Functional importance and paralog-specificity of the intrinsically disordered RsmE C-terminus region in Pseudomonas fluorescens Pf0-1

ABSTRACT RsmE and its homologs function as RNA-binding post-transcriptional regulators that control the production of diverse secondary metabolites. Pseudomonads harbor varying numbers of RsmE paralogs that are often generalized to overlap in function. However, recent studies indicate that these paralogs bind to both overlapping and unique sets of mRNA. In Pseudomonas fluorescens Pf0-1, RsmE exclusively regulates the production of multiple extracellular secretions, distinguishing it from its paralogs, RsmA and RsmI. While the majority of the three paralogs’ core sequences are highly conserved, each possesses a vastly different C-terminus region. The C-terminus tails are generalized to be functionless, as they are intrinsically disordered and devoid of known mRNA binding sites. Here, we challenge this notion through analyses of various naturally emergent RsmE variants that differentially impact repressive function solely from changes in the C-terminus tail. Engineered Rsm chimeras containing the various paralog cores and tails further confirmed the functional importance of the C-terminus tail, as neither replacing the RsmE tail with the RsmA tail nor attaching the RsmE tail to a different paralog core restored repression. However, the RsmI tail complemented function in the presence of the RsmE core, indicating that RsmE’s functional specificity lies within the core despite the essentiality of the C-terminus. Bioinformatic analyses also revealed that the C-terminus tail composition of RsmA to be the most unique among the paralogs and each tail sequence is uniquely and highly conserved across diverse proteins, not only in bacteria, but also in eukaryotic species. IMPORTANCE The post-transcriptional regulator RsmE controls the production of various extracellular secretions in Pseudomonas fluorescens Pf0-1, making it functionally unique from its paralogs, RsmA and RsmI. The three paralogs share highly conserved sequences and secondary structures save for their disordered C-termini, which are generalized to be functionless. Here, we demonstrate that the absence of the RsmE C-terminus tail completely abolishes native function and that various alterations to the tail differentially impact repression of extracellular secretions. The results described here strongly support functional uniqueness of Rsm paralogs, challenge the supposed dispensability of their C-terminus tails, and deepen our understanding of RsmE-regulation, which modulates biofilm formation and virulence in clinically significant bacteria.