1
|
Bhar S, Yoon CS, Mai K, Han J, Prajapati DV, Wang Y, Steffen CL, Bailey LS, Basso KB, Butcher RA. An acyl-CoA thioesterase is essential for the biosynthesis of a key dauer pheromone in C. elegans. Cell Chem Biol 2024; 31:1011-1022.e6. [PMID: 38183989 PMCID: PMC11102344 DOI: 10.1016/j.chembiol.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/02/2023] [Accepted: 12/10/2023] [Indexed: 01/08/2024]
Abstract
Methyl ketone (MK)-ascarosides represent essential components of several pheromones in Caenorhabditis elegans, including the dauer pheromone, which triggers the stress-resistant dauer larval stage, and the male-attracting sex pheromone. Here, we identify an acyl-CoA thioesterase, ACOT-15, that is required for the biosynthesis of MK-ascarosides. We propose a model in which ACOT-15 hydrolyzes the β-keto acyl-CoA side chain of an ascaroside intermediate during β-oxidation, leading to decarboxylation and formation of the MK. Using comparative metabolomics, we identify additional ACOT-15-dependent metabolites, including an unusual piperidyl-modified ascaroside, reminiscent of the alkaloid pelletierine. The β-keto acid generated by ACOT-15 likely couples to 1-piperideine to produce the piperidyl ascaroside, which is much less dauer-inducing than the dauer pheromone, asc-C6-MK (ascr#2, 1). The bacterial food provided influences production of the piperidyl ascaroside by the worm. Our work shows how the biosynthesis of MK- and piperidyl ascarosides intersect and how bacterial food may impact chemical signaling in the worm.
Collapse
Affiliation(s)
- Subhradeep Bhar
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Chi-Su Yoon
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kevin Mai
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Jungsoo Han
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Dilip V Prajapati
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Yuting Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Candy L Steffen
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
2
|
Lee D, Fox B, Palomino D, Panda O, Tenjo F, Koury E, Evans K, Stevens L, Rodrigues P, Kolodziej A, Schroeder F, Andersen E. Natural genetic variation in the pheromone production of C. elegans. Proc Natl Acad Sci U S A 2023; 120:e2221150120. [PMID: 37339205 PMCID: PMC10293855 DOI: 10.1073/pnas.2221150120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/10/2023] [Indexed: 06/22/2023] Open
Abstract
From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. These signals are encoded by different types and mixtures of ascarosides, whose modular structures further enhance the diversity of this nematode pheromone language. Interspecific and intraspecific differences in this ascaroside pheromone language have been described previously, but the genetic basis and molecular mechanisms underlying the variation remain largely unknown. Here, we analyzed natural variation in the production of 44 ascarosides across 95 wild Caenorhabditis elegans strains using high-performance liquid chromatography coupled to high-resolution mass spectrometry. We discovered wild strains defective in the production of specific subsets of ascarosides (e.g., the aggregation pheromone icas#9) or short- and medium-chain ascarosides, as well as inversely correlated patterns between the production of two major classes of ascarosides. We investigated genetic variants that are significantly associated with the natural differences in the composition of the pheromone bouquet, including rare genetic variants in key enzymes participating in ascaroside biosynthesis, such as the peroxisomal 3-ketoacyl-CoA thiolase, daf-22, and the carboxylesterase cest-3. Genome-wide association mappings revealed genomic loci harboring common variants that affect ascaroside profiles. Our study yields a valuable dataset for investigating the genetic mechanisms underlying the evolution of chemical communication.
Collapse
Affiliation(s)
- Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Biology, Kyung Hee University, Seoul02447, Republic of Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Bennett W. Fox
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Diana Fajardo Palomino
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Oishika Panda
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Francisco J. Tenjo
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Emily J. Koury
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Kathryn S. Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Tree of Life, Wellcome Sanger Institute, CambridgeCB10 1SA, United Kingdom
| | - Pedro R. Rodrigues
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Aiden R. Kolodziej
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Frank C. Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY14850
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14850
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| |
Collapse
|
3
|
Xu Z, Chen Z, Zhang H. Adaptation and evolution of the sea anemone
Alvinactis
sp. to deep‐sea hydrothermal vents: A comparison using transcriptomes. Ecol Evol 2022; 12:e9309. [PMID: 36188500 PMCID: PMC9486505 DOI: 10.1002/ece3.9309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Sea anemones are diverse and ecologically successful members of Anthozoa. They are often found in intertidal and shallow waters, although a few of them inhabit harsher living conditions, such as deep‐sea hydrothermal vents. Here, we sequenced the transcriptome of the vent sea anemone Alvinactis sp., which was collected from Edmond vent along the central Indian Ocean ridge at a depth of 3275 m, to explore the molecular mechanisms related to adaptation to vents. Compared with another deep‐sea anemone (Paraphelliactis xishaensis) and five shallow water sea anemones, a total of 117 positively selected genes and 46 significantly expanded gene families were found in Alvinactis sp. specifically that may be related to its vent‐specific aspect of adaptation. In addition, 127 positively selected genes and 23 significantly expanded gene families that were found in both Alvinactis sp. and P. xishaensis. Among these, vent‐specific adaptations of Alvinactis sp. may involve genetic alterations in peroxisome, ubiquitin‐mediated protein degradation, oxidative phosphorylation, and endocytosis, and its deep‐sea adaptation may involve changes in genetic information processing. Differentially expressed genes between Alvinactis sp. and the deep‐sea anemone P. xishaensis were enriched in a variety of pathways related to adaptation, such as energy metabolism, genetic information processing, endocytosis, and peroxisomes. Overall, we provided the first transcriptome of sea anemones that inhabit vents, which enriches our knowledge of deep‐sea hydrothermal vent adaptation and the diversity of sea anemones.
Collapse
Affiliation(s)
- Zehui Xu
- Institute of Deep‐sea Science and Engineering, Chinese Academy of Sciences Sanya China
- University of Chinese Academy of Sciences Beijing China
| | - Zeyu Chen
- University of Chinese Academy of Sciences Beijing China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
| | - Haibin Zhang
- Institute of Deep‐sea Science and Engineering, Chinese Academy of Sciences Sanya China
| |
Collapse
|
4
|
Li N, Hua B, Chen Q, Teng F, Ruan M, Zhu M, Zhang L, Huo Y, Liu H, Zhuang M, Shen H, Zhu H. A sphingolipid-mTORC1 nutrient-sensing pathway regulates animal development by an intestinal peroxisome relocation-based gut-brain crosstalk. Cell Rep 2022; 40:111140. [PMID: 35905721 DOI: 10.1016/j.celrep.2022.111140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 05/23/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022] Open
Abstract
The mTOR-dependent nutrient-sensing and response machinery is the central hub for animals to regulate their cellular and developmental programs. However, equivalently pivotal nutrient and metabolite signals upstream of mTOR and developmental-regulatory signals downstream of mTOR are not clear, especially at the organism level. We previously showed glucosylceramide (GlcCer) acts as a critical nutrient and metabolite signal for overall amino acid levels to promote development by activating the intestinal mTORC1 signaling pathway. Here, through a large-scale genetic screen, we find that the intestinal peroxisome is critical for antagonizing the GlcCer-mTORC1-mediated nutrient signal. Mechanistically, GlcCer deficiency, inactive mTORC1, or prolonged starvation relocates intestinal peroxisomes closer to the apical region in a kinesin- and microtubule-dependent manner. Those apical accumulated peroxisomes further release peroxisomal-β-oxidation-derived glycolipid hormones that target chemosensory neurons and downstream nuclear hormone receptor DAF-12 to arrest the animal development. Our data illustrate a sophisticated gut-brain axis that predominantly orchestrates nutrient-sensing-dependent development in animals.
Collapse
Affiliation(s)
- Na Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Beilei Hua
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fukang Teng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meiyu Ruan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengnan Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Li Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yinbo Huo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Hongqin Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huali Shen
- Institutes of Biomedical Sciences, Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huanhu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
5
|
Wang Y, Li C, Zhang J, Xu X, Fu L, Xu J, Zhu H, Hu Y, Li C, Wang M, Wu Y, Zou X, Liang B. Polyunsaturated fatty acids promote the rapid fusion of lipid droplets in Caenorhabditis elegans. J Biol Chem 2022; 298:102179. [PMID: 35752365 PMCID: PMC9352923 DOI: 10.1016/j.jbc.2022.102179] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/27/2022] Open
Abstract
Lipid droplets (LDs) are intracellular organelles that dynamically regulate lipids and energy homeostasis in the cell. LDs can grow through either local lipid synthesis or LD fusion. However, how lipids involving in LD fusion for LD growth is largely unknown. Here, we show that genetic mutation of acox-3 (acyl-CoA oxidase), maoc-1 (enoyl-CoA hydratase), dhs-28 (3-hydroxylacyl-CoA dehydrogenase), and daf-22 (3-ketoacyl-CoA thiolase), all involved in the peroxisomal β-oxidation pathway in Caenorhabditis elegans, led to rapid fusion of adjacent LDs to form giant LDs (gLDs). Mechanistically, we show that dysfunction of peroxisomal β-oxidation results in the accumulation of long-chain fatty acid-CoA and phosphocholine, which may activate the sterol-binding protein 1/sterol regulatory element–binding protein to promote gLD formation. Furthermore, we found that inactivation of either FAT-2 (delta-12 desaturase) or FAT-3 and FAT-1 (delta-15 desaturase and delta-6 desaturase, respectively) to block the biosynthesis of polyunsaturated fatty acids (PUFAs) with three or more double bonds (n≥3-PUFAs) fully repressed the formation of gLDs; in contrast, dietary supplementation of n≥3-PUFAs or phosphocholine bearing these PUFAs led to recovery of the formation of gLDs in peroxisomal β-oxidation–defective worms lacking PUFA biosynthesis. Thus, we conclude that n≥3-PUFAs, distinct from other well-known lipids and proteins, promote rapid LD fusion leading to LD growth.
