Taubert S (2016) Cell Syst "Caenorhabditis elegans Gets Metabolic Network Models."

Taubert S

[Cell Syst, 2016]

Two genome-scale network models for Caenorhabditis elegans offer a powerful new way to delineate context-dependent metabolic activity in the worm.

S Taubert et al. (2004) European Worm Meeting "CHARACTERIZATION OF THE C. ELEGANS NUCLEAR HORMONE RECEPTOR NHR-49"

S Taubert, K Yamamoto, M Van Gilst

[European Worm Meeting, 2004]

Nuclear Hormone receptors (NHRs) are a family of ligand-regulated transcription factors involved in diverse metazoan functions, such as sexual differentiation, organ development, and regulation of metabolism. The C. elegans genome contains over 270 NHR genes, approximately five times as many as the human genome. For most of these no function has been described yet. We focus on characterizing NHR-49, which regulates fat metabolism, and lifespan (Marc van Gilst and Keith R. Yamamoto, unpublished). Interestingly, this mirrors the functions of human Peroxisome-proliferator-activated-receptor a (PPARa), while the sequence of NHR-49 suggests similarity to another human receptor, Hepatocye Nuclear Receptor 4a (HNF4a). Since HNF4a dimerizes via its ligand-binding-domain (LBD), we utilized yeast two-hybrid based technology to assess whether the LBDs of NHR-49 and 12 related HNF4a-like NHRs, can also homodimerize. While several of these LBDs readily dimerized (including NHR-49), some others did not (such as DAF-12). Since the homodimerization of NHR-49's LBD is predicted to occur via two conserved salt-bridges (E5/K55 and E50/R93), we mutated the E50 and K55 residues to alanines. We will present the effect of these mutations on LBD homodimerization and activation of a transcriptional reporter in yeast. In an attempt to identify ligands of NHR-49 we treated worms with clofibrate, a synthetic PPARa ligand used to treat hyperlipidemia. This treatment caused a strong reduction of worm body fat levels, and was accompanied by lethality at higher concentrations. However, similar effects were observed in a strain harboring an NHR-49 deletion, suggesting that the effects of clofibrate are independent of NHR-49. We are currently characterizing changes in the transcriptional program in response to clofibrate treatment.

Taubert S et al. (2008) PLoS Genet "The Mediator subunit MDT-15 confers metabolic adaptation to ingested material."

Yamamoto KR, Hansen M, Taubert S, van Gilst MR, Cooper SB

[PLoS Genet, 2008]

In eukaryotes, RNA polymerase II (Pol(II)) dependent gene expression requires accessory factors termed transcriptional coregulators. One coregulator that universally contributes to Pol(II)-dependent transcription is the Mediator, a multisubunit complex that is targeted by many transcriptional regulatory factors. For example, the Caenorhabditis elegans Mediator subunit MDT-15 confers the regulatory actions of the sterol response element binding protein SBP-1 and the nuclear hormone receptor NHR-49 on fatty acid metabolism. Here, we demonstrate that MDT-15 displays a broader spectrum of activities, and that it integrates metabolic responses to materials ingested by C. elegans. Depletion of MDT-15 protein or mutation of the mdt-15 gene abrogated induction of specific detoxification genes in response to certain xenobiotics or heavy metals, rendering these animals hypersensitive to toxin exposure. Intriguingly, MDT-15 appeared to selectively affect stress responses related to ingestion, as MDT-15 functional defects did not abrogate other stress responses, e.g., thermotolerance. Together with our previous finding that MDT-15:NHR-49 regulatory complexes coordinate a sector of the fasting response, we propose a model whereby MDT-15 integrates several transcriptional regulatory pathways to monitor both the availability and quality of ingested materials, including nutrients and xenobiotic compounds.

Taubert S et al. (2011) Mol Cell Endocrinol "Nuclear hormone receptors in nematodes: evolution and function."

Taubert S, Ward JD, Yamamoto KR

[Mol Cell Endocrinol, 2011]

