Essentiality of WalRK for growth in Bacillus subtilis and its role during heat stress

Structural analysis of the peptidoglycan DL-endopeptidase CwlO complexed with its inhibitory protein IseA

Peptidoglycan DL-endopeptidases locally cleave the peptide stem of peptidoglycan in the bacterial cell wall. This process facilitates bacterial growth and division by loosening the rigid peptidoglycan layer. IseA binds to the active site of multiple DL-endopeptidases and inhibits excessive peptidoglycan degradation that leads to cell lysis. To better understand how IseA inhibits DL-endopeptidase activity, we determined the crystal structure of the peptidoglycan DL-endopeptidase CwlO/IseA complex and compared it with that of the peptidoglycan DL-endopeptidase LytE/IseA complex. Structural analyses showed significant differences between the hydrophobic pocket-binding residues of the DL-endopeptidases (F361 of CwlO and W237 of LytE). Additionally, binding assays showed that the F361 mutation of CwlO to the bulkier hydrophobic residue, tryptophan, increased its binding affinity for IseA, whereas mutation to alanine reduced the affinity. These analyses revealed that the hydrophobic pocket-binding residue of DL-endopeptidases determines IseA-binding affinity and is required for substrate-mimetic inhibition by IseA.

The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus

IMPORTANCE

The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.

Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages

Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.

Regulation of peptidoglycan hydrolases: localization, abundance, and activity

Most bacteria are surrounded by a cell wall composed of peptidoglycan (PG) that specifies shape and protects the cell from osmotic rupture. Growth, division, and morphogenesis are intimately linked to the synthesis of this exoskeleton but also its hydrolysis. The enzymes that cleave the PG meshwork require careful control to prevent aberrant hydrolysis and loss of envelope integrity. Bacteria employ diverse mechanisms to control the activity, localization, and abundance of these potentially autolytic enzymes. Here, we discuss four examples of how cells integrate these control mechanisms to finely tune cell wall hydrolysis. We highlight recent advances and exciting avenues for future investigation.

Imbalance of peptidoglycan biosynthesis alters the cell surface charge of Listeria monocytogenes

The bacterial cell wall is composed of a thick layer of peptidoglycan and cell wall polymers, which are either embedded in the membrane or linked to the peptidoglycan backbone and referred to as lipoteichoic acid (LTA) and wall teichoic acid (WTA), respectively. Modifications of the peptidoglycan or WTA backbone can alter the susceptibility of the bacterial cell towards cationic antimicrobials and lysozyme. The human pathogen Listeria monocytogenes is intrinsically resistant towards lysozyme, mainly due to deacetylation and O-acetylation of the peptidoglycan backbone via PgdA and OatA. Recent studies identified additional factors, which contribute to the lysozyme resistance of this pathogen. One of these is the predicted ABC transporter, EslABC. An eslB mutant is hyper-sensitive towards lysozyme, likely due to the production of thinner and less O-acetylated peptidoglycan. Using a suppressor screen, we show here that suppression of eslB phenotypes could be achieved by enhancing peptidoglycan biosynthesis, reducing peptidoglycan hydrolysis or alterations in WTA biosynthesis and modification. The lack of EslB also leads to a higher negative surface charge, which likely stimulates the activity of peptidoglycan hydrolases and lysozyme. Based on our results, we hypothesize that the portion of cell surface exposed WTA is increased in the eslB mutant due to the thinner peptidoglycan layer and that latter one could be caused by an impairment in UDP-N-acetylglucosamine (UDP-GlcNAc) production or distribution.

