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In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions
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SYSNO ASEP 0556783 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions Author(s) Giacobelli, V. G. (CZ)
Fujishima, K. (JP)
Lepšík, Martin (UOCHB-X) RID, ORCID
Tretyachenko, V. (CZ)
Kadavá, T. (CZ)
Makarov, M. (CZ)
Bednárová, Lucie (UOCHB-X) RID, ORCID
Novák, Petr (MBU-M) RID, ORCID
Hlouchová, Klára (UOCHB-X) ORCIDArticle number msac032 Source Title Molecular Biology and Evolution. - : Oxford University Press - ISSN 0737-4038
Roč. 39, č. 3 (2022)Number of pages 11 s. Language eng - English Country US - United States Keywords RNA-protein interaction ; genetic code evolution ; protein evolution ; mRNA-display OECD category Biochemistry and molecular biology R&D Projects EF16_019/0000729 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) ED1.1.00/02.0109 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Research Infrastructure e-INFRA CZ - 90140 - CESNET, zájmové sdružení právnických osob Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 ; MBU-M - RVO:61388971 UT WOS 000764264700001 EID SCOPUS 85125682104 DOI 10.1093/molbev/msac032 Annotation RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10(10) library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2023 Electronic address https://doi.org/10.1093/molbev/msac032
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