The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

Loedige, Inga; Jakob, Leonhard; Treiber, Thomas; Ray, Debashish; Stotz, Mathias; Treiber, Nora; Hennig, Janosch; Cook, Kate B.; Morris, Quaid; Hughes, Timothy R.; Engelmann, Julia C.; Krahn, Michael P.; Meister, Gunter

doi:10.1016/j.celrep.2015.09.068

Cited by 90 publications

(183 citation statements)

References 51 publications

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“…Top2 was previously shown to directly interact with RNA (Rzepecki and Fisher 2000). Flr binds actin and contains a WD40 domain, which is usually implicated in protein-protein interactions but can also have potential RNA-binding properties (Lau et al 2009;Stirnimann et al 2010;Kwon et al 2013;Loedige et al 2015). Correspondingly, we found RNA crosslinking evidence for about 30 out of 95 WD40 domain-harboring proteins of the early fly proteome (Supplemental Fig.…”

Section: Discussionmentioning

confidence: 61%

The mRNA-bound proteome of the early fly embryo

et al. 2016

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Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRNA interactome capture methods to identify RBPs bound to polyadenylated transcripts within the first 2 h of Drosophila melanogaster embryogenesis. We identified a high-confidence set of 476 putative RBPs and confirmed RNA-binding activities for most of 24 tested candidates. Most proteins in the interactome are known RBPs or harbor canonical RBP features, but 99 exhibited previously uncharacterized RNA-binding activity. mRNA-bound RBPs and TFs exhibit distinct expression dynamics, in which the newly identified RBPs dominate the first 2 h of embryonic development. Integrating our resource with in situ hybridization data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation.

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Section: Discussionmentioning

confidence: 61%

The mRNA-bound proteome of the early fly embryo

et al. 2016

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“…The predicted WD40 repeat fold of Gemin5 did not help in understanding its RNA-binding mode, as WD40 repeat domains have not been well characterized as RNA-binding proteins. To date, the crystal structure of only one WD40-like protein bound to RNA has been determined (Loedige et al 2015). Our results revealed for the first time the mechanism by which two WD40 repeat domains form an integral RNA-binding unit, as indicated by the importance of the interface between the two WD40 repeat domains in RNA binding.…”

Section: Discussionmentioning

confidence: 71%

“…To date, only very limited information is available about the structural basis for sequence-specific RNA binding by WD40-like domains (Loedige et al 2015), but more examples of RNA-interacting WD40 repeat domains are turning up in the rapidly developing high-resolution cryo-electron microscopy (cryo-EM) studies of spliceosomal complexes (Yan et al 2015Agafonov et al 2016;Galej et al 2016;Rauhut et al 2016;Wan et al 2016). To facilitate mechanistic understanding of snRNP assembly and elucidate the structural basis for RNA recognition by the unorthodox RNA-binding module, we determined the structure of the WD40 repeat domains of Gemin5 in complex with RNA fragments encompassing the Sm site.…”

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confidence: 99%

Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5

et al. 2016

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Assembly of the spliceosomal small nuclear ribonucleoparticle (snRNP) core requires the participation of the multisubunit SMN (survival of motor neuron) complex, which contains SMN and several Gemin proteins. The SMN and Gemin2 subunits directly bind Sm proteins, and Gemin5 is required for snRNP biogenesis and has been implicated in snRNA recognition. The RNA sequence required for snRNP assembly includes the Sm site and an adjacent 3 ′ stem-loop, but a precise understanding of Gemin5's RNA-binding specificity is lacking. Here we show that the N-terminal half of Gemin5, which is composed of two juxtaposed seven-bladed WD40 repeat domains, recognizes the Sm site. The tandem WD40 repeat domains are rigidly held together to form a contiguous RNA-binding surface. RNA-contacting residues are located mostly on loops between β strands on the apical surface of the WD40 domains. Structural and biochemical analyses show that base-stacking interactions involving four aromatic residues and hydrogen bonding by a pair of arginines are crucial for specific recognition of the Sm sequence. We also show that an adenine immediately 5 ′ to the Sm site is required for efficient binding and that Gemin5 can bind short RNA oligos in an alternative mode. Our results provide mechanistic understandings of Gemin5's snRNA-binding specificity as well as valuable insights into the molecular mechanism of RNA binding by WD40 repeat proteins in general.

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“…This high sequence conservation between the yeast and human proteins indicates that the involved binding interface might be conserved, although a direct interaction between human AATF and NOL10 remains to be experimentally confirmed. Interestingly, WD40 repeats have also been implicated in protein–RNA interactions (64–66). We can thus not exclude that the WD40 domain of NOL10 may contact RNA in addition.…”

Section: Discussionmentioning

confidence: 99%

Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis

Bammert

Jonas

Ungricht

et al. 2016

Nucleic Acids Research

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Mammalian AATF/Che-1 is essential for embryonic development, however, the underlying molecular mechanism is unclear. By immunoprecipitation of human AATF we discovered that AATF forms a salt-stable protein complex together with neuroguidin (NGDN) and NOL10, and demonstrate that the AATF-NGDN-NOL10 (ANN) complex functions in ribosome biogenesis. All three ANN complex members localize to nucleoli and display a mutual dependence with respect to protein stability. Mapping of protein-protein interaction domains revealed the importance of both the evolutionary conserved WD40 repeats in NOL10 and the UTP3/SAS10 domain in NGDN for complex formation. Functional analysis showed that the ANN complex supports nucleolar steps of 40S ribosomal subunit biosynthesis. All complex members were required for 18S rRNA maturation and their individual depletion affected the same nucleolar cleavage steps in the 5′ETS and ITS1 regions of the ribosomal RNA precursor. Collectively, we identified the ANN complex as a novel functional module supporting the nucleolar maturation of 40S ribosomal subunits. Our data help to explain the described role of AATF in cell proliferation during mouse development as well as its requirement for malignant tumor growth.

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The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

Cited by 90 publications

References 51 publications

The mRNA-bound proteome of the early fly embryo

The mRNA-bound proteome of the early fly embryo

Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5

Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis

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