Collapse
Affiliation(s)
- Yanli Wang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Chunxia Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Jingjing Zhang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Xiumei Xu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Lin Fu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Jie Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan province, Kunming Institute of Zoology, CAS, Kunming, Yunnan 650223, China
| | - Hong Zhu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Ying Hu
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Chengbin Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Mengjie Wang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China
| | - Yingjie Wu
- Shandong Provincial Hospital, School of Laboratory Animal & Shandong Laboratory Animal Center, Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250021, China; Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Liaoning Provence Key Lab of Genome Engineered Animal Models Dalian Medical University, Dalian, Liaoning 116044, China.
| | - Xiaoju Zou
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China.
| | - Bin Liang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650500, China.
| |
Collapse
|
6
|
Ma X, Hou M, Liu C, Li J, Ba Q, Wang H. Cadmium accelerates bacterial oleic acid production to promote fat accumulation in Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126723. [PMID: 34325294 DOI: 10.1016/j.jhazmat.2021.126723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/30/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Environmental cadmium, with a high dietary intake and long biological half-life, is a severe health risk by harming physiological function directly or through gut microbiota. However, the toxicity mechanisms of environmental cadmium on microbes and host systems remain unclear. Herein, we established three C. elegans and E. coli cultivated systems to investigate the vital role of microorganisms in cadmium-induced lipid toxicity and depict the interaction between environmental cadmium, bacteria, and the host. We found that only nematodes in the system with live bacteria, rather than UV-killed bacteria or no bacteria, could be induced to fat accumulation by cadmium exposure, suggesting that bacteria mediated the effect of environmental cadmium on body fat. Cadmium caused perturbation of metabolite in bacteria, most notably oleic acid, elevated the synthesis genes expression, and enhanced the bacterial oleic acid production, which further promoted the expression of lipid metabolism-related genes and fat deposition in C. elegans regardless of the cultivated system. Finally, we showed the potential protective effect of Vitamin D3 which prevented cadmium- or oleic acid-induced fat storage significantly. In conclusion, this study illustrates the mechanism underlying cadmium-induced lipid accumulation in body through bacterial metabolites and reveals the interplay between environmental cadmium, microorganisms, and the host.
Collapse
Affiliation(s)
- Xueqi Ma
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200025, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Hou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chaobao Liu
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China
| | - Jingquan Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qian Ba
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Hui Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
7
|
Huang PW, Xu YS, Sun XM, Shi TQ, Gu Y, Ye C, Huang H. Development of an Efficient Gene Editing Tool in Schizochytrium sp. and Improving Its Lipid and Terpenoid Biosynthesis. Front Nutr 2022; 8:795651. [PMID: 34970583 PMCID: PMC8712325 DOI: 10.3389/fnut.2021.795651] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Schizochytrium sp. HX-308 is a marine microalga with fast growth and high lipid content, which has potential as microbial cell factories for lipid compound biosynthesis. It is significant to develop efficient genetic editing tool and discover molecular target in Schizochytrium sp. HX-308 for lipid compound biosynthesis. In this study, we developed an efficient gene editing tool in HX-308 which was mediated by Agrobacterium tumefaciens AGL-1. Results showed that the random integration efficiency reached 100%, and the homologous recombination efficiency reached about 30%. Furthermore, the metabolic pathway of lipid and terpenoid biosynthesis were engineered. Firstly, the acetyl-CoA c-acetyltransferase was overexpressed in HX-308 with a strong constitutive promoter. With the overexpression of acetyl-CoA c-acetyltransferase, more acetyl-CoA was used to synthesize terpenoids, and the production of squalene, β-carotene and astaxanthin was increased 5.4, 1.8, and 2.4 times, respectively. Interestingly, the production of saturated fatty acids and polyunsaturated fatty acids also changed. Moreover, three Acyl-CoA oxidase genes which catalyze the first step of β-oxidation were knocked out using homologous recombination. Results showed that the production of lipids increased in the three knock-out strains. Our results demonstrated that the A. tumefaciens-mediated transformation method will be of great use for the study of function genes, as well as developing Schizochytrium sp. as a strong cell factory for producing high value products.
Collapse
Affiliation(s)
- Peng-Wei Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| |
Collapse
|
8
|
Gao C, Li Q, Yu J, Li S, Cui Q, Hu X, Chen L, Zhang SO. Endocrine pheromones couple fat rationing to dauer diapause through HNF4α nuclear receptors. SCIENCE CHINA-LIFE SCIENCES 2021; 64:2153-2174. [PMID: 34755252 DOI: 10.1007/s11427-021-2016-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 12/21/2022]
Abstract
Developmental diapause is a widespread strategy for animals to survive seasonal starvation and environmental harshness. Diapaused animals often ration body fat to generate a basal level of energy for enduring survival. How diapause and fat rationing are coupled, however, is poorly understood. The nematode Caenorhabditis elegans excretes pheromones to the environment to induce a diapause form called dauer larva. Through saturated forward genetic screens and CRISPR knockout, we found that dauer pheromones feed back to repress the transcription of ACOX-3, MAOC-1, DHS-28, DAF-22 (peroxisomal β-oxidation enzymes dually involved in pheromone synthesis and fat burning), ALH-4 (aldehyde dehydrogenase for pheromone synthesis), PRX-10 and PRX-11 (peroxisome assembly and proliferation factors). Dysfunction of these pheromone enzymes and factors relieves the repression. Surprisingly, transcription is repressed not by pheromones excreted but by pheromones endogenous to each animal. The endogenous pheromones regulate the nuclear translocation of HNF4α family nuclear receptor NHR-79 and its co-receptor NHR-49, and, repress transcription through the two receptors. The feedback repression maintains pheromone homeostasis, increases fat storage, decreases fat burning, and prolongs dauer lifespan. Thus, the exocrine dauer pheromones possess an unexpected endocrine function to mediate a peroxisome-nucleus crosstalk, coupling dauer diapause to fat rationing.
Collapse
Affiliation(s)
- Cheng Gao
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Qi Li
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jialei Yu
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shiwei Li
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Qingpo Cui
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Hu
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Lifeng Chen
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shaobing O Zhang
- Laboratory of Metabolic Genetics, College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| |
Collapse
|
9
|
Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan. Nat Commun 2021; 12:4912. [PMID: 34389721 PMCID: PMC8363725 DOI: 10.1038/s41467-021-24682-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis. The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.
Collapse
|
10
|
Wasson JA, Harris G, Keppler-Ross S, Brock TJ, Dar AR, Butcher RA, Fischer SEJ, Kagias K, Clardy J, Zhang Y, Mango SE. Neuronal control of maternal provisioning in response to social cues. SCIENCE ADVANCES 2021; 7:7/34/eabf8782. [PMID: 34417172 PMCID: PMC8378817 DOI: 10.1126/sciadv.abf8782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues between generations are not well understood. Here, we show that, in Caenorhabditis elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRFamide (Phe-Met-Arg-Phe)-like peptides. Parental FMRFamide-like peptide signaling dampens oxidative stress resistance and promotes the deposition of mRNAs for translational components in progeny, which, in turn, reduces gene silencing. This study identifies a previously unknown pathway for intergenerational communication that links neuronal responses to maternal provisioning. We suggest that loss of social cues in the parental environment represents an adverse environment that stimulates stress responses across generations.
Collapse
Affiliation(s)
| | - Gareth Harris
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Biology, California State University Channel Islands, Camarillo, CA, USA
| | | | | | - Abdul R Dar
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Sylvia E J Fischer
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Konstantinos Kagias
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.
| | - Susan E Mango
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
11
|
Shi H, Huang X, Chen X, Yang Y, Wang Z, Yang Y, Wu F, Zhou J, Yao C, Ma G, Du A. Acyl-CoA oxidase ACOX-1 interacts with a peroxin PEX-5 to play roles in larval development of Haemonchus contortus. PLoS Pathog 2021; 17:e1009767. [PMID: 34270617 PMCID: PMC8354476 DOI: 10.1371/journal.ppat.1009767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/10/2021] [Accepted: 06/29/2021] [Indexed: 11/19/2022] Open
Abstract
Hypobiosis (facultative developmental arrest) is the most important life-cycle adaptation ensuring survival of parasitic nematodes under adverse conditions. Little is known about such survival mechanisms, although ascarosides (ascarylose with fatty acid-derived side chains) have been reported to mediate the formation of dauer larvae in the free-living nematode Caenorhabditis elegans. Here, we investigated the role of a key gene acox-1, in the larval development of Haemonchus contortus, one of the most important parasitic nematodes that employ hypobiosis as a routine survival mechanism. In this parasite, acox-1 encodes three proteins (ACOXs) that all show a fatty acid oxidation activity in vitro and in vivo, and interact with a peroxin PEX-5 in peroxisomes. In particular, a peroxisomal targeting signal type1 (PTS1) sequence is required for ACOX-1 to be recognised by PEX-5. Analyses on developmental transcription and tissue expression show that acox-1 is predominantly expressed in the intestine and hypodermis of H. contortus, particularly in the early larval stages in the environment and the arrested fourth larval stage within host animals. Knockdown of acox-1 and pex-5 in parasitic H. contortus shows that these genes play essential roles in the post-embryonic larval development and likely in the facultative arrest of this species. A comprehensive understanding of these genes and the associated β-oxidation cycle of fatty acids should provide novel insights into the developmental regulation of parasitic nematodes, and into the discovery of novel interventions for species of socioeconomic importance.
