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In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions

VG. Giacobelli, K. Fujishima, M. Lepšík, V. Tretyachenko, T. Kadavá, M. Makarov, L. Bednárová, P. Novák, K. Hlouchová

. 2022 ; 39 (3) : . [pub] 20220302

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc22019235

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 1010 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.

Citace poskytuje Crossref.org

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$a RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 1010 library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.
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$a Fujishima, Kosuke $u Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan $u Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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$a Lepšík, Martin $u Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
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$a Tretyachenko, Vyacheslav $u Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
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$a Kadavá, Tereza $u Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
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$a Novák, Petr $u Institute of Microbiology, Czech Academy of Sciences, Vestec, Czech Republic
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$a Hlouchová, Klára $u Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic $u Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
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