, ClpC, ClpX, ClpE, and CcpA were among the members identified in the MecA-associated complex. Further analysis using a bacterial two-hybrid system confirmed CcpA, ClpX, and ClpE as members of the MecA interactome. These results further suggest that MecA in S. mutans is more than an adapter of the Clp-proteolytic machinery, although the mechanism that underlies the Clp-independent regulation and its impact on S. mutans pathophysiology await further investigation.

IMPORTANCE

MecA is known as an adaptor protein that works in concerto with ATPase ClpC and protease ClpP in the regulated proteolysis machinery. The results presented here provide further evidence that MecA in S. mutans, a keystone cariogenic bacterium, plays a significant role in its ability to facilitate mixed-species biofilm formation, a trait critical to its cariogenicity. Proteomics analysis, along with affinity pull-down and bacterial two-hybrid system, further confirm that MecA can also regulate S. mutans physiology and biofilm formation through pathways independent of the Clp proteolytic machinery, although how it functions independently of Clp awaits further investigation.

Developmentally-regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation

Bacillus subtilis sporulation entails a dramatic transformation of the two cells required to assemble a dormant spore, with the larger mother cell engulfing the smaller forespore to produce the cell-within-a-cell structure that is a hallmark of endospore formation. Sporulation also entails metabolic differentiation, whereby key metabolic enzymes are depleted from the forespore but maintained in the mother cell. This reduces the metabolic potential of the forespore, which becomes dependent on mother-cell metabolism and the SpoIIQ-SpoIIIA channel to obtain metabolic building blocks necessary for development. We demonstrate that metabolic differentiation depends on the ClpCP protease and a forespore-produced protein encoded by the yjbA gene, which we have renamed MdfA (metabolic differentiation factor A). MdfA is conserved in aerobic endospore-formers and required for spore resistance to hypochlorite. Using mass spectrometry and quantitative fluorescence microscopy, we show that MdfA mediates the depletion of dozens of metabolic enzymes and key transcription factors from the forespore. An accompanying study by Massoni, Evans and collaborators demonstrates that MdfA is a ClpC adaptor protein that directly interacts with and stimulates ClpCP activity. Together, these results document a developmentally-regulated proteolytic pathway that reshapes forespore metabolism, reinforces differentiation, and is required to produce spores resistant to the oxidant hypochlorite.

Mass spectrometry and split luciferase complementation assays reveal the MecA protein interactome of Streptococcus mutans

MecA is a highly conserved adaptor protein encoded by prokaryotes from the Bacillota phylum. MecA mutants exhibit similar pleiotropic defects in a variety of organisms, although most of these phenotypes currently lack a mechanistic basis. MecA mediates ClpCP-dependent proteolysis of its substrates, but only several such substrates have been reported in the literature and there are suggestions that proteolysis-independent regulatory mechanisms may also exist. Here, we provide the first comprehensive characterization of the MecA interactome and further assess its regulatory role in Clp-dependent proteolysis. Untargeted coimmunoprecipitation assays coupled with mass spectrometry revealed that the MecA ortholog from the oral pathobiont Streptococcus mutans likely serves as a major protein interaction network hub by potentially complexing with >100 distinct protein substrates, most of which function in highly conserved metabolic pathways. The interactome results were independently verified using a newly developed prokaryotic split luciferase complementation assay (SLCA) to detect MecA protein-protein interactions in vivo. In addition, we further develop a new application of SLCA to support in vivo measurements of MecA relative protein binding affinities. SLCA results were independently verified using targeted coimmunoprecipitation assays, suggesting the general utility of this approach for prokaryotic protein-protein interaction studies. Our results indicate that MecA indeed regulates its interactome through both Clp-dependent proteolysis as well as through an as-yet undefined proteolysis-independent mechanism that may affect more than half of its protein interactome. This suggests a significant aspect of the MecA regulatory function still has yet to be discovered.IMPORTANCEDespite multiple decades of study, the regulatory mechanism and function of MecA have remained largely a mystery. The current study provides the first detailed roadmap to investigate these functions in other medically significant bacteria. Furthermore, this study developed new genetic approaches to assay prokaryotic protein-protein interactions via the split luciferase complementation assay (SLCA). SLCA technology is commonly employed in eukaryotic genetic research but has not yet been established for studies of bacterial protein-protein interactions. The SLCA protein binding affinity assay described here is a new technological advance exclusive to the current study and has not been reported elsewhere.

Identification of ClpP Dual Isoform Disruption as an Anti-sporulation Strategy for Clostridioides difficile

The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. By extension, the identification of druggable targets that significantly attenuate sporulation would have a significant impact on thwarting C. difficile infection. Using a new CRISPR-Cas9 nickase genome editing methodology, stop codons were inserted early in the coding sequence for clpP1 and clpP2 to generate C. difficile mutants that no longer produced the corresponding isoforms of caseinolytic protease P (ClpP). The data show that genetic ablation of ClpP isoforms leads to altered sporulation phenotypes with the clpP1/clpP2 double mutant exhibiting asporogenic behavior. A small screen of known ClpP inhibitors in a fluorescence-based biochemical assay identified bortezomib as an inhibitor of C. difficile ClpP that produces dose-dependent inhibition of purified ClpP. Incubation of C. difficile cultures in the presence of bortezomib reveals anti-sporulation effects approaching that observed in the clpP1/clpP2 double mutant. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as C. difficile anti-sporulating agents. IMPORTANCE Due to diverse roles of ClpP and the reliance of pathogens upon this system for infection, it has emerged as a target for antimicrobial development. Biology regulated by ClpP is organism-dependent and has not been defined in C. difficile. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as anti-sporulating agents. The identification of new approaches and/or drug targets that reduce C. difficile sporulation would be transformative and are expected to find high utility in prophylaxis, transmission attenuation, and relapse prevention. Discovery of the ClpP system as a major driver to sporulation also provides a new avenue of inquiry for advancing the understanding of sporulation.

Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis

Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., Bacillus subtilis and Staphylococcus aureus, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., Mycobacterium tuberculosis, Listeria monocytogenes, and Chlamydia trachomatis, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.

Deficiency of MecA in Streptococcus mutans Causes Major Defects in Cell Envelope Biogenesis, Cell Division, and Biofilm Formation

MecA is an adaptor protein that guides the ClpC/P-mediated proteolysis. A S. mutans MecA-deficient mutant was constructed by double-crossover allelic exchange and analyzed for the effects of such a deficiency on cell biology and biofilm formation. Unlike the wild-type, UA159, the mecA mutant, TW416, formed mucoid and smooth colonies, severely clumped in broth and had a reduced growth rate. Transmission electron microscopy analysis revealed that TW416 grows primarily in chains of giant “swollen” cells with multiple asymmetric septa, unlike the coccoid form of UA159. As compared to UA159, biofilm formation by TW416 was significantly reduced regardless of the carbohydrate sources used for growth (P < 0.001). Western blot analysis of TW416 whole cell lysates showed a reduced expression of the glucosyltransferase GtfC and GtfB, as well as the P1 and WapA adhesins providing an explanation for the defective biofilm formation of TW416. When analyzed by a colorimetric assay, the cell wall phosphate of the mutant murein sacculi was almost 20-fold lower than the parent strain (P < 0.001). Interestingly, however, when analyzed using immunoblotting of the murein sacculi preps with UA159 whole cell antiserum as a probe, TW416 was shown to possess significantly higher signal intensity as compared to the wild-type. There is also evidence that MecA in S. mutans is more than an adaptor protein, although how it modulates the bacterial pathophysiology, including cell envelope biogenesis, cell division, and biofilm formation awaits further investigation.