Metazoan Maelstrom is an RNA-binding protein that has evolved from an ancient nuclease active in protists

Abstract

Piwi-interacting RNAs (piRNAs) guide Piwi argonautes to their transposon targets for silencing. The highly conserved protein Maelstrom is linked to both piRNA biogenesis and effector roles in this pathway. One defining feature of Maelstrom is the predicted MAEL domain of unknown molecular function. Here, we present the first crystal structure of the MAEL domain from Bombyx Maelstrom, which reveals a nuclease fold. The overall architecture resembles that found in Mg 2+ -or Mn 2+ -dependent DEDD nucleases, but a clear distinguishing feature is the presence of a structural Zn 2+ ion coordinated by the conserved ECHC residues. Strikingly, metazoan Maelstrom orthologs across the animal kingdom lack the catalytic DEDD residues, and as we show for Bombyx Maelstrom are inactive as nucleases. However, a MAEL domain-containing protein from amoeba having both sequence motifs (DEDD and ECHC) is robustly active as an exoribonuclease. Finally, we show that the MAEL domain of Bombyx Maelstrom displays a strong affinity for single-stranded RNAs. Our studies suggest that the ancient MAEL nuclease domain evolved to function as an RNA-binding module in metazoan Maelstrom.

MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

“…Diffraction data from crystals of the selenomethionyl derivate of the MAEL domain of B. mori Maelstrom (for crystallization conditions, see Chen et al, 2015) were collected using an X-ray beam of 10 mm in diameter with a flux of $9.5 Â 10 10 photons s À1 at the peak of the Se K absorption edge ( = 0.979 Å ) on beamline ID23-1 at the ESRF. Crystals of this system (20-50 mm in the largest dimension) diffract rather poorly; therefore, in order to increase the data multiplicity to Multi-crystal data collection and SAD structure solution from crystals of thermolysin.…”

“…The first of these, thermolysin, contains one catalytic Zn 2+ ion and three Ca 2+ ions per protein chain (316 residues), producing a theoretical anomalous diffraction ratio (hÁF/F i) of $2% for data collected at the peak of the Zn K absorption edge. The second, the selenomethionyl derivative of the MAEL domain of B. mori Maelstrom (Chen et al, 2015), produces a theoretical anomalous diffraction ratio of 4.0% for data collected at the peak of the Se K absorption edge. However, the crystals of this system diffract rather poorly (see Table 1).…”

The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease

“…This finding suggests that Exu evolved from active exonucleases and lost its catalytic activity along the arthropod stem lineage. Other EXO-domain proteins have been shown to bind RNA 51,55,56 . In particular, Maelstrom has recently been shown to lack canonical EXO activity, and it features a Zn 2+ -binding insertion that plays a functional role in RNA binding and the piwi-interacting-RNA pathway 55,57 .…”

Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster

“…In protists, the MAEL domain was predicted to degrade RNA and may directly destroy nascent transcripts (Zhang et al, 2008a). In insects, the MAEL domain interacts with singlestranded RNA (Chen et al, 2015;Matsumoto et al, 2015); we speculate that fly Mael may have retained a role in destabilizing RNA. In this view, Mael may promote premature termination or degradation of nascent transcripts.…”