Collapse
Affiliation(s)
- Hengzhi Shi
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaocui Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhao Wang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yimin Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Wu
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingru Zhou
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, St. Kitts & Nevis
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Veterinary Biosciences, Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (GM); (AD)
| | - Aifang Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail: (GM); (AD)
| |
Collapse
|
12
|
Yu Y, Zhang YK, Manohar M, Artyukhin AB, Kumari A, Tenjo-Castano FJ, Nguyen H, Routray P, Choe A, Klessig DF, Schroeder FC. Nematode Signaling Molecules Are Extensively Metabolized by Animals, Plants, and Microorganisms. ACS Chem Biol 2021; 16:1050-1058. [PMID: 34019369 DOI: 10.1021/acschembio.1c00217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Many bacterivorous and parasitic nematodes secrete signaling molecules called ascarosides that play a central role regulating their behavior and development. Combining stable-isotope labeling and mass spectrometry-based comparative metabolomics, here we show that ascarosides are taken up from the environment and metabolized by a wide range of phyla, including plants, fungi, bacteria, and mammals, as well as nematodes. In most tested eukaryotes and some bacteria, ascarosides are metabolized into derivatives with shortened fatty acid side chains, analogous to ascaroside biosynthesis in nematodes. In plants and C. elegans, labeled ascarosides were additionally integrated into larger, modular metabolites, and use of different ascaroside stereoisomers revealed the stereospecificity of their biosynthesis. The finding that nematodes extensively metabolize ascarosides taken up from the environment suggests that pheromone editing may play a role in conspecific and interspecific interactions. Moreover, our results indicate that plants, animals, and microorganisms may interact with associated nematodes via manipulation of ascaroside signaling.
Collapse
Affiliation(s)
- Yan Yu
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ying K. Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Alexander B. Artyukhin
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
| | - Anshu Kumari
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
| | | | - Hung Nguyen
- Holoclara, Inc., Pasadena, California 91101, United States
| | - Pratyush Routray
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Andrea Choe
- Holoclara, Inc., Pasadena, California 91101, United States
| | - Daniel F. Klessig
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
13
|
Watanabe K, Perez CMT, Kitahori T, Hata K, Aoi M, Takahashi H, Sakuma T, Okamura Y, Nakashimada Y, Yamamoto T, Matsuyama K, Mayuzumi S, Aki T. Improvement of fatty acid productivity of thraustochytrid, Aurantiochytrium sp. by genome editing. J Biosci Bioeng 2020; 131:373-380. [PMID: 33386277 DOI: 10.1016/j.jbiosc.2020.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/12/2023]
Abstract
Thraustochytrid strains belonging to the genus Aurantiochytrium accumulate significant amounts of lipids including polyunsaturated fatty acids and carotenoids and, therefore, are expected to be used for industrial production of various valuable materials. Although various efforts such as chemical mutagenesis and homologous gene recombination have been made to improve lipid productivity of Aurantiochytrium species, low specificity and efficiency in the conventional methods hinder the research progress. Here, we attempted to apply a genome editing technology, the CRISPR-Cas9 system as an alternative molecular breeding technique for Aurantiochytrium species to accelerate the metabolic engineering. The efficiency of specific gene knock-in by the homologous recombination increased more than 10-folds by combining the CRISPR-Cas9 system. As a result of disrupting the genes associated with β-oxidation of fatty acids by the improved method, the genome edited strains with higher fatty acid productivity were isolated, demonstrating for the first time that the CRISPR-Cas9 system was effective for molecular breeding of the strains in the genus Aurantiochytrium to improve lipid productivity.
Collapse
Affiliation(s)
- Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Charose Marie Ting Perez
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tomoki Kitahori
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Kosuke Hata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Masato Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tetsushi Sakuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | | | - Shinzo Mayuzumi
- Idemitsu Kosan Co., Ltd., 1280 Kami-izumi, Sodegaura, Chiba 299-0293, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
| |
Collapse
|
14
|
Zhang B, Zhao L, Ning J, Wickham JD, Tian H, Zhang X, Yang M, Wang X, Sun J. miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling. BMC Biol 2020; 18:184. [PMID: 33246464 PMCID: PMC7697373 DOI: 10.1186/s12915-020-00926-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/11/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Survival to cold stress in insects living in temperate environments requires the deployment of strategies that lead to physiological changes involved in freeze tolerance or freeze avoidance. These strategies may consist of, for instance, the induction of metabolic depression, accumulation of cryoprotectants, or the production of antifreeze proteins, however, little is known about the way such mechanisms are regulated and the signals involved in their activation. Ascarosides are signaling molecules usually known to regulate nematode behavior and development, whose expression was recently found to relate to thermal plasticity in the Japanese pine sawyer beetle Monochamus alternatus. Accumulating evidence also points to miRNAs as another class of regulators differentially expressed in response to cold stress, which are predicted to target genes involved in cold adaptation of insects. Here, we demonstrate a novel pathway involved in insect cold acclimation, through miRNA-mediated regulation of ascaroside function. RESULTS We initially discovered that experimental cold acclimation can enhance the beetle's cold hardiness. Through screening and functional verification, we found miR-31-5p, upregulated under cold stress, significantly contributes to this enhancement. Mechanistically, miR-31-5p promotes production of an ascaroside (asc-C9) in the beetle by negatively targeting the rate-limiting enzyme, acyl-CoA oxidase in peroxisomal β-oxidation cycles. Feeding experiments with synthetic asc-C9 suggests it may serve as a signal to promote cold acclimation through metabolic depression and accumulation of cryoprotectants with specific gene expression patterns. CONCLUSIONS Our results point to important roles of miRNA-mediated regulation of ascaroside function in insect cold adaptation. This enhanced cold tolerance may allow higher survival of M. alternatus in winter and be pivotal in shaping its wide distribution range, greatly expanding the threat of pine wilt disease, and thus can also inspire the development of ascaroside-based pest management strategies.
Collapse
Affiliation(s)
- Bin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jing Ning
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jacob D Wickham
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haokai Tian
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meiling Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 10049, China.
| |
Collapse
|
15
|
Yu Y, Le HH, Curtis BJ, Wrobel CJJ, Zhang B, Maxwell DN, Pan JY, Schroeder FC. An Untargeted Approach for Revealing Electrophilic Metabolites. ACS Chem Biol 2020; 15:3030-3037. [PMID: 33074644 DOI: 10.1021/acschembio.0c00706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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 via LC-MS. In the model system Caenorhabditis elegans, parallel treatment with 14NH2OH and 15NH2OH revealed >1000 labeled metabolites, e.g., derived from peptide, fatty acid, and ascaroside pheromone biosyntheses. Results from NH2OH treatment of a pheromone biosynthesis mutant, acox-1.1, 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 Aspergillus and human cell lines indicate applicability toward uncovering reactive metabolomes in diverse living systems.
Collapse
Affiliation(s)
- Yan Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian J. Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Chester J. J. Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Bingsen Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Danielle N. Maxwell
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Judy Y. Pan
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
16
|
Abstract
For the first 25 years after the landmark 1974 paper that launched the field, most C. elegans biologists were content to think of their subjects as solitary creatures. C. elegans presented no shortage of fascinating biological problems, but some of the features that led Brenner to settle on this species-in particular, its free-living, self-fertilizing lifestyle-also seemed to reduce its potential for interesting social behavior. That perspective soon changed, with the last two decades bringing remarkable progress in identifying and understanding the complex interactions between worms. The growing appreciation that C. elegans behavior can only be meaningfully understood in the context of its ecology and evolution ensures that the coming years will see similarly exciting progress.
Collapse
Affiliation(s)
- Douglas S Portman
- Departments of Biomedical Genetics, Neuroscience, and Biology, Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY, USA
| |
Collapse
|
17
|
Le HH, Wrobel CJ, Cohen SM, Yu J, Park H, Helf MJ, Curtis BJ, Kruempel JC, Rodrigues PR, Hu PJ, Sternberg PW, Schroeder FC. Modular metabolite assembly in Caenorhabditis elegans depends on carboxylesterases and formation of lysosome-related organelles. eLife 2020; 9:61886. [PMID: 33063667 PMCID: PMC7641594 DOI: 10.7554/elife.61886] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.
Collapse
Affiliation(s)
- Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Chester Jj Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Sarah M Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Jingfang Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Joseph C Kruempel
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, United States
| | - Pedro Reis Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Patrick J Hu
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| |
Collapse
|
18
|
Yilmaz LS, Li X, Nanda S, Fox B, Schroeder F, Walhout AJ. Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels. Mol Syst Biol 2020; 16:e9649. [PMID: 33022146 PMCID: PMC7537831 DOI: 10.15252/msb.20209649] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/04/2023] Open
Abstract
Metabolism is a highly compartmentalized process that provides building blocks for biomass generation during development, homeostasis, and wound healing, and energy to support cellular and organismal processes. In metazoans, different cells and tissues specialize in different aspects of metabolism. However, studying the compartmentalization of metabolism in different cell types in a whole animal and for a particular stage of life is difficult. Here, we present MEtabolic models Reconciled with Gene Expression (MERGE), a computational pipeline that we used to predict tissue-relevant metabolic function at the network, pathway, reaction, and metabolite levels based on single-cell RNA-sequencing (scRNA-seq) data from the nematode Caenorhabditis elegans. Our analysis recapitulated known tissue functions in C. elegans, captured metabolic properties that are shared with similar tissues in human, and provided predictions for novel metabolic functions. MERGE is versatile and applicable to other systems. We envision this work as a starting point for the development of metabolic network models for individual cells as scRNA-seq continues to provide higher-resolution gene expression data.
Collapse
Affiliation(s)
- Lutfu Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xuhang Li
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shivani Nanda
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bennett Fox
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank Schroeder
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Albertha Jm Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
19
|
Faghih N, Bhar S, Zhou Y, Dar AR, Mai K, Bailey LS, Basso KB, Butcher RA. A Large Family of Enzymes Responsible for the Modular Architecture of Nematode Pheromones. J Am Chem Soc 2020; 142:13645-13650. [PMID: 32702987 DOI: 10.1021/jacs.0c04223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nematode Caenorhabditis elegans produces a broad family of pheromones, known as the ascarosides, that are modified with a variety of groups derived from primary metabolism. These modifications are essential for the diverse activities of the ascarosides in development and various behaviors, including attraction, aggregation, avoidance, and foraging. The mechanism by which these different groups are added to the ascarosides is poorly understood. Here, we identify a family of over 30 enzymes, which are homologous to mammalian carboxylesterase (CES) enzymes, and show that a number of these enzymes are responsible for the selective addition of specific modifications to the ascarosides. Through stable isotope feeding experiments, we demonstrate the in vivo activity of the CES-like enzymes and provide direct evidence that the acyl-CoA synthetase ACS-7, which was previously implicated in the attachment of certain modifications to the ascarosides in C. elegans, instead activates the side chains of certain ascarosides for shortening through β-oxidation. Our data provide a key to the combinatorial logic that gives rise to different modified ascarosides, which should greatly facilitate the exploration of the specific biological functions of these pheromones in the worm.
