Synergistic and Global Effect of C‐terminus of Hfq in Small RNA Regulation

Abstract

Hfq, a homohexameric RNA chaperone, is known for stabilizing small noncoding RNAs (sRNAs) and facilitating riboregulation by promoting sRNA base pairing with target mRNAs. The proteins encoded by these target mRNAs are often involved in virulence and stress responses. Hfq has a conserved N‐terminal region sufficient for most of its function and a poorly conserved disordered C‐terminus (CT). The length of the C‐terminus varies among bacteria; it is 37 aa in E. coli. Since the role of C‐terminus of Hfq has been poorly understood we have investigated its role in vivo in small RNA stability and function. Mutant derivatives of Hfq were expressed from the chromosomal locus, allowing in vivo comparisons with the wild‐type (WT) Hfq, expressed under similar conditions and at physiological levels. While deletion of the CT (Hfq65) had modest phenotypes, combinations of this deletion with a weak mutation (K31A) in the distal face of the protein was fully defective for function in different assays. This strong synergistic phenotype of CT deletion with K31A allowed us to further dissect the CT. Loss of the region between 65–72aa, the best conserved part of the CT, was critical for the synergistic defect. These results suggest that the initial region of the CT supports the function of the distal face, where many mRNAs and a subset of sRNAs are known to bind. To understand the global effect of CT on interacting RNAs, we compared RNA seq data of Hfq immunoprecipitation for WT and Hfq65. Overall, Hfq binding RNA patterns were not much affected. However, consistent with previous findings, and with the cooperation of the CT with the distal face of Hfq, Hfq65 was most defective in the accumulation of the sRNAs (Class II) that bind the proximal and distal faces of Hfq. Some class I sRNAs, which bind the proximal and rim face of Hfq, were also modestly depleted in Hfq65, suggesting the possibility of a broader role for the CT. The mechanistic aspects of CT collaboration with the Hfq core are under investigation. Our results suggest that the C‐terminus collaborates with the Hfq distal face, reinforcing the specificity and strength of RNA binding to Hfq.Support or Funding InformationThis research was supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.