Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy

Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy Full article

Journal

Nucleic Acids Research
ISSN: 0305-1048 , E-ISSN: 1362-4962

Output data

Year: 2019, Volume: 47, Number: 22, Pages: 11850-11860 Pages count : 11 DOI: 10.1093/nar/gkz1039

Authors

Malygin Alexey A. ^1,2,3 , Krumkacheva Olesya A. ^2,3,4 , Graifer Dmitry M. ^1,2,3 , Timofeev Ivan O. ^2,3,4 , Ochkasova Anastasia S. ^1,2 , Meschaninova Maria I. ^1,2 , Venyaminova Alya G. ^1,2 , Fedin Matvey V. ^3,4 , Bowman Michael ^2,5 , Karpova Galina G. ^1,2,3 , Bagryanskaya Elena G. ^2,3

Affiliations

1	Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk 630090, Russia
2	N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk 630090, Russia
3	Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
4	International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
5	University of Alabama, Tuscaloosa, AL 35487-0336, USA

The features of previously unexplored labile complexes of human 40S ribosomal subunits with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of RNAs to the ribosomal protein uS3 through its peptide 55-64 located outside the mRNA channel, were studied by EPR spectroscopy methods. Analysis of subatomic 40S subunit models showed that a likely site for labile RNA binding is a cluster of positively charged amino acid residues between the mRNA entry site and uS3 peptide 55-64. This is consistent with our finding that the 3'-terminal mRNA fragment hanging outside the 40S subunit prevents the cross-linking of an RNA derivative to this peptide. To detect labile complexes of 40S subunits with RNA by DEER/PELDOR spectroscopy, an undecaribonucleotide derivative with nitroxide spin labels at terminal nucleotides was utilized. We demonstrated that the 40S subunit channel occupancy with mRNA does not affect the RNA derivative binding and that uS3 peptide 55-64 is not involved in binding interactions. Replacing the RNA derivative with a DNA one revealed the importance of ribose 2'-OH groups for the complex formation. Using the single-label RNA derivatives, the distance between the mRNA entry site and the loosely bound RNA site on the 40S subunit was estimated.

Malygin A.A. , Krumkacheva O.A. , Graifer D.M. , Timofeev I.O. , Ochkasova A.S. , Meschaninova M.I. , Venyaminova A.G. , Fedin M.V. , Bowman M. , Karpova G.G. , Bagryanskaya E.G.
Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy

Nucleic Acids Research. 2019. V.47. N22. P.11850-11860. DOI: 10.1093/nar/gkz1039 WOS Scopus РИНЦ OpenAlex

Full text from publisher

Submitted:	Sep 9, 2019
Accepted:	Nov 5, 2019
Published online:	Nov 14, 2019

Web of science:	WOS:000522289000031
Scopus:	2-s2.0-85076329269
Elibrary:	43212973
OpenAlex:	W2986131283

DB	Citing
Web of science	12
Scopus	13
Elibrary	13
OpenAlex	13