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Coig R, Harrison BR, Johnson RS, MacCoss MJ, Promislow DEL. Tissue-specific metabolomic signatures for a doublesex model of reduced sexual dimorphism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612537. [PMID: 39345368 PMCID: PMC11429604 DOI: 10.1101/2024.09.11.612537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Sex has a major effect on the metabolome. However, we do not yet understand the degree to which these quantitative sex differences in metabolism are associated with anatomical dimorphism and modulated by sex-specific tissues. In the fruit fly, Drosophila melanogaster , knocking out the doublesex ( dsx ) gene gives rise to adults with intermediate sex characteristics. Here we sought to determine the degree to which this key node in sexual development leads to sex differences in the fly metabolome. We measured 91 metabolites across head, thorax and abdomen in Drosophila , comparing the differences between distinctly sex-dimorphic flies with those of reduced sexual dimorphism: dsx null flies. Notably, in the reduced dimorphism flies, we observed a sex difference in only 1 of 91 metabolites, kynurenate, whereas 51% of metabolites (46/91) were significantly different between wildtype XX and XY flies in at least one tissue, suggesting that dsx plays a major role in sex differences in fly metabolism. Kynurenate was consistently higher in XX flies in both the presence and absence of functioning dsx . We observed tissue-specific consequences of knocking out dsx . Metabolites affected by sex were significantly enriched in branched chain amino acid metabolism and the mTOR pathway. This highlights the importance of considering variation in genes that cause anatomical sexual dimorphism when analyzing sex differences in metabolic profiles and interpreting their biological significance.
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He Z, Fang Y, Zhang F, Liu Y, Cheng X, Wang J, Li D, Chen D, Wu F. Adenine nucleotide translocase 2 (Ant2) is required for individualization of spermatogenesis of Drosophila melanogaster. INSECT SCIENCE 2024; 31:1055-1072. [PMID: 38112480 DOI: 10.1111/1744-7917.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
Successful completion of spermatogenesis is crucial for the perpetuation of the species. In Drosophila, spermatid individualization, a process involving changes in mitochondrial structure and function is critical to produce functional mature sperm. Ant2, encoding a mitochondrial adenine nucleotide translocase, is highly expressed in male testes and plays a role in energy metabolism in the mitochondria. However, its molecular function remains unclear. Here, we identified an important role of Ant2 in spermatid individualization. In Ant2 knockdown testes, spermatid individualization complexes composed of F-actin cones exhibited a diffuse distribution, and mature sperms were absent in the seminal vesicle, thus leading to male sterility. The most striking effects in Ant2-knockdown spermatids were decrease in tubulin polyglycylation and disruption of proper mitochondria derivatives function. Excessive apoptotic cells were also observed in Ant2-knockdown testes. To further investigate the phenotype of Ant2 knockdown in testes at the molecular level, complementary transcriptome and proteome analyses were performed. At the mRNA level, 868 differentially expressed genes were identified, of which 229 genes were upregulated and 639 were downregulated induced via Ant2 knockdown. iTRAQ-labeling proteome analysis revealed 350 differentially expressed proteins, of which 117 proteins were upregulated and 233 were downregulated. The expression of glutathione transferase (GstD5, GstE5, GstE8, and GstD3), proteins involved in reproduction were significantly regulated at both the mRNA and protein levels. These results indicate that Ant2 is crucial for spermatid maturation by affecting mitochondrial morphogenesis.
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Affiliation(s)
- Zhen He
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Yang Fang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Fengchao Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Yang Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xinkai Cheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Jiajia Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Dechen Li
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Dengsong Chen
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
| | - Fan Wu
- Industrial Crops Institute, Hubei Academy of Agriculture Sciences, Wuhan, China
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Rand MD, Tennessen JM, Mackay TFC, Anholt RRH. Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science. Curr Protoc 2023; 3:e870. [PMID: 37639638 PMCID: PMC10463236 DOI: 10.1002/cpz1.870] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The use of Drosophila melanogaster for studies of toxicology has grown considerably in the last decade. The Drosophila model has long been appreciated as a versatile and powerful model for developmental biology and genetics because of its ease of handling, short life cycle, low cost of maintenance, molecular genetic accessibility, and availability of a wide range of publicly available strains and data resources. These features, together with recent unique developments in genomics and metabolomics, make the fly model especially relevant and timely for the development of new approach methodologies and movements toward precision toxicology. Here, we offer a perspective on how flies can be leveraged to identify risk factors relevant to environmental exposures and human health. First, we review and discuss fundamental toxicologic principles for experimental design with Drosophila. Next, we describe quantitative and systems genetics approaches to resolve the genetic architecture and candidate pathways controlling susceptibility to toxicants. Finally, we summarize the current state and future promise of the emerging field of Drosophila metabolomics for elaborating toxic mechanisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Matthew D. Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
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Zhang JQ, Qiao Y, Li D, Hao S, Zhang F, Zhang X, Li A, Qin XM. Aqueous extract from Astragalus membranaceus can improve the function degradation and delay aging on Drosophila melanogaster through antioxidant mechanism. Rejuvenation Res 2022; 25:181-190. [PMID: 35726384 DOI: 10.1089/rej.2021.0081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Astragali radix is the dry root of the leguminous plants Astragalus membranaceus (Fisch.) Bge. Var. mongholicus (Bge.) Hsiao and Astragalus membranaceus (Fisch.) Bge. Astragali radix is mostly used clinically as a decoction. A number of pharmacological studies shows that Astragalus extract can increase telomerase activity, and has anti-oxidation, anti-inflammatory, immune regulation, anti-cancer, lowering blood lipid, lowering blood sugar and other effects. However, the anti-aging mechanism of aqueous extract from Astragali Radix (ARE) is still unclear. In this study, we evaluated the anti-aging effect of ARE on Drosophila melanogaster (D. melanogaster) and investigated the underlying mechanism. The results of lifespan assay showed that 1.25 mg/mL of ARE can significantly prolong the lifespan of D. melanogaster in a natural aging model, and protect against H2O2 and paraquat. Meanwhile, ARE can improve flies climbing ability and food intake. Metabolomics and the glutamate content assay suggested that ARE prevented an age-dependent increase in glutamate levels in D. melanogaster. Furthermore, ARE showed a dose-dependent effect on the scavenging ability of DPPH in vitro. Superoxide dismutase and catalase activities in the aging group also increased after the intervention of ARE. The data and the findings described here support the notion that ARE may play a preventive role in aging by improving the climbing ability, eliminating harmful free radicals accumulated in D. melanogaster and triggering antioxidant responses.