Genome Analysis Coupled With Transcriptomics Reveals the Reduced Fitness of a Hot Spring Cyanobacterium Mastigocladus laminosus UU774 Under Exogenous Nitrogen Supplement

The present study focuses on the stress response of a filamentous, AT-rich, heterocystous cyanobacterium Mastigocladus laminosus UU774, isolated from a hot spring, Taptapani, located in the eastern part of India. The genome of UU774 contains an indispensable fragment, scaffold_38, of unknown origin that is implicated during severe nitrogen and nutrition stress. Prolonged exposure to nitrogen compounds during starvation has profound adverse effects on UU774, leading to loss of mobility, loss of ability to fight pathogens, reduced cell division, decreased nitrogen-fixing ability, reduced ability to form biofilms, reduced photosynthetic and light-sensing ability, and reduced production of secreted effectors and chromosomal toxin genes, among others. Among genes showing extreme downregulation when grown in a medium supplemented with nitrogen with the fold change > 5 are transcriptional regulator gene WalR, carbonic anhydrases, RNA Polymerase Sigma F factor, fimbrial protein, and twitching mobility protein. The reduced expression of key enzymes involved in the uptake of phosphate and enzymes protecting oxygen-sensitive nitrogenases is significant during the presence of nitrogen. UU774 is presumed to withstand heat by overexpressing peptidases that may be degrading abnormally folded proteins produced during heat. The absence of a key gene responsible for heterocyst pattern formation, patS, and an aberrant hetN without a functional motif probably lead to the formation of a chaotic heterocyst pattern in UU774. We suggest that UU774 has diverged from Fischerella sp. PCC 9339, another hot spring species isolated in the United States.

The WalRK Two-Component System Is Essential for Proper Cell Envelope Biogenesis in Clostridioides difficile

The WalR-WalK two-component regulatory system (TCS) is found in all Firmicutes, in which it regulates the expression of multiple genes required for remodeling the cell envelope during growth and division. Unlike most TCSs, WalRK is essential for viability, so it has attracted interest as a potential antibiotic target. In this study, we used overexpression of WalR and CRISPR interference to investigate the Wal system of Clostridioides difficile, a major cause of hospital-associated diarrhea in high-income countries. We confirmed that the wal operon is essential and identified morphological defects and cell lysis as the major terminal phenotypes of altered wal expression. We also used transcriptome sequencing (RNA-seq) to identify over 150 genes whose expression changes in response to WalR levels. This gene set is enriched in cell envelope genes and includes genes encoding several predicted PG hydrolases and proteins that could regulate PG hydrolase activity. A distinct feature of the C. difficile cell envelope is the presence of an S-layer, and we found that WalR affects expression of several genes which encode S-layer proteins. An unexpected finding was that some Wal-associated phenotypic defects were inverted in comparison to what has been reported for other Firmicutes. For example, downregulation of Wal signaling caused C. difficile cells to become longer rather than shorter, as in Bacillus subtilis. Likewise, downregulation of Wal rendered C. difficile more sensitive to vancomycin, whereas reduced Wal activity is linked to increased vancomycin resistance in Staphylococcus aureus. IMPORTANCE The WalRK two-component system (TCS) is essential for coordinating synthesis and turnover of peptidoglycan in Firmicutes. We investigated the WalRK TCS in Clostridioides difficile, an important bacterial pathogen with an atypical cell envelope. We confirmed that WalRK is essential and regulates cell envelope biogenesis, although several of the phenotypic changes we observed were opposite to what has been reported for other Firmicutes. We also identified over 150 genes whose expression is controlled either directly or indirectly by WalR. Overall, our findings provide a foundation for future investigations of an important regulatory system and potential antibiotic target in C. difficile.

Glucolipids and lipoteichoic acids affect the activity of SigI, an alternative sigma factor, and WalKR, an essential two-component system, in Bacillus subtilis

In a Bacillus subtilis ugtP mutant lacking glucolipids, SigI was activated in the log phase, and the activation of SigI in the mutant was suppressed by the expression of native ugtP. By contrast, SigI was inhibited in a yfnI mutant lacking one of the lipoteichoic acid (LTA) synthase genes, and the inhibition was suppressed by the expression of yfnI. A series of mutation analyses of the sigI promoter revealed that the two WalR binding sites were involved in the increase of P_sigI -lacZ activity in the ugtP mutant and decrease of the lacZ activity in the yfnI mutant. Transcription from the SigI recognition sequence was enhanced in the ugtP mutant, whereas yfnI disruption inhibited the transcription from the SigA recognition sequence in the sigI promoter. We found that not only SigI but also WalKR, the essential two-component system, was activated in the ugtP mutant and inhibited in the yfnI mutant. The walK mutants with activated WalR exhibited abnormal morphology, but this phenotype was suppressed by the addition of MgSO₄ . We conclude that glucolipids and LTA are key compounds in the maintenance of normal cell surface structure in B. subtilis.

