Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family

The Pseudomonas aeruginosa Secreted Protein PA3611 Promotes Bronchial Epithelial Cell Epithelial-Mesenchymal Transition via Integrin αvβ6-Mediated TGF-β1-Induced p38/NF-κB Pathway Activation

Pseudomonas aeruginosa (PA) is an important pathogen that has been proven to colonize and cause infection in the respiratory tract of patients with structural lung diseases and to lead to bronchial fibrosis. The development of pulmonary fibrosis is a complication of PA colonization of the airway, resulting from repeated infection, damage and repair of the epithelium. Bronchial epithelial cell epithelial-mesenchymal transition (EMT) plays a vital role in bronchial fibrosis. To date, research on bronchial epithelial cell EMT caused by PA-secreted virulence factors has not been reported. Here, we found that PA3611 protein stimulation induced bronchial epithelial cell EMT with mesenchymal cell marker upregulation and epithelial cell marker downregulation. Moreover, integrin αvβ6 expression and TGF-β1 secretion were markedly increased, and p38 MAPK phosphorylation and NF-κB p65 subunit phosphorylation were markedly enhanced. Further research revealed that PA3611 promoted EMT via integrin αvβ6-mediated TGF-β1-induced p38/NF-κB pathway activation. The function of PA3611 was also verified in PA-infected rats, and the results showed that ΔPA3611 reduced lung inflammation and EMT. Overall, our results revealed that PA3611 promoted EMT via integrin αvβ6-mediated TGF-β1-induced p38/NF-κB pathway activation, suggesting that PA3611 acts as a crucial virulence factor in bronchial epithelial cell EMT and is a potential target for the clinical treatment of bronchial EMT and fibrosis caused by chronic PA infection.

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities

The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment. IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities' adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.