A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

ABSTRACT: The common oral microbe Fusobacterium nucleatum has recently gained attention when it was found to colonize tumors throughout the human body. Fusobacteria are also interesting in regard to bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. Here, to search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that copurified with 19 different sRNAs. Our approach recovered a 6S RNA-RNA polymerase complex in this species and discovered high enrichment of the KH domain proteins KhpA and KhpB with almost any tested sRNA, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the cellular stability of several of their targets. RNA-seq analysis and cell biological assays suggest that KhpA/B have several physiological functions, including a strong requirement for ethanolamine utilization. Our RBP search and discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Fusobacterium Nucleatum Subsp. Nucleatum Atcc 23726

SUBMITTER: Falk Ponath  

LAB HEAD: Jörg Vogel

PROVIDER: PXD046416 | Pride | 2024-02-08

REPOSITORIES: Pride