Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria

Abstract

The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.

Integrative analysis reveals RNA G-Quadruplexes in UTRs are selectively constrained and enriched for functional associations

“…Indeed, the RNA-binding protein GRSF1 has been shown to bind and promote G4 melting within mitochondrial-transcribed RNAs that, in turn, facilitates their degradasome-mediated decay 23 . In both K562 and HepG2 cells, we observe similar enrichment for GRSF1 binding over 5' and 3' UTR pG4 sequences, leading us to speculate that a similar mechanism may exist to melt pG4 sequences, and promote degradation of their parent RNA transcripts in human cells.…”

“…This analysis revealed enrichment for proteins that have been implicated in RNA G4 binding (GRSF1, FUS), and those that, to our knowledge, have not previously been associated with RNA G4 structures (PRPF4, GTF2F1, and CSTF2T). GRSF1 is a cytoplasmic protein involved in viral mRNA translation, and has recently been shown to play a role in the degradation of G4-containing RNAs in mitochondria 22,23 . Other proteins with significant enrichment for pG4 Table 4).…”

Mitochondrial Gene Expression and Beyond—Novel Aspects of Cellular Physiology

“…While the complex of leucine rich pentatricopeptide repeat containing and SRA stem-loop interacting RNA binding proteins (LRPPRC-SLIRP complex) was suggested to suppress the degradosome-mediated decay of mitochondrial protein-coding RNAs [102]. G-rich RNA sequence binding factor 1 (GRSF1) was recently found to enhance the degradosome activity towards mtRNAs containing a G-quadruplex (G4), which are mostly non-coding mtRNAs [106].…”

“…It was postulated that GRSF1 participates in the initial stages of polycistronic mtRNA precursor processing [116] and in the translation of some mt-mRNAs [115]. Recent findings, however, reported that GRSF1 takes part in the RNA surveillance pathway, showing that GRSF1 cooperates with the mitochondrial degradosome to regulate mtRNAs that contain G4s [106]. Vertebrates' mitochondrial genomes have exceptional GC skews, i.e., high guanine content on one strand.…”

“…Since G4s are stable, their presence in RNA can hinder its degradation; nevertheless, steady-state levels of mt-ncRNAs that can form G4s are extremely low. GRSF1 was found to positively regulate the degradosome-dependent decay of G4-containing mitochondrial non-coding transcripts by binding and melting G4 structures, which in turn facilitates their degradation [106,117].…”