Identifier: R-HSA-9836573
Compartment:
mitochondrial matrix
The human mitochondrial genome encodes two rRNAs, 22 tRNAs, and 13 proteins. The mitochondrial genome is transcribed from two divergent promoters into two large precursor RNAs, one from each strand, that are endonucleolytically processed into individual mRNAs, tRNAs, and rRNAs (Mercer et al. 2011, reviewed in Barchiesi and Vascotto 2019, Jedynak-Slyvka et al. 2021, Rackham and Filipovska 2022). Heavy strand (H-strand) DNA is significantly more G-rich than light strand (L-strand) DNA. Transcripts from the H-strand encode eight monocistronic mRNAs, two bicistronic mRNAs (MT-ATP8/6 and MT-ND4L/4), 14 tRNAs, and two rRNAs. Transcripts from the L‑strand encode only one mRNA (MT‑ND6), one long non-coding RNA (lncRNA), lncND6, which is antisense to MT-ND6, and eight tRNAs, and two long non-coding RNAs designated as lncND5, and lncCyt b RNA that are antisense to the coding mRNAs MT-ND5 and MT-CYB (CYTB, MT-Cytb) (Rackham et al. 2011). The L-strand and H-strand transcripts are complementary and, therefore, have the potential to form large double-stranded RNAs (dsRNAs), yet very little dsRNA is observed in wild-type mitochondria.
Both dsRNAs and normal mRNAs, tRNAs, and rRNAs are hydrolyzed by the SUPV3L1:PNPT1 complex, called the degradosome, which is located mostly in mitochondrial RNA granules (MRGs) adjacent to the DNA-containing nucleoid (reviewed in Borowski et al. 2010, Rorbach and Minczuk 2012, Kotrys and Szczesny 2019, Rackham and Filipovska 2022). Degradation appears to occur in subregions of MRGs called D-foci (Borowski et al. 2013, Van Haute et al. 2015). SUPV3L1 is a helicase that unwinds double-stranded RNA (Shu et al. 2004, Wang et al. 2009, Dhir et al. 2018, Jain et al. 2022) to provide single-stranded substrate to the PNPT1 exonuclease (Wang et al. 2009, Lin et al. 2012). Additionally, G quadruplex structures in a subset of RNAs are unwound by GRSF1 to provide substrates to the SUPV3L1:PNPT1 complex (Antonicka et al. 2013, Pietras et al. 2018). However, other RNAs are stabilized by GRSF1 (Antonicka et al. 2013). The PNPT1 3'-5' exonuclease hydrolyzes RNAs to yield 4-5 nucleotide "nanoRNAs" which are further hydrolyzed to mononucleotides by the REXO2 dimer (Bruni et al. 2013, Szewczyk et al. 2020).
Degradation of mitochondrial RNAs is regulated by RNA-binding proteins: FASTK, FASTKD1-5, and the SLIRP:LRPPRC complex (Sasarman et al. 2010, Chujo et al. 2021, Ruzzenente et al. 2012, Jourdain et al. 2017, Siira et al. 2017, reviewed in Rackham and Filipovska 2022). SLIRP:LRPPRC binds throughout the mitochondrial transcriptome, including 12S rRNA, 16S rRNA, and 13 mRNAs, and acts to stabilize RNA structures, inhibit hybridization of complementary RNAs, and extend the half-lives of RNAs (Sasarman et al. 2010, Chujo et al. 2012, Siira et al. 2017). Fas-activated serine/threonine kinase (FASTK) and its homologs FASTKD1-5 bind particular mitochondrial RNAs and affect their stability and processing (reviewed in Jourdain et al. 2017, Rackham and Filipovska 2022).