A Mitochondrial-Derived Peptide Exercises the Nuclear Option

The vast majority of mitochondrial proteins are encoded by nuclear genes, giving the nucleus ultimate control of mitochondrial biogenesis, dynamics, and function. However, in this issue Kim et al., 2018Kim K.H. Son J.M. Benayoun B.A. Lee C. The mitochondrial-encoded peptide MOTS-c translocates to the nucleus to regulate nuclear gene expression in response to metabolic stress.Cell Metab. 2018; 28 (this issue): 516-524Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar demonstrate a reversal of fortune, whereby an mtDNA-encoded peptide, MOTS-c, is targeted to the nucleus to signal changes in gene expression. The vast majority of mitochondrial proteins are encoded by nuclear genes, giving the nucleus ultimate control of mitochondrial biogenesis, dynamics, and function. However, in this issue Kim et al., 2018Kim K.H. Son J.M. Benayoun B.A. Lee C. The mitochondrial-encoded peptide MOTS-c translocates to the nucleus to regulate nuclear gene expression in response to metabolic stress.Cell Metab. 2018; 28 (this issue): 516-524Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar demonstrate a reversal of fortune, whereby an mtDNA-encoded peptide, MOTS-c, is targeted to the nucleus to signal changes in gene expression. The human genome comprises nuclear DNA, half a which is contributed by each parent, and mitochondrial DNA (mtDNA), which is maternally inherited. Mitochondria are complex organelles, containing ∼1,200 proteins, the vast majority of which are encoded by nuclear genes, translated by cytoplasmic ribosomes, and imported into the organelle. The genes for only thirteen oxidative phosphorylation complex subunits are housed by the ∼16.5-kb circular mtDNA. At least, that was the dogma until a host of other mtDNA-encoded peptides were discovered. Though the first of these mitochondrial-derived peptides (MDPs), humanin, was somewhat controversial, there is now solid evidence that mtDNA encodes this and other physiologically active peptides, the list of which continues to grow (Kim et al., 2017Kim S.J. Xiao J. Wan J. Cohen P. Yen K. Mitochondrially derived peptides as novel regulators of metabolism.J. Physiol. 2017; 595: 6613-6621Crossref PubMed Scopus (106) Google Scholar). The activity and stress status of mitochondria is relayed back to the nucleus via "retrograde signaling" pathways to enact changes in gene expression of nucleus-encoded mitochondrial proteins and other factors needed to maintain overall mitochondrial and cellular homeostasis (Quirós et al., 2016Quirós P.M. Mottis A. Auwerx J. Mitonuclear communication in homeostasis and stress.Nat. Rev. Mol. Cell Biol. 2016; 17: 213-226Crossref PubMed Scopus (411) Google Scholar). These pathways are still being defined in mammals, but mitochondrial retrograde stress relays involving altered mitochondrial ATP production, reactive oxygen species (ROS) generation, and unfolded/improperly imported proteins, among others, have been documented (Shadel and Horvath, 2015Shadel G.S. Horvath T.L. Mitochondrial ROS signaling in organismal homeostasis.Cell. 2015; 163: 560-569Abstract Full Text Full Text PDF PubMed Scopus (691) Google Scholar). There is also evidence that certain primarily mitochondria-resident proteins translocate or are dually targeted to the nucleus, some of which are clearly involved in mitochondria-nuclear communication (Lionaki et al., 2016Lionaki E. Gkikas I. Tavernarakis N. Differential protein distribution between the nucleus and mitochondria: implications in aging.Front. Genet. 2016; 7: 162Crossref PubMed Scopus (22) Google Scholar). For example, the mitochondrial enzymes fumarase and pyruvate dehydrogenase have roles in regulating histone modifications. However, Kim et al., 2018Kim K.H. Son J.M. Benayoun B.A. Lee C. The mitochondrial-encoded peptide MOTS-c translocates to the nucleus to regulate nuclear gene expression in response to metabolic stress.Cell Metab. 