Nuclear hormone receptors (NHRs) are proteins that regulate gene expression in response to developmental, environmental, and nutritional signals. The activity of some NHRs is selectively and reversibly modulated by small molecular weight compounds. However, for others - termed "orphan" receptors - no such ligands have (yet) been identified, and at least some NHRs may lack natural ligands. NHRs exhibit a stereotyped architecture, with conserved N-terminal DNA-binding domains (DBDs) and more variable C-terminal ligand-binding domains (LBDs). NHRs control the transcription of remarkably diverse and specific gene networks, apparently by integrating multiple regulatory inputs that interact with distinct receptor surfaces; these inputs include small molecule ligands, transcriptional coregulators, and response elements, the genomic sites to which the receptors bind. NHRs comprise an ancient superfamily found in all metazoans, and recent findings have revealed NHR-like regulatory factors in fungi. Here, we consider NHR function and evolution in nematodes, roundworms that inhabit terrestrial, marine, and freshwater habitats; we focus in particular on the well-established experimental organism Caenorhabditis elegans. Interestingly, the C. elegans genome encodes a massively expanded NHR family; we speculate that some of the multiple physiological activities governed by individual mammalian NHRs may be distributed among multiple members of the C. elegans family, potentially focusing and simplifying functional analyses. Accordingly, investigations of relevant NHR cofactors, ligands, and response elements might also prove to be simpler; moreover, the abbreviated intergenic regions of the C. elegans genome will facilitate the assignment of response elements to target genes. Finally, the growing interest in medically relevant nematodes is providing novel insights into the function and evolution of NHRs.

Stefan Taubert et al. (2004) West Coast Worm Meeting "Biochemical Characterization of the C. elegans Nuclear Hormone Receptor NHR-49"

Keith R Yamamoto, Stefan Taubert, Marc Van Gilst

[West Coast Worm Meeting, 2004]

Nuclear Hormone receptors (NHRs) are a family of ligand-regulated transcription factors involved in diverse metazoan functions, such as sexual differentiation, organ development, and regulation of metabolism. The C. elegans genome contains over 270 NHR genes, approximately five times as many as the human genome. For most of these no function has been described yet. We focus on characterizing NHR-49, which regulates fat metabolism, and lifespan (Marc van Gilst and Keith R. Yamamoto, unpublished). Interestingly, this mirrors the functions of human Peroxisome-proliferator-activated-receptor a (PPARalpha), while the sequence of NHR-49 suggests similarity to another human receptor, Hepatocye Nuclear Receptor 4alpha (HNF4alpha). Since HNF4alpha dimerizes via its ligand-binding-domain (LBD), we utilized yeast two-hybrid based technology to assess whether the LBDs of NHR-49 and 12 related HNF4alpha-like NHRs, can also homodimerize. While several of these LBDs readily dimerized (including NHR-49), some others did not (such as DAF-12). Since the homodimerization of NHR-49's LBD is predicted to occur via two conserved salt-bridges (E5/K55 and E50/R93), we mutated the E50 and K55 residues to alanines. We will present the effect of these mutations on LBD homodimerization and activation of a transcriptional reporter in yeast. In an attempt to identify ligands of NHR-49 we treated worms with clofibrate, a synthetic PPARa ligand used to treat hyperlipidemia. This treatment caused a strong reduction of worm body fat levels, and was accompanied by lethality at higher concentrations. However, similar effects were observed in a strain harboring an NHR-49 deletion, suggesting that the effects of clofibrate are independent of NHR-49. We are currently characterizing changes in the transcriptional program in response to clofibrate treatment.

Taubert, Stefan et al. (2009) International Worm Meeting "Transcriptional Regulation by the conserved regulatory complex Mediator in C. elegans."

Taubert, Stefan, Porter, Jess, Blackwell, T. Keith

[International Worm Meeting, 2009]

The multi-subunit complex Mediator is a conserved transcriptional regulatory complex for transcription factors (TFs) such as Nuclear Hormone Receptors (NHRs). Although Mediator is globally required for PolII-dependent transcription, some of its subunits confer specific biological functions. Others and we found that the C. elegans Mediator subunit MDT-15 cooperates with the TFs SBP-1/SREBP [1] and NHR-49 [2] to control certain aspects of lipid biology such as the fasting response, and fatty acid desaturation; through the latter, MDT-15 also impinges on global worm health and life span. Recently, we found that MDT-15 is also involved in systemic detoxification, as mdt-15 depletion or mutation abrogates the induction of (i) Phase II detoxification genes in response to a hydrophobic toxin, (ii) metal responsive genes in response to heavy metals [3], and (iii) genes that respond to oxidative stress (unpublished). As many of these physiological processes are under control of the Insulin/IGF-1 signaling (IIS), we are currently testing whether MDT-15 is involved in IIS signaling, potentially as a cofactor of the IIS target TFs DAF-16 and SKN-1. Thus, we propose that MDT-15 is a key component of a regulatory network that monitors the availability and quality of ingested materials. Moreover, the fact that individual components of the Mediator complex selectively confer regulatory action has prompted us to discover the targets and biological functions of other Mediator subunits such as the Mediator kinase CDK-8. Preliminary data suggest that this protein affects processes such as worm development and host defense. In summary, Mediator is a highly dynamic and versatile regulatory complex that serves to integrate and fine-tune diverse biological processes. 1. Yang et al, 2006, Nature. 2. Taubert et al, 2006, Genes & Development. 3. Taubert et al, 2008, PLoS Genetics.

