Peptidoglycan Modification by the Catalytic Domain of Streptococcus pneumoniae OatA Follows a Ping-Pong Bi-Bi Mechanism of Action

WssI from the Gram-Negative Bacterial Cellulose Synthase is an O-acetyltransferase that Acts on Cello-oligomers with Several Acetyl Donor Substrates

In microbial biofilms, bacterial cells are encased in a self-produced matrix of polymers (e.g., exopolysaccharides) that enable surface adherence and protect against environmental stressors. For example, the wrinkly spreader phenotype of Pseudomonas fluorescens colonizes food/water sources and human tissue to form robust biofilms that can spread across surfaces. This biofilm largely consists of bacterial cellulose produced by the cellulose synthase proteins encoded by the wss operon, which also occurs in other species, including pathogenic Achromobacter species. Although phenotypic mutant analysis of the wssFGHI genes has previously shown that they are responsible for acetylation of bacterial cellulose, their specific roles remain unknown and distinct from the recently identified cellulose phosphoethanolamine modification found in other species. Here we have purified the C-terminal soluble form of WssI from P. fluorescens and A. insuavis and demonstrated acetyl-esterase activity with chromogenic substrates. The kinetic parameters (k_cat/K_M values of 13 and 8.0 M^-1∙ s^-1, respectively) indicate that these enzymes are up to four times more catalytically efficient than the closest characterized homolog, AlgJ from the alginate synthase. Unlike AlgJ and its cognate alginate polymer, WssI also demonstrated acetyltransferase activity onto cellulose oligomers (e.g., cellotetraose to cellohexaose) with multiple acetyl-donor substrates (pNP-Ac, MU-Ac and acetyl-CoA). Finally, a high-throughput screen identified three low micromolar WssI inhibitors that may be useful for chemically interrogating cellulose acetylation and biofilm formation.

Determination of lysophosphatidylcholine using peroxidase-mimic PVP/PtRu nanozyme

Lysophosphatidylcholine (LPC) can be used as a biomarker for diseases such as cancer, diabetes, atherosclerosis, and sepsis. In this study, we demonstrated the ability of nanozymes to displace the natural derived enzyme in enzyme-based assays for the measurement of LPC. Synthesized polyvinylpyrrolidone-stabilized platinum-ruthenium nanozymes (PVP/PtRu NZs) had a uniform size of 2.48 ± 0.24 nm and superb peroxidase-mimicking activity. We demonstrated that the nanozymes had high activity over a wide pH and temperature range and high stability after long-term storage. The LPC concentration could be accurately analyzed through the absorbance and fluorescence signals generated by the peroxidation reaction using the synthesized nanozyme with substrates such as 3,3',5,5'-tetramethylbenzidine (TMB) and 10-acetyl-3,7-dihydroxyphenoxazine (Ampliflu™ Red). LPC at a concentration of 0-400 µM was used for the analysis, and the coefficient of determination (R²) was 0.977, and the limit of detection (LOD) was 23.1 µM by colorimetric assay. In the fluorometric assay, the R² was 0.999, and the LOD was 8.97 µM. The spiked recovery values for the determination of LPC concentration in human serum samples were 102-115%. Based on these results, we declared that PVP/PtRu NZs had an ability comparable to that of the native enzyme horseradish peroxidase (HRP) in the enzyme-based LPC detection method.

Identification of critical residues of O-antigen-modifying O-acetyltransferase B (OacB) of Shigella flexneri

Background

Shigellosis is an acute gastrointestinal disease caused primarily by the bacterium Shigella flexneri. Upon ingestion, S. flexneri initiates a serotype-specific immune response that targets the O-antigen of the pathogen’s lipopolysaccharide. O-antigen subunits are modified by the addition of chemical moieties, which give rise to new serotypes of S. flexneri. Nineteen different serotypes of S. flexneri have been recognized. A recently identified O-antigen-modifying enzyme, O-acetyltransferase B (OacB), which adds an acetyl residue at either position 3 or 4 of Rhamnose^III (3/4-O-acetylation) in serotypes 1a, 1b, 2a, 5a, 7a, Y, and 6 and position 6 of N- acetylglucosamine (6-O-acetylation) in serotypes 2a, 3a, Y and Yv of the O-antigen subunits. Critical residues in other proteins involved in O-antigen modifications such as glucosyltransferases (Gtrs) and acetyltransferase (Oac) of S. flexneri have been identified, whereas identification of important amino acids in OacB function is yet to be determined.

