Functional Characterization of CutA: A Conserved Protein Involved in Bacterial Stress Adaptation

Abstract

A substantial fraction of proteins remains functionally uncharacterized, forming the so-called dark proteome, which includes evolutionarily conserved proteins that are likely essential for cellular physiology. One such protein is CutA, a small homotrimeric protein conserved across all domains of life, from cyanobacteria to humans. Despite its pronounced structural similarity to the nitrogen regulatory protein PII, a central hub for metabolic signal integration, the physiological role of CutA has remained elusive. Early studies suggested a function in copper tolerance, but this hypothesis has remained controversial. Motivated by its broad conservation, structural similarity to PII, and the lack of a clearly defined cellular function, this study aimed to provide further insight into the potential roles of CutA.

As model systems, CutA from Escherichia coli and cyanobacterial CutA homologs, primarily from Synechococcus elongatus PCC 7942, were investigated. Physiological analyses of wild-type and ΔcutA strains revealed impaired recovery from environmental stress conditions in the absence of CutA, indicating a contribution to cellular stress resilience. To investigate potential molecular interactions, native metabolomics was employed to screen for ligands of CutA. From crude cyanobacterial extracts, a previously uncharacterized pteridine was identified, purified, and structurally characterized. Further analyses confirmed that this pteridine binds to CutA from both E. coli and S. elongatus, and that CutA also interacts with additional pteridines as well as with copper. In addition, associations with proteins involved in fatty acid biosynthesis, a process essential for cell envelope integrity, were observed under stress conditions. Together, these results provide new insight into the physiological relevance of CutA and support the view that this PII-like protein participates in stress-adaptive cellular processes, potentially linking metal homeostasis to the maintenance of cellular integrity.