Human Mitochondrial mRNAs Are Stabilized with Polyadenylation Regulated by Mitochondria-specific Poly(A) Polymerase and Polynucleotide Phosphorylase

Abstract

Mammalian mitochondrial (mt) mRNAs have short poly(A) tails at their 3 termini that are post-transcriptionally synthesized by mt poly(A) polymerase (PAP). The polyadenylation of mt mRNAs is known to be a key process needed to create UAA stop codons that are not encoded in mtDNA. In some cases, polyadenylation is required for the tRNA maturation by editing of its 3 terminus. However, little is known about the functional roles the poly(A) tail of mt mRNAs plays in mt translation and RNA turnover. Here we show human mt PAP (hmtPAP) and human polynucleotide phosphorylase (hPNPase) control poly(A) synthesis in human mitochondria. Partial inactivation of hmtPAP by RNA interference using small interfering RNA in HeLa cells resulted in shortened poly(A) tails and decreased steady state levels of some mt mRNAs as well as their translational products. Moreover, knocking down hmtPAP generated markedly defective mt membrane potentials and reduced oxygen consumption. In contrast, knocking down hPNPase showed significantly extended poly(A) tails of mt mRNAs. These results demonstrate that the poly(A) length of human mt mRNAs is controlled by polyadenylation by hmtPAP and deadenylation by hPNPase, and polyadenylation is required for the stability of mt mRNAs.

Genetic aspects of mitochondrial genome evolution

“…The mRNAs are typically polyadenylated (Bobrowicz et al, 2008), although non-poly(A) mRNAs are also detectable ). An interesting feature of mitochondrial mRNAs is that many of the stop codons are complete only by polyadenylation (7 in human, 6 in cod, and at least 4 in fruit fly) so that they completely lack 3'UTRs (Nagaike et al, 2005;Stewart and Beckenbach, 2009). This appears to be a very frequent phenomenon without a distinctive phylogenetic distribution according to the RefSeq annotation.…”

Population-level expression variability of mitochondrial DNA-encoded genes in humans

“…To simultaneously estimate the expression of mtDNA and nuclear genes, in the present study we revisited published RNA-seq data 8,9 that included a large number of polyadenylated [10][11][12][13] mitochondrial transcripts. We quantified between-individual variation in the expression of mtDNA genes in HapMap samples of European (CEU) and African (YRI) ancestry to evaluate this variation at the population level.…”

Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3′ tails in Trypanosoma brucei mitochondria

“…Instead, an encoded dodecamer sequence regulates RNA stability in this system (10). In human mitochondria, it appears that polyadenylation positively or negatively regulates steady-state levels of mitochondrial mRNAs in a transcript-specific manner (11)(12)(13).…”

“…Recently, a new class of PAPs was described in several eukaryotes. Members of this class include Cid1p and Cid13p in the fission yeast Schizosaccharomyces pombe (29,30), GLD-2 in Caenorhabditis elegans (31), and hmtPAP in human mitochondria (11,12). Members of this novel PAP family diverge from canonical PAPs, exhibiting relatively low homology within the catalytic domain.…”

“…Indeed, Wang et al have reported that in C. elegans, an RNA-binding protein termed GLD-3 binds to and stimulates the polyadenylation activity of GLD-2 (31). Another member of the novel PAP family, hmtPAP, has been shown to be the bona fide mitochondrial PAP in humans (11,12). Mitochondria from cells in which hmtPAP expression was downregulated by RNA interference (RNAi) showed decreased poly(A) tail lengths.…”