Proteomic Profiling Reveals Intracellular Regulatory Network Disturbance Induced by QseB Deletion in Glaesserella parasuis

The highly conserved QseB/QseC two-component system (TCS) in Glaesserella parasuis (G. parasuis) regulates gene expression, with QseC as a histidine kinase and QseB as a response regulator. This study employed data-independent acquisition (DIA) quantitative proteomics to investigate the effects of qseB deletion on bacterial morphology, proteome, and molecular regulation. Electron microscopy revealed that the ΔqseB mutant exhibited ultrastructural damage, including cell shrinkage, membrane impairment, cell wall separation, and protoplast dissolution, indicating that the loss of qseB resulted in severe compromise of cellular structural integrity. A total of 1493 proteins were identified by DIA quantitative proteomics. Fifty-five proteins were differentially expressed between the ΔqseB mutant and the wild-type strain SC1401. Among them, 24 were upregulated and 31 were downregulated. Upregulated proteins were mainly heat shock proteins (DnaK, HslV/U, ClpB), molecular chaperones (GroL, HtpG, HslO), and co-chaperone GroES, along with translation inhibitors RaiA and RsfS. These proteins participate in stress response, protein folding, and proteostasis maintenance. The downregulated proteins included QseC, LolB, CarB, ThiL, and Tgt, which are linked to TCSs, quorum sensing, and transport functions. KEGG analysis indicated that the differentially expressed proteins are involved in RNA degradation, amino acid metabolism, and ABC transporters. Protein–protein interaction (PPI) network analysis identified 10 core hub proteins, including GroEL, HslU, and QseC. These proteins may play key roles in maintaining cellular homeostasis. Integrated multi-omics analysis identified three genes (dnaK, hslU, hslO) that were differentially expressed in both transcriptomic and proteomic data. qRT-PCR results confirmed these findings. In summary, loss of qseB disrupts the QseB/QseC system. This affects stress response, metabolism, and cell structure. These changes may affect bacterial fitness and host adaptation, providing clues for understanding the pathogenic mechanisms of G. parasuis.