Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation

Abstract

G-quadruplexes are four-stranded nucleic acid structures occurring in the genomes of all living organisms and viruses. It is increasingly evident that these structures play important molecular roles; generally, by modulating gene expression and overall genome integrity. For a long period, G-quadruplexes have been studied specifically in the context of human promoters, telomeres, and associated diseases (cancers, neurological disorders). Several of the proteins for binding G-quadruplexes are known, providing promising targets for influencing G-quadruplex-related processes in organisms. Nonetheless, in plants, only a small number of G-quadruplex binding proteins have been described to date. Thus, we aimed to bioinformatically inspect the available protein sequences to find the best protein candidates with the potential to bind G-quadruplexes. Two similar glycine and arginine-rich G-quadruplex-binding motifs were described in humans. The first is the so-called “RGG motif”-RRGDGRRRGGGGRGQGGRGRGGGFKG, and the second (which has been recently described) is known as the “NIQI motif”-RGRGRGRGGGSGGSGGRGRG. Using this general knowledge, we searched for plant proteins containing the above mentioned motifs, using two independent approaches (BLASTp and FIMO scanning), and revealed many proteins containing the G4-binding motif(s). Our research also revealed the core proteins involved in G4 folding and resolving in green plants, algae, and the key plant model organism, Arabidopsis thaliana. The discovered protein candidates were annotated using STRINGdb and sorted by their molecular and physiological roles in simple schemes. Our results point to the significant role of G4-binding proteins in the regulation of gene expression in plants.

The Arabidopsis tDR Ala forms G‐quadruplex structures that can be unwound by the DExH1 DEA(D/H)‐box RNA helicase

“…In plants, G4 and rG4 motifs appear widespread, but detecting them in vivo remains challenging, and their potential biological roles remain to be better understood (Griffin & Bass, 2018; Liu et al., 2022; Ma et al., 2022; Volnà et al., 2021). It was recently demonstrated that rG4 structures exist in vivo and can act as regulators (Yang et al., 2020).…”

“…Human G4‐binding proteins with another motif (RGRGRGRGGGSGGSGGRGRG) called NIKI for “Novel Interesting Quadruplex Interaction” were also found (Brazda et al., 2018). Plant proteins containing GAR or NIKI motifs have been identified and speculated to interact with G4 structures (Volnà et al., 2021). Among them, seven RNA helicases were identified, including DExH1 (Figure S6).…”

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation

“…Many G4-binding proteins in animals and humans are known [ 43 ]. Recently, it has been shown that proteins in barley seedlings can bind to PQSs and form DNA–protein complexes [ 44 ], so we can expect that G4-binding proteins also will be present in plant genomes [ 45 ].…”

Dissecting G-Quadruplexes and I-Motifs in Cis-Regulatory Regions of Mammals and Plants

“…The motif-binding potential of G-quadruplexes having vital roles in gene regulation was done by using a plant model organism "Arabidopsis thaliana (Thale cress)". 17 Research studies on Hordeum vulgare (Barley) clearly state that the DNA-binding proteins in barley seedlings are rich in potential G-quadruplexes, although the genome is rich in i-motifs. 18 .…”