title: Molecular recognition of mRNA 5' cap by 3' poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins.
abstract: The mRNA 5' cap structure plays a pivotal role in coordination of eukaryotic translation and mRNA degradation. Poly(A)-specific ribonuclease (PARN) is a dimeric exoribonuclease that efficiently degrades mRNA 3' poly(A) tails while also simultaneously interacting with the mRNA 5' cap. The cap binding amplifies the processivity of PARN action. We used surface plasmon resonance kinetic analysis, quantitative equilibrium fluorescence titrations and circular dichroism to study the cap binding properties of PARN. The molecular mechanism of 5' cap recognition by PARN has been demonstrated to differ from interactions seen for other known cap-binding proteins in that: i) the auxiliary biological function of 5' cap binding by the 3' degrading enzyme is accomplished by negative cooperativity of PARN dimer subunits; ii) non-coulombic interactions are major factors in the complex formation; and iii) PARN has versatile activity toward alternative forms of the cap. These characteristics contribute to stabilization of the PARN-cap complex needed for the deadenylation processivity. Our studies provide a consistent biophysical basis for elucidation of the processive mechanism of PARN-mediated 3' mRNA deadenylation and provide a new framework to interpret the role of the 5' cap in mRNA degradation.
authors.affiliation: Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland. Electronic address: annan@ifpan.edu.pl.
authors.forename: Anna
authors.initials: A
authors.lastname: Niedzwiecka
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Nilsson
authors.affiliation: Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland.
authors.forename: Remigiusz
authors.initials: R
authors.lastname: Worch
authors.affiliation: Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland.
authors.forename: Janusz
authors.initials: J
authors.lastname: Stepinski
authors.affiliation: Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland; Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
authors.forename: Edward
authors.initials: E
authors.lastname: Darzynkiewicz
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Virtanen
mesh_terms: D005095:Exoribonucleases / Q000737:chemistry*; D007700:Kinetics; D009994:Osmolar Concentration; D011487:Protein Conformation; D039381:RNA Cap-Binding Proteins / Q000737:chemistry*; D012315:RNA Caps / Q000737:chemistry*; D012333:RNA, Messenger / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D005095:Exoribonucleases; D039381:RNA Cap-Binding Proteins; D012315:RNA Caps; D012333:RNA, Messenger
keywords: Circular dichroism; Fluorescence spectroscopy; PARN; Protein–ligand interactions; Surface plasmon resonance; mRNA 5′ cap