Stefan Taubert et al. (2007) International Worm Meeting "A conserved C. elegans Mediator subunit, MDT-15, selectively confers stress responses."

Malene Hansen, Stefan Taubert, Marc R. Van Gilst, Keith R. Yamamoto

[International Worm Meeting, 2007]

The conserved multi-subunit complex Mediator is an important transcriptional coregulator for many metazoan Transcription Factors (TFs), including the physiologically relevant Nuclear Hormone Receptors (NHRs). In C. elegans, the Mediator subunit MDT-15 affects energy metabolism, the stress response to fasting, and longevity through the TFs SBP-1 [1] and NHR-49 [2]. In this study, using expression profiling, we found that MDT-15 differentially affected various stress responses in vivo. Depletion of mdt-15 by RNA interference (RNAi), or a mutation within the mdt-15 gene, prevented toxin-induced mRNA accumulation of detoxification genes such as GSTs, UGTs and CYP450s. Consistent with the gene expression data, mdt-15 RNAi causes toxin hypersensitivity. Moreover, Cadmium- and Zinc-induced mRNA accumulation of several metal-responsive genes was also compromised in mdt-15(-) animals. In contrast, MDT-15 depletion caused the opposite effect on heat-shock protein expression: Several HSP genes were overexpressed at ambient temperature, and hyper-induced upon heat-shock. Interestingly, we found that multiple NHRs and other conserved TFs interact with MDT-15 in a yeast-two-hybrid assay. These findings suggest that MDT-15 integrates multiple stress-responsive TFs to modulate gene expression to adjust to adverse physiological conditions. In addition, MDT-15s previously described role in energy metabolism suggests that this protein may link energy homeostasis to systemic detoxification. Finally, the prevalence of intestinal genes among MDT-15 targets implies that MDT-15 is an important functional specifier of gut identity. In summary, our data demonstrate an exciting new function for a specific Mediator subunit as an important physiological integrator in C. elegans, and potentially also in higher metazoans. 1.Yang et al, 2006, Nature 442(7103):700-4. 2.Taubert et al., 2006, Genes & Development, 2 0(9):1137-49.

Taubert S et al. (2006) Genes Dev "A Mediator subunit, MDT-15, integrates regulation of fatty acid metabolism by NHR-49-dependent and -independent pathways in C. elegans."

Yamamoto KR, Taubert S, Hansen M, van Gilst MR

[Genes Dev, 2006]

The Caenorhabditis elegans Nuclear Hormone Receptor NHR-49 coordinates expression of fatty acid (FA) metabolic genes during periods of feeding and in response to fasting. Here we report the identification of MDT-15, a subunit of the C. elegans Mediator complex, as an NHR-49-interacting protein and transcriptional coactivator. Knockdown of mdt-15 by RNA interference (RNAi) prevented fasting-induced mRNA accumulation of NHR-49 targets in vivo, and fasting-independent expression of other NHR-49 target genes, including two FA-Delta9-desaturases (fat-5, fat-7). Interestingly, mdt-15 RNAi affected additional FA-metabolism genes (including the third FA-Delta9-desaturase, fat-6) that are regulated independently of NHR-49, suggesting that distinct unidentified regulatory factors also recruit MDT-15 to selectively modulate metabolic gene expression. The deregulation of FA-Delta9-desaturases by knockdown of mdt-15 correlated with dramatically decreased levels of unsaturated FAs and multiple deleterious phenotypes (short life span, sterility, uncoordinated locomotion, and morphological defects). Importantly, dietary addition of specific polyunsaturated FAs partially suppressed these pleiotropic phenotypes. Thus, failure to properly govern FA-Delta9-desaturation contributed to decreased nematode viability. Our findings imply that a single subunit of the Mediator complex, MDT-15, integrates the activities of several distinct regulatory factors to coordinate metabolic and hormonal regulation of FA metabolism.