Collapse
Affiliation(s)
- Nasser Faghih
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Subhradeep Bhar
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Yue Zhou
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Kevin Mai
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| |
Collapse
|
20
|
Dong C, Weadick CJ, Truffault V, Sommer RJ. Convergent evolution of small molecule pheromones in Pristionchus nematodes. eLife 2020; 9:55687. [PMID: 32338597 PMCID: PMC7224695 DOI: 10.7554/elife.55687] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
The small molecules that mediate chemical communication between nematodes-so-called 'nematode-derived-modular-metabolites' (NDMMs)-are of major interest because of their ability to regulate development, behavior, and life-history. Pristionchus pacificus nematodes produce an impressive diversity of structurally complex NDMMs, some of which act as primer pheromones that are capable of triggering irreversible developmental switches. Many of these NDMMs have only ever been found in P. pacificus but no attempts have been made to study their evolution by profiling closely related species. This study brings a comparative perspective to the biochemical study of NDMMs through the systematic MS/MS- and NMR-based analysis of exo-metabolomes from over 30 Pristionchus species. We identified 36 novel compounds and found evidence for the convergent evolution of complex NDMMs in separate branches of the Pristionchus phylogeny. Our results demonstrate that biochemical innovation is a recurrent process in Pristionchus nematodes, a pattern that is probably typical across the animal kingdom.
Collapse
Affiliation(s)
- Chuanfu Dong
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cameron J Weadick
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
21
|
Label-Free Proteomics of the Fetal Pancreas Identifies Deficits in the Peroxisome in Rats with Intrauterine Growth Restriction. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1520753. [PMID: 31781323 PMCID: PMC6874927 DOI: 10.1155/2019/1520753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/31/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Aim The objective of the present study was to identify differentially expressed proteins (DEPs) in the pancreas of a fetus with intrauterine growth restriction (IUGR) and to investigate the molecular mechanisms leading to adulthood diabetes in IUGR. Methods The IUGR rat model was induced by maternal protein malnutrition. The fetal pancreas was collected at embryonic day 20 (E20). Protein was extracted, pooled, and subjected to label-free quantitative proteomic analysis. Bioinformatics analysis (GO and IPA) was performed to define the pathways and networks associated with DEPs. LC-MS results were confirmed by western blotting and/or quantitative PCR (q-PCR). The principal parameters of oxidative stress-superoxide dismutase (Sod) were determined in blood samples of fetal rats. Results A total of 57 DEPs (27 upregulated, 30 downregulated) were identified with a 1.5-fold change threshold and a p value ≤ 0.05 between the IUGR and the control pancreas. Bioinformatics analysis revealed that these proteins play important roles in peroxisome biogenesis and fission, fatty acid beta-oxidation (FAO), mitotic cell cycle, and histone modification. The peroxin Pex14 was downregulated in the IUGR pancreas as confirmed by western blotting and q-PCR. Pmp70, a peroxisomal membrane protein involved in the transport of fatty acids, was upregulated. Hsd17b4 and Acox1/2, which catalyze different steps of peroxisomal FAO, were dysregulated. Sod plasma concentrations in the IUGR fetus were higher than those in the control, suggesting partial compensation for oxidative stress. Multiple DEPs were related to the regulation of the cell cycle, including reduced Cdk1, Mcm2, and Brd4. The histone acetylation regulators Hdac1/2 were downregulated, whereas Sirt1/3 and acetylated H3K56 were increased in the IUGR fetal pancreas. Conclusion The present study identified DEPs in the fetal pancreas of IUGR rats by proteomic analysis. Downregulation of pancreas peroxins and dysregulation of enzymes involved in peroxisomal FAO may impair the biogenesis and function of the peroxisome and may underlie the development of T2 diabetes mellitus in adult IUGR rats. Disorders of cell cycle regulators may induce cell division arrest and lead to smaller islets. The present data provide new insight into the role of the peroxisome in the development of the pancreas and may be valuable in furthering our understanding of the pathogenesis of IUGR-induced diabetes.
Collapse
|
22
|
MDT-28/PLIN-1 mediates lipid droplet-microtubule interaction via DLC-1 in Caenorhabditis elegans. Sci Rep 2019; 9:14902. [PMID: 31624276 PMCID: PMC6797801 DOI: 10.1038/s41598-019-51399-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
Ectopic lipid accumulation in lipid droplets (LD) has been linked to many metabolic diseases. In this study, DHS-3::GFP was used as a LD marker in C. elegans and a forward genetic screen was carried out to find novel LD regulators. There were 140 mutant alleles identified which were divided into four phenotypic categories: enlarged, aggregated, aggregated and small, and decreased. After genetic mapping, mutations in three known LD regulatory genes (maoc-1, dhs-28, daf-22) and a peroxisome-related gene (acox-3) were found to enlarge LDs, demonstrating the reliability of using DHS-3 as a living marker. In the screen, the cytoskeleton protein C27H5.2 was found to be involved in LD aggregation, as was the LD resident/structure-like protein, MDT-28/PLIN-1. Using yeast two-hybrid screening and pull-down assays, MDT-28/PLIN-1 was found to bind to DLC-1 (dynein light chain). Fluorescence imaging confirmed that MDT-28/PLIN-1 mediated the interaction between DHS-3 labeled LDs and DLC-1 labeled microtubules. Furthermore, MDT-28/PLIN-1 was directly bound to DLC-1 through its amino acids 1–210 and 275–415. Taken together, our results suggest that MDT-28/PLIN-1 is involved in the regulation of LD distribution through its interaction with microtubule-related proteins.
Collapse
|
23
|
Ascaroside Pheromones: Chemical Biology and Pleiotropic Neuronal Functions. Int J Mol Sci 2019; 20:ijms20163898. [PMID: 31405082 PMCID: PMC6719183 DOI: 10.3390/ijms20163898] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Pheromones are neuronal signals that stimulate conspecific individuals to react to environmental stressors or stimuli. Research on the ascaroside (ascr) pheromones in Caenorhabditis elegans and other nematodes has made great progress since ascr#1 was first isolated and biochemically defined in 2005. In this review, we highlight the current research on the structural diversity, biosynthesis, and pleiotropic neuronal functions of ascr pheromones and their implications in animal physiology. Experimental evidence suggests that ascr biosynthesis starts with conjugation of ascarylose to very long-chain fatty acids that are then processed via peroxisomal β-oxidation to yield diverse ascr pheromones. We also discuss the concentration and stage-dependent pleiotropic neuronal functions of ascr pheromones. These functions include dauer induction, lifespan extension, repulsion, aggregation, mating, foraging and detoxification, among others. These roles are carried out in coordination with three G protein-coupled receptors that function as putative pheromone receptors: SRBC-64/66, SRG-36/37, and DAF-37/38. Pheromone sensing is transmitted in sensory neurons via DAF-16-regulated glutamatergic neurotransmitters. Neuronal peroxisomal fatty acid β-oxidation has important cell-autonomous functions in the regulation of neuroendocrine signaling, including neuroprotection. In the future, translation of our knowledge of nematode ascr pheromones to higher animals might be beneficial, as ascr#1 has some anti-inflammatory effects in mice. To this end, we propose the establishment of pheromics (pheromone omics) as a new subset of integrated disciplinary research area within chemical ecology for system-wide investigation of animal pheromones.
Collapse
|
24
|
Dolke F, Dong C, Bandi S, Paetz C, Glauser G, von Reuß SH. Ascaroside Signaling in the Bacterivorous Nematode Caenorhabditis remanei Encodes the Growth Phase of Its Bacterial Food Source. Org Lett 2019; 21:5832-5837. [PMID: 31305087 DOI: 10.1021/acs.orglett.9b01914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel class of species-specific modular ascarosides that integrate additional fatty acid building blocks was characterized in the nematode Caenorhabditis remanei using a combination of HPLC-ESI-(-)-MS/MS precursor ion scanning, microreactions, HR-MS/MS, MSn, and NMR techniques. The structure of the dominating component carrying a cyclopropyl fatty acid moiety was established by total synthesis. Biogenesis of this female-produced male attractant depends on cyclopropyl fatty acid synthase (cfa), which is expressed in bacteria upon entering their stationary phase.
Collapse
Affiliation(s)
- Franziska Dolke
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Chuanfu Dong
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Siva Bandi
- Laboratory for Bioanalytical Chemistry, Institute of Chemistry , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| | - Christian Paetz
- Research Group Biosynthesis/NMR , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Gaétan Glauser
- Neuchâtel Platform for Analytical Chemistry (NPAC) , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| | - Stephan H von Reuß
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany.,Laboratory for Bioanalytical Chemistry, Institute of Chemistry , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland.,Neuchâtel Platform for Analytical Chemistry (NPAC) , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| |
Collapse
|
25
|
Butcher RA. Natural products as chemical tools to dissect complex biology in C. elegans. Curr Opin Chem Biol 2019; 50:138-144. [PMID: 31102973 DOI: 10.1016/j.cbpa.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
The search for novel pheromones, hormones, and other types of natural products in the nematode Caenorhabditis elegans has accelerated over the last 10-15 years. Many of these natural products perturb fundamental processes such as developmental progression, metabolism, reproductive and somatic aging, and various behaviors and have thus become essential tools for probing these processes, which are difficult to study in higher organisms. Furthermore, given the similarity between C. elegans and parasitic nematodes, these natural products could potentially be used to manipulate the development and behavior of parasitic nematodes and target the infections caused by them.
