Project 1: A laboratory test of evolutionary aging theories
Our high‐throughput chemical genetic screen of chemical compounds from several commercial libraries has revealed that lithocholic bile acid (LCA), and some other bile acids, can slow yeast chronological aging [Aging 2010; 2:393-414]. The robust geroprotective effect of exogenously added LCA is due to its ability to enter chronologically aging yeast cells, be sorted to both mitochondrial membranes and alter mitochondrial lipidome [Aging 2013; 5:551-574]. This elicits considerable changes in mitochondrial morphology and functionality, thus allowing mitochondria to operate as a signaling platform that institutes and maintains an aging-delaying pattern of the entire cell [Cell Cycle 2015; 14:1643-1656].
LCA and other bile acids are mildly toxic molecules that cause a so-called ″hormetic″ stress response in animals; because bile acids elicit chemical hormesis, they act as endobiotic geroprotective regulators that can delay the onset and slow the progression of animal aging [Cell Metab 2008; 7:200-203]. Yeast cells do not synthesize LCA and other bile acids found in animals [Aging 2010; 2:461-470]. To explain how these natural molecules can delay yeast chronological aging, we proposed a hypothesis of the hormetic selective forces driving the evolution of longevity regulation mechanisms within ecosystems [Aging 2010; 2:461-470]. This hypothesis posits that after animals inhabiting an ecosystem release bile acids into the environment, these mildly toxic chemicals may create hormetic selective force that drives the evolution of certain protective mechanisms in yeast within this ecosystem. These mechanisms protect yeast against bile acid-induced cellular damage [Aging 2010; 2:461-470]. Our hypothesis further suggests that some of these mechanisms of protection against broad cellular damage elicited by bile acids can also protect yeast against damage and stress accumulated purely with age. Therefore, those yeast species that have developed such longevity regulation mechanisms are expected to live longer [Aging 2010; 2:461-470].
As a laboratory test of this hypothesis, we conducted a multistep selection of long-lived yeast species by a lasting exposure of yeast cells to different concentrations of exogenously added LCA [Front Genet. 2016; 7:216]. This test yielded twenty long-lived yeast mutants, three of which were capable of maintaining their considerably prolonged chronological lifespans after numerous passages in medium without LCA [Front Genet. 2016; 7:216]. Our genetic analyses have revealed that the extended longevity of each of the three selected long-lived yeast mutants was a polygenic genetic trait caused by mutations in more than two nuclear genes [Front Genet. 2016; 7:216]. In further support of the hypothesis on hormetic selective forces driving the ecosystemic evolution of longevity regulation mechanisms, none of the yeast cells that were not exposed to exogenous bile acids had chronological lifespan above a species-specific age [Front Genet. 2016; 7:216]. Thus, unlike yeast cells exposed to exogenous LCA, yeast cells that were not subjected to such exposure were unable to develop mechanisms of protection against age-related damage and to live longer [Front Genet. 2016; 7:216].
We then used the selected long-lived yeast mutants for a laboratory test of evolutionary theories of programmed or non-programmed aging [Aging 2016; 8:2568-2589]. Programmed aging theories assume that all organisms have evolved certain active mechanisms for limiting their lifespans at a species-specific age, whereas non-programmed aging theories postulate that such mechanisms cannot exist because organismal lifespan is limited at a species-specific age due to the lack of any evolutionary force [Aging 2016; 8:2568-2589]. In support of programmed aging theories, we found that the dominant polygenic trait increasing the chronological lifespan of each of the three selected long-lived mutants 1) does not alter the key features of early-life fitness, including the exponential growth rate, efficiency of post-exponential growth and fecundity; 2) enhances other key features of early-life fitness by increasing cell resistance to chronic exogenous stresses and by decreasing cell susceptibility to exogenously induced modes of programmed death; and 3) lowers the relative fitness of the mutant strain in direct competition with the parental wild-type strain exhibiting shorter lifespan, thus being forced out of the ecosystem by the strain whose lifespan is limited at a species-specific age [Aging 2016; 8:2568-2589].
