Yu Y et al. (2020) ACS Chem Biol "Untargeted Approach for Revealing Electrophilic Metabolites."

Maxwell DN, Zhang B, Le HH, Schroeder FC, Wrobel CJJ, Yu Y, Curtis BJ, Pan JY

[ACS Chem Biol, 2020]

Reactive electrophilic intermediates such as coenzyme A esters play central roles in metabolism but are difficult to detect with conventional strategies. Here, we introduce hydroxylamine-based stable isotope labeling to convert reactive electrophilic intermediates into stable derivatives that are easily detectable <i>via</i> LC-MS. In the model system <i>Caenorhabditis elegans</i>, parallel treatment with ¹⁴NH₂OH and ¹⁵NH₂OH revealed &gt;1000 labeled metabolites, e.g., derived from peptide, fatty acid, and ascaroside pheromone biosyntheses. Results from NH₂OH treatment of a pheromone biosynthesis mutant, <i>acox-1.1</i>, suggested upregulation of thioesterase activity, which was confirmed by gene expression analysis. The upregulated thioesterase contributes to the biosynthesis of a specific subset of ascarosides, determining the balance of dispersal and attractive signals. These results demonstrate the utility of NH₂OH labeling for investigating complex biosynthetic networks. Initial results with <i>Aspergillus</i> and human cell lines indicate applicability toward uncovering reactive metabolomes in diverse living systems.

Yu Y et al. (2011) Biochem J "HID-1 is a novel player in the regulation of neuropeptide sorting."

Xu T, Yu Y, Wang L, Liu L, Xu P, Xia Z, Song E, Zhan Y, Jiu Y

[Biochem J, 2011]

Peptide hormones and neuropeptides are packaged and stored in a specialized intracellular organelle called the dense core vesicle. It remains elusive how peptide cargoes are correctly sorted. In the present study, we show that a highly conserved Golgi-localized protein named HID-1 acts to prevent mis-sorting of peptide cargoes to lysosomes for degradation via a PtdIns3P-dependent trafficking pathway. Epistasis analysis suggests that rab-2 is epistatic to hid-1.

Yu Y et al. (2024) Elife "Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity."

Yu Y, Hu PW, Zhao Q, Zhang Q, Jing B, Gao SM, Sabatini DM, Guan Y, Wang MC, Liu J, Jung SY, Abu-Remaileh M

[Elife, 2024]

Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked to longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using deep proteomic profiling, we systemically profiled lysosome-associated proteins linked with four different longevity mechanisms. We discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we further elucidated lysosomal heterogeneity across tissues as well as the increased enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity across multiple scales and provides resources for understanding the contribution of lysosomal protein dynamics to signal transduction, organelle crosstalk and organism longevity.

Yu, Y. et al. (2019) International Worm Meeting "A rapid untargeted technique for identifying activated compounds in living systems."

Yu, Y., Le, H.

[International Worm Meeting, 2019]

In metabolism, most compounds that undergo chemical transformations get activated as thiol esters with Coenzyme A, which then undergo diverse biosynthetic transformations. Such compounds include intermediates of fatty acid metabolism1 and ascarosides2 in C. elegans, and it is likely that the vast majority of activated metabolites have remained unknown. Using conventional metabolomics protocols, such thiol esters will either undergo hydrolysis or react with another molecules in the worm lysate, e.g. proteins, and become invisible in LCMS analysis. We developed a protocol to capture CoA-derivatives and other activated intermediates using a simple trapping reagent, hydroxylamine (NH2OH), Treatment with hydroxylamine during preparation of worms for metabolomic analysis converts thiol esters into the corresponding hydroxamic acids, which can be easily detected and identified using high-resolution LC-MS. Using a new software platform we have developed for comparative metabolomics in worms and other model systems, Metaboseek (https://metaboseek.com/ ), changes in the production of several 1,000 activated intermediates and other metabolites in different mutants or in response to different environmental conditions can be assessed. I will present results using these approaches for the comparison of the activated metabolome of several fatty acid metabolism mutants. 1. Stryer, L. (1995). "Fatty acid metabolism." In: Biochemistry (Fourth Ed.). New York: W.H. Freeman and Company. pp. 603-628. ISBN 0 7167 2009 4. 2. Von Reuss, S. "Comparative Metabolomics Reveals Biogenesis of Ascarosides, a Modular Library of Small-Molecule Signals in C. elegans." J. Am. Chem. Soc. 2012, 134, 1817-1824

Yu Y et al. (2000) Mol Cell Biol "Architectural transcription factors and the SAGA complex function in parallel pathways to activate transcription."

