Journal Article

Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3

Nakel, Katharina, Fabien Bonneau, Christian R. Eckmann, Elena Conti

2015

Overview

The Caenorhabditis elegans germ-line development defective (GLD)-2–GLD-3 complex up-regulates the expression of genes required for meiotic progression. GLD-2–GLD-3 acts by extending the short poly(A) tail of germ-line–specific mRNAs, switching them from a dormant state into a translationally active state. GLD-2 is a cytoplasmic noncanonical poly(A) polymerase that lacks the RNA-binding domain typical of the canonical nuclear poly(A)-polymerase Pap1. The activity of C. elegans GLD-2 in vivo and in vitro depends on its association with the multi-K homology (KH) domain-containing protein, GLD-3, a homolog of Bicaudal-C. We have identified a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, and determined its structure at 2.3-Å resolution. The structure shows that the N-terminal domain of GLD-3 does not fold into the predicted KH domain but wraps around the catalytic domain of GLD-2. The picture that emerges from the structural and biochemical data are that GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. The RNA-binding cleft of GLD-2 has distinct structural features compared with the poly(A)-polymerases Pap1 and Trf4. Consistently, GLD-2 has distinct biochemical properties: It displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3′ end. GLD-2 thus appears to have evolved specialized nucleotidyl-transferase properties that match the 3′ end features of dormant cytoplasmic mRNAs. The efficient translation of the vast majority of eukaryotic mRNAs requires the presence of a poly(A) tail. Although the poly(A) tail was originally thought of as a stable modification, it is now clear that it is much more dynamic. Poly(A) tails can be shortened by deadenylases, leading to mRNA decay or translational repression. The short poly(A) tails of translationally inactive mRNAs can also be reextended by cytoplasmic noncanonical poly(A) polymerases, activating their translation. This mechanism of translational control is found predominantly in metazoan oocytes and neurons and is mediated by germ-line development defective (GLD)-2. Here, we report the molecular mechanism with which Caenorhabditis elegans GLD-2 is activated by GLD-3, a homologue of Bicaudal-C, and identify the unusual substrate specificity of this class of noncanonical poly(A) polymerases.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Animals / Binding sites / Biological Sciences / Caenorhabditis elegans / Caenorhabditis elegans - enzymology / Caenorhabditis elegans Proteins - chemistry / Caenorhabditis elegans Proteins - metabolism / Crystallography, X-Ray / Cytoplasm / Cytoplasm - enzymology / cytoplasmic poly(A)-polymerase / cytoplasmic polyadenylation / Gene expression / germ-line maturation / messenger RNA / Models, Molecular / neurons / noncanonical poly(A)-polymerase / oocytes / Pancreatitis-Associated Proteins / Polynucleotide Adenylyltransferase - chemistry / Polynucleotide Adenylyltransferase - metabolism / posttranscriptional regulation / Protein Conformation / Ribonucleic acid / RNA / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - metabolism / substrate specificity / translation (genetics) / Worms