In sum, our laboratory test of evolutionary aging theories provided evidence that yeast cells have evolved some active mechanisms for limiting their lifespan upon reaching a certain chronological age. Furthermore, it seems that these mechanisms can drive the evolution of yeast longevity towards maintaining a finite yeast lifespan within ecosystems. One could hypothesize that these mechanisms may involve the ability of the parental wild-type strain to secrete into growth medium certain compounds (small molecules and/or proteins) capable of inhibiting growth or even killing long-lived yeast mutants. Because these compounds may be responsible for the maintenance of a finite yeast lifespan within ecosystems, it would be important to identify them.
Project 2: Mechanism of liponecrosis, a distinct mode of programmed cell death
We identified a form of cell death called ″liponecrosis″ [Cell Cycle 2014; 13:138-147]. It can be elicited by an exposure of the yeast Saccharomyces cerevisiae to exogenous palmitoleic acid (POA). Our data imply that liponecrosis is 1) a programmed, regulated form of cell death rather than an accidental, unregulated cellular process; and 2) an age-related form of cell death. Cells committed to liponecrotic death: 1) do not exhibit features characteristic of apoptotic cell death; 2) do not display plasma membrane rupture, a hallmark of programmed necrotic cell death; 3) akin to cells committed to necrotic cell death, exhibit an increased permeability of the plasma membrane for propidium iodide; 4) do not display excessive cytoplasmic vacuolization, a hallmark of autophagic cell death; 5) akin to cells committed to autophagic death, exhibit a non-selective en masse degradation of cellular organelles and require the cytosolic serine/threonine protein kinase Atg1p for executing the death program; and 6) display a hallmark feature that has not been reported for any of the currently known cell death modalities – namely, an excessive accumulation of lipid droplets where non-esterified fatty acids (including POA) are deposited in the form of neutral lipids. We therefore concluded that liponecrotic cell death subroutine differs from the currently known subroutines of programmed cell death (PCD). Our data suggest a hypothesis that liponecrosis is a cell death module dynamically integrated into a so-called PCD network, which also includes the apoptotic, necrotic and autophagic modules of PCD [Cell Cycle 2014; 13:138-147].
Our recent study has revealed the following mechanism for liponecrotic PCD [Cell Cycle 2014; 13:3707-3726]. Exogenously added POA is incorporated into POA-containing phospholipids that then amass in the endoplasmic reticulum membrane, mitochondrial membranes and the plasma membrane. The buildup of the POA-containing phospholipids in the plasma membrane reduces the level of phosphatidylethanolamine in its extracellular leaflet, thereby increasing plasma membrane permeability for small molecules and committing yeast to liponecrotic PCD. The excessive accumulation of POA-containing phospholipids in mitochondrial membranes impairs mitochondrial functionality and causes the excessive production of reactive oxygen species in mitochondria. The resulting rise in cellular reactive oxygen species above a critical level contributes to the commitment of yeast to liponecrotic PCD by: 1) oxidatively damaging numerous cellular organelles, thereby triggering their massive macroautophagic degradation; and 2) oxidatively damaging various cellular proteins, thus impairing cellular proteostasis. Several cellular processes in yeast exposed to POA can protect cells from liponecrosis. They include: 1) POA oxidation in peroxisomes, which reduces the flow of POA into phospholipid synthesis pathways; 2) POA incorporation into neutral lipids, which prevents the excessive accumulation of POA-containing phospholipids in cellular membranes; 3) mitophagy, a selective macroautophagic degradation of dysfunctional mitochondria, which sustains a population of functional mitochondria needed for POA incorporation into neutral lipids; and 4) a degradation of damaged, dysfunctional and aggregated cytosolic proteins, which enables the maintenance of cellular proteostasis.
In the future, it would be important to explore a mechanism through which the observed depletion of phosphatidylethanolamine in the outer (extracellular) leaflet of the plasma membrane enclosing yeast cells exposed to POA elevates the permeability of this cellular membrane for small molecules, thereby committing yeast to liponecrotic PCD. Another challenge for the future will be to define mechanisms by which the observed buildup of POA-containing phospholipids in both mitochondrial membranes of yeast cells exposed to POA alters such vital mitochondrial processes as respiration, membrane potential maintenance, ATP synthesis and reactive oxygen species production – thus contributing to the commitment of yeast to liponecrotic PCD. Moreover, it would be interesting to establish the identities of numerous oxidatively damaged and aggregated proteins that accumulate in yeast cells exposed to POA and to explore a pro-survival mechanism underlying the degradation of these proteins in a Yca1p (metacaspase)- and Nma111p-dependent manner.
