Selection, development and structural characterization of 2' FY-RNA aptamers for pyoverdine

ABSTRACT: Pyoverdines are siderophores employed by a variety of pseudomonas species to capture essential iron by which their growth is supported in many environments in which they can be harmful or helpful to coinhabiting species or the organisms that they inhabit. Of the Pseudomonas fluorescens group, the pyoverdine of each pseudomonad species is constituted of a central chromophore and a unique peptide component that is produced by nonribosomal peptide synthetases. Pyoverdine Pf5 (PYO-Pf5) is the product of pseudomonas protegens, a species that supports plant growth, particularly in soils with limiting iron. To explore the dynamics of P. protegens activity in soil, we have selected 2’ FY modified RNA aptamers that selectively recognize PYO-Pf5 with high affinities. Two 2’FY-RNA aptamers, with different base sequences, were selected that specifically bind pyoverdine-Pf5 (PYO-Pf5) over pseudobactin (PSB), a related pyoverdine, and two other siderophores, enterobactin and ornibactin. The 2’FY-RNA aptamers were shown to be G-quadruplexes by computational prediction, N-methyl mesoporphyrin IX (NMM) binding and CD spectroscopy. They were compared with their counterparts (same base sequence) in RNA and DNA for function and structure. Whereas the 2’FY-RNA and RNA forms bound PYO-Pf5 and had circular dichroism (CD) spectra typical of a G-quadruplex, the DNA forms neither bound PYO-Pf5 nor showed diagnostic NMM binding or CD spectra for G-quadruplexes. The impact of 2’ moiety in aptamers on their structure and function have been explored and results revealed that the nature of the chemical group at the 2’ position influences binding activity and structure.The aptamers will be applied to a nanoporous aluminum oxide biosensor to detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.

ORGANISM(S): synthetic construct

PROVIDER: GSE224685 | GEO | 2025/12/31

REPOSITORIES: GEO