Yu Y, Eriksson P, Stillman DJ

[Mol Cell Biol, 2000]

Recent work has shown that transcription of the yeast HO gene involves the sequential recruitment of a series of transcription factors. We have performed a functional analysis of HO regulation by determining the ability of mutations in SIN1, SIN3, RPD3, and SIN4 negative regulators to permit HO expression in the absence of certain activators. Mutations in the SIN1 (=SPT2) gene do not affect HO regulation, in contrast to results of other studies using an HO:lacZ reporter, and our data show that the regulatory properties of an HO:lacZ reporter differ from that of the native HO gene. Mutations in SIN3 and RPD3, which encode components of a histone deacetylase complex, show the same pattern of genetic suppression, and this suppression pattern differs from that seen in a sin4 mutant. The Sin4 protein is present in two transcriptional regulatory complexes, the RNA polymerase II holoenzyme/mediator and the SAGA histone acetylase complex. Our genetic analysis allows us to conclude that Swi/Snf chromatin remodeling complex has multiple roles in HO activation, and the data suggest that the ability of the SBF transcription factor to bind to the HO promoter may be affected by the acetylation state of the HO promoter. We also demonstrate that the Nhp6 architectural transcription factor, encoded by the redundant NHP6A and NHP6B genes, is required for HO expression. Suppression analysis with sin3, rpd3, and sin4 mutations suggests that Nhp6 and Gcn5 have similar functions. A gcn5 nhp6a nhp6b triple mutant is extremely sick, suggesting that the SAGA complex and the Nhp6 architectural transcription factors function in parallel pathways to activate transcription. We find that disruption of SIN4 allows this strain to grow at a reasonable rate, indicating a critical role for Sin4 in detecting structural changes in chromatin mediated by Gcn5 and Nhp6. These studies underscore the critical role of chromatin structure in regulating HO gene expression.

Yu Y et al. (2020) Environ Pollut "Toxicity of lindane induced by oxidative stress and intestinal damage in Caenorhabditis elegans."

Xiang M, Chen H, Wang Y, Yu Y, Han Y, Hua X, Li Z

[Environ Pollut, 2020]

Lindane, a lipophilic pollutant, may be toxic to organisms. To explore the toxic effects of lindane and the underlying mechanisms of this toxicity, the animal model Caenorhabditis elegans (C.elegans) was exposed to lindane for 3dat environmentally relevant concentrations (0.01-100ng/L) and the physiological, biochemical, and molecular indices were evaluated. Subacute exposure to 10-100ng/L of lindane caused adverse physiological effects on the development, reproduction, and locomotion behaviors in C.elegans. Exposure to 1-100ng/L of lindane increased the accumulation of Nile red and blue food dye, which suggested high permeability of the intestine in nematodes. Lindane exposure also significantly influenced the expression of genes related to intestinal development (e.g., mtm-6 and opt-2). Moreover, reactive oxygen species production, lipofuscin accumulation, and expression of oxidation resistance genes (e.g., sod-5 and isp-1) were significantly increased in C.elegans exposed to 10-100ng/L of lindane, which indicated that lindane exposure induced oxidative stress. According to Pearson correlation analyses, oxidative stress and intestinal damage were significantly correlated with the adverse physiological effects of lindane. Therefore, the adverse effects of lindane may have been induced by intestinal damage and oxidative stress, and mtm-6, opt-2, sod-5, isp-1, and mev-1 might play important roles in the toxicity of lindane.

Yu Y et al. (2024) Chemosphere "Chronic neurotoxicity of Tetrabromobisphenol A: Induction of oxidative stress and damage to neurons in Caenorhabditis elegans."

Tan S, Yu Y, Xiang M, Xie D, Ling H, Yi C, Yang Y, Chen H, Guo H, Hua X

[Chemosphere, 2024]

Tetrachlorobisphenol A (TCBPA) has been used as an alternative flame retardant in various fields. However, the long-term effects of TCBPA on the nervous system remain unclear. Thus, Caenorhabditis elegans (L4 larvae) were selected as a model animal to investigate the neurotoxic effects and underlying mechanisms after 10&#x202f;d of TCBPA exposure. Exposure to TCBPA (0.01-100&#x202f;&#x3bc;g/L) decreased locomotive behavior in a concentration-dependent manner. In addition, reactive oxygen species (ROS) formation and lipofuscin accumulation were significantly increased, and the expression of sod-3 was upregulated in the exposed nematodes, indicating that TCBPA exposure induced oxidative damage. Furthermore, 100&#x202f;&#x3bc;g/L TCBPA exposure caused a reduction in dopamine and serotonin levels, and damage in dopaminergic and serotoninergic neurons, which was further confirmed by the downregulated expression of related genes (e.g., dop-1, dop-3, cat-1, and mod-1). Molecular docking analysis demonstrated the potential of TCBPA to bind to the neurotransmitter receptor proteins DOP-1, DOP-3, and MOD-1. These results indicate that chronic exposure to TCBPA induces neurotoxic effects on locomotive behavior, which is associated with oxidative stress and damage to dopaminergic and serotoninergic neurons.

