Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii

Abstract

The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.

Keywords:

• Lsm proteins
• Hfq
• archaea
• RNA–protein interactions
• translation regulation
• crystal structure

Acknowledgements

We are indebted to Dr Alexei Kazakov (IBI RAS, Pushchino, Russia) for assistance in SPR measurements which were performed based on Scientific Instrumentation Facility of Pushchino Research Centre “Structural and functional studies of biological systems”. We are very grateful to S. Nikonov and A. Korepanov for reading of the manuscript and helpful discussion.