Collapse
Affiliation(s)
- Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States.
| |
Collapse
|
26
|
Zhou Y, Zhang X, Butcher RA. Tryptophan Metabolism in Caenorhabditis elegans Links Aggregation Behavior to Nutritional Status. ACS Chem Biol 2019; 14:50-57. [PMID: 30586284 DOI: 10.1021/acschembio.8b00872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Caenorhabditis elegans uses aggregation pheromones to communicate its nutritional status and recruit fellow members of its species to food sources. These aggregation pheromones include the IC-ascarosides, ascarosides modified with an indole-3-carbonyl (IC) group on the 4'-position of the ascarylose sugar. Nothing is known about the biosynthesis of the IC modification beyond the fact that it is derived from tryptophan. Here, we show that C. elegans produces endogenously several indole-containing metabolites, including indole-3-pyruvic acid (IPA), indole-3-acetic acid (IAA; auxin), and indole-3-carboxylic acid, and that these metabolites are intermediates in the biosynthetic pathway from tryptophan to the IC group. Stable isotope-labeled IPA and IAA are incorporated into the IC-ascarosides. Importantly, we show that flux through the biosynthetic pathway is affected by the activity of the pyruvate dehydrogenase complex (PDC). Knockdown of the PDC by RNA interference leads to an accumulation of upstream metabolites and a reduction in downstream metabolites in the pathway. Our results show that production of aggregation pheromones is linked to PDC activity and that aggregation behavior may reflect a favorable metabolic state in the worm. Lastly, we show that treatment of C. elegans with indole-containing metabolites in the pathway induces the biosynthesis of the IC-ascarosides. Because the natural environment of C. elegans is rotting plant material, indole-containing metabolites in this environment could potentially stimulate pheromone biosynthesis and aggregation behavior in the worm. Thus, there may be important links between tryptophan metabolism in C. elegans and in plants and bacteria that enable interkingdom signaling.
Collapse
Affiliation(s)
- Yue Zhou
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Xinxing Zhang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
27
|
McGrath PT, Ruvinsky I. A primer on pheromone signaling in Caenorhabditis elegans for systems biologists. ACTA ACUST UNITED AC 2018; 13:23-30. [PMID: 30984890 DOI: 10.1016/j.coisb.2018.08.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Individuals communicate information about their age, sex, social status, and recent life history with other members of their species through the release of pheromones, chemical signals that elicit behavioral or physiological changes in the recipients. Pheromones provide a fascinating example of information exchange: animals have evolved intraspecific languages in the presence of eavesdroppers and cheaters. In this review, we discuss the recent work using the nematode C. elegans to decipher its chemical language through the analysis of ascaroside pheromones. Genetic dissection has started to identify the enzymes that produce pheromones and the neural circuits that process these signals. Ecological experiments have characterized the biotic environment of C. elegans and its relatives, including ecological relationships with a variety of species that sense or release similar blends of ascarosides. Systems biology approaches should be fruitful in understanding the organization and function of communication systems in C. elegans.
Collapse
Affiliation(s)
- Patrick T McGrath
- Department of Biological Sciences, Department of Physics; Georgia Institute of Technology, Atlanta, GA 30332.
| | - Ilya Ruvinsky
- Department of Molecular Biosciences; Northwestern University, Evanston, IL 60208.
| |
Collapse
|
28
|
White CV, Herman MA. Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction Between Caenorhabditis elegans and Stenotrophomonas maltophilia. Front Cell Infect Microbiol 2018; 8:266. [PMID: 30177956 PMCID: PMC6109753 DOI: 10.3389/fcimb.2018.00266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
The bacterivorous nematode Caenorhabditis elegans is an excellent model for the study of innate immune responses to a variety of bacterial pathogens, including the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia. The study of this interaction has ecological and medical relevance as S. maltophilia is found in association with C. elegans and other nematodes in the wild and is an emerging opportunistic bacterial pathogen. We identified 393 genes that were differentially expressed when exposed to virulent and avirulent strains of S. maltophilia and an avirulent strain of E. coli. We then used a probabilistic functional gene network model (WormNet) to determine that 118 of the 393 differentially expressed genes formed an interacting network and identified a set of highly connected genes with eight or more predicted interactions. We hypothesized that these highly connected genes might play an important role in the defense against S. maltophila and found that mutations of six of seven highly connected genes have a significant effect on nematode survival in response to these bacteria. Of these genes, C48B4.1, mpk-2, cpr-4, clec-67, and lys-6 are needed for combating the virulent S. maltophilia JCMS strain, while dod-22 was solely involved in response to the avirulent S. maltophilia K279a strain. We further found that dod-22 and clec-67 were up regulated in response to JCMS vs. K279a, while C48B4.1, mpk-2, cpr-4, and lys-6 were down regulated. Only dod-22 had a documented role in innate immunity, which demonstrates the merit of our approach in the identification of novel genes that are involved in combating S. maltophilia infection.
Collapse
Affiliation(s)
- Corin V White
- Ecological Genomics Institute, Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Michael A Herman
- Ecological Genomics Institute, Division of Biology, Kansas State University, Manhattan, KS, United States
| |
Collapse
|
29
|
Zhao L, Ahmad F, Lu M, Zhang W, Wickham JD, Sun J. Ascarosides Promote the Prevalence of Ophiostomatoid Fungi and an Invasive Pathogenic Nematode, Bursaphelenchus xylophilus. J Chem Ecol 2018; 44:701-710. [PMID: 30033490 DOI: 10.1007/s10886-018-0996-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/08/2018] [Accepted: 07/12/2018] [Indexed: 01/28/2023]
Abstract
Understanding the coevolution of pathogens and their associated mycoflora depend upon a proper elucidation of the basis of their chemical communication. In the case of pine wilt disease, the mutual interactions between cerambycid beetles, invasive pathogenic nematodes, (Bursaphelenchus xylophilus) and their symbiotic ophiostomatoid fungi provide a unique opportunity to understand the role of small molecules in mediating their chemical communication. Nematodes produce ascarosides, a highly conserved family of small molecules that serve essential functions in nematode biology and ecology. Here we demonstrated that the associated fungi, one of the key natural food resources of pine wood nematodes, can detect and respond to these ascarosides. We found that ascarosides significantly increase the growth of L. pini-densiflorae and Sporothrix sp. 1, which are native fungal species in China that form a symbiotic relationship with pinewood nematodes. Hyphal mass of L. pini-densiflorae increased when treated with asc-C5 compared to other ophiostomatoid species. Field results demonstrated that in forests where higher numbers of PWN were isolated from beetle galleries, L. pini-densiflorae had been prevalent; the same results were confirmed in laboratory studies. Furthermore, when treated with asc-C5, L. pini-densiflorae responded by increasing its production of spores, which leads to a higher likelihood of dispersal by insect vectors, hence explaining the dominance of L. pini-densiflorae over S. sp. 1 in the Tianwang and Nanlu Mountains within the Northern Forestry Centre of China. These findings provide an emphatic representation of coevolution of pine wood nematode and its associated fungi. Our results lay a broader foundation for a better understanding of inter-kingdom mutualisms and the chemical signals that mediate their establishment.
Collapse
Affiliation(s)
- Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Faheem Ahmad
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, 45550, Pakistan
| | - Min Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jacob D Wickham
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 10049, China.
| |
Collapse
|
30
|
Zhou Y, Wang Y, Zhang X, Bhar S, Jones Lipinski RA, Han J, Feng L, Butcher RA. Biosynthetic tailoring of existing ascaroside pheromones alters their biological function in C. elegans. eLife 2018; 7:33286. [PMID: 29863473 PMCID: PMC5986272 DOI: 10.7554/elife.33286] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
Caenorhabditis elegans produces ascaroside pheromones to control its development and behavior. Even minor structural differences in the ascarosides have dramatic consequences for their biological activities. Here, we identify a mechanism that enables C. elegans to dynamically tailor the fatty-acid side chains of the indole-3-carbonyl (IC)-modified ascarosides it has produced. In response to starvation, C. elegans uses the peroxisomal acyl-CoA synthetase ACS-7 to activate the side chains of medium-chain IC-ascarosides for β-oxidation involving the acyl-CoA oxidases ACOX-1.1 and ACOX-3. This pathway rapidly converts a favorable ascaroside pheromone that induces aggregation to an unfavorable one that induces the stress-resistant dauer larval stage. Thus, the pathway allows the worm to respond to changing environmental conditions and alter its chemical message without having to synthesize new ascarosides de novo. We establish a new model for biosynthesis of the IC-ascarosides in which side-chain β-oxidation is critical for controlling the type of IC-ascarosides produced. Small roundworms such as Caenorhabditis elegans release chemical signals called ascarosides in order to communicate with other worms of the same species. Using the ascarosides, the worm can tell its friends, for example, how crowded the neighborhood is and whether there is enough food. The ascarosides thus help the worms in the population decide whether the neighborhood is good – meaning they should hang around, eat, and make babies – or whether the neighborhood is bad. If so, the worms should develop into a larval stage specialized for dispersal that will allow them to find a better neighborhood. Roundworms make the ascarosides by attaching a long chemical ‘side chain’ to an ascarylose sugar. Further chemical modifications allow the worms to produce different signals. In general, to signal a good neighborhood, worms attach a structure called an indole group to the ascarosides. To signal a bad neighborhood, worms make the side chain very short. But how does a worm control which ascarosides it makes? Zhou, Wang et al. now show that C. elegans can change the meaning of its chemical message by modifying the ascarosides that it has already produced instead of making new ones from scratch. Specifically, as their neighborhood runs out of food, C. elegans can use an enzyme called ACS-7 to initiate the shortening of the side chains of indole-ascarosides. The worm can thus change a favorable ascaroside signal that causes the worms to group together into an unfavorable ascaroside signal that causes the worms to enter their dispersal stage. Although Zhou, Wang et al. have focused on chemical communication in C. elegans, the findings could easily apply to the many other species of roundworm that produce ascarosides. Knowing how worms communicate will help us to understand how worms respond to their environment. This knowledge could potentially be used to interfere with the lifecycles and survival of parasitic worm species that harm health and crops.