Project 3: Mitochondria operate as signaling platforms in yeast aging
Mitochondria are vital to physiology and health of eukaryotic organisms across phyla. These organelles generate the majority of cellular ATP and create biosynthetic intermediates for amino acids, nucleotides and lipids [Cell 2012; 148:1145-1159]. Mitochondria can also operate as signaling platforms and structural scaffolds for coordinating diverse cellular responses to changes in a variety of physiological conditions [BMC Biol 2014; 12:34; Int J Mol Sci 2015; 16:5528-5554]. Therefore, the functional state of mitochondria is crucial for a plethora of cellular processes, including cell growth, division, differentiation, homeostasis, metabolism, stress response, signaling, immune response, survival and death [Cell 2012; 148:1145-1159; BMC Biol 2014; 12:34; Int J Mol Sci 2015; 16:5528-5554; Genes Dev 2013; 27:2615-2627]. Because mitochondrial functionality gradually declines with age in evolutionarily distant organisms, such age-related deterioration of mitochondrial function is regarded as the universal hallmark of cellular and organismal aging [Cell 2013; 153:1194-1217]. The budding yeast Saccharomyces cerevisiae, a unicellular eukaryote, has been intensively used as a model organism for uncovering mechanisms linking mitochondrial functionality and cellular aging [Int J Mol Sci 2015; 16:5528-5554].
Our recent studies have revealed how a geroprotective chemical compound delays yeast chronological aging by causing an age-related remodeling of mitochondrial lipidome [Aging 2013; 5: 551-574], how such remodeling elicits changes to mitochondrial morphology and functionality [Aging 2013; 5: 551-574], and how such changes enable mitochondria to operate as signaling platforms that exploit a distinct set of transcription factors to choreograph a longevity-extending transcriptional program for many nuclear genes [Cell Cycle 2015; 14:1643-1656]. We found that exogenously added lithocholic bile acid (LCA), which is known to slow the chronological aging of S. cerevisiae, enters yeast cell, amasses within a double membrane delimiting mitochondria and resides primarily in the inner mitochondrial membrane [Aging 2013; 5: 551-574]. After being confined to mitochondrial membranes, LCA elicits specific changes in the concentrations of mitochondrial membrane phospholipids; these changes occur in an age-related fashion and are believed to be due to a characteristic remodeling of pathways for phospholipid synthesis and movement within both mitochondrial membranes [Aging 2013; 5: 551-574]. The resulting major changes in mitochondrial membrane lipidome cause a substantial enlargement of mitochondria, decrease the number of these organelles, significantly increase the total length on mitochondrial cristae, and reduce the extent of connectivity between these cristae and the inner mitochondrial membrane [Aging 2013; 5: 551-574]. These extensive alterations in mitochondrial abundance and morphology incite a distinct pattern of changes in the age-related chronology of such key longevity-defining processes as mitochondrial respiration, membrane potential maintenance, ATP synthesis and reactive oxygen species homeostasis [Aging 2013; 5: 551-574]. Such specific changes to the age-related chronology of mitochondrial functionality allow mitochondria to function as signaling platforms that coordinate a stepwise establishment of a distinct transcriptional program for many nuclear genes [Cell Cycle 2015; 14:1643-1656]. The observed age-related rewiring of transcriptional patterns is choreographed by a distinct set of transcription factors [Cell Cycle 2015; 14:1643-1656]. These transcription factors respond to different aspects of altered mitochondrial functionality in yeast cells exposed to LCA; they include the following regulators of transcription: 1) the Rtg1, Rtg2 and Rtg3 protein components of the mitochondrial retrograde signaling pathway; 2) the Sfp1 protein component of the mitochondrial back-signaling pathway; 3) the Aft1 transcription factor modulated by the concentrations of iron-sulfur clusters, which function as inorganic cofactors of numerous mitochondrial, nuclear and cytosolic proteins; 4) a transcription factor involved in the unfolded protein response pathway of mitochondria-to-nucleus communications; this pathway is elicited in response to reduced concentrations of the mitochondrial protease Yme1 and the mitochondrial peptide exporter Mdl1; and 5) the transcription factors Yap1, Msn2/Msn4, Skn7 and Hog1, all modulated by mitochondrially generated reactive oxygen species [Cell Cycle 2015; 14:1643-1656]. Based on these observations, we proposed a model for how LCA-driven changes in mitochondrial proteome and functionality early and late in life of chronologically aging yeast coordinate a stepwise development of an aging-delaying cellular pattern and its maintenance throughout lifespan [Cell Cycle 2015; 14:1643-1656].
