Haynes C et al. (2015) J Cell Biol "Cole Haynes: on the trail of mitochondrial dysfunction."

Powell K, Haynes C

[J Cell Biol, 2015]

Baker B M et al. (2010) Aging, Metabolism, Stress, Pathogenesis, and Small RNAs, Madison, WI "The Mitochondrial UPR, a Stress Response to Maintain Organelle Protein Homeostasis and Function"

Baker B M, Haynes C M

[Aging, Metabolism, Stress, Pathogenesis, and Small RNAs, Madison, WI, 2010]

Protein folding in eukaryotic cells is compartmentalized. The load of unfolded proteins confronting the compartment specific machinery of the cytosol, ER and mitochondria varies with cell type, age and physiological state. Signaling pathways that adjust the folding capacity of each organelle to its load of unfolded proteins are collectively referred to as unfolded protein responses (UPR). Dysfunction of these pathways compromises the ability of cells to cope with compartment-specific stress and may contribute to diseases of aging and protein misfolding. Compartment-specific protein folding sensors responsive to chaperone occupancy signal a transcriptional response that selectively upregulates compartment-specific machinery to fold or degrade unfolded/misfolded proteins. Through a genetic screen we have identified several components that make up a signal transduction pathway that regulates expression of mitochondrial chaperone genes. The most upstream component of the UPRmt is a matrix-localized orthologue of the bacterial protease ClpXP, a protease known to play a role in protein quality control. UPRmt signaling occurs as unfolded proteins accumulate beyond the mitochondrial chaperone capacity. The excess unfolded proteins are degraded by ClpXP to prevent the accumulation of deleterious proteins or aggregation. Genetic and biochemical evidence indicate that HAF-1, a mitochondrial-localized ABC transporter contributes to signaling the UPRmt by pumping ClpXP-derived peptides across the mitochondrial inner membrane. We have recently identified a novel bZip transcription factor, ZC376.7, required for mitochondrial chaperone expression, the downstream effector of ClpP-mediated peptide efflux in signaling the UPRmt. These observations are consistent with unfolded protein degradation and peptide efflux in signaling changes in the mitochondrial matrix protein folding state or chaperone occupancy to activate the UPRmt and reestablish homeostasis within the organelle. Furthermore, we have established a role for this pathway in stress resistance to conditions that perturb mitochondrial function and will discuss further its involvement in development and aging. Haynes et al., 2007. ClpP mediates activation of a mitochondrial unfolded protein response in C.elegans. Developmental Cell 13, 467-80. Haynes et al., 2010. The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans. Molecular Cell 26, 529-40.

Soo, Sonja K et al. (2021) MicroPubl Biol

Van Raamsdonk, Jeremy M, Soo, Sonja K

[MicroPubl Biol, 2021]

The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway that promotes cell survival and restores mitochondrial function when mitochondrial health is compromised (Haynes et al. 2013; Jovaisaite et al. 2014; Shpilka and Haynes 2018). While a mitoUPR was first reported in mammalian cells (Zhao et al. 2002), the initial work on the mitoUPR in C. elegans was performed by Yoneda et al. who found that treatment with ethidium bromide, which affects the replication and expression of mitochondrial DNA, increased the expression of the mitochondrial chaperone gene hsp-6 (Yoneda et al. 2004). Based on this observation, they generated hsp-6p::gfp and hsp-60p::gfp reporter strains to further study the mitoUPR. They found that either RNA interference (RNAi) targeting spg-7, the worm homolog of paraplegin, or RNAi targeting other genes encoding mitochondrial proteins resulted in activation of the hsp-6p::gfp and hsp-60p::gfp reporter strains (Yoneda et al. 2004).

Broadley SA et al. (2008) Trends Cell Biol "Mitochondrial stress signaling: a pathway unfolds."

