The Drosha-DGCR8 complex initiates microRNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of approximately 33 bp, with a terminal loop and flanking segments. The terminal loop is unessential, whereas the flanking ssRNA segments are critical for processing. The cleavage site is determined mainly by the distance (approximately 11 bp) from the stem-ssRNA junction. Purified DGCR8, but not Drosha, interacts with pri-miRNAs both directly and specifically, and the flanking ssRNA segments are vital for this binding to occur. Thus, DGCR8 may function as the molecular anchor that measures the distance from the dsRNA-ssRNA junction. Our current study thus facilitates the prediction of novel microRNAs and will assist in the rational design of small hairpin RNAs for RNA interference.

A complex of Drosha with DGCR8 (or its homolog Pasha) cleaves primary microRNA (pri-miRNA) substrates into precursor miRNA and initiates the microRNA maturation process. Drosha provides the catalytic site for this cleavage, whereas DGCR8 or Pasha provides a frame for anchoring substrate pri-miRNAs. To clarify the molecular basis underlying recognition of pri-miRNA by DGCR8 and Pasha, we determined the crystal structure of the human DGCR8 core (DGCR8S, residues 493-720). In the structure, the two double-stranded RNA-binding domains (dsRBDs) are arranged with pseudo two-fold symmetry and are tightly packed against the C-terminal helix. The H2 helix in each dsRBD is important for recognition of pri-miRNA substrates. This structure, together with fluorescent resonance energy transfer and mutational analyses, suggests that the DGCR8 core recognizes pri-miRNA in two possible orientations. We propose a model for DGCR8's recognition of pri-miRNA.

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Tumor suppressor programmed cell death protein 4 (PDCD4) inhibits the translation initiation factor eIF4A, an RNA helicase that catalyzes the unwinding of secondary structure at the 5 -untranslated region of mRNAs and controls the initiation of translation. Here, we determined the crystal structure of the human eIF4A and PDCD4 complex. The structure reveals that one molecule of PDCD4 binds to the two eIF4A molecules through the two different binding modes. While the two MA3 domains of PDCD4 bind to one eIF4A molecule, the C-terminal MA3 domain alone of the same PDCD4 also interacts with another eIF4A molecule. The eIF4A-PDCD4 complex structure suggests that the MA3 domain(s) of PDCD4 binds perpendicular to the interface of the two domains of eIF4A, preventing the domain closure of eIF4A and blocking the binding of RNA to eIF4A, both of which are required events in the function of eIF4A helicase. The structure, together with biochemical analyses, reveals insights into the inhibition mechanism of eIF4A by PDCD4 and provides a framework for designing chemicals that target eIF4A.translation inhibition ͉ tumor suppressor ͉ RNA helicase ͉ domain closure ͉ MA3 domain P rogrammed cell death protein 4 (PDCD4) is a translation inhibitor that suppresses neoplastic transformation in cultured cells and transgenic mice (1-3). Loss or reduced expression of PDCD4 has been implicated in the development and progression of a variety of aggressive human cancers (4-6). PDCD4 is regulated by the S6K1 kinase and the SCF ␤TRCP ubiquitin ligase in response to the activation of the mTOR pathway by mitogens, and the controlled degradation of PDCD4 is essential for efficient protein synthesis and consequently for cell growth and proliferation (7).PDCD4 is believed to perform its tumor suppressor function primarily through interaction with eIF4A and eIF4G, which are components of mRNA-binding complex eIF4F (8). eIF4A is a DEAD-box RNA helicase, with two domains, that unwinds the secondary structures in 5Ј-untranslated region (UTR) and cap of mRNA and thereby facilitates ribosome scanning (8). eIF4G is an adaptor protein that coordinates assembly of translation factors and the small ribosomal subunit (8). PDCD4 is believed to inhibit cap-dependent translation by directly inhibiting the helicase activity of eIF4A or by competing with eIF4G for binding to eIF4A and preventing assembly into a eukaryotic initiation complex, eIF4F, or both (1, 9, 10).PDCD4 is formed with the two MA3 domains at its middle (mMA3) and C-terminal regions (cMA3) (9, 11-13). Mutational and NMR binding analysis have shown that PDCD4 uses both MA3 domains to interact with eIF4A and prevents translation (9, 10). However, other studies have demonstrated that the cMA3 domain alone is sufficient for the inhibition of RNA helicase and translation (12). The interactions between eIF4A and PDCD4 have been analyzed in several mutational and NMR mapping studies (1, 9, 10). Nevertheless, it is unclear from these studies how PDCD4 inhibits eIF4A at the molecular level. To elucidate ...

Glutamate is the major excitatory neurotransmitter in the mammalian CNS and acts on both ionotropic and metabotropic glutamate receptors (mGluRs). The mGluRs are widely distributed in the CNS and modulate a variety of neuronal processes including neurotransmitter release and ion channel function. In hippocampus and cortex, mGluR5 is highly expressed and plays an important role in the regulation of synaptic plasticity. CaM binding dynamically regulates mGluR5 surface expression; however, the mechanisms linking CaM to mGluR5 trafficking are not clear. Recent studies showed that CaM binding to mGluR7 regulates its trafficking in a phosphorylation-dependent manner by disrupting the binding of PICK1. The E3 ligase seven in absentia homolog (Siah)-1A binds to mGluR5 and competes with CaM binding making it an intriguing molecule to regulate phosphorylation-dependent trafficking of mGluR5. In the present study, we find that CaM competes with Siah-1A for mGluR5 binding in a phosphorylation-dependent manner in rat hippocampal neurons. Specifically, phosphorylation of mGluR5 S901 favors Siah-1A binding by displacing CaM. We identified critical residues regulating Siah-1A binding to mGluR5 and showed that binding is essential for the Siah-1A effects on mGluR5 trafficking. Siah-1A binding decreases mGluR5 surface expression and increases endosomal trafficking and lysosomal degradation of mGluR5. Thus CaM-regulated Siah-1A binding to mGluR5 dynamically regulates mGluR5 trafficking. These findings support a conserved role for CaM in regulating mGluR trafficking by PKC-dependent regulation of receptor binding proteins.