NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A

Topology-driven negative sampling enhances generalizability in protein-protein interaction prediction

MOTIVATION

Unraveling the human interactome to uncover disease-specific patterns and discover drug targets hinges on accurate protein-protein interaction (PPI) predictions. However, challenges persist in machine learning (ML) models due to a scarcity of quality hard negative samples, shortcut learning, and limited generalizability to novel proteins.

RESULTS

In this study, we introduce a novel approach for strategic sampling of protein-protein noninteractions (PPNIs) by leveraging higher-order network characteristics that capture the inherent complementarity-driven mechanisms of PPIs. Next, we introduce Unsupervised Pre-training of Node Attributes tuned for PPI (UPNA-PPI), a high throughput sequence-to-function ML pipeline, integrating unsupervised pre-training in protein representation learning with Topological PPNI (TPPNI) samples, capable of efficiently screening billions of interactions. By using our TPPNI in training the UPNA-PPI model, we improve PPI prediction generalizability and interpretability, particularly in identifying potential binding sites locations on amino acid sequences, strengthening the prioritization of screening assays and facilitating the transferability of ML predictions across protein families and homodimers. UPNA-PPI establishes the foundation for a fundamental negative sampling methodology in graph machine learning by integrating insights from network topology.

AVAILABILITY AND IMPLEMENTATION

Code and UPNA-PPI predictions are freely available at https://github.com/alxndgb/UPNA-PPI.

ComQXPA Quorum Sensing Dynamic Regulation Enhanced Fengycin Production of Bacillus subtilis

Fengycin is an antifungal drug that could be used as a biocontrol agent if it could be produced in high amounts. The ComQXPA quorum sensing (QS) system is a natural mechanism, regulating cell density-dependent behaviors in Bacillus subtilis. This study employed the QS-targeted promoter PsrfA to express the pps gene cluster in B. subtilis, coupling the ComQXPA system to produce fengycin. Mutations in the ComA regulatory protein-binding site RE3 exhibited a 2.45-fold increase in promoter expression intensity and resulted in an elevation of fengycin production from 489 to 1832 mg/L, a 2.74-fold enhancement. Transcriptomic analysis revealed the upregulation of genes associated with carbon source uptake and utilization and metabolic pathways related to amino acids and fatty acids, which are precursors for fengycin synthesis. Additionally, knockout of rapJ and rapE increased fengycin production to 3190 mg/L. In a coculture system constructed with Corynebacterium glutamicum, fengycin production reached 4005 mg/L. This work provides a strategy for dynamically regulating fengycin synthesis.

Controlled interkingdom cell-cell communication between Saccharomyces cerevisiae and Bacillus subtilis using quorum-sensing peptides

Understanding communication among microorganisms through the array of signal molecules and establishing controlled signal transfer between different species is a major goal of the future of biotechnology, and controlled multispecies bioreactor cultivations will open a wide range of applications. In this study, we used two quorum-sensing peptides from Bacillus subtilis - namely, the competence and sporulation factor (CSF) and regulator of the activity of phosphatase RapF (PhrF)-to establish a controlled interkingdom communication system between prokaryotes and eukaryotes. For this purpose, we engineered B. subtilis as a reporter capable of detecting the CSF and PhrF peptides heterologously produced by the yeast Saccharomyces cerevisiae. The reporter strain included the ComA-dependent srfAA promoter fused to the bioluminescence or fluorescence reporter gene(s) to monitor promoter activity measured in a multimode microplate reader. The first measurements of srfAA promoter activity showed a specific response of the reporter strain to the peptides CSF and PhrF. Based on this, systematic mutagenesis of genes that modulate the activity of ComA in the reporter strain resulted in increased activity of the promoter and, thereby, higher sensitivity to the heterologously produced CSF/PhrF. The robustness of the signal transfer was further confirmed in co-cultivation studies in both liquid and solid media. The reporter strain exhibited an up to 5-fold increase in promoter activity in the presence of quorum-sensing peptides-producing cells of S. cerevisiae. In summary, a quorum sensing peptide-driven interkingdom crosstalk between yeast and bacteria was successfully established, which might serve as a basis for controlled protein expression in co-cultivations, establishing biological sensor-actuator systems or study cell-cell interaction and metabolite exchange in bioreactors cultivations.

