Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa
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The RNA degradosome, a multi-protein complex regulating mRNA in bacteria, assembles on the RNase E C-terminal domain (CTD) in Pseudomonadota (Proteobacteria) via short linear motifs (SLiMs). The composition of the Pseudomonas aeruginosa RNA degradosome is largely unknown, and its RNase E CTD shows limited similarity to those in models like Escherichia coli or Caulobacter crescentus . Our study characterizes the function of conserved SLiMs in P. aeruginosa RNase E, including a duplicated sequence termed the “REER-repeats” region. This region, along with AR1 and AR4 SLiMs, mediates RNA binding and localizes the degradosome in subcellular foci. Pull-down and bacterial two-hybrid assays identified PNPase and RhlB as interacting proteins, with direct interactions confirmed via protein binding assays. The NDPR and AR1 SLiMs mediate these interactions, respectively. Transcriptome analyses and phenotypic assays of RNase E CTD mutants revealed growth defects in specific conditions and virulence defects, revealing the importance of RNase E CTD RNA binding and RNA degradosome scaffolding for P. aeruginosa adaptability.
Author Summary
In this study, we investigate the RNA degradosome in Pseudomonas aeruginosa , a bacterium known for causing multiple types of human infections and for its multi-drug resistance. The RNA degradosome is a crucial multi-protein complex that regulates RNA levels, helping bacteria to rapidly adapt to various environments. We identified the key components of this complex in P. aeruginosa and mapped their interactions. Our findings also reveal that interaction between this complex and RNA is important for bacterial growth, particularly in cold conditions and during infection. We finally compare our findings with the RNA degradosome in other species, noting significant evolutionary convergence and unique characteristics in P. aeruginosa .
Our research sheds light on the complex mechanisms bacteria use to manage RNA and adapt to their surroundings, which could eventually inform new strategies to combat bacterial infections and resistance.
