Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

Aleksandra Pajak; Isabelle Laine; Paula Clemente; Najla El-Fissi; Florian A Schober; Camilla Maffezzini; Javier Calvo-Garrido; Rolf Wibom; Roberta Filograna; Ashish Dhir; Anna Wedell; Christoph Freyer; Anna Wredenberg

doi:10.1371/journal.pgen.1008240

Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo

PLoS Genet. 2019 Jul 31;15(7):e1008240. doi: 10.1371/journal.pgen.1008240. eCollection 2019 Jul.

Authors

Aleksandra Pajak^{1

2}, Isabelle Laine^{1

2}, Paula Clemente^{1

2}, Najla El-Fissi^{1

2}, Florian A Schober^{2

3}, Camilla Maffezzini^{1

2}, Javier Calvo-Garrido^{2

3}, Rolf Wibom^{1

4}, Roberta Filograna^{1

2}, Ashish Dhir⁵, Anna Wedell^{2

3

4}, Christoph Freyer^{1

2

4}, Anna Wredenberg^{1

2

4}

Affiliations

¹ Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
² Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
³ Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
⁴ Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
⁵ Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.

Abstract

The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood. Additionally, upstream processes, such as transcript maturation, have been linked to some of these factors, suggesting either dual roles or tightly interconnected mechanisms of mitochondrial RNA metabolism. To get a better understanding of the turn-over of mitochondrial RNAs in vivo, we manipulated the mitochondrial mRNA degrading complex in Drosophila melanogaster models and studied the molecular consequences. Additionally, we investigated if and how these factors interact with the mitochondrial poly(A) polymerase, MTPAP, as well as with the mitochondrial mRNA stabilising factor, LRPPRC. Our results demonstrate a tight interdependency of mitochondrial mRNA stability, polyadenylation and the removal of antisense RNA. Furthermore, disruption of degradation, as well as polyadenylation, leads to the accumulation of double-stranded RNAs, and their escape out into the cytoplasm is associated with an altered immune-response in flies. Together our results suggest a highly organised and inter-dependable regulation of mitochondrial RNA metabolism with far reaching consequences on cellular physiology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
DEAD-box RNA Helicases / genetics
DEAD-box RNA Helicases / metabolism
DNA-Directed RNA Polymerases / genetics
DNA-Directed RNA Polymerases / metabolism
Drosophila Proteins / genetics
Drosophila Proteins / metabolism*
Drosophila melanogaster / genetics*
Drosophila melanogaster / metabolism
Female
Male
Neoplasm Proteins / genetics
Neoplasm Proteins / metabolism
Polyadenylation
Polyribonucleotide Nucleotidyltransferase / genetics
Polyribonucleotide Nucleotidyltransferase / metabolism
RNA Stability
RNA, Antisense / chemistry
RNA, Antisense / metabolism
RNA, Double-Stranded / chemistry
RNA, Double-Stranded / metabolism
RNA, Mitochondrial / chemistry*
RNA, Mitochondrial / metabolism*

Substances

Drosophila Proteins
Neoplasm Proteins
RNA, Antisense
RNA, Double-Stranded
RNA, Mitochondrial
DNA-Directed RNA Polymerases
Polyribonucleotide Nucleotidyltransferase
DEAD-box RNA Helicases
SUV3 protein, Drosophila

Grants and funding

This study was supported by the Swedish Research Council [AW (VR2016-02179), AWe (VR2016-01082)]; Knut & Alice Wallenberg Foundation [AW and AWe (KAW 2013.0026)). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement n°715009). AW is a Ragnar Söderberg fellow in Medicine (M77/13). Confocal imaging was performed at the Live Cell Imaging unit/Nikon Centre of Excellence, Department of Biosciences and Nutrition, Karolinska Institutet, Sweden, supported by grants from the Knut and Alice Wallenberg Foundation, the Swedish Research Council, the Centre for Innovative Medicine and the Jonasson donation to the School of Technology and Health, Kungliga Tekniska Högskolan, Sweden. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.