Abstract Nucleases are specialized enzymes known for degrading nucleic acids in diverse cellular processes. Among them, EXD2 contributes to genome maintenance by digesting a broad range of nucleic acid substrates, including non-canonical RNA–DNA hybrids (RDHs). However, the molecular mechanism underlying the interplay of EXD2 with these hybrid structures has remained elusive. Here, using an optical tweezers-based single-molecule approach, we unveil that EXD2 cooperatively binds to and slowly digests mechanically tensioned RDHs. On the other hand, the cooperative binding of a high amount of EXD2 onto a relaxed RDH drives their co-condensation. Moreover, EXD2 is capable of recognizing damage sites along RDHs and inducing damaged RDH condensation even at low protein concentrations. Surprisingly, this co-condensation, in contrast, protects RDHs from timely degradation by other nucleases. Consistently, we unveil that overexpressed EXD2 colocalizes with mitochondrial RDHs and, rather than cleavage, prevents them from fast degradation. Therefore, EXD2 is a promiscuous moonlighting enzyme that can exert opposing activities toward RDHs. Our findings provide a mechanistic understanding of the functional roles of EXD2 in cells.
Meng Hu, Yinghong Chen, Yanan Li et al.· Nucleic Acids Research· 0 citations
Amyloid fibrils are highly ordered protein assemblies characterized by a cross-β architecture. A wide range of proteins can adopt amyloid states, contributing to both disease-related pathology and normal physiological function. While animal-derived amyloids have been extensively examined in atomic detail, amyloid fibrils formed by plant proteins remain relatively understudied. Here we systematically assess three major seed storage proteins—oat 12S globulin, soybean 7S globulin, and rice glutelin—under harsh cooking-like conditions (pH 2, 85 °C). Oat globulin and rice glutelin readily form fibrils in both purified preparations and whole-seed extracts, whereas soybean globulin forms fibrils only in purified preparations and remains largely amorphous in whole-seed extracts. Using cryo-electron microscopy, we determine the structure of oat globulin fibrils at 3.9 Å resolution. The fibril core adopts a compact triangular architecture with pseudo-threefold symmetry and is stabilized by extensive hydrophobic and aromatic packing. Our findings establish the molecular basis of amyloid formation in plant seeds and expand the structural landscape of amyloid fibrils beyond animal and microbial systems, providing a foundation for understanding amyloid formation in plant- and food-derived proteins. Plant seed storage proteins can form amyloid fibrils under cooking-like conditions. Zhang et al. systematically compare three major plant seed storage proteins and determine the cryo-EM structures of oat globulin fibrils, providing molecular insight into amyloid assembly by plant-derived proteins.