The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs

ComA-like transcription factors regulate the quorum response in numerous Gram-positive bacteria. ComA proteins belong to the tetrahelical helix-turn-helix superfamily of transcriptional activators, which bind as homodimers to inverted sequence repeats in the DNA. Here, we report that ComA from Bacillus subtilis recognizes a topologically distinct motif, in which the binding elements form a direct repeat. We provide in vitro and in vivo evidence that the canonical and non-canonical site play an important role in facilitating type I and type II promoter activation, respectively, by interacting with different subunits of RNA polymerase. We furthermore show that there is a variety of contexts in which the non-canonical site can occur and identify new direct target genes that are located within the integrative and conjugative element ICEBs1. We therefore suggest that ComA acts as a multifunctional transcriptional activator and provides a striking example for complexity in protein–DNA interactions that evolved in the context of quorum sensing.

Effect of inulin on efficient production and regulatory biosynthesis of bacillomycin D in Bacillus subtilis fmbJ

The effect of inulin on the production of bacillomycin D and the levels of mRNA of bacillomycin D synthetase genes: bmyA (BYA), bmyB (BYB), bmyC (BYC), the thioesterase gene (TE) and regulating genes: AbrB, ComA, DegU, PhrC, SigmaH and Spo0A in Bacillus subtilis fmbJ were investigated. The production of bacillomycin D was enhanced with the increase of biomass concentration. The maximum production and productivity of bacillomycin D were found to be 1227.49 mg/L and 10.23 mg/L h. Inulin significantly improved the expression of bacillomycin D synthetase genes: bmyA (BYA), bmyB (BYB), bmyC (BYC) and the thioesterase gene (TE). Also, inulin up-regulated ComA, DegU, SigmaH and Spo0A and therefore promoted the high production of bacillomycin D. Our results provided a practical approach for efficient production of bacillomycin D and a meaningful explanation for regulatory mechanism of bacillomycin D biosynthesis.

Structural basis of response regulator inhibition by a bacterial anti-activator protein

The complex interplay between the response regulator ComA, the anti-activator RapF, and the signaling peptide PhrF controls competence development in Bacillus subtilis. More specifically, ComA drives the expression of genetic competence genes, while RapF inhibits the interaction of ComA with its target promoters. The signaling peptide PhrF accumulates at high cell density and upregulates genetic competence by antagonizing the interaction of RapF and ComA. How RapF functions mechanistically to inhibit ComA activity and how PhrF in turn antagonizes the RapF-ComA interaction were unknown. Here we present the X-ray crystal structure of RapF in complex with the ComA DNA binding domain. Along with biochemical and genetic studies, the X-ray crystal structure reveals how RapF mechanistically regulates ComA function. Interestingly, we found that a RapF surface mimics DNA to block ComA binding to its target promoters. Furthermore, RapF is a monomer either alone or in complex with PhrF, and it undergoes a conformational change upon binding to PhrF, which likely causes the dissociation of ComA from the RapF-ComA complex. Finally, we compare the structure of RapF complexed with the ComA DNA binding domain and the structure of RapH complexed with Spo0F. This comparison reveals that RapF and RapH have strikingly similar overall structures, and that they have evolved different, non-overlapping surfaces to interact with diverse cellular targets. To our knowledge, the data presented here reveal the first atomic level insight into the inhibition of response regulator DNA binding by an anti-activator. Compounds that affect the interaction of Rap and Rap-like proteins with their target domains could serve to regulate medically and commercially important phenotypes in numerous Bacillus species, such as sporulation in B. anthracis and sporulation and the production of Cry protein endotoxin in B. thuringiensis.