Results

Hydrophobicity analysis showed that OacB is a transmembrane protein with 11 transmembrane segments, 12 loops, and periplasmic N- and cytoplasmic C- termini. Bioinformatics analyses revealed that OacB contains acetyltransferase-3 domain and several conserved residues. Using site-directed mutagenesis, selected amino acids were mutated to alanine to elucidate their role in the mechanism of action of OacB. Seven amino acids R47, H58, F98, W71, R116, R119, and S146 were found critical for the OacB function.

Conclusion

In the absence of a three-dimensional structure of the serotype converting enzyme, O-acetyltransferase B (OacB), a clear role of important residues in the mechanism of action is precluded. Therefore, in this study, using site-directed mutagenesis, seven residues critical to the function of OacB were identified. The lack of agglutination of cell expressing mutant OacB in the presence of the antiserum indicated the functional role of the corresponding residues. Hence, this study provides significant information about key residues in OacB which might be involved in forming the catalytic sites of this O-antigen modifying enzyme of S. flexneri.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12860-022-00415-8.

Mechanism of Staphylococcus aureus peptidoglycan O-acetyltransferase A as an O-acyltransferase

The O-acetylation of exopolysaccharides, including the essential bacterial cell wall polymer peptidoglycan, confers resistance to their lysis by exogenous hydrolases. Like the enzymes catalyzing the O-acetylation of exopolysaccharides in the Golgi of animals and fungi, peptidoglycan O-acetyltransferase A (OatA) is predicted to be an integral membrane protein comprised of a membrane-spanning acyltransferase-3 (AT-3) domain and an extracytoplasmic domain; for OatA, these domains are located in the N- and C-terminal regions of the enzyme, respectively. The recombinant C-terminal domain (OatA_C) has been characterized as an SGNH acetyltransferase, but nothing was known about the function of the N-terminal AT-3 domain (OatA_N) or its homologs associated with other acyltransferases. We report herein the experimental determination of the topology of Staphylococcus aureus OatA_N, which differs markedly from that predicted in silico. We present the biochemical characterization of OatA_N as part of recombinant OatA and demonstrate that acetyl-CoA serves as the substrate for OatA_N Using in situ and in vitro assays, we characterized 35 engineered OatA variants which identified a catalytic triad of Tyr-His-Glu residues. We trapped an acetyl group from acetyl-CoA on the catalytic Tyr residue that is located on an extracytoplasmic loop of OatA_N Further enzymatic characterization revealed that O-acetyl-Tyr represents the substrate for OatA_C We propose a model for OatA action involving the translocation of acetyl groups from acetyl-CoA across the cytoplasmic membrane by OatA_N and their subsequent intramolecular transfer to OatA_C for the O-acetylation of peptidoglycan via the concerted action of catalytic Tyr and Ser residues.

PVP-stabilized PtRu nanozymes with peroxidase-like activity and its application for colorimetric and fluorometric glucose detection

Nanozymes have significant advantages over natural enzymes. The intrinsic peroxidase-like activity of Pt-based nanomaterials can be enhanced by alloying with other transition metals, such as Ru, that have great catalytic activity. In this study, we used polyvinylpyrrolidone (PVP) to synthesize well-dispersed and homogeneous nanostructures. PVP-stabilized Pt-Ru nanozymes (PVP/PtRu NZs) were synthesized and characterized. The PVP/PtRu NZs had an average size of 3.54 ± 0.84 nm and exhibited an intense peroxidase-like activity. The PVP/PtRu NZs were used as peroxidase mimics for colorimetric and fluorometric glucose determination by the glucose oxidase and PVP/PtRu NZs cascade reaction. In the colorimetric assay, the linearly detectable range was 0.25-3.0 mM, with an R² and limit of detection (LOD) of 0.988 and 138 μM, respectively. In the fluorometric assay, a linear relationship was found when the glucose concentration was between 5.0 and 300 μM (R² = 0.997), with an LOD of 1.11 μM. Compared to the colorimetric assay, the fluorometric assay had greater sensitivity and a lower detection limit for the determination of glucose. Moreover, the PVP/PtRu NZs had high storage stability over a month and great recovery values in human serum and artificial urine, with a range of 94-106 %. From these results, PVP/PtRu NZs are expected to be used as promising peroxidase mimics in various fields such as biosensing, pharmaceutical processing, and the food industry.

Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too

Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme's kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions.

Structural basis for the O-acetyltransferase function of the extracytoplasmic domain of OatA from Staphylococcus aureus

Many bacteria possess enzymes that modify the essential cell-wall polymer peptidoglycan by O-acetylation. This modification occurs in numerous Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus, a common cause of human infections. O-Acetylation of peptidoglycan protects bacteria from the lytic activity of lysozyme, a mammalian innate immune enzyme, and as such is important for bacterial virulence. The O-acetylating enzyme in Gram-positive bacteria, O-acetyltransferase A (OatA), is a two-domain protein consisting of an N-terminal integral membrane domain and a C-terminal extracytoplasmic domain. Here, we present the X-ray crystal structure at 1.71 Å resolution and the biochemical characterization of the C-terminal domain of S. aureus OatA. The structure revealed that this OatA domain adopts an SGNH-hydrolase fold and possesses a canonical catalytic triad. Site-specific replacement of active-site amino acids revealed the presence of a water-coordinating aspartate residue that limits esterase activity. This residue, although conserved in staphyloccocal OatA and most other homologs, is not present in the previously characterized streptococcal OatA. These results provide insights into the mechanism of acetyl transfer in the SGNH/GDSL hydrolase family and highlight important evolutionary differences between homologous OatA enzymes. Furthermore, this study enhances our understanding of PG O-acetyltransferases, which could guide the development of novel antibacterial drugs to combat infections with multidrug-resistant bacterial pathogens.

Environment Shapes the Accessible Daptomycin Resistance Mechanisms in Enterococcus faecium

Daptomycin binds to bacterial cell membranes and disrupts essential cell envelope processes, leading to cell death. Bacteria respond to daptomycin by altering their cell envelopes to either decrease antibiotic binding to the membrane or by diverting binding away from septal targets. In Enterococcus faecalis, daptomycin resistance is typically coordinated by the three-component cell envelope stress response system, LiaFSR. Here, studying a clinical strain of multidrug-resistant Enterococcus faecium containing alleles associated with activation of the LiaFSR signaling pathway, we found that specific environments selected for different evolutionary trajectories, leading to high-level daptomycin resistance. Planktonic environments favored pathways that increased cell surface charge via yvcRS upregulation of dltABCD and mprF, causing a reduction in daptomycin binding. Alternatively, environments favoring complex structured communities, including biofilms, evolved both diversion and repulsion strategies via divIVA and oatA mutations, respectively. Both environments subsequently converged on cardiolipin synthase (cls) mutations, suggesting the importance of membrane modification across strategies. Our findings indicate that E. faecium can evolve diverse evolutionary trajectories to daptomycin resistance that are shaped by the environment to produce a combination of resistance strategies. The accessibility of multiple and different biochemical pathways simultaneously suggests that the outcome of daptomycin exposure results in a polymorphic population of resistant phenotypes, making E. faecium a recalcitrant nosocomial pathogen.

Peptidoglycan O-Acetylation as a Virulence Factor: Its Effect on Lysozyme in the Innate Immune System

The peptidoglycan sacculus of both Gram-positive and Gram-negative bacteria acts as a protective mesh and provides structural support around the entirety of the cell. The integrity of this structure is of utmost importance for cell viability and so naturally is the first target for attack by the host immune system during bacterial infection. Lysozyme, a muramidase and the first line of defense of the innate immune system, targets the peptidoglycan sacculus hydrolyzing the β-(1→4) linkage between repeating glycan units, causing lysis and the death of the invading bacterium. The O-acetylation of N-acetylmuramoyl residues within peptidoglycan precludes the productive binding of lysozyme, and in doing so renders it inactive. This modification has been shown to be an important virulence factor in pathogens such as Staphylococcus aureus and Neisseria gonorrhoeae and is currently being investigated as a novel target for anti-virulence therapies. This article reviews interactions made between peptidoglycan and the host immune system, specifically with respect to lysozyme, and how the O-acetylation of the peptidoglycan interrupts these interactions, leading to increased pathogenicity.

