DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells

Journal Article · · Nucleic Acids Research
DOI: https://doi.org/10.1093/nar/gky412 · OSTI ID:1439776

Abstract The circadian protein Nocturnin (NOCT) belongs to the exonuclease, endonuclease and phosphatase superfamily and is most similar to the CCR4-class of deadenylases that degrade the poly-adenosine tails of mRNAs. NOCT-deficient mice are resistant to high-fat diet induced weight gain, and exhibit dysregulation of bone formation. However, the mechanisms by which NOCT regulates these processes remain to be determined. Here, we describe a pair of high-resolution crystal structures of the human NOCT catalytic domain. The active site of NOCT is highly conserved with other exoribonucleases, and when directed to a transcript in cells, NOCT can reduce translation and abundance of that mRNA in a manner dependent on key active site residues. In contrast to the related deadenylase CNOT6L, purified recombinant NOCT lacks in vitro ribonuclease activity, suggesting that unidentified factors are necessary for enzymatic activity. We also find the ability of NOCT to repress reporter mRNAs in cells depends upon the 3′ end of the mRNA, as reporters terminating with a 3′ MALAT1 structure cannot be repressed by NOCT. Together, these data demonstrate that NOCT is an exoribonuclease that can degrade mRNAs to inhibit protein expression, suggesting a molecular mechanism for its regulatory role in lipid metabolism and bone development.

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1439776
Alternate ID(s):
OSTI ID: 1460872
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 12 Vol. 46; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (65)

Nocturnin, a Deadenylase in Xenopus laevis Retina journal February 2003
Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases journal June 2000
Xenopus CAF1 requires NOT1-mediated interaction with 4E-T to repress translation in vivo journal May 2015
Structure of the PAN3 Pseudokinase Reveals the Basis for Interactions with the PAN2 Deadenylase and the GW182 Proteins journal August 2013
Cellular magnesium homeostasis journal August 2011
First evidence of nocturnin in fish: two isoforms in goldfish differentially regulated by feeding journal February 2018
The structure of the Pan2–Pan3 core complex reveals cross-talk between deadenylase and pseudokinase journal June 2014
Features and development of Coot journal March 2010
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
PAN3 Encodes a Subunit of the Pab1p-Dependent Poly(A) Nuclease in Saccharomyces cerevisiae journal October 1996
The Anti-Proliferative Activity of BTG/TOB Proteins Is Mediated via the Caf1a (CNOT7) and Caf1b (CNOT8) Deadenylase Subunits of the Ccr4-Not Complex journal December 2012
PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells journal September 2015
A circadian-regulated gene, Nocturnin , promotes adipogenesis by stimulating PPAR-γ nuclear translocation journal May 2010
Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity journal May 2007
The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors journal June 2015
Mouse CAF1 Can Function As a Processive Deadenylase/3′–5′-Exonuclease in Vitro but in Yeast the Deadenylase Function of CAF1 Is Not Required for mRNA Poly(A) Removal journal June 2004
Poly(A)-specific ribonuclease is a nuclear ribosome biogenesis factor involved in human 18S rRNA maturation journal April 2017
The highways and byways of mRNA decay journal February 2007
curled Encodes the Drosophila Homolog of the Vertebrate Circadian Deadenylase Nocturnin journal July 2009
Human Pumilio Proteins Recruit Multiple Deadenylases to Efficiently Repress Messenger RNAs journal September 2012
Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity journal July 2010
X‐ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex journal December 2003
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information journal January 2003
Reconstitution, Activities, and Structure of the Eukaryotic RNA Exosome journal December 2006
Identification of Multiple RNA Features That Influence CCR4 Deadenylation Activity journal April 2003
Distinct modes of recruitment of the CCR 4– NOT complex by Drosophila and vertebrate Nanos journal March 2016
Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation journal May 2014
mRNA deadenylation by PARN is essential for embryogenesis in higher plants journal July 2004
GlobPlot: exploring protein sequences for globularity and disorder journal July 2003
Capturing snapshots of APE1 processing DNA damage journal October 2015
Multifunctional deadenylase complexes diversify mRNA control journal April 2008
The π-helix translates structure into function journal January 2000
Mammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP-Dependent Deadenylation journal September 2009
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures journal July 2005
Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix journal June 2014
The circadian clock, metabolism and obesity journal February 2017
Model-Based Clustering of Non-Gaussian Panel Data Based on Skew-tDistributions journal January 2010
Tethered function assays using 3′ untranslated regions journal February 2002
Identification of local variations within secondary structures of proteins journal April 2015
Poly(A)-specific ribonuclease (PARN): An allosterically regulated, processive and mRNA cap-interacting deadenylase journal March 2013
Nocturnin Regulates Circadian Trafficking of Dietary Lipid in Intestinal Enterocytes journal August 2011
The Ccr4–Not Deadenylase Subunits CNOT7 and CNOT8 Have Overlapping Roles and Modulate Cell Proliferation journal September 2009
Immediate early response of the circadian polyA ribonuclease nocturnin to two extracellular stimuli journal May 2007
ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function journal April 2013
CCR4-Associated Factor CAF1 Is an Essential Factor for Spermatogenesis journal July 2004
Cnot7-Null Mice Exhibit High Bone Mass Phenotype and Modulation of BMP Actions journal August 2007
Translational Repression by Deadenylases journal July 2010
Inference from Iterative Simulation Using Multiple Sequences journal November 1992
boa : An R Package for MCMC Output Convergence Assessment and Posterior Inference journal January 2007
PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria journal June 2011
Structural basis for the recruitment of the human CCR4–NOT deadenylase complex by tristetraprolin journal May 2013
Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors journal January 2017
Oligo-astheno-teratozoospermia in mice lacking Cnot7, a regulator of retinoid X receptor beta journal April 2004
Electrostatics of nanosystems: Application to microtubules and the ribosome journal August 2001
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations journal July 2004
Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase Nocturnin journal November 2015
I-TASSER: a unified platform for automated protein structure and function prediction journal March 2010
Non-alcoholic fatty liver disease, obesity and the metabolic syndrome journal August 2014
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules journal May 2016
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations journal May 2007
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes journal June 2006
miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT journal October 2011
Nocturnin Expression Is Induced by Fasting in the White Adipose Tissue of Restricted Fed Mice journal February 2011
Long noncoding RNAs: Re-writing dogmas of RNA processing and stability journal January 2016
An essential role for the circadian‐regulated gene Nocturnin in osteogenesis: the importance of local timekeeping in skeletal homeostasis journal November 2011