Broadley SA, Hartl FU

[Trends Cell Biol, 2008]

Disruption of protein homeostasis in mitochondria elicits a cellular response, which upregulates mitochondrial chaperones and other factors that serve to remodel the mitochondrial-folding environment. In a recent study, Haynes and colleagues uncovered a novel signal transduction pathway underlying this process. The upstream mitochondrial component of this pathway is an orthologue of Escherichia coli ClpP, which functions in the bacterial heat-shock response. These findings suggest that molecular aspects of stress sensing might be conserved between bacteria and mitochondria.

Berry, Brandon J. et al. (2021) MicroPubl Biol

Wojtovich, Andrew P., Berry, Brandon J., Nieves, Tyrone O.

[MicroPubl Biol, 2021]

Mitochondria are organelles that make ATP by generating a proton gradient across the inner membrane through the action of the electron transport chain (ETC). The gradient is composed of a membrane potential (m) and a concentration gradient (pH). In addition to energy production, mitochondria are recognized as signaling organelles (Chandel 2015), and m powers diverse signaling outputs that mitochondria coordinate. One such signaling response is the mitochondrial unfolded protein response (UPRmt). Some ETC complex components are encoded by mitochondrial or nuclear genes and require coordination between the genomes for proper stoichiometry (Shpilka and Haynes 2018). The UPRmt is a protein homeostasis response that is activated when nuclear and mitochondrial gene expression are not correctly coordinated (Melber and Haynes 2018). When the expression of mitochondrial and nuclear encoded proteins is mismatched, the UPRmt is activated. In C. elegans, the UPRmt is controlled by the transcription factor ATFS-1, which is normally trafficked to mitochondria and degraded. When nuclear:mitochondrial gene expression is perturbed, ATFS-1 is blocked from entering mitochondria and is instead trafficked to the nucleus where a host of chaperones and stress-response genes are activated and transcribed.

Benedetti C et al. (2006) Genetics "Ubiquitin-like protein 5 positively regulates chaperone gene expression in the mitochondrial unfolded protein response."

Yang Y, Haynes C, Ron D, Harding HP, Benedetti C

[Genetics, 2006]

Perturbation of the protein folding environment in the mitochondrial matrix selectively upregulates the expression of nuclear genes encoding mitochondrial chaperones. To identify components of the signal transduction pathway(s) mediating this mitochondrial unfolded protein response (UPRmt) we first isolated a temperature sensitive mutation (zc32) that conditionally activates the UPRmt in C. elegans and subsequently searched for suppressors by systematic inactivation of genes. RNAi of ubl-5, a gene encoding an ubiquitin like protein, suppresses activation of the UPRmt markers hsp-60::gfp and hsp-6::gfp by the zc32 mutation and by other manipulations that promote mitochondrial protein misfolding. ubl-5 (RNAi) inhibits the induction of endogenous mitochondrial chaperone encoding genes hsp-60 and hsp-6 and compromises animals'' ability to cope with mitochondrial stress. Mitochondrial morphology and assembly of multi-subunit mitochondrial complexes of biotinylated proteins are also perturbed in ubl-5(RNAi) worms, indicating that UBL-5 also counteracts physiological levels of mitochondrial stress. Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding.

Osman, Hadley C et al. MicroPubl Biol

Lucanic, Mark, Hall, David, Osman, Hadley C, Sedore, Christine A, Foulger, Anna, Jackson, E Grace, Battistoni, Elena T, Lithgow, Gordon J, Guo, Max, Driscoll, Monica, Phillips, Patrick

[MicroPubl Biol, 2021]

The Caenorhabditis Intervention Testing Program (CITP) is a multi-institutional, National Institute on Aging (NIA)-funded consortium with the goal of identifying compounds that will robustly extend lifespan with reproducible effects across genetically diverse Caenorhabditis species and strains (Lucanic et al., 2017). Compounds are prioritized for testing based on computational prediction for lifespan or healthspan effects (Coleman-Hulbert et al., 2019), predicted or known interactions with documented lifespan-regulating pathways, or previous reports for lifespan or healthspan extension in laboratory animals. In this case, diuron was of interest to CITP based on the report of a positive effect on the lifespan of C. elegans strain TJ1060 (spe-9;fer-15) (Lucanic et al., 2018; personal communication). Diuron (1-(3,4-dichlorophenyl)-3,3-dimethylurea) is an herbicide that inhibits photosynthesis by binding photosystem II (Haynes et al., 2000). Diuron has been previously tested in nematode species for toxicity (Neury-Ormanni et al., 2019) and reproductive effects (Mugova et al., 2018), and in both cases showed detrimental effects at high doses only.