Our recent findings provided evidence that 1) LCA initially creates a distinct pro-longevity pattern of mitochondrial lipidome by proportionally decreasing phosphatidylethanolamine and cardiolipin concentrations to maintain equimolar concentrations of these phospholipids, and by increasing phosphatidic acid concentration; 2) this pattern of mitochondrial lipidome allows to establish a specific, aging-delaying pattern of mitochondrial proteome; and 3) this pattern of mitochondrial proteome plays an essential role in creating a distinctive, geroprotective pattern of mitochondrial functionality [Oncotarget 2017; 8:30672-30691].
In sum, we demonstrated that the geroprotective chemical compound LCA can delay the onset and slow the progression of chronological aging in yeast by causing an age-related remodeling of mitochondrial lipidome. Our findings revealed that such remodeling of mitochondrial lipidome alters mitochondrial morphology and functionality, thereby enabling mitochondria to act as signaling platforms that can 1) choreograph a longevity-extending transcriptional program for many nuclear genes governed by a distinct set of transcription factors; and 2) orchestrate a gradual establishment and long-term maintenance of a longevity-extending cellular pattern. Thus, targeting the discovered role of mitochondria as signaling platforms in yeast aging has potential as a novel therapeutic strategy for slowing aging, improving health, attenuating age-related pathologies and delaying the onset of age-related diseases in humans.
Project 4: Discovery of plant extracts that greatly delay yeast chronological aging and have different effects on longevity-defining cellular processes
We discovered six plant extracts that increase yeast chronological lifespan to a significantly greater extent than any of the presently known longevity-extending chemical compounds [Oncotarget 2016; 7:16542-16566]. One of these extracts is the most potent longevity-extending pharmacological intervention yet described. We show that each of the six plant extracts is a geroprotector which delays the onset and decreases the rate of yeast chronological aging by eliciting a hormetic stress response. We also show that each of these extracts has different effects on cellular processes that define longevity in organisms across phyla. These effects include the following: 1) increased mitochondrial respiration and membrane potential; 2) augmented or reduced concentrations of reactive oxygen species; 3) decreased oxidative damage to cellular proteins, membrane lipids, and mitochondrial and nuclear genomes; 4) enhanced cell resistance to oxidative and thermal stresses; and 5) accelerated degradation of neutral lipids deposited in lipid droplets. Our findings provide new insights into mechanisms through which chemicals extracted from certain plants can slow biological aging.
Project 5: Six plant extracts delay yeast chronological aging through different signaling pathways
We discovered six plant extracts that slow yeast chronological aging more efficiently than any chemical compound yet described [Oncotarget 2016; 7:16542-16566]. The rate of aging in yeast is controlled by an evolutionarily conserved network of integrated signaling pathways and protein kinases. We assessed how single-gene-deletion mutations eliminating each of these pathways and kinases affect the aging-delaying efficiencies of the six plant extracts. Our findings imply that these extracts slow aging in the following ways: 1) plant extract 4 decreases the efficiency with which the pro-aging TORC1 pathway inhibits the anti-aging SNF1 pathway; 2) plant extract 5 mitigates two different branches of the pro-aging PKA pathway; 3) plant extract 6 coordinates processes that are not assimilated into the network of presently known signaling pathways/protein kinases; 4) plant extract 8 diminishes the inhibitory action of PKA on SNF1; 5) plant extract 12 intensifies the anti-aging protein kinase Rim15; and 6) plant extract 21 inhibits a form of the pro-aging protein kinase Sch9 that is activated by the pro-aging PKH1/2 pathway [Oncotarget 2016; 7:50845-50863].