Shane L. Rea, Ph.D.
My laboratory utilizes the nematode Caenorhabditis elegans (Figure 1) as a facile model organism to help us understand the fundamental mechanisms of aging and mitochondrial dysfunction in humans (Rea et al., 2010). Research spanning three decades has revealed that nematode lifespan is controlled by a roughly equal mix of genetics, environment and random factors. The genetic toolbox of C. elegans is extensive (http://www.wormbook.org/) and many genes in worms are now known that influence lifespan (http://genomics.senescence.info/species/). Likewise, the ability to culture hundreds of thousands of genetically identical individuals in controlled environments has permitted identification of multiple environmental factors that influence aging. Such approaches have also provided insight into “random” aging factors, intractable in most other organisms (Rea et al., 2005).
The primary focus of my group is on a class of long-lived C. elegans called the Mitochondrial (Mit) mutants (Rea and Johnson, 2003; Rea, 2005). These animals contain one of several mutations in their mitochondrial electron transport chain (ETC) that paradoxically lengthen life (Figure 2). Life extension following ETC disruption has also been observed in other species, including mice (Dell'Agnello et al., 2007). We aim to understand precisely how such life extension unfolds in Mit mutants.
My group recently employed gas-chromatography-mass spectrometry (GC-MS) to map the exometabolome of long-lived mitochondrial mutants (Butler et al., 2012). The exometabolome represents all those metabolites that pass out of cells into the environment and is distinct from intestinal waste products. From the composition of the exometabolome we reconstructed the metabolism active inside Mit mutants. From these studies we made two important findings: (i) three, highly conserved, a-ketoacid dehydrogenase enzymes of intermediary metabolism are central to the Mit mutant metabolome (namely, branched-chain ketoacid dehydrogenase, pyruvate dehydrogenase and a-ketoglutarate dehydrogenase) (Figure 3) (Butler et al., 2013); (ii) Mit mutants.
uniquely generate several metabolic end products that can act as signaling molecules in their own right (Figure 4) (Mishur, Khan, et al. submitted). In fact, these latter molecules are closely related to another group of signaling molecules in humans called oncometabolites that target enzymes belonging to the a-ketoglutarate-dependent hydroxylase family and are involved in the etiology of some cancers (Xu et al., 2011). Currently we are using a variety of techniques that span chemistry, biochemistry and genetics, to explore how a-ketoacid dehydrogenases and the unique metabolic profile of Mit mutants lead to their life extension. We are actively pursuing members of the large a-ketoglutarate-dependent hydroxylase family, since these proteins control a diverse range of processes including epigenetic programing, response to hypoxia and nucleic acid repair (McDonough et al., 2010), all of which are processes known to be involved in the life extension of Mit mutants.
A second area of research related to longevity specification in Mit mutants that we have been actively pursing involves the role of DNA damage response (DDR) proteins. We previously found that p53 is activated in Mit mutants and that it is involved in the longevity specification of these animals (Ventura et al., 2009). Surprisingly, we have found no evidence for nDNA damage in Mit mutants. Instead, in our most recent work we have discovered that changes in transcriptional activity underlie DDR activation and indeed, quite unexpectedly, discovered that DDR activation ultimately impinges on cytoplasmic ribosomal activity to limit animal growth rate and lifespan. We have essentially uncovered the elements of an exciting new mitochondrial-nucleus-ribosome signaling axis that acts to dictate length of life and we are now actively exploring this line of investigation.
More recently my group has been using systems biology tools in a novel approach to understand mechanisms of cellular aging. We have focused on the single-celled yeast Saccharomyces cerevisiae. We have been exploiting in silico metabolic models that were originally developed by the chemical engineering field to predict global metabolic configurations that are associated with increased replicative lifespan in S. cerevisiae (which is the equivalent of extended lifespan in higher organisms). These models contain several hundred genes and over a thousand individual reactions. We have mapped real-world lifespan data onto these models and in our first set of modeling experiments we were able to account for 30% of the variance observed in lifespan. This is an incredible finding because it implies that metabolic configuration, per se, is responsible for a large fraction of the differences seen in lifespan between individual yeast.
Butler, J.A., Mishur, R.J., Bhaskaran, S., and Rea, S.L. (2013). A metabolic signature for long life in the Caenorhabditis elegans Mit mutants. Aging Cell 12, 130-138.
Butler, J.A., Mishur, R.J., Bokov, A.F., Hakala, K.W., Weintraub, S.T., and Rea, S.L. (2012). Profiling the Anaerobic Response of C. elegans Using GC-MS. PLoS ONE 7, e46140.
Dell'Agnello, C., Leo, S., Agostino, A., Szabadkai, G., Tiveron, C., Zulian, A., Prelle, A., Roubertoux, P., Rizzuto, R., and Zeviani, M. (2007). Increased longevity and refractoriness to Ca2+-dependent neurodegeneration in Surf1 knockout mice. Hum Mol Genet 16, 431-444.
McDonough, M.A., Loenarz, C., Chowdhury, R., Clifton, I.J., and Schofield, C.J. (2010). Structural studies on human 2-oxoglutarate dependent oxygenases. Current opinion in structural biology 20, 659-672.
Rea, S., and Johnson, T.E. (2003). A metabolic model for life span determination in Caenorhabditis elegans. Dev Cell 5, 197-203.
Rea, S.L. (2005). Metabolism in the Caenorhabditis elegans Mit mutants. Experimental Gerontology 40, 841-849.
Rea, S.L., Graham, B.H., Nakamaru-Ogiso, E., Kar, A., and Falk, M.J. (2010). Bacteria, yeast, worms, and flies: Exploiting simple model organisms to investigate human mitochondrial diseases. Developmental Disabilities Research Reviews 16, 200-218.
Rea, S.L., Wu, D., Cypser, J.R., Vaupel, J.W., and Johnson, T.E. (2005). A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans. Nat Genet 37, 894-898.
Ventura, N., Rea, S.L., Schiavi, A., Torgovnick, A., Testi, R., and Johnson, T.E. (2009). p53/CEP-1 increases or decreases lifespan, depending on level of mitochondrial bioenergetic stress. Aging Cell 8, 380-393.
Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.H., Ito, S., Yang, C., Xiao, M.T., Liu, L.X., et al. (2011). Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of alpha-Ketoglutarate-Dependent Dioxygenases. Cancer Cell 19, 17-30.
Maruf Khan, Ph.D.
Bhaskaran, S., Butler, J.A., Becerra, S., Fassio, V., Girotti, M., and Rea, S.L. (2011). Breaking Caenorhabditis elegans the easy way using the Balch homogenizer: An old tool for a new application. Analytical Biochemistry.