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Lüdke, D.

Publications and source records attributed to Lüdke, D..

3 recordsLinked to original sources

Granule microenvironment regulates the dual functions of FMR1

Fragile X Messenger Ribonucleoprotein 1 (FMR1) is an evolutionarily conserved RNA binding protein with important functions in cognition and female reproduction, and its disruption is associated with neurodevelopmental and reproductive disorders including the Fragile X syndrome. FMR1 is best known for its role as a translation repressor. However, several recent studies also suggest a role of FMR1 as a translation enhancer raising fundamental questions about the molecular regulation of these opposing functions. In this study, we identify FMR1 as part of the oskar mRNA-protein complex in the Drosophila oocyte and study the role of FMR1 as a translational enhancer of oskar. We provide the molecular mechanism for the dual functions of FMR1 and show that the two major RNA-binding domains of FMR1, the KH domains and the RGG box, play distinct separable roles in regulating translation. The KH domains enhance translation of mRNAs while the RGG box containing C-terminal domain (CTD) is required to repress translation. We further show that the condensation propensity of FMR1 containing granules regulates the two antagonistic functions, such that phase separation by FMR1-CTD creates the molecular microenvironment necessary for the repressive activity, whereas reduction in phase separation is associated with increased translation. Our findings highlight the importance of biomolecular condensates not just as a means of molecular compartmentalization but as a fundamental regulatory principle that dictates the functional output of modular protein domains.

molecular biology↗

AI-guided discovery of atypical protein assemblies

Artificial intelligence (AI) systems such as AlphaFold have transformed structural biology by enabling accurate prediction of protein structures. However, their capacity to uncover new classes of macromolecular assemblies remains largely untapped. We developed the Structural Novelty Index (SNI), a quantitative framework for identifying protein complexes that diverge from canonical architectures. As one implementation of SNI, we developed SNINRC-Hexa, to identify unconventional resistosomes formed by nucleotide-binding, leucine-rich repeat immune receptors (NLRs). We used it to analyze AlphaFold 3 models of 637 non-redundant NRC proteins from 346 genomes representing 85 plant species. This analysis identified candidates with predicted architectures distinct from the canonical hexameric resistosomes of NRC proteins. Biochemical purification and negative-stain transmission electron microscopy of NRC7 orthologs from multiple species supported the SNI prediction and revealed an unexpected undecameric (11-mer) assembly. Our results establish SNI as a scalable approach for discovering atypical protein complexes.

bioinformatics↗

Functional requirement of the Arabidopsis importin-α nuclear transport receptor family in autoimmunity mediated by the NLR protein SNC1

IMPORTIN-3/MOS6 (MODIFIER OF SNC1, 6) is one of nine importin- isoforms in Arabidopsis that recruit nuclear localization signal (NLS)-containing cargo proteins to the nuclear import machinery. IMP-3/MOS6 is required genetically for full autoimmunity of the nucleotide-binding leucine-rich repeat (NLR) immune receptor mutant snc1 (suppressor of npr1-1, constitutive 1) and MOS6 also contributes to basal disease resistance. Here, we investigated the contribution of the other importin- genes to both types of immune responses, and we analyzed potential interactions of all importin- isoforms with SNC1. By using reverse-genetic analyses in Arabidopsis and protein-protein interaction assays in N. benthamiana we provide evidence that among the nine -importins in Arabidopsis, IMP-3/MOS6 is the main nuclear transport receptor of SNC1, and that IMP-3/MOS6 is required selectively for autoimmunity of snc1 and basal resistance to mildly virulent Pseudomonas syringae in Arabidopsis. SIGNIFICANCE STATEMENTSpecific requirement for the Arabidopsis -importin MOS6 in snc1-mediated autoimmunity is explained by selective formation of MOS6-SNC1 nuclear import complexes.

plant biology↗