Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2

• Published in: The Journal of biological chemistry 2024-11, Vol.300 (11), p.107903, Article 107903
• Main Authors: Pougy, Karina C., Moraes, Beatriz S., Malizia-Motta, Clara L.F., Lima, Luís Maurício T.R., Sachetto-Martins, Gilberto, Almeida, Fabio C.L., Pinheiro, Anderson S.
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - chemistry; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; AtCSP2; AtGRP2; cold shock; NMR; Protein Binding; Protein Domains; RNA; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1016/j.jbc.2024.107903

AtGRP2 is a glycine-rich, RNA-binding protein that plays pivotal roles in abiotic stress response and flowering time regulation in Arabidopsis thaliana. AtGRP2 consists of an N-terminal cold shock domain (CSD) and two C-terminal CCHC-type zinc knuckles interspersed with glycine-rich regions. Here, we investigated the structure, dynamics, and nucleic acid–binding properties of AtGRP2-CSD. The 2D [1H,15N] heteronuclear single quantum coherence spectrum of AtGRP2-CSD1–79 revealed the presence of a partially folded intermediate in equilibrium with the folded state. The addition of 11 residues at the C terminus stabilized the folded conformation. The three-dimensional structure of AtGRP2-CSD1–90 unveiled a β-barrel composed of five antiparallel β-strands and a 310 helical turn, along with an ordered C-terminal extension, a conserved feature in eukaryotic CSDs. Direct contacts between the C-terminal extension and the β3–β4 loop further stabilized the CSD fold. AtGRP2-CSD1–90 exhibited nucleic acid binding via solvent-exposed residues on strands β2 and β3, as well as the β3–β4 loop, with higher affinity for DNA over RNA, particularly favoring pyrimidine-rich sequences. Furthermore, DNA binding induced rigidity in the β3–β4 loop, evidenced by 15N-{1H} NOE values. Mutation of residues W17, F26, and F37, in the central β-sheet, completely abolished DNA binding, highlighting the significance of π-stacking interactions in the binding mechanism. These results shed light on the mechanism of nucleic acid recognition employed by AtGRP2, creating a framework for the development of biotechnological strategies aimed at enhancing plant resistance to abiotic stresses.