LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain

Abstract

LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.

Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules

“…Two LOTUS variants have been distinguished: the minimal LOTUS (mLOTUS) and the extended LOTUS (eLOTUS), whose defining feature is an additional C-terminal alpha-helix in a region that appears disordered in minimal LOTUS domains ( Jeske et al, 2017 ). A recent study has identified binding of RNA G-quadruplex secondary structures as an ancient conserved function of mLOTUS domains across kingdoms, and suggests that protein binding by eLOTUS domains may be a more recent evolutionary innovation ( Ding et al, 2020 ).…”

“…MIP-1 and MIP-2 can self-associate and form heterodimers through their LOTUS domains, and MIP-2 also interacts with MIP-1 through its largely disordered C-terminal region. Although we do not know if MIPs bind RNAs directly, this is a distinct possibility given the tendency of many IDRs to bind RNA and the evolutionary conservation of G-quadruplex binding among LOTUS domains ( Ding et al, 2020 ).…”

Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules

“…(Right) Predicted three-dimensional structures of LOTUS1 (top) and LOTUS2 (bottom) domains in MIP-1 and MIP-2 (also see Figure S1). study has identified binding of RNA G-quadruplex secondary structures as an ancient conserved function of mLOTUS domains across kingdoms, and suggests that protein binding by eLOTUS domains may be a more recent evolutionary innovation (Ding et al, 2020).…”

The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline

“…[23] The function of these G-rich and G4 interactions remains unclear but could be instrumental to the role of LOTUS in RNA metabolism and regulation. [23] TDRD5 and TDRD7 contain LOTUS domains paired with Tudor scaffolding domains. [24] Tudor domains have been shown to bind methylated arginines and lysines, with some preference for Argonaute proteins and histone tails.…”

“…[21,22] In addition to interfacing with proteins, LOTUS domains also bind RNA with a preference for G-rich RNAs and those that form a G-quadruplex (G4) secondary structure. [23] The function of these G-rich and G4 interactions remains unclear but could be instrumental to the role of LOTUS in RNA metabolism and regulation. [23] TDRD5 and TDRD7 contain LOTUS domains paired with Tudor scaffolding domains.…”