ABSTRACT
Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.
Subject(s)
Adenosine Triphosphatases/chemistry , Adenosine Triphosphate/analogs & derivatives , DEAD-box RNA Helicases/chemistry , Organelle Biogenesis , RNA Helicases/chemistry , RNA/chemistry , Ribonucleoproteins, Small Nucleolar/chemistry , Adenosine Triphosphatases/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphate/metabolism , Animals , Binding Sites , Cloning, Molecular , Crystallography, X-Ray , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Kinetics , Mice , Models, Molecular , Protein Binding , Protein Biosynthesis , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , RNA/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Ribonucleoproteins, Small Nucleolar/genetics , Ribonucleoproteins, Small Nucleolar/metabolism , Ribosomes/genetics , Ribosomes/metabolism , Substrate SpecificityABSTRACT
Meiosis arrest female 1 (MARF1) is a cytoplasmic RNA binding protein that is essential for meiotic progression of mouse oocytes, in part by limiting retrotransposon expression. MARF1 is also expressed in somatic cells and tissues; however, its mechanism of action has yet to be investigated. Human MARF1 contains a NYN-like domain, two RRMs and eight LOTUS domains. Here we provide evidence that MARF1 post-transcriptionally silences targeted mRNAs. MARF1 physically interacts with the DCP1:DCP2 mRNA decapping complex but not with deadenylation machineries. Importantly, we provide a 1.7 Å resolution crystal structure of the human MARF1 NYN domain, which we demonstrate is a bona fide endoribonuclease, the activity of which is essential for the repression of MARF1-targeted mRNAs. Thus, MARF1 post-transcriptionally represses gene expression by serving as both an endoribonuclease and as a platform that recruits the DCP1:DCP2 decapping complex to targeted mRNAs.
Subject(s)
Cell Cycle Proteins/metabolism , Endoribonucleases/metabolism , RNA Interference , Trans-Activators/metabolism , Amino Acid Sequence , Animals , Binding Sites , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Crystallography, X-Ray , Endoribonucleases/chemistry , Endoribonucleases/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , HEK293 Cells , HeLa Cells , Humans , Mice , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Cleavage , RNA, Messenger/chemistry , RNA, Messenger/genetics , RNA, Messenger/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Trans-Activators/chemistry , Trans-Activators/geneticsABSTRACT
The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6. LSM14 binds DDX6 via a unique non-contiguous motif with distinct directionality as compared to other DDX6-interacting proteins. Together with mutational and proteomic studies, the LSM14-DDX6 structure reveals that LSM14 has adopted a divergent mode of binding DDX6 in order to support the formation of mRNA silencing complexes and P-body assembly.
Subject(s)
DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/metabolism , Protein Interaction Domains and Motifs , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/metabolism , RNA Interference/physiology , RNA, Messenger/metabolism , Ribonucleoproteins/chemistry , Ribonucleoproteins/metabolism , Amino Acid Sequence , Animals , Binding Sites , Caenorhabditis elegans , Crystallography, X-Ray , DEAD-box RNA Helicases/genetics , Drosophila melanogaster , Eukaryotic Initiation Factor-4E/metabolism , HeLa Cells , Humans , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Mutation , Protein Binding , Protein Conformation , Protein Structure, Secondary , Proteins/chemistry , Proteins/metabolism , Proteomics , Proto-Oncogene Proteins/genetics , Rec A Recombinases/chemistry , Recombinant Proteins/chemistry , Ribonucleoproteins/genetics , Sequence AlignmentABSTRACT
In response to viral infections, the mammalian innate immune system induces the production of the second messenger 2'-5' oligoadenylate (2-5A) to activate latent ribonuclease L (RNase L) that restricts viral replication and promotes apoptosis. A subset of rotaviruses and coronaviruses encode 2',5'-phosphodiesterase enzymes that hydrolyze 2-5A, thereby inhibiting RNase L activation. We report the crystal structure of the 2',5'-phosphodiesterase domain of group A rotavirus protein VP3 at 1.39 Å resolution. The structure exhibits a 2H phosphoesterase fold and reveals conserved active site residues, providing insights into the mechanism of 2-5A degradation in viral evasion of host innate immunity.
Subject(s)
Capsid Proteins/chemistry , Phosphoric Diester Hydrolases/chemistry , Rotavirus/enzymology , Catalytic Domain , Crystallography, X-Ray , Hydrogen Bonding , Models, Molecular , Protein Structure, SecondaryABSTRACT
Cyclic nucleotide regulation is an important target for drug development, particularly for treatment and prophylaxis of cardiovascular diseases. Determination of cyclic nucleotide levels for screening and monitoring of cyclic nucleotide modulating drug action is necessary, yet the techniques available are cumbersome and not sufficiently accurate. Here we present an approach based on the detection of cyclic nucleotide-dependent protein phosphorylation. By use of a common substrate of cyclic nucleotide-dependent protein kinases, the protein vasodilator-stimulated phosphoprotein (VASP) featuring two phosphorylation sites specifically phosphorylated by these kinases, an assay was developed for the monitoring of intracellular cyclic nucleotide levels. The assay was tested with human platelets ex vivo treated with stimulants of nucleotide cyclases, kinases, and phosphodiesterase inhibitors. Phosphorylation of the protein VASP correlates with intracellular cyclic nucleotide concentration (R(2)>0.90 for cGMP and cAMP); however, VASP phosphorylation is more sensitive to elevated cyclic nucleotide levels and significantly more stable over time. Quantification of VASP phosphorylation offers a reliable and robust tool for fast and easy monitoring of cyclic nucleotide levels and is also applicable to unprocessed biological matrices. Owing to these properties, VASP is a promising biomarker for screening and monitoring of cyclic nucleotide modulating drugs.