Nhan, J. et al. (2019) International Worm Meeting "Transcriptional redirection of activated SKN-1/NRF2 abates the negative metabolic outcomes of a perceived pathogen infection."

Curran, S., Yen, C.A., Ruter, D., Naresh, N.U., Dalton, H., Pukkila-Worley , R., Haynes, C., Nhan, J., Anderson, S.

[International Worm Meeting, 2019]

Optimal health requires continuous transcriptional fidelity of gene expression. SKN-1/NRF2 is a cytoprotective transcription factor in C. elegans that regulates the expression of cellular defenses during stress, including: nutrient deprivation, redox imbalance, and xenobiotic and pathogen exposure. Constitutive activation of SKN-1 results in pleiotropic outcomes, including shortened lifespan and protective redistribution of somatic fat to the germline. We measured lipid distribution between the soma and germ tissues after manipulation of SKN-1 activity. Modulating the epigenetic landscape refines SKN-1 activity away from innate immunity targets and alleviates negative metabolic outcomes. Similarly, paraquat exposure redirects SKN-1 activity toward oxidative stress responses and away from pathogen response genes, which restores lipid distribution across tissues. Lastly, activating p38 MAPK signaling is sufficient to drive SKN-1-dependent loss of somatic fat. These data reveal a coordination of organismal metabolic homeostasis with pathogen responses and identifies mechanisms for counteracting the pleiotropic consequences of aberrant transcriptional activity.

Haroon, S et al. (2017) International Worm Meeting "A novel model of mtDNA disease uncovers multiple biological pathways that control disease progression."

Haroon, S, Bielas, J, Haynes, C, Ericson, N, Vermulst, M, Fritsch, C, Gidalevitz, T, Li, A

[International Worm Meeting, 2017]

Mutations in the mitochondrial genome (mtDNA) are detrimental to human health since disrupting mitochondrial function disables high-energy consuming cells like neurons and muscle fibers. Mutations in mtDNA accumulated during natural aging or inherited by children lead to diseases characterized by neuromuscular dysfunction. Currently, there are no treatments or cures for mtDNA disease. We want to identify novel therapeutic targets by discovering biological pathways that can be exploited to ameliorate mtDNA disease. In order to accomplish this goal, we are using a new worm model for mtDNA disease that carries an error-prone allele of polg-1, the polymerase that replicates the mitochondrial genome. Remarkably, this model exhibits hallmark features of mtDNA disease in humans, which include mtDNA instability, mitochondrial dysfunction, loss of neuromuscular function and a shortened lifespan. The mimicry of mammalian disease progression in the polg-1 mutant worms make them ideal for discovery experiments. With a small, targeted RNAi screen of 130 genes, the knockdown of 22 genes were identified to rescue mtDNA disease. These genes belong to different biological processes, including the IGF/Insulin signaling (IIS) pathway, mitochondrial unfolded protein response (UPRmt), autophagy and apoptosis. Studies with genetic mutants show that reducing either the IIS pathway and or mitophagy ameliorates mtDNA disease in polg-1 mutant worms by improving mtDNA copy number, mitochondrial function and tissue function. Furthermore, constitutively activating the UPRmt also improves these phenotypes in the polg-1 mutants. Currently, we are further dissecting the IIS pathway by studying the gene expression pattern in wildtype, in single mutants (polg-1, daf-2, daf-16), and in the double mutants (daf-16;polg-1, polg-1;daf-2) to understand the mechanism by which IIS regulates mtDNA disease progression.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.