2018; 28 (this issue): 516-524Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar have apparently discovered a unique twist on retrograde signaling through which the mtDNA-encoded MOTS-c peptide is targeted to the nucleus to directly regulate nuclear gene expression. While confirming that MOTS-c displayed cytoplasmic and mitochondria localization, Kim and colleagues also noticed signs of nuclear localization. Following this lead, the authors showed not only that there is a legitimate pool of MOTS-c in the nucleus basally in HEK293 cells, but also that, when exposed to nutrient starvation or oxidant stress, these cells accumulate more MOTS-c in the nucleus. This was accompanied by a reduction in mitochondrial MOTS-c and required AMP kinase, which was shown previously to be activated downstream of the effects of MOTS-c on one-carbon and purine metabolism (Lee et al., 2015Lee C. Zeng J. Drew B.G. Sallam T. Martin-Montalvo A. Wan J. Kim S.J. Mehta H. Hevener A.L. de Cabo R. Cohen P. The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance.Cell Metab. 2015; 21: 443-454Abstract Full Text Full Text PDF PubMed Scopus (340) Google Scholar). Increased ROS is a common downstream consequence of all the stress conditions tested that led to MOTS-c nuclear localization. Accordingly, nuclear accumulation was inhibited by antioxidant treatment. Thus, it remains unclear if energy stress (i.e., ATP depletion), redox signaling, or both are impinging on AMP kinase to control MOTS-c nuclear import. The authors next focused intently on what MOTS-c is doing in the nucleus in the first place. Here they made the exciting discovery that it interacts both with nuclear DNA regulatory elements and transcription factors. One key node of regulation identified was the activation of genes with antioxidant response elements (AREs), which are binding sites for the major oxidative stress-response transcription factor NRF2, as well as other related factors, ATF1, ATF7, and JUND. Based on co-immunoprecipitation experiments, MOTS-c binds to NRF2 complexes under stress, and in vitro assays show direct binding of the peptide to ARE DNA. Thus, a complex mode of regulation is proposed that involves MOTS-c binding both regulatory DNA elements and a cadre of related transcription factors to fine-tune target gene expression. Though not pursued in earnest by Kim et al., 2018Kim K.H. Son J.M. Benayoun B.A. Lee C. The mitochondrial-encoded peptide MOTS-c translocates to the nucleus to regulate nuclear gene expression in response to metabolic stress.Cell Metab. 2018; 28 (this issue): 516-524Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar, it is noteworthy that MOTS-c apparently has a negative role in regulating transcription factors for immune genes, in particular those that mediate interferon responses. It is interesting to speculate that this is somehow related to recent reports that both mtDNA and mitochondrial double-stranded RNA (dsRNA) activate type-1 interferon signaling responses when released into the cytoplasm (Dhir et al., 2018Dhir A. Dhir S. Borowski L.S. Jimenez L. Teitell M. Rötig A. Crow Y.J. Rice G.I. Duffy D. Tamby C. et al.Mitochondrial double-stranded RNA triggers antiviral signalling in humans.Nature. 2018; 560: 238-242Crossref PubMed Scopus (253) Google Scholar, West et al., 2015West A.P. Khoury-Hanold W. Staron M. Tal M.C. Pineda C.M. Lang S.M. Bestwick M. Duguay B.A. Raimundo N. MacDuff D.A. et al.Mitochondrial DNA stress primes the antiviral innate immune response.Nature. 2015; 520: 553-557Crossref PubMed Scopus (89) Google Scholar). While predicted MDPs have been found in the mitochondrial mRNA genes, it is curious that the rRNA genes seem to be enriched in these (Kim et al., 2017Kim S.J. Xiao J. Wan J. Cohen P. Yen K. Mitochondrially derived peptides as novel regulators of metabolism.J. Physiol. 