Collapse
Affiliation(s)
- Yue Zhou
- Department of Chemistry, University of Florida, Gainesville, United States
| | - Yuting Wang
- Department of Chemistry, University of Florida, Gainesville, United States
| | - Xinxing Zhang
- Department of Chemistry, University of Florida, Gainesville, United States
| | - Subhradeep Bhar
- Department of Chemistry, University of Florida, Gainesville, United States
| | | | - Jungsoo Han
- Department of Chemistry, University of Florida, Gainesville, United States
| | - Likui Feng
- Department of Chemistry, University of Florida, Gainesville, United States
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, United States
| |
Collapse
|
31
|
Falcke JM, Bose N, Artyukhin AB, Rödelsperger C, Markov GV, Yim JJ, Grimm D, Claassen MH, Panda O, Baccile JA, Zhang YK, Le HH, Jolic D, Schroeder FC, Sommer RJ. Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis. Cell Chem Biol 2018; 25:787-796.e12. [PMID: 29779955 DOI: 10.1016/j.chembiol.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/28/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022]
Abstract
In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.
Collapse
Affiliation(s)
- Jan M Falcke
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gabriel V Markov
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Joshua J Yim
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dominik Grimm
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Marc H Claassen
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dino Jolic
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| |
Collapse
|
32
|
Zhang X, Wang Y, Perez DH, Jones Lipinski RA, Butcher RA. Acyl-CoA Oxidases Fine-Tune the Production of Ascaroside Pheromones with Specific Side Chain Lengths. ACS Chem Biol 2018. [PMID: 29537254 DOI: 10.1021/acschembio.7b01021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Caenorhabditis elegans produces a complex mixture of ascaroside pheromones to control its development and behavior. Acyl-CoA oxidases, which participate in β-oxidation cycles that shorten the side chains of the ascarosides, regulate the mixture of pheromones produced. Here, we use CRISPR-Cas9 to make specific nonsense and missense mutations in acox genes and determine the effect of these mutations on ascaroside production in vivo. Ascaroside production in acox-1.1 deletion and nonsense strains, as well as a strain with a missense mutation in a catalytic residue, confirms the central importance of ACOX-1.1 in ascaroside biosynthesis and suggests that ACOX-1.1 functions in part by facilitating the activity of other acyl-CoA oxidases. Ascaroside production in an acox-1.1 strain with a missense mutation in an ATP-binding site at the ACOX-1.1 dimer interface suggests that ATP binding is important for the enzyme to function in ascaroside biosynthesis in vivo. Ascaroside production in strains with deletion, nonsense, and missense mutations in other acox genes demonstrates that ACOX-1.1 works with ACOX-1.3 in processing ascarosides with 7-carbon side chains, ACOX-1.4 in processing ascarosides with 9- and 11-carbon side chains, and ACOX-3 in processing ascarosides with 13- and 15-carbon side chains. It also shows that ACOX-1.2, but not ACOX-1.1, processes ascarosides with 5-carbon ω-side chains. By modeling the ACOX structures, we uncover characteristics of the enzyme active sites that govern substrate preferences. Our work demonstrates the role of specific acyl-CoA oxidases in controlling the length of ascaroside side chains and thus in determining the mixture of pheromones produced by C. elegans.
Collapse
Affiliation(s)
- Xinxing Zhang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yuting Wang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - David H. Perez
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
33
|
Dong C, Reilly DK, Bergame C, Dolke F, Srinivasan J, von Reuss SH. Comparative Ascaroside Profiling of Caenorhabditis Exometabolomes Reveals Species-Specific (ω) and (ω - 2)-Hydroxylation Downstream of Peroxisomal β-Oxidation. J Org Chem 2018; 83:7109-7120. [PMID: 29480728 DOI: 10.1021/acs.joc.8b00094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical communication in nematodes such as the model organism Caenorhabditis elegans is modulated by a variety of glycosides based on the dideoxysugar l-ascarylose. Comparative ascaroside profiling of nematode exometabolome extracts using a GC-EIMS screen reveals that several basic components including ascr#1 (asc-C7), ascr#2 (asc-C6-MK), ascr#3 (asc-ΔC9), ascr#5 (asc-ωC3), and ascr#10 (asc-C9) are highly conserved among the Caenorhabditis. Three novel side chain hydroxylated ascaroside derivatives were exclusively detected in the distantly related C. nigoni and C. afra. Molecular structures of these species-specific putative signaling molecules were elucidated by NMR spectroscopy and confirmed by total synthesis and chemical correlations. Biological activities were evaluated using attraction assays. The identification of (ω)- and (ω - 2)-hydroxyacyl ascarosides demonstrates how GC-EIMS-based ascaroside profiling facilitates the detection of novel ascaroside components and exemplifies how species-specific hydroxylation of ascaroside aglycones downstream of peroxisomal β-oxidation increases the structural diversity of this highly conserved class of nematode signaling molecules.
Collapse
Affiliation(s)
- Chuanfu Dong
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knoell Strasse 8 , D-07745 Jena , Germany.,Department for Integrative Evolutionary Biology , Max Planck Institute for Developmental Biology , Max-Planck-Ring 9 , D-72076 Tübingen , Germany
| | - Douglas K Reilly
- Department of Biology and Biotechnology , Worcester Polytechnic Institute , 60 Prescott Street , Worcester , Massachusetts 01605 , United States
| | - Célia Bergame
- Laboratory of Bioanalytical Chemistry , University of Neuchatel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| | - Franziska Dolke
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knoell Strasse 8 , D-07745 Jena , Germany
| | - Jagan Srinivasan
- Department of Biology and Biotechnology , Worcester Polytechnic Institute , 60 Prescott Street , Worcester , Massachusetts 01605 , United States
| | - Stephan H von Reuss
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knoell Strasse 8 , D-07745 Jena , Germany.,Laboratory of Bioanalytical Chemistry , University of Neuchatel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| |
Collapse
|
34
|
Chen XF, Tian MX, Sun RQ, Zhang ML, Zhou LS, Jin L, Chen LL, Zhou WJ, Duan KL, Chen YJ, Gao C, Cheng ZL, Wang F, Zhang JY, Sun YP, Yu HX, Zhao YZ, Yang Y, Liu WR, Shi YH, Xiong Y, Guan KL, Ye D. SIRT5 inhibits peroxisomal ACOX1 to prevent oxidative damage and is downregulated in liver cancer. EMBO Rep 2018; 19:embr.201745124. [PMID: 29491006 DOI: 10.15252/embr.201745124] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes account for ~35% of total H2O2 generation in mammalian tissues. Peroxisomal ACOX1 (acyl-CoA oxidase 1) is the first and rate-limiting enzyme in fatty acid β-oxidation and a major producer of H2O2 ACOX1 dysfunction is linked to peroxisomal disorders and hepatocarcinogenesis. Here, we show that the deacetylase sirtuin 5 (SIRT5) is present in peroxisomes and that ACOX1 is a physiological substrate of SIRT5. Mechanistically, SIRT5-mediated desuccinylation inhibits ACOX1 activity by suppressing its active dimer formation in both cultured cells and mouse livers. Deletion of SIRT5 increases H2O2 production and oxidative DNA damage, which can be alleviated by ACOX1 knockdown. We show that SIRT5 downregulation is associated with increased succinylation and activity of ACOX1 and oxidative DNA damage response in hepatocellular carcinoma (HCC). Our study reveals a novel role of SIRT5 in inhibiting peroxisome-induced oxidative stress, in liver protection, and in suppressing HCC development.
Collapse
Affiliation(s)
- Xiu-Fei Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng-Xin Tian
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Ren-Qiang Sun
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng-Li Zhang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Sha Zhou
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Jin
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Lei-Lei Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Jie Zhou
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Kun-Long Duan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Jia Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chao Gao
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhou-Li Cheng
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Fang Wang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jin-Ye Zhang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi-Ping Sun
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong-Xiu Yu
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Zheng Zhao
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yi Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei-Ren Liu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Ying-Hong Shi
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun-Liang Guan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dan Ye
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
35
|
Artyukhin AB, Zhang YK, Akagi AE, Panda O, Sternberg PW, Schroeder FC. Metabolomic "Dark Matter" Dependent on Peroxisomal β-Oxidation in Caenorhabditis elegans. J Am Chem Soc 2018; 140:2841-2852. [PMID: 29401383 PMCID: PMC5890438 DOI: 10.1021/jacs.7b11811] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peroxisomal β-oxidation (pβo) is a highly conserved fat metabolism pathway involved in the biosynthesis of diverse signaling molecules in animals and plants. In Caenorhabditis elegans, pβo is required for the biosynthesis of the ascarosides, signaling molecules that control development, lifespan, and behavior in this model organism. Via comparative mass spectrometric analysis of pβo mutants and wildtype, we show that pβo in C. elegans and the satellite model P. pacificus contributes to life stage-specific biosynthesis of several hundred previously unknown metabolites. The pβo-dependent portion of the metabolome is unexpectedly diverse, e.g., intersecting with nucleoside and neurotransmitter metabolism. Cell type-specific restoration of pβo in pβo-defective mutants further revealed that pβo-dependent submetabolomes differ between tissues. These results suggest that interactions of fat, nucleoside, and other primary metabolism pathways can generate structural diversity reminiscent of that arising from combinatorial strategies in microbial natural product biosynthesis.
