The Negative Regulative Roles of BdPGRPs in the Imd Signaling Pathway of Bactrocera dorsalis

Peptidoglycan recognition proteins (PGRPs) are key regulators in insects’ immune response, functioning as sensors to detect invading pathogens and as scavengers of peptidoglycan (PGN) to reduce immune overreaction. However, the exact function of PGRPs in Bactrocera dorsalis is still unclear. In this study, we identified and functionally characterized the genes BdPGRP-LB, BdPGRP-SB1 and BdPGRP-SC2 in B. dorsalis. The results showed that BdPGRP-LB, BdPGRP-SB1 and BdPGRP-SC2 all have an amidase-2 domain, which has been shown to have N-Acetylmuramoyl-l-Alanine amidase activity. The transcriptional levels of BdPGRP-LB and BdPGRP-SC2 were both high in adult stages and midgut tissues; BdPGRP-SB1 was found most abundantly expressed in the 2nd instar larvae stage and adult fat body. The expression of BdPGRP-LB and BdPGRP-SB1 and AMPs were significantly up-regulated after injury infected with Escherichia coli at different time points; however, the expression of BdPGRP-SC2 was reduced at 9 h, 24 h and 48 h following inoculation with E. coli. By injection of dsRNA, BdPGRP-LB, BdPGRP-SB1 and BdPGRP-SC2 were knocked down by RNA-interference. Silencing of BdPGRP-LB, BdPGRP-SB1 and BdPGRP-SC2 separately in flies resulted in over-activation of the Imd signaling pathway after bacterial challenge. The survival rate of the ds-PGRPs group was significantly reduced compared with the ds-egfp group after bacterial infection. Taken together, our results demonstrated that three catalytic PGRPs family genes, BdPGRP-LB, BdPGRP-SB1 and BdPGRP-SC2, are important negative regulators of the Imd pathway in B. dorsalis.

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C. difficile, MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn2+, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

Characterization of PGRP-LB and immune deficiency in the white-backed planthopper Sogatella furcifera (Hemiptera: Delphacidae)

Peptidoglycan recognition proteins (PGRPs) participate in insect defense against bacterial pathogens by recognizing bacterial cell wall peptidoglycans (PGNs). Here, we identified the PGRP-LB gene in the white-backed planthopper Sogatella furcifera (SfPGRP-LB). SfPGRP-LB is a secreted protein with a typical PGN-binding domain and five conserved amino acid (aa) residues required for amidase activity. Expression analysis showed that the SfPGRP-LB transcript levels were significantly higher in the midgut than in other tissues. Silencing SfPGRP-LB with dsRNA significantly downregulated the expression of Toll pathway genes Toll and Dorsal and Imd pathway genes Imd and Relish after Escherichia coli challenge. However, only Toll and Dorsal expressions were downregulated after Staphylococcus aureus challenge. E. coli and S. aureus challenges rapidly and strongly upregulated SfPGRP-LB expression. Recombinantly expressed SfPGRP-LB (rSfPGRP-LB) had strong affinities for E. coli Dap-type PGN and S. aureus Lys-type PGN and agglutinated the bacteria. However, rSfPGRP-LB inhibited S. aureus but not E. coli growth. Furthermore, rSfPGRP-LB had amidase activity, degraded Lys-type PGN, and destroyed S. aureus cell walls but had no such effects on E. coli Dap-type PGN. Thus, SfPGRP-LB recognizes and binds various bacterial PGNs but only has amidase activity against Lys-type PGN.

Allosteric activation of CwlD amidase activity by the GerS lipoprotein during Clostridioides difficile spore formation

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. Spore germination depends on the degradation of the protective spore peptidoglycan layer known as the spore cortex. Cortex degradation is mediated by enzymes that recognize the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL). In C. difficile, MAL synthesis depends on the activity of the CwlD amidase and the GerS lipoprotein, which directly binds CwlD. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind zinc stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to zinc, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of zinc co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

