Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA

Abstract

RNA decay is a key element of mitochondrial RNA metabolism. To date, the only well-documented machinery that plays a role in mtRNA decay in humans is the complex of polynucleotide phosphorylase (PNPase) and SUV3 helicase, forming the degradosome. REXO2, a homolog of prokaryotic oligoribonucleases present in humans both in mitochondria and the cytoplasm, was earlier shown to be crucial for maintaining mitochondrial homeostasis, but its function in mitochondria has not been fully elucidated. In the present study, we created a cellular model that enables the clear dissection of mitochondrial and non-mitochondrial functions of human REXO2. We identified a novel mitochondrial short RNA, referred to as ncH2, that massively accumulated upon REXO2 silencing. ncH2 degradation occurred independently of the mitochondrial degradosome, strongly supporting the hypothesis that ncH2 is a primary substrate of REXO2. We also investigated the global impact of REXO2 depletion on mtRNA, revealing the importance of the protein for maintaining low steady-state levels of mitochondrial antisense transcripts and double-stranded RNA. Our detailed biochemical and structural studies provide evidence of sequence specificity of the REXO2 oligoribonuclease. We postulate that REXO2 plays dual roles in human mitochondria, ‘scavenging’ nanoRNAs that are produced by the degradosome and clearing short RNAs that are generated by RNA processing.

Human Mitochondrial RNA Processing and Modifications: Overview

“…The final products of PNPase/SUV3-mediated mtRNA degradation are short oligonucleotides that are removed by RNA exonuclease 2 (REXO2) [ 118 ]. REXO2 has 3′ to 5′ oligonuclease activity toward short single-stranded RNAs and DNAs, and its silencing results in the accumulation of short RNA species and double-stranded RNAs [ 119 ]. Furthermore, REXO2 knockout results in the disruption of mitochondrial protein synthesis [ 118 ].…”

“…Furthermore, REXO2 knockout results in the disruption of mitochondrial protein synthesis [ 118 ]. REXO2 activity in mitochondria is considered to enable the recycling of monoribonucleotides and prevent the accumulation of short oligoribonucleotides that could affect degradosome function and stimulate promoter-independent transcription [ 119 , 120 , 121 ].…”

Non-coding RNA Regulated Cross-Talk Between Mitochondria and Other Cellular Compartments

“…In the cytosol, these RNAs engage a MDA5-driven immune signaling pathway that activates a type I interferon response ( Dhir et al, 2018 ). The mitochondrial IMS degradation machinery that restricts the release of mitochondrial dsRNAs could therefore play a vital role in restricting this auto immune response ( Liu et al, 2017 ; Huang et al, 2018 ; Maciej et al, 2020 ). Whether it is also involved in defense against the invasion of RNA viruses remains to be investigated.…”

Loading messenger RNAs onto ribosomes in human mitochondria: lessons learned from a bacterial toxin

“…Mitochondrial degradosome, a complex of RNA helicase SUV3 and ribonuclease PNPase, is involved in mtRNA decay [16]. Products of degradosome‐mediated degradation are removed by REXO2 oligoribonuclease [17]…”

“…Mitochondrial degradosome, a complex of RNA helicase SUV3 and ribonuclease PNPase, is involved in mtRNA decay [16]. Products of degradosome-mediated degradation are removed by REXO2 oligoribonuclease [17] molecule unprotected and prone to degradation. An unresolved issue is whether the LRPPRC/SLIRP complex dissociates from mt-mRNA immediately before translation or whether it is simply displaced from mt-mRNA by the ribosome during translation.…”