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

• Published in: Journal of biomolecular structure & dynamics 2017-06, Vol.35 (8), p.1615-1628
• Main Authors: Nikulin, Alexey, Mikhailina, Alisa, Lekontseva, Natalia, Balobanov, Vitalii, Nikonova, Ekaterina, Tishchenko, Svetlana
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; archaea; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Binding Sites; Cloning, Molecular; crystal structure; Crystallography, X-Ray; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; Genetic Vectors - chemistry; Genetic Vectors - metabolism; Hfq; Host Factor 1 Protein - chemistry; Host Factor 1 Protein - genetics; Host Factor 1 Protein - metabolism; Kinetics; Lsm proteins; Methanocaldococcus - chemistry; Methanocaldococcus - metabolism; Models, Molecular; Poly A - chemistry; Poly A - metabolism; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA, Archaeal - metabolism; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; RNA-protein interactions; Sequence Alignment; Sequence Homology, Amino Acid; translation regulation
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2016.1189849

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.