Deep Profiling of the Proteome Dynamics of Pseudomonas aeruginosa Reference Strain PAO1 under Different Growth Conditions

As one of the most common bacterialpathogens causing nosocomialinfections, Pseudomonas aeruginosa ishighly adaptable to survive under various conditions. Here, we profiledthe abundance dynamics of 3489 proteins across different growth stagesin the P. aeruginosa reference strainPAO1 using data-independent acquisition-based quantitative proteomics.The proteins differentially expressed during the planktonic growthexhibit several distinct patterns of expression profiles and are relevantto various biological processes, highlighting the continuous adaptationof the PAO1 proteome during the transition from the acceleration phaseto the stationary phase. By contrasting the protein expressions ina biofilm to planktonic cells, the known roles of T6SS, phenazinebiosynthesis, quorum sensing, and c-di-GMP signaling in the biofilmformation process were confirmed. Additionally, we also discoveredseveral new functional proteins that may play roles in the biofilmformation process. Lastly, we demonstrated the general concordanceof protein expressions within operons across various growth states,which permits the study of coexpression protein units, and reversely,the study of regulatory components in the operon structure. Takentogether, we present a high-quality and valuable resource on the proteomicdynamics of the P. aeruginosa referencestrain PAO1, with the potential of advancing our understanding ofthe overall physiology of Pseudomonas bacteria.

Automated summary

In this study, the abundance dynamics of proteins in Pseudomonas aeruginosa reference strain PAO1 were analyzed using data-independent acquisition-based quantitative proteomics. The differentially expressed proteins during planktonic growth exhibited diverse expression patterns relevant to various biological processes, highlighting the continuous adaptation of the PAO1 proteome. By comparing protein expressions in biofilm and planktonic cells, the roles of known factors in biofilm formation were confirmed and new functional proteins were discovered. This study provides a valuable resource for understanding the proteomic dynamics of P. aeruginosa and advancing our knowledge of its physiology.