The fitness of an organism lies in its ability to adapt to the ever-changing and challenging environment. Failure to appropriately respond to different stresses and maintain homeostasis could result in multiple diseases. The Liu lab has broad interests in stress response and homeostatic regulation. In particular, we are interested in the molecular mechanisms that govern cellular and organismal responses to mitochondrial stress (low-energy level) and nutrient scarcity (low-nutrient level). In addition, we are currently active exploring the physiological function and regulation of N6-methyldeoxyadenine (DNA 6mA) in stress responses.

During the past five years, we study mitochondrial stress and contribute at three levels: 1) Molecular level: we reported the coupling of mitochondrial stress response with immune response, finished a genome-wide RNAi screen in C. elegans and reported the essential function of mevalonate and ceramide signaling, and SUMO peptidase ULP-4 in mitochondrial unfolded protein response; 2) Tissue level: we found that neuropeptide FLP-2 is required to mediate cell non-autonomous mitochondrial stress response initiated in the nervous system; 3) Organism level: we reported that histone H3K4me3 and DNA 6mA methylation mediate transgenerational inheritance of mitochondrial stress adaptation. (Nature 2014; Cell Research 2016; Nature Cell Biology 2018; eLife 2019)

For nutrient scarcity response, we also combine the power of worm genetics, cell biology and biochemistry, and reported that 1) CUL3-RBX1-KLHL22 functions as ubiquitin E3 ligase to mediate responses to amino acids levels; 2) Metformin extends C. elegans lifespan through lysosome-mediated coordination of TORC1 and AMPK pathways. (eLife 2017; Nature 2018)

Mitochondrial Stress Response

Mitochondria bear a trace of their bacterial origin but are almost entirely composed of proteins encoded by the nuclear genome. Proper function of mitochondria is often challenged by intrinsic factors such as reactive oxygen species (ROS) and unfolded proteins, or extrinsic stimuli such as pathogens and xenobiotics. Animals respond to mitochondrial stress with the activation of a mitochondrial-to-nuclear communication, known as mitochondrial unfolded protein response (UPRmt) that buffers mitochondrial protein-folding environment and restores the mito-nuclear balance of electron transport chain (ETC) components. UPRmt also elicits global changes to reset metabolic state, and promote animal fitness through immune responses and lifespan extension. Failure to sense or repair damaged mitochondria has been implicated in aging and numerous diseases such as neurodegenerative disorders.

To understand the molecular mechanism of UPRmt, I have finished a genome-wide RNAi screen in the Ruvkun lab to derive strains of C. elegans that are “blind” to mitochondrial perturbation, and therefore did not activate stress reporters such as mitochondrial chaperone reporter hsp-6p::gfp. We identified around fifty genes that are essential for the induction of UPRmt. The initial analysis of the screen hits allowed us to demonstrate the important functions of the mevalonate and ceramide signaling in UPRmt (Liu et al., Nature 2014).

Our lab continued to carry out in-depth studies of other hits from the initial screen, with the hope to delineate the signaling cascade of UPRmt. For instance, ulp-4, an ortholog of human SUMO1 specific peptidase, is one of the hits from our primary screen. We found that during mitochondrial stress, ULP-4 is required to remove SUMO moiety from DVE-1 and ATFS-1, two transcription factors of UPRmt pathway. DeSUMOylation of DVE-1 changes its sub-cellular localization, whereas deSUMOylation of ATFS-1 increases its stability and transcriptional activity. We further showed that ULP-4 is required for UPRmt-mediated innate immunity and lifespan extension (Gao et al., eLife 2019).

Nutrient Scarcity Response

The ability to sense mitochondrial function or nutrient levels, and coordinate their growth and reproduction is crucial for the survival of organisms. Deregulation of these responses have been implicated in many diseases, such as metabolic disorders and cancer.

During nutrient deprivation, animals activate catabolic pathways such as lipophagy and fatty acids oxidation to break down lipids to provide energy for other biological processes. In order to understand how animal sense nutrient scarcity and activate catabolism, we generated reporter strains in C. elegans to fuse the promoter of lipl-3 (a lipase functioning in lipolysis) and acs-2 (an acyl-CoA synthetase functioning in fatty acids beta-oxidation) to green fluorescent protein. We further showed that these two strains could be effectively used as reporters to nutrient levels, which activate GFP signal under fasting condition. We then screened cherry-picked RNAi libraries of kinases, phosphatases, nuclear hormone receptors and transcription factors, likely candidates to transduce starvation signals and engage target genes for defects in GFP reporter activation under nutrient scarcity, or constitutive GFP activation with food supply. We also carried out a cherry-picked RNAi screen to test candidate genes that have been reported to play a role in fat storage, feeding response and lysosomal function. We are carrying out in-depth studies to analyze our screen hits (unpublished).

In addition to C. elegans, we also study responses to nutrient scarcity in mammals. In particular, we focus on mechanisms that allow cells to detect levels of amino acids, major nutrients essential for proper cellular functions. The mechanistic target of rapamycin complex 1 (mTORC1) is a master modulator that responds to fluctuations in amino acids levels. Deregulation of mTORC1 has been linked with metabolic diseases, cancer and ageing. In response to amino acids, mTORC1 is recruited by the Rag GTPases to the lysosome, its site of activation. The GATOR1 complex, consisting of DEPDC5, NPRL3 and NPRL2, displays GAP activity to inactivate Rag GTPases under amino acid-deficient conditions. We found that CUL3-RBX1-KLHL22 functions as ubiquitin E3 ligase to mediate the ubiquitination and degradation of DEPDC5, leading to mTORC1 activation under amino acids-sufficient condition. We also revealed the biological significance of KLHL22 and showed that deficient of KLHL22 promotes C. elegans lifespan and inhibits tumor growth in nude mice (Chen et al., Nature 2018).

N6-methyldeoxyadenine in stress response

The ability to sense mitochondrial function or nutrient levels, and coordinate their growth and reproduction is crucial for the survival of organisms. Deregulation of these responses have been implicated in many diseases, such as metabolic disorders and cancer.

N6-methyldeoxyadenine (6mA), a major type of DNA methylation in bacteria, represents a part of restriction-modification systems to discriminate host genome from invader DNA. With the recent advent of more sensitive detection techniques, 6mA has also been detected in some eukaryotes. However, the physiological function of this epigenetic mark in eukaryotes remains elusive. Heritable changes in DNA 5mC methylation have been associated with transgenerational inheritance of responses to a high-fat diet, thus raising the exciting possibility that 6mA may also be transmitted across generations and serve as a carrier of inheritable information. Using Caenorhabditis elegans as a model, we reported that histone H3K4me3 and DNA 6mA modifications are required for the transmission of mitochondrial stress adaptations to progeny. The global level of 6mA is significantly elevated following mitochondrial perturbation. N6-methyldeoxyadenine marks mitochondrial stress response genes and promotes their transcription to alleviate mitochondrial stress in progeny. These findings suggest that 6mA is a precisely regulated epigenetic mark that modulates stress response and signals transgenerational inheritance in C. elegans (Ma et al., Nature Cell Biology 2018).

We combine worm genetics with biochemistry to identify additional 6mA modifiers or erasers, and hope to understand the physiological function and regulation of these enzymes.