Stefan Taubert et al. (2005) International Worm Meeting "Characterization of a novel NHR-cofactor interaction pair regulating fatty acid desaturation, starvation response, and normal longevity in C. elegans"

Marc Van Gilst, Stefan Taubert, Keith R Yamamoto

[International Worm Meeting, 2005]

Nuclear Hormone Receptors (NHRs) are ligand-regulated transcription factors (TFs) that govern processes such as organism development, sexual differentiation, and energy homeostasis in metazoans. The genome of C. elegans encodes 284 putative NHRs, the function of most of which is elusive. One of these, NHR-49, regulates transcription of genes involved in fat metabolism. Interestingly, NHR-49 is required for gene expression during periods of feeding, e.g. the fatty acid (FA) desaturase fat-7, as well as for upregulation of certain metabolic genes during periods of starvation (e.g. acs-2). Thus, NHR-49 function strikingly resembles the role of the mammalian NHR Peroxisome Proliferator-Activated-Receptor . To investigate molecular mechanisms underlying NHR-49 regulation of fat homeostasis we aimed to isolate transcriptional cofactors of NHR-49. We performed a yeast-two-hybrid-screen using the NHR-49 ligand-binding-domain as bait. One positive clone expresses a cDNA orthologous to a subunit of yeast Mediator. This multi-subunit-protein-complex acts as a transcriptional coactivator for many distinct TFs, including several human NHRs. However, the Mediator subunit we identified has not previously been reported to interact with NHRs in any organism, therefore representing a novel NHR-cofactor interaction pair. To address the role of this potential NHR-49 cofactor in vivo we utilized feeding RNAi. In N2 L4 worms, RNAi specific to this Mediator subunit prevented starvation-induced mRNA upregulation of NHR-49 targets (determined by qRT-PCR). Similarly, starvation-independent expression of all three FA 9-desaturases (fat-5, -6 and 7) was reduced in worms feeding on Mediator-subunit RNAi. Interestingly, fat-6 is regulated in an NHR-49 independent fashion, suggesting that another TF controls its expression through the same Mediator-subunit. The coordinate regulation of the 9-desaturases suggests that this Mediator-subunit governs FA-desaturation in C. elegans. To verify this hypothesis we analyzed the FA-composition of N2 worms by GC-MS. We found that Mediator-subunit RNAi significantly reduced levels of C18 and C20 mono-or poly-unsaturated FAs. Curiously, prolonged Mediator-subunit RNAi treatment caused larval developmental defects, adult sterility, uncoordinated locomotory behavior, and premature death. Thus, we propose that proper regulation of FA-desaturation by distinct TF-Mediator complexes is important for normal nematode viability. Interestingly, this Mediator subunit is conserved in mammals, suggesting that a similar regulatory loop may be important in higher metazoans.

Stefan Taubert et al. (2008) C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting "The Mediator Subunit MDT-15 Integrates the Genomic Responses to Fasting, Xenobiotic Toxins, Heavy Metals, and Oxidative Stress"

Stefan Taubert, Malene Hansen, Keith Blackwell, Marc Van Gilst, Keith Yamamoto, Jess Porter, Samantha Cooper

[C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting, 2008]

The multi-subunit complex Mediator is a conserved transcriptional coregulator for transcription factors (TFs) such as Nuclear Hormone Receptors (NHRs). Although Mediator is globally required for Pol-dependent transcription, some of its subunits confer specific biological functions. Others and we found that the C. elegansMediator subunit MDT-15 cooperates with the TFs SBP-1 [1] and NHR-49 [2] to control certain aspects of lipid biology. Importantly, MDT-15 affects worm health and life span by controlling fatty acid desaturation. Here, we show that MDT-15 is prominently involved in systemic detoxification. Specifically,depletion of MDT-15 protein or mutation of the mdt-15 gene abrogates the induction of (i) Phase 2 detoxification genes such as cyp-35C1 in response to the hydrophobic toxin fluoranthene, (ii) of metal responsive genes such as the metallothionein mtl-1 in response to cadmium, and (iii) of oxidative stress response genes such as glutathione-S-transferases (gst) in response to arsenite. Moreover, mdt-15(-) animals are hypersensitive to fluoranthene. Intriguingly, MDT-15''s role in stress response is selectively related to dietary uptake, as MDT-15 functional defects do not abrogate the diet-independent response to heat-shock. Taken together with our finding that MDT-15 and NHR-49 coordinate a sector of the fasting response, we propose that MDT-15 integrates several regulatory pathways to monitor both the availability and quality of ingested materials. Thus, in addition to maintaining normal health and longevity by assuring appropriate fatty acid desaturation, we hypothesize that MDT-15 also contributes to normal life span by governing metabolism and elimination of toxic compounds. Finally, some MDT-15 targets such as gst genes are regulated by insulin/IGF-1 signaling in C.elegans, and mdt-15 potentially as well [3]; hence, MDT-15 may affect lipid and detoxification metabolic pathways in the context of insulin/IGF-1 signaling.