Crystal Structure of Nitrilase-Like Protein Nit2 from Kluyveromyces lactis

The nitrilase superfamily, including 13 branches, plays various biological functions in signaling molecule synthesis, vitamin metabolism, small-molecule detoxification, and posttranslational modifications. Most of the mammals and yeasts have Nit1 and Nit2 proteins, which belong to the nitrilase-like (Nit) branch of the nitrilase superfamily. Recent studies have suggested that Nit1 is a metabolite repair enzyme, whereas Nit2 shows ω-amidase activity. In addition, Nit1 and Nit2 are suggested as putative tumor suppressors through different ways in mammals. Yeast Nit2 (yNit2) is a homolog of mouse Nit1 based on similarity in sequence. To understand its specific structural features, we determined the crystal structure of Nit2 from Kluyveromyces lactis (KlNit2) at 2.2 Å resolution and compared it with the structure of yeast-, worm-, and mouse-derived Nit2 proteins. Based on our structural analysis, we identified five distinguishable structural features from 28 structural homologs. This study might potentially provide insights into the structural relationships of a broad spectrum of nitrilases.

Vibrio fischeri amidase activity is required for normal cell division, motility, and symbiotic competence

N-acetylmuramoyl-L-alanine amidases are periplasmic hydrolases that cleave the amide bond between N-acetylmuramic acid and alanine in peptidoglycan. Unlike many Gram-negative bacteria that encode redundant periplasmic amidases, Vibrio fischeri appears to encode a single protein that is homologous to AmiB of V. cholerae. We screened a V. fischeri transposon-mutant library for strains altered in biofilm production and discovered a biofilm over-producing strain with an insertion in amiB (VF_2326). Further characterization of biofilm enhancement suggested that this phenotype was due to over-production of cellulose, and it was dependent on the bcsA cellulose synthase. Additionally, the amiB mutant was nonmotile, perhaps due to defects in its ability to septate during division. The amidase mutant was unable to compete with wild type for colonization of V. fischeri’s symbiotic host, the squid Euprymna scolopes. In single-strain inoculations, host squid inoculated with the mutant eventually became colonized, but with much less efficiency than squid inoculated with wild type. This observation was consistent with the pleiotropic effects of the amiB mutation and led us to speculate that motile suppressors of the amiB mutant were responsible for partially restored colonization. In culture, motile suppressor mutants carried point mutations in a single gene (VF_1477), resulting in a partial restoration of wild-type motility. In addition, these point mutations reversed the effect of the amiB mutation on cellulosic biofilm production. These data are consistent with V. fischeri AmiB possessing amidase activity; they also suggest that AmiB suppresses cellulosic biofilm formation but promotes successful host colonization. Importance Peptidoglycan (PG) is a critical microbe-associated molecular pattern (MAMP) that is sloughed by cells of V. fischeri during symbiotic colonization of squid. Specifically, this process induces significant remodeling of a specialized symbiotic light organ within the squid mantle cavity. This phenomenon is reminiscent of the loss of ciliated epithelium in patients with whooping cough due to production of PG monomers by Bordetella pertussis. Furthermore, PG processing machinery can influence susceptibility to anti-microbials. In this study, we report roles for the V. fischeri PG-amidase AmiB, including the beneficial colonization of squid, underscoring the urgency to more deeply understand PG processing machinery and the downstream consequences of their activities.

Biocatalysts Based on Bacterial Strain Cells with Amidase Activity for Synthesis of Acrylic Acid from Acrylamide

A biocatalytic process for synthesis of acrylic acid was studied in the presence of Rhodococcus erythropolis 4-1 and Alcaligenes faecalis 2 strains with the pronounced amidase activity. The optimal pH of the process was 6–7 for R. erythropolis 4-1 and 7–7.5 for A. faecalis 2, optimal temperature 20–50 °C for both strains, optimal concentration of acrylamide 150 mM for R. erythropolis 4-1 and 250 mM for A. faecalis 2. At the stepwise addition of the substrate, the synthesis was more effective with A. faecalis 2 than with R. erythropolis 4-1. Freezing at –20 °C was shown preferable for storing the biocatalysts. The amidase activity of both humid and dry stored A. faecalis 2 cells immobilized on activated glutaric aldehyde and non-activated chitosan was not decreased.