2017; 595: 6613-6621Crossref PubMed Scopus (106) Google Scholar). This might suggest a role for MDPs in sensing mitochondrial ribosome biogenesis as an indicator of overall mitochondrial health. Other than the oxidative phosphorylation complexes (I, III, IV, and V), mitochondrial ribosomes are the only other entity in mammalian cells that contain products derived from both genomes (ribosomal proteins from the nucleus, two rRNAs from mtDNA). This potentially makes mitochondrial ribosome assembly an ideal sensor that integrates mtDNA and nuclear gene expression, protein import efficiency, and large complex assembly capacity. If so, expression of humanin and MOTS-c (and perhaps other MDPs) from these loci might be part of an intricate mitochondrial stress-sensing mechanism. Coincidentally, in yeast, there is a small peptide, Tar1p, encoded antisense to the nuclear 25S rDNA gene that functions in mitochondria (Bonawitz et al., 2008Bonawitz N.D. Chatenay-Lapointe M. Wearn C.M. Shadel G.S. Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction.Curr. Genet. 2008; 54: 83-94Crossref PubMed Scopus (23) Google Scholar), which might suggest there is also coordination of nucleolar ribosome biogenesis and mitochondria function. MOTS-c, like its predecessor humanin, has now been implicated in many physiological processes that involve a multitude of proposed sites of sites of action, including intracellular, extracellular, and in the general circulation. They both are involved in cellular and systemic metabolic regulation and provide resistance to many stress and disease conditions and hence are of significant therapeutic interest (Kim et al., 2017Kim S.J. Xiao J. Wan J. Cohen P. Yen K. Mitochondrially derived peptides as novel regulators of metabolism.J. Physiol. 2017; 595: 6613-6621Crossref PubMed Scopus (106) Google Scholar, Lee et al., 2016Lee C. Kim K.H. Cohen P. MOTS-c: a novel mitochondrial-derived peptide regulating muscle and fat metabolism.Free Radic. Biol. Med. 2016; 100: 182-187Crossref PubMed Scopus (105) Google Scholar). While research on the cellular and physiological effects of MDPs has taken center stage so far, many questions about the basic biology of MDPs remain. For example, humanin is postulated to exist as two peptides, a truncated one that is translated inside mitochondria (by mitochondrial ribosomes) and the other outside of mitochondria by cytoplasmic ribosomes. MOTS-c, on the other hand, is argued to be translated exclusively in the cytoplasm. Cytoplasmic translation of humanin or MOTS-c would require the release of mitochondrial 16S or 12S rRNA (or fragments thereof) into the cytoplasm, respectively. If and how this is accomplished and regulated remains unclear. If this occurs frequently, how are these mtRNAs not recognized by antiviral immune receptors as recently reported (Dhir et al., 2018Dhir A. Dhir S. Borowski L.S. Jimenez L. Teitell M. Rötig A. Crow Y.J. Rice G.I. Duffy D. Tamby C. et al.Mitochondrial double-stranded RNA triggers antiviral signalling in humans.Nature. 2018; 560: 238-242Crossref PubMed Scopus (253) Google Scholar)? Can 12S and 16S rRNAs be differentially released from mitochondria so that humanin or MOTS-c are produced exclusively by specific cell types or in response to different environmental or physiological stimuli? Or is their production regulated not at the RNA release stage, but at the level of translation, perhaps by post-transcriptional modification (e.g., methylation)? Lastly, as the Kim et al. study nicely points out, where MDPs travel within the cell matters. Even the simple redistribution between mitochondria and the nucleus appears to have wide-ranging effects that are only just now being unraveled. Clearly, MDP biology is a burgeoning field with fertile ground for new investigation. G.S.S. is the Audrey Geisel Chair in Biomedical Science, and this work was supported by NIH R01 AR0698876 and R33 ES025636. The Mitochondrial-Encoded Peptide MOTS-c Translocates to the Nucleus to Regulate Nuclear Gene Expression in Response to Metabolic StressKim et al.Cell MetabolismJuly 5, 2018In BriefThe mitochondrial genome is regulated by factors encoded in the nucleus. Kim et al. now show that, reciprocally, MOTS-c, a mitochondrial-encoded peptide, can dynamically translocate to the nucleus in response to metabolic stress and regulate adaptive nuclear gene expression. Their findings suggest that mitonuclear communication is genetically integrated. Full-Text PDF Open Archive