Conserved domains and structural motifs that differentiate closely related Rex1 and Rex3 DEDDh Exoribonuclease families are required for their function in yeast

Abstract

The DEDD family of exonucleases has expanded through evolution whilst retaining a well conserved catalytic domain. One subgroup of DEDD exoribonucleases with very closely related catalytic domain sequences includes the yeast enzymes Rex1 (RNA exonuclease 1) and Rex3, the metazoan REXO1 (RNA exonuclease 1 homologue) and Rexo5 proteins, and the plant protein Sdn5 (small RNA degrading nuclease). Comparison of Alphafold models for these proteins reveals that Rex1, Rexo5 and Sdn5 are structural homologues, consisting of a central catalytic domain inserted within a discontinuous alkaline phosphatase (AlkP) domain. The core AlkP domain of Rex1-related proteins contains distinct surface insertions in different eukaryotic lineages. Yeast Rex1 contains three loops that are modelled to be directed towards the DEDD domain, one of which forms an extended helical arch that is conserved across fungi and plants but absent in metazoan homologues. We show that the arch and an adjacent loop are required for Rex1-mediated processing of 5S rRNA and tRNA in Saccharomyces cerevisiae. Rex3 structural homologues, including REXO1, contain a KIX domain (CREB kinase-inducible domain (KID) interacting domain) and a cysteine- and histidine-rich domain (CHORD) adjacent to a C-terminal DEDD domain. In contrast to Rex1, Rex3 proteins are found in metazoans and fungi but not in plants or algae. Deletion of the KIX domain within yeast Rex3 blocked its function in RNase MRP processing. Taken together, this work identifies evolutionarily conserved structural hallmarks of Rex1 and Rex3 enzymes and demonstrates that these features are required for Rex1- and Rex3-mediated RNA processing pathways in vivo.