Yu Y et al. (2022) Chemosphere "Tetrachlorobisphenol A mediates reproductive toxicity in Caenorhabditis elegans via DNA damage-induced apoptosis."

Xiang M, Yu Y, Chen H, Yang Y, Dang Y, Hua X

[Chemosphere, 2022]

Tetrachlorobisphenol A (TCBPA), an alternative to tetrabromobisphenol A (TBBPA), is ubiquitous in the environment and could potentially impact the reproductive system of organisms. However, the mechanisms underlying TCBPA-mediated reproductive effects remain unclear. Herein, we exposed Caenorhabditis elegans (C. elegans, L4 larvae) to TCBPA at environmentally relevant doses (0-100 &#956;g/L) for 24 h. Exposure to TCBPA at concentrations of 1-100 &#956;g/L impaired fertility of C. elegans, as indicated by brood size. After staining, the number of germline cells decreased in a dose-dependent manner, whereas germline cell corpses increased in exposed nematodes (10-100 &#956;g/L TCBPA). Moreover, the expression of genes related to the germline apoptosis pathway was regulated following exposure to 100 &#956;g/L TCBPA, indicating the potential role of DNA damage in TCBPA-induced apoptosis. Apoptosis was nearly abolished in ced-4 and ced-3 mutants and blocked in hus-1, egl-1, cep-1, and ced-9 mutants. Numerous foci were detected in TCBPA (100 &#956;g/L)-exposed hus-1::GFP strains. These results indicate that TCBPA induces hus-1-mediated DNA damage and further causes apoptosis via a cep-1-dependent pathway. Our data provide evidence that TCBPA causes reproductive toxicity via DNA damage-induced apoptosis.

Yu Y et al. (2017) Nat Commun "High-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation."

Yu Y, Liu H, Mutlu AS, Wang MC

[Nat Commun, 2017]

High-throughput screens at microscopic resolution can uncover molecular mechanisms of cellular dynamics, but remain technically challenging in live multicellular organisms. Here we present a genetic screening method using photo-highlighting for candidate selection on microscopes. We apply this method to stimulated Raman scattering (SRS) microscopy and systematically identify 57 Caenorhabditis elegans mutants with altered lipid distribution. Four of these mutants target the components of the Bone Morphogenetic Protein (BMP) signaling pathway, revealing that BMP signaling inactivation causes exhaustion of lipid reserves in somatic tissues. Using SRS-based isotope tracing assay to quantitatively track lipid synthesis and mobilization, we discover that the BMP signaling mutants have increased rates of lipid mobilization. Furthermore, this increase is associated with the induction of mitochondrial -oxidation and mitochondrial fusion. Together these studies demonstrate a photo-highlighting microscopic strategy for genome-scale screens, leading to the discovery of new roles for BMP signaling in linking mitochondrial homeostasis and lipid metabolism.High-throughput genetic screens in animals could benefit from an easy way to mark positive hits. Here the authors introduce photo-highlighting using a photoconvertible fluorescent protein, and in combination with stimulated Raman scattering (SRS) microscopy, define a role for BMP signaling in lipid metabolism in C. elegans.

Yu Y et al. (2021) Chemosphere "Glutamatergic transmission associated with locomotion-related neurotoxicity to lindane over generations in Caenorhabditis elegans."

Chen X, Chen H, Hua X, Yang Y, Xiang M, Yu Y, Wang Z, Han Y

[Chemosphere, 2021]

Organochlorine pesticide lindane in the environment and biota results in the potential risks on ecosystem and human health. Lindane can adversely affect the locomotion and nervous system, yet the potential neurotoxicity of lindane over generations remains uncertain. In this study, the neurotoxicity and underlying mechanisms in Caenorhabditis elegans (C. elegans) were investigated after parental (P0) exposure to lindane at environmentally relevant concentrations over generations. Exposure to lindane at concentrations of 10-100 ng/L significantly decreased body bends and head thrashes in P0 generation. Significant decrease of fluorescence labeled different neurotransmitters, and clear morphological changes by exposure to lindane at 10-100 ng/L suggested that lindane could induce the neuronal damage in C. elegans. During the transgenerational process, decreased locomotive behaviors were also observed in F1-F3 generations, and head thrashes returned to normal levels in F4 generation. Moreover, lindane exposure down-regulated the expression of dat-1, dop-1, glr-1 and mod-1genes, while up-regulated unc-30 gene in P0 generation, which recovered to normal levels in F4 generation. Interestingly, eat-4 continued to be regulated from inhibition to stimulation in P0-F4 generations, suggesting that glutamatergic transmission may more contribute to the neurotoxicity of lindane over generations.