Collapse
Affiliation(s)
- Alexander B. Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Ying K. Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Allison E. Akagi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| |
Collapse
|
36
|
Kim S, Kim KJ. Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs. Biochem Biophys Res Commun 2017; 495:1628-1634. [PMID: 29198706 DOI: 10.1016/j.bbrc.2017.11.191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/31/2023]
Abstract
Acyl-CoA oxidase (ACOX) plays an important role in fatty acid degradation. The enzyme catalyzes the first reaction in peroxisomal fatty acid β-oxidation by reducing acyl-CoA to 2-trans-enoyl-CoA. The yeast Yarrowia lipolytica is able to utilize fatty acids, fats, and oil as carbon sources to produce valuable bioproducts. We determined the crystal structure of ACOX1 from Y. lipolytica (YlACOX1) at a resolution of 2.5 Å. YlACOX1 forms a homodimer, and the monomeric structure is composed of four domains, the Nα, Nβ, Cα1, and Cα2. The FAD cofactor is bound at the dimerization interface between the Nβ- and Cα1-domains. The substrate-binding tunnel formed by the interface between the Nα-, Nβ-, and Cα1-domains is located proximal to FAD. Amino acid and structural comparisons of YlACOX1 with other ACOXs show that the substrate-binding pocket of YlACOX1 is much smaller than that of the medium- or long-chain ACOXs but is rather similar to that of the short-chain ACOXs. Moreover, the hydrophilicity of residues constituting the end region of the substrate-binding pocket in YlACOX1 is quite similar to those in the short-chain ACOXs but different from those of the medium- or long-chain ACOXs. These observations provide structural insights how YlACOX1 prefers short-chain dicarboxylyl-CoAs as a substrate.
Collapse
Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.
| |
Collapse
|
37
|
von Reuss SH, Dolke F, Dong C. Ascaroside Profiling of Caenorhabditis elegans Using Gas Chromatography-Electron Ionization Mass Spectrometry. Anal Chem 2017; 89:10570-10577. [PMID: 28866881 DOI: 10.1021/acs.analchem.7b02803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nematodes such as the model organism Caenorhabditis elegans produce various homologous series of l-ascarylose-derived glycolipids called ascarosides, which include several highly potent signals in intra and interspecies communication as well as cross-kingdom interactions. Given their low concentrations and large number of structurally similar components, mass spectrometric screens based on high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) are commonly employed for ascaroside detection and quantification. Here, we describe a complementary gas chromatography-electron ionization mass spectrometry (GC-EIMS) screen that utilizes an ascarylose-derived K1-fragment ion signal at m/z 130.1 [C6H14OSi]+● to highlight known as well as yet unidentified ascaroside components in TMS-derivatized crude nematode exometabolome extracts. GC-EIMS-based ascaroside profiling of wild-type and mutant C. elegans facilitates the analysis of all basic ascarosides using the same ionization technique while providing excellent resolution for the complete homologous series with side chains ranging from 3 to 33 carbons. Combined screening for m/z 130.1 along with side chain-specific J1 [M - 173]+ and J2 [M - 291]+ fragment ions, as well as additional characteristic marker ions from α-cleavage, enables convenient structure assignment of ca. 200 components from wild-type and peroxisomal β-oxidation mutants including (ω - 1)-linked acyl, enoyl, β-hydroxyacyl, and 2-ketoalkyl ascarosides along with their (ω)-linked or α-methyl isomers and ethanolamide derivatives, as well as 2-hydroxyalkyl ascarosides. Given the widespread availability of GC-MS and its increasing popularity in metabolomics, this method will promote the identification of ascarosides in C. elegans and other nematodes.
Collapse
Affiliation(s)
- Stephan H von Reuss
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology , D-07745 Jena, Germany
| | - Franziska Dolke
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology , D-07745 Jena, Germany
| | - Chuanfu Dong
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology , D-07745 Jena, Germany
| |
Collapse
|
38
|
Small-molecule pheromones and hormones controlling nematode development. Nat Chem Biol 2017; 13:577-586. [PMID: 28514418 DOI: 10.1038/nchembio.2356] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Abstract
The existence of small-molecule signals that influence development in Caenorhabditis elegans has been known for several decades, but only in recent years have the chemical structures of several of these signals been established. The identification of these signals has enabled connections to be made between these small molecules and fundamental signaling pathways in C. elegans that influence not only development but also metabolism, fertility, and lifespan. Spurred by these important discoveries and aided by recent advances in comparative metabolomics and NMR spectroscopy, the field of nematode chemistry has the potential to expand dramatically in the coming years. This Perspective will focus on small-molecule pheromones and hormones that influence developmental events in the nematode life cycle (ascarosides, dafachronic acids, and nemamides), will cover more recent work regarding the biosynthesis of these signals, and will explore how the discovery of these signals is transforming our understanding of nematode development and physiology.
Collapse
|
39
|
Abstract
The nematode Caenorhabditis elegans produces tens, if not hundreds, of different ascarosides as pheromones to communicate with other members of its species. Overlapping mixtures of these pheromones affect the development of the worm and a variety of different behaviors. The ascarosides represent a unique tool for dissecting the neural circuitry that controls behavior and that connects to important signaling pathways, such as the insulin and TGFβ pathways, that lie at the nexus of development, metabolism, and lifespan in C. elegans. However, the exact physiological roles of many of the ascarosides are unclear, especially since many of these pheromones likely have multiple functions depending on their concentrations, the presence of other pheromones, and a variety of other factors. Determining these physiological roles will be facilitated by top-down approaches to characterize the pheromone receptors and their function, as well as bottom-up approaches to characterize the pheromone biosynthetic enzymes and their regulation.
Collapse
Affiliation(s)
- Rebecca A Butcher
- University of Florida, Department of Chemistry, Gainesville, FL 32611, USA.
| |
Collapse
|
40
|
Panda O, Akagi AE, Artyukhin AB, Judkins JC, Le HH, Mahanti P, Cohen SM, Sternberg PW, Schroeder FC. Biosynthesis of Modular Ascarosides in
C. elegans. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Allison E. Akagi
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA
| | - Alexander B. Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Joshua C. Judkins
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Parag Mahanti
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Sarah M. Cohen
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA
| | - Paul W. Sternberg
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| |
Collapse
|
41
|
Panda O, Akagi AE, Artyukhin AB, Judkins JC, Le HH, Mahanti P, Cohen SM, Sternberg PW, Schroeder FC. Biosynthesis of Modular Ascarosides in C. elegans. Angew Chem Int Ed Engl 2017; 56:4729-4733. [PMID: 28371259 DOI: 10.1002/anie.201700103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/20/2017] [Indexed: 11/11/2022]
Abstract
The nematode Caenorhabditis elegans uses simple building blocks from primary metabolism and a strategy of modular assembly to build a great diversity of signaling molecules, the ascarosides, which function as a chemical language in this model organism. In the ascarosides, the dideoxysugar ascarylose serves as a scaffold to which diverse moieties from lipid, amino acid, neurotransmitter, and nucleoside metabolism are attached. However, the mechanisms that underlie the highly specific assembly of ascarosides are not understood. We show that the acyl-CoA synthetase ACS-7, which localizes to lysosome-related organelles, is specifically required for the attachment of different building blocks to the 4'-position of ascr#9. We further show that mutants lacking lysosome-related organelles are defective in the production of all 4'-modified ascarosides, thus identifying the waste disposal system of the cell as a hotspot for ascaroside biosynthesis.
Collapse
Affiliation(s)
- Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Allison E Akagi
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Joshua C Judkins
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Parag Mahanti
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Sarah M Cohen
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.,Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Paul W Sternberg
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
42
|
Ding H, Shi H, Shi Y, Guo X, Zheng X, Chen X, Zhou Q, Yang Y, Du A. Characterization and function analysis of a novel gene, Hc-maoc-1, in the parasitic nematode Haemonochus contortus. Parasit Vectors 2017; 10:67. [PMID: 28166831 PMCID: PMC5294872 DOI: 10.1186/s13071-017-1991-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enoyl-CoA hydratase (MAOC) is required for the biosynthesis of the fatty acid-derive side chains of the ascaroside via peroxisome β-oxidation in the free-living nematode Caenorhabditis elegans. The derivative of dideoxy-sugar, ascarylose is used as dauer pheromones or daumones to induce development of the stress-resistant dauer larvae stage. METHODS Hc-maoc-1 gene was obtained by searching the Wellcome Trusts Sanger Institute's H. contortus genomic database. qRT-PCR was performed to analyse the transcriptional levels of Hc-maoc-1 with different developmental stages as templates. IFA was carried out to determine the expression pattern in L3 larvae and micro-injection was used to verify the promoter activity of 5'-flanking region of Hc-maoc-1. Overexpression and RNAi experiments were applied in N2 strain to ascertain the gene function of Hc-maoc-1. RESULTS The full-length cDNA of Hc-maoc-1 was 900 bp in length, which contained eight exons separated by seven introns and possessed the Hotdog domain and the MaoC-like domain, together with several other residues and a hydratase 2 motif. It was transcribed throughout the lifecycle and peaked in the fourth-stage larvae (L4) of H. contortus; however, its transcription level decreased in diapausing L4. The protein expression and location of Hc-MAOC-1 were mainly in the intestine of L3 larvae. Overexpression of Ce-maoc-1 and Hc-maoc-1 in C. elegans showed extended lifespan and increased body size. The protein Ce-MAOC-1 and Hc-MAOC-1 were localized in the intestine with a punctate pattern. In C. elegans, knockdown of Ce-maoc-1 conferred shortened lifespan and body lengths, decreased brood size and increased lipid storage. CONCLUSION Caenorhabditis elegans was used as a model organism to ascertain the function of Hc-maoc-1 in H. contortus. Our results showed the similar characteristics and functions with Ce-maoc-1 and provided evidences of the potential functions of Hc-maoc-1 in biosynthesis of daumones in H. contortus.
