Designing protein mutants with both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants with improved stability and activity without any prior experimental mutagenesis data for the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive ability compared to current state-of-the-art models on the public mutagenesis dataset across 283 protein assays. Furthermore, we validated PRIME’s predictions on five proteins, examining the impact of the top 30 to 45 single-site mutations on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize nonnatural nucleic acid or resilience to extreme alkaline conditions. More than 30% of PRIME-recommended mutants exhibited superior performance compared to their premutation counterparts across all proteins and desired properties. We developed an efficient and effective method based on PRIME to rapidly obtain multisite mutants with enhanced activity and stability. Hence, PRIME demonstrates broad applicability in protein engineering.

Transmissible gastroenteritis virus (TGEV) is a coronavirus causing diarrhea with high incidence in swine herds. Its persistent infection might lead to epithelial-mesenchymal transition (EMT) of swine intestinal epithelial cells, followed by subsequent infections of other pathogens. Enterococcus faecalis (E. faecalis) is a member of the enteric microorganisms and an opportunistic pathogen. There is no report of secondary E. faecalis infection to TGEV, even though they both target to the intestinal tracts. To investigate the interactions between TGEV and E. faecalis, we set up an in vitro infection model by the swine IPEC-J2 cells. Dynamic changes of cell traits, including EMT and cell motility, were evaluated through qPCR, Western blot, electronic microscopy, scratch test, Transwell migration test and invasion test, respectively. The adhesion and invasion tests of E. faecalis were taken to verify the impact of the preceding TGEV infection. The cell morphology and molecular marker evaluation results showed that the TGEV persistent infection induced EMT on IPEC-J2 cells; increased cellular motility and invasion potential were also observed. Spontaneously, the expression levels of fibronectin (FN) and the membrane protein integrin-α5, which are dominant bacterial receptors on IPEC-J2 cells, were upgraded. It indicated that the bacteria E. faecalis adhered to IPEC-J2 cells through the FN receptor, and then invaded the cells by binding with the integrin-α5, suggesting that both molecules were critical for the adhesion and invasion of E. faecalis to IPEC-J2 cells. Additionally, it appeared that E. faecalis alone might trigger certain EMT phenomena, implying a vicious circle might occur. Generally, bacterial and viral co-infections are frustrating yet common in both human and veterinary medicines, and our observations on enteric TGEV and E. faecalis interactions, especially the diversity of bacterial invasion strategies, might provide new insights into the mechanisms of E. faecalis pathogenicity.

Aims The study aimed to investigate the prevalence and conservation of endocarditis and biofilm-associated pili (ebp) genes in Enterococcus faecalis originated from animals and the potential of developing Ebp into serological diagnostic and vaccine targets. Methods and Results In this work, we investigated the prevalence and conservation of ebp genes in 116 strains of E. faecalis originated from animals by using PCR and sequencing methods. The results demonstrated the presence of ebp genes (ebpA, ebpB and ebpC) in all 116 strains of E. faecalis, and their amino acid homology ranges from 96.6% to 100.0%. Moreover, the phylogenetic analysis of ebp genes in all 164 E. faecalis strains (including 48 reference strains) revealed that ebp genes show no significant correlation with species origins and regions of E. faecalis, indicating that ebp genes are conserved features in E. faecalis, even though it evolved under environmental pressures from various regions and origins. Given that EbpA1 as a part of the adhesion protein EbpA has immunogenicity, we further determined whether amino acid mutations have effects on the function and 3D structure of EbpA1. The results showed that two of the 26 mutations, at amino acids positions 178 and 387, had deleterious effects on the biological function of EbpA1 protein, while all mutations had no effect on the 3D structure or binding pockets of EbpA1 protein. Conclusions This study suggests that ebp genes are prevalent and conserved in E. faecalis originated from diverse animal origins and regions. EbpA1 could be a potential target for serological diagnosis and vaccine development to prevent E. faecalis infection. Significance and Impact of Study The current study provides data to support further research on Ebp as a serological diagnostic and vaccine target against E. faecalis infection.