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Affiliation(s)
- Jian-Qin Zhang
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
| | - Yuqi Qiao
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
| | - Daqi Li
- Shanxi Agricultural University, 74600, College of Plant Protection, Taiyuan, Shanxi , China;
| | - Shenghui Hao
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
| | - Fusheng Zhang
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
| | - Xubo Zhang
- Shanxi University, 12441, Institute of Applied Biology, Taiyuan, Shanxi , China;
| | - Aiping Li
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
| | - Xue-Mei Qin
- Shanxi University, 12441, Modern Research Center for Traditional Chinese Medicine, Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province,the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan, Shanxi , China;
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5
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Williamson NG, Walsh CM, Kijimoto T. Comparative metabolomic analysis of polyphenic horn development in the dung beetle Onthophagus taurus. PLoS One 2022; 17:e0265222. [PMID: 35298496 PMCID: PMC8929603 DOI: 10.1371/journal.pone.0265222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Organisms alter their phenotypes in response to changing environmental conditions. The developmental basis of this phenomenon, phenotypic plasticity, is a topic of broad interest in many fields of biology. While insects provide a suitable model for studying the genetic basis of phenotypic plasticity, the physiological aspects of plasticity are not fully understood. Here, we report the physiological basis of polyphenism, an extreme form of phenotypic plasticity by utilizing a dung beetle species, Onthophagus taurus. We highlighted the metabolome between sexes as well as two distinct male morphs—large and small horns. Unlike results from previous transcriptomic studies, the comparative metabolomic study revealed that differences in metabolite level were more prominent between animals with different body sizes than different sexes. Our results also indicate that specific metabolites and biochemical pathways may be active during horn size determination.
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Affiliation(s)
- Naomi G. Williamson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Callee M. Walsh
- Shared Research Facilities, West Virginia University, Morgantown, West Virginia, United States of America
| | - Teiya Kijimoto
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
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6
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Harrison BR, Hoffman JM, Samuelson A, Raftery D, Promislow DEL. Modular Evolution of the Drosophila Metabolome. Mol Biol Evol 2022; 39:msab307. [PMID: 34662414 PMCID: PMC8760934 DOI: 10.1093/molbev/msab307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Comparative phylogenetic studies offer a powerful approach to study the evolution of complex traits. Although much effort has been devoted to the evolution of the genome and to organismal phenotypes, until now relatively little work has been done on the evolution of the metabolome, despite the fact that it is composed of the basic structural and functional building blocks of all organisms. Here we explore variation in metabolite levels across 50 My of evolution in the genus Drosophila, employing a common garden design to measure the metabolome within and among 11 species of Drosophila. We find that both sex and age have dramatic and evolutionarily conserved effects on the metabolome. We also find substantial evidence that many metabolite pairs covary after phylogenetic correction, and that such metabolome coevolution is modular. Some of these modules are enriched for specific biochemical pathways and show different evolutionary trajectories, with some showing signs of stabilizing selection. Both observations suggest that functional relationships may ultimately cause such modularity. These coevolutionary patterns also differ between sexes and are affected by age. We explore the relevance of modular evolution to fitness by associating modules with lifespan variation measured in the same common garden. We find several modules associated with lifespan, particularly in the metabolome of older flies. Oxaloacetate levels in older females appear to coevolve with lifespan, and a lifespan-associated module in older females suggests that metabolic associations could underlie 50 My of lifespan evolution.
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Affiliation(s)
- Benjamin R Harrison
- Department of Lab Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ariana Samuelson
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Daniel Raftery
- Department of Anesthesiology & Pain Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Daniel E L Promislow
- Department of Lab Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
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7
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Poma G, Cuykx M, Da Silva KM, Iturrospe E, van Nuijs AL, van Huis A, Covaci A. Edible insects in the metabolomics era. First steps towards the implementation of entometabolomics in food systems. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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8
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Scolari F, Khamis FM, Pérez-Staples D. Beyond Sperm and Male Accessory Gland Proteins: Exploring Insect Reproductive Metabolomes. Front Physiol 2021; 12:729440. [PMID: 34690804 PMCID: PMC8529219 DOI: 10.3389/