Development of a High Throughput Screen for the Identification of Inhibitors of Peptidoglycan O-Acetyltransferases, New Potential Antibacterial Targets

The O-acetylation of peptidoglycan occurs in many Gram-negative and most Gram-positive pathogens and this modification to the essential wall polymer controls the lytic activity of the autolysins, particularly the lytic transglycosylases, and inhibits that of the lysozymes of innate immunity systems. As such, the peptidoglycan O-acetyltransferases PatA/B and OatA are recognized as virulence factors. In this study, we present the high throughput screening of small compound libraries to identify the first known inhibitors of these enzymes. The fluorometric screening assay developed involved monitoring the respective O-acetyltransferases as esterases using 4-methylumbelliferylacetate as substrate. Pilot screens of 3921 compounds validated the usefulness of the HTS protocol. A number of potential inhibitors were identified amongst a total of 145,000 low molecular-weight compounds, some of which were common to both enzymes, while others were unique to each. After eliminating a number of false positives in secondary screens, dose response curves confirmed the apparent specificity of a benzothiazolyl-pyrazolo-pyridine as an inhibitor of Neisseria gonorrhoeae PatB, and several coumarin-based compounds as inhibitors of both this PatB and OatA from Staphylococcus aureus. The benzothiazolyl-pyrazolo-pyridine was determined to be a non-competitive inhibitor of PatB with a Ki of 126 µM. At 177 µg/mL and close to its solubility limit, this compound caused a 90% reduction in growth of N. gonorrhoeae, while growth of Escherichia coli, a bacterium that lacks PatB and, hence, does not produce O-acetylated peptidoglycan, was unaffected. These data provide preliminary proof of concept that peptidoglycan O-acetyltransferases would serve as useful antibacterial targets.

Mechanistic Pathways for Peptidoglycan O-Acetylation and De-O-Acetylation

The post-synthetic O-acetylation of the essential component of bacterial cell walls, peptidoglycan (PG), is performed by many pathogenic bacteria to help them evade the lytic action of innate immunity responses. Occurring at the C-6 hydroxyl of N-acetylmuramoyl residues, this modification to the glycan backbone of PG sterically blocks the activity of lysozymes. As such, the enzyme responsible for this modification in Gram-positive bacteria is recognized as a virulence factor. With Gram-negative bacteria, the O-acetylation of PG provides a means of control of their autolysins at the substrate level. In this review, we discuss the pathways for PG O-acetylation and de-O-acetylation and the structure and function relationship of the O-acetyltransferases and O-acetylesterases that catalyze these reactions. The current understanding of their mechanisms of action is presented and the prospects of targeting these systems for the development of novel therapeutics are explored.

New Insights Into Wall Polysaccharide O-Acetylation

The extracellular matrix of plants, algae, bacteria, fungi, and some archaea consist of a semipermeable composite containing polysaccharides. Many of these polysaccharides are O-acetylated imparting important physiochemical properties to the polymers. The position and degree of O-acetylation is genetically determined and varies between organisms, cell types, and developmental stages. Despite the importance of wall polysaccharide O-acetylation, only recently progress has been made to elucidate the molecular mechanism of O-acetylation. In plants, three protein families are involved in the transfer of the acetyl substituents to the various polysaccharides. In other organisms, this mechanism seems to be conserved, although the number of required components varies. In this review, we provide an update on the latest advances on plant polysaccharide O-acetylation and related information from other wall polysaccharide O-acetylating organisms such as bacteria and fungi. The biotechnological impact of understanding wall polysaccharide O-acetylation ranges from the design of novel drugs against human pathogenic bacteria to the development of improved lignocellulosic feedstocks for biofuel production.