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:
Hfq; Lsm proteins; RNA–protein interactions; archaea; crystal structure; translation regulation.
MeSH terms
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Amino Acid Sequence
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Archaeal Proteins / chemistry*
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Archaeal Proteins / genetics
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Archaeal Proteins / metabolism
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Binding Sites
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Cloning, Molecular
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Crystallography, X-Ray
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Escherichia coli / genetics
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Escherichia coli / metabolism
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Gene Expression
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Genetic Vectors / chemistry
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Genetic Vectors / metabolism
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Host Factor 1 Protein / chemistry*
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Host Factor 1 Protein / genetics
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Host Factor 1 Protein / metabolism
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Kinetics
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Methanocaldococcus / chemistry*
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Methanocaldococcus / metabolism
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Models, Molecular
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Poly A / chemistry
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Poly A / metabolism
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Protein Binding
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Protein Conformation, alpha-Helical
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Protein Conformation, beta-Strand
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Protein Interaction Domains and Motifs
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RNA, Archaeal / chemistry*
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RNA, Archaeal / genetics
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RNA, Archaeal / metabolism
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RNA, Messenger / chemistry*
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RNA, Messenger / genetics
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RNA, Messenger / metabolism
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RNA-Binding Proteins / chemistry*
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RNA-Binding Proteins / genetics
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RNA-Binding Proteins / metabolism
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Recombinant Proteins / chemistry
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Recombinant Proteins / genetics
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Recombinant Proteins / metabolism
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Sequence Alignment
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Sequence Homology, Amino Acid
Substances
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Archaeal Proteins
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Host Factor 1 Protein
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RNA, Archaeal
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RNA, Messenger
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RNA-Binding Proteins
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Recombinant Proteins
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Poly A