The WalR-WalK signaling pathway modulates the activities of both CwlO and LytE through control of the peptidoglycan deacetylase PdaC in Bacillus subtilis

The WalR-WalK two component signaling system in Bacillus subtilis functions in the homeostatic control of the peptidoglycan (PG) hydrolases LytE and CwlO that are required for cell growth. When the activities of these enzymes are low, WalR activates transcription of lytE and cwlO and represses transcription of iseA, a secreted inhibitor of LytE. Conversely, when PG hydrolases activity is too high, WalR-dependent expression of lytE and cwlO is reduced and iseA is de-repressed. In a screen for additional factors that regulate this signaling pathway, we discovered that over-expression of the membrane-anchored PG deacetylase PdaC increases WalR-dependent gene expression. We show that increased expression of PdaC, but not catalytic mutants, prevents cell wall cleavage by both LytE and CwlO, explaining the WalR activation. Importantly, the pdaC gene, like iseA, is repressed by active WalR. We propose that de-repression of pdaC when PG hydrolase activity is too high results in modification of the membrane-proximal layers of the PG, protecting the wall from excessive cleavage by the membrane-tethered CwlO. Thus, the WalR-WalK system homeostatically controls the levels and activities of both elongation-specific cell wall hydrolases. Importance: Bacterial growth and division requires a delicate balance between the synthesis and remodeling of the cell wall exoskeleton. How bacteria regulate the potentially autolytic enzymes that remodel the cell wall peptidoglycan remains incompletely understood. Here, we provide evidence that the broadly conserved WalR-WalK two-component signaling system homeostatically controls both the levels and activities of two cell wall hydrolases that are critical for cell growth.

Homeostatic control of cell wall hydrolysis by the WalRK two-component signaling pathway in Bacillus subtilis

Bacterial cells are encased in a peptidoglycan (PG) exoskeleton that protects them from osmotic lysis and specifies their distinct shapes. Cell wall hydrolases are required to enlarge this covalently closed macromolecule during growth, but how these autolytic enzymes are regulated remains poorly understood. Bacillus subtilis encodes two functionally redundant D,L-endopeptidases (CwlO and LytE) that cleave peptide crosslinks to allow expansion of the PG meshwork during growth. Here, we provide evidence that the essential and broadly conserved WalR-WalK two component regulatory system continuously monitors changes in the activity of these hydrolases by sensing the cleavage products generated by these enzymes and modulating their levels and activity in response. The WalR-WalK pathway is conserved among many Gram-positive pathogens where it controls transcription of distinct sets of PG hydrolases. Cell wall remodeling in these bacteria may be subject to homeostatic control mechanisms similar to the one reported here.

Essentiality and function of WalK/WalR two-component system: the past, present, and future of research

The WalK/WalR two-component system (TCS), originally identified in Bacillus subtilis, is very highly conserved in gram-positive bacteria, including several important pathogens. The WalK/WalR TCS appears to be involved in the growth of most bacterial species encoding it. Previous studies have indicated conserved functions of this system, defining this signal transduction pathway as a crucial regulatory system for cell wall metabolism. Because of such effects on essential functions, this system is considered a potential target for anti-infective therapeutics. In this review, we discuss the role of WalK/WalR TCS in different bacterial cells, focusing on the function of the genes in its regulon as well as the variations in walRK operon structure, its auxiliary proteins, and the composition of its regulon. We also discuss recent experimental data addressing its essential function and the potential type of signal being sensed by B. subtilis. This review also focuses on the potential future research.