Collapse
Affiliation(s)
- Haojie Ding
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Hengzhi Shi
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yu Shi
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiaolu Guo
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiuping Zheng
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xueqiu Chen
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Qianjin Zhou
- Faculty of Life Science and Biotechnology, Ningbo University, Ningbo, 315211, China
| | - Yi Yang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Aifang Du
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
43
|
Greene JS, Brown M, Dobosiewicz M, Ishida IG, Macosko EZ, Zhang X, Butcher RA, Cline DJ, McGrath PT, Bargmann CI. Balancing selection shapes density-dependent foraging behaviour. Nature 2016; 539:254-258. [PMID: 27799655 PMCID: PMC5161598 DOI: 10.1038/nature19848] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 09/14/2016] [Indexed: 02/04/2023]
Abstract
The optimal foraging strategy in a given environment depends on the number of competing individuals and their behavioural strategies. Little is known about the genes and neural circuits that integrate social information into foraging decisions. Here we show that ascaroside pheromones, small glycolipids that signal population density, suppress exploratory foraging in Caenorhabditis elegans, and that heritable variation in this behaviour generates alternative foraging strategies. We find that natural C. elegans isolates differ in their sensitivity to the potent ascaroside icas#9 (IC-asc-C5). A quantitative trait locus (QTL) regulating icas#9 sensitivity includes srx-43, a G-protein-coupled icas#9 receptor that acts in the ASI class of sensory neurons to suppress exploration. Two ancient haplotypes associated with this QTL confer competitive growth advantages that depend on ascaroside secretion, its detection by srx-43 and the distribution of food. These results suggest that balancing selection at the srx-43 locus generates alternative density-dependent behaviours, fulfilling a prediction of foraging game theory.
Collapse
Affiliation(s)
- Joshua S Greene
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Maximillian Brown
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - May Dobosiewicz
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Itzel G Ishida
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Evan Z Macosko
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Xinxing Zhang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - Devin J Cline
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Cornelia I Bargmann
- Howard Hughes Medical Institute, Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA
| |
Collapse
|
44
|
Shou Q, Feng L, Long Y, Han J, Nunnery JK, Powell DH, Butcher RA. A hybrid polyketide-nonribosomal peptide in nematodes that promotes larval survival. Nat Chem Biol 2016; 12:770-2. [PMID: 27501395 PMCID: PMC5030153 DOI: 10.1038/nchembio.2144] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 06/16/2016] [Indexed: 11/18/2022]
Abstract
Polyketides and nonribosomal peptides are two important types of natural products that are produced by many species of bacteria and fungi but are exceedingly rare in metazoans. Here, we elucidate the structure of a hybrid polyketide-nonribosomal peptide from Caenorhabditis elegans that is produced in the canal-associated neurons (CANs) and promotes survival during starvation-induced larval arrest. Our results uncover a novel mechanism by which animals respond to nutrient fluctuations to extend survival.
Collapse
Affiliation(s)
| | | | - Yaoling Long
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Jungsoo Han
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | | | - David H. Powell
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | | |
Collapse
|
45
|
Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2016; 113:10055-60. [PMID: 27551084 DOI: 10.1073/pnas.1608262113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal β-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.
Collapse
|
46
|
Ascarosides coordinate the dispersal of a plant-parasitic nematode with the metamorphosis of its vector beetle. Nat Commun 2016; 7:12341. [PMID: 27477780 PMCID: PMC4974635 DOI: 10.1038/ncomms12341] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/23/2016] [Indexed: 11/24/2022] Open
Abstract
Insect vectors are required for the transmission of many species of parasitic nematodes, but the mechanisms by which the vectors and nematodes coordinate their life cycles are poorly understood. Here, we report that ascarosides, an evolutionarily conserved family of nematode pheromones, are produced not only by a plant-parasitic nematode, but also by its vector beetle. The pinewood nematode and its vector beetle cause pine wilt disease, which threatens forest ecosystems world-wide. Ascarosides secreted by the dispersal third-stage nematode LIII larvae promote beetle pupation by inducing ecdysone production in the beetle and up-regulating ecdysone-dependent gene expression. Once the beetle develops into the adult stage, it secretes ascarosides that attract the dispersal fourth-stage nematode LIV larvae, potentially facilitating their movement into the beetle trachea for transport to the next pine tree. These results demonstrate that ascarosides play a key role in the survival and spread of pine wilt disease. Many species of nematodes use pheromones called ascarosides to coordinate their behaviour and development. Here, Zhao et al. demonstrate that the beetle vector of the pinewood nematode (Bursaphelenchus xylophilus) also uses and responds to ascarosides in its interactions with the nematodes.
Collapse
|
47
|
Dong C, Dolke F, von Reuss SH. Selective MS screening reveals a sex pheromone in Caenorhabditis briggsae and species-specificity in indole ascaroside signalling. Org Biomol Chem 2016; 14:7217-25. [PMID: 27381649 DOI: 10.1039/c6ob01230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The indole ascarosides (icas) represent a highly potent class of nematode-derived modular signalling components that integrate structural inputs from amino acid, carbohydrate, and fatty acid metabolism. Comparative analysis of the crude exo-metabolome of hermaphroditic Caenorhabditis briggsae using a highly sensitive mass spectrometric screen reveals an indole ascaroside blend dominated by two new components. The structures of isolated icas#2 and icas#6.2 were determined by NMR spectroscopy and confirmed by total synthesis and chemical correlation. Low atto- to femtomolar amounts of icas#2 and icas#6.2 act in synergism to attract males indicating a function as sex pheromone. Comparative analysis of 14 Caenorhabditis species further demonstrates that species-specific indole ascaroside biosynthesis is highly conserved in the Elegans group. Functional characterization of the dominating indole ascarosides icas#2, icas#3, and icas#9 reveals a high degree of species-specificity and considerable variability with respect to gender-specificity, thus, confirming that indole ascarosides modulate different biological functions within the Elegans group. Although the nematode response was usually most pronounced towards conspecific signals, Caenorhabditis brenneri, the only species of the Elegans group that does not produce any indole ascarosides, exhibits a robust response to icas#2 suggesting the potential for interspecies interactions.
Collapse
Affiliation(s)
- Chuanfu Dong
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knoell Strasse 8, D-07745 Jena, Germany.
| | | | | |
Collapse
|
48
|
Markov GV, Meyer JM, Panda O, Artyukhin AB, Claaßen M, Witte H, Schroeder FC, Sommer RJ. Functional Conservation and Divergence of daf-22 Paralogs in Pristionchus pacificus Dauer Development. Mol Biol Evol 2016; 33:2506-14. [PMID: 27189572 DOI: 10.1093/molbev/msw090] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and integrates building blocks from diverse primary metabolic pathways. Despite this complexity of small-molecule structures and functions, little is known about the biosynthesis of small molecules in nematodes outside C. elegans Here, we show that the genes encoding enzymes of the peroxisomal β-oxidation pathway involved in small-molecule biosynthesis evolve rapidly, including gene duplications and domain switching. The thiolase daf-22, the most downstream factor in C. elegans peroxisomal β-oxidation, has duplicated in P. pacificus, resulting in Ppa-daf-22.1, which still contains the sterol-carrier-protein (SCP) domain that was lost in C. elegans daf-22, and Ppa-daf-22.2. Using the CRISPR/Cas9 system, we induced mutations in both P. pacificus daf-22 genes and identified an unexpected complexity of functional conservation and divergence. Under well-fed conditions, ascaroside biosynthesis proceeds exclusively via Ppa-daf-22.1 In contrast, starvation conditions induce Ppa-daf-22.2 activity, resulting in the production of a specific subset of ascarosides. Gene expression studies indicate a reciprocal up-regulation of both Ppa-daf-22 genes, which is, however, independent of starvation. Thus, our study reveals an unexpected functional complexity of dauer development and evolution.
Collapse
Affiliation(s)
- Gabriel V Markov
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Jan M Meyer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Oishika Panda
- Boyce Thompson Institute, Cornell University Department of Chemistry and Chemical Biology, Cornell University
| | | | - Marc Claaßen
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Hanh Witte
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University Department of Chemistry and Chemical Biology, Cornell University
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| |
Collapse
|
49
|
Identification of a dTDP-rhamnose biosynthetic pathway that oscillates with the molting cycle in Caenorhabditis elegans. Biochem J 2016; 473:1507-21. [PMID: 27009306 PMCID: PMC4888466 DOI: 10.1042/bcj20160142] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 03/23/2016] [Indexed: 01/08/2023]
Abstract
The rhamnose biosynthetic pathway, which is highly conserved across nematode species, was characterized in the nematode Caenorhabditis elegans. The pathway is up-regulated before each larval molt, suggesting that rhamnose biosynthesis plays a role in cuticle or surface coat synthesis. L-Rhamnose is a common component of cell-wall polysaccharides, glycoproteins and some natural products in bacteria and plants, but is rare in fungi and animals. In the present study, we identify and characterize a biosynthetic pathway for dTDP-rhamnose in Caenorhabditis elegans that is highly conserved across nematode species. We show that RML-1 activates glucose 1-phosphate (Glc-1-P) in the presence of either dTTP or UTP to yield dTDP-glucose or UDP-glucose, respectively. RML-2 is a dTDP-glucose 4,6-dehydratase, converting dTDP-glucose into dTDP-4-keto-6-deoxyglucose. Using mass spectrometry and NMR spectroscopy, we demonstrate that coincubation of dTDP-4-keto-6-deoxyglucose with RML-3 (3,5-epimerase) and RML-4 (4-keto-reductase) produces dTDP-rhamnose. RML-4 could only be expressed and purified in an active form through co-expression with a co-regulated protein, RML-5, which forms a complex with RML-4. Analysis of the sugar nucleotide pool in C. elegans established the presence of dTDP-rhamnose in vivo. Targeting the expression of the rhamnose biosynthetic genes by RNAi resulted in significant reductions in dTDP-rhamnose, but had no effect on the biosynthesis of a closely related sugar, ascarylose, found in the ascaroside pheromones. Therefore, the rhamnose and ascarylose biosynthetic pathways are distinct. We also show that transcriptional reporters for the rhamnose biosynthetic genes are expressed highly in the embryo, in the hypodermis during molting cycles and in the hypodermal seam cells specifically before the molt to the stress-resistant dauer larval stage. These expression patterns suggest that rhamnose biosynthesis may play an important role in hypodermal development or the production of the cuticle or surface coat during molting.
Collapse
|
50
|
Witting M, Schmitt-Kopplin P. The Caenorhabditis elegans lipidome. Arch Biochem Biophys 2016; 589:27-37. [DOI: 10.1016/j.abb.2015.06.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/02/2015] [Accepted: 06/04/2015] [Indexed: 12/30/2022]
|