KaiC-like proteins improve stress resistance in environmental Pseudomonas species

Abstract

KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria that are not known to have or need a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC-like proteins found in environmental Pseudomonas species. Using a bioinformatic approach, we describe the diversity and distribution of members of this protein family in the Pseudomonas genus and sketch, through comparative genomics, a conserved minimal interaction network comprising a histidine kinase and a response regulator. We then characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in sulfur uptake and alternative carbon source utilization in P. protegens. As expected, it physically interacts with its cognate histidine kinase and response regulator. Moreover, KaiC homologs are phosphorylated at one (P. putida) or two (P. protegens) sites and KaiC phosphorylation patterns change over time; however, in Pseudomonas species, changes in KaiC phosphorylation are driven by the age of the culture rather than by circadian cues as is the case in Cyanobacteria. In this study, through thorough bioinformatic and experimental analyses, we shed light onto the functional diversification and evolution of a unique protein family, diversely involved in bacterial rhythmic interactions with their environment. By so doing, we present a striking example of a protein whose general purpose is conserved in evolution, but whose molecular mechanics and participation in bacterial physiology can change dramatically across species.