Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1

• Published in: RNA (Cambridge) 2022-04, Vol.28 (4), p.493-507
• Main Authors: Daniels, Peter W, Hama Soor, Taib, Levicky, Quentin, Hettema, Ewald H, Mitchell, Phil
• Format: Article
• Language: English
• Subjects: Endoribonucleases - metabolism; Exoribonucleases - genetics; Exoribonucleases - metabolism; Genetic analysis; Homology; Localization; Nuclease; Nucleotide sequence; Ribonuclease T; RNA processing; RNA Processing, Post-Transcriptional; RNA, Transfer - chemistry; rRNA 5S; Saccharomyces cerevisiae - metabolism; Structure-function relationships; tRNA
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.078939.121

The 3' exonucleolytic processing of stable RNAs is conserved throughout biology. Yeast strains lacking the exoribonuclease Rex1 are defective in the 3' processing of stable RNAs, including 5S rRNA and tRNA. The equivalent RNA processing steps in are carried out by RNase T. Rex1 is larger than RNase T, the catalytic DEDD domain being embedded within uncharacterized amino- and carboxy-terminal regions. Here we report that both amino- and carboxy-terminal regions of Rex1 are essential for its function, as shown by genetic analyses and 5S rRNA profiling. Full-length Rex1, but not mutants lacking amino- or carboxy-terminal regions, accurately processed a 3' extended 5S rRNA substrate. Crosslinking analyses showed that both amino- and carboxy-terminal regions of Rex1 directly contact RNA in vivo. Sequence homology searches identified YFE9 in and SDN5 in as closely related proteins to Rex1. In addition to the DEDD domain, these proteins share a domain, referred to as the RYS ( ex1, FE9 and DN5) domain, that includes elements of both the amino- and caroxy-terminal flanking regions. We also characterize a nuclear localization signal in the amino-terminal region of Rex1. These studies reveal a novel dual domain structure at the core of Rex1-related ribonucleases, wherein the catalytic DEDD domain and the RYS domain are aligned such that they both contact the bound substrate. The domain organization of Rex1 is distinct from that of other previously characterized DEDD family nucleases and expands the known repertoire of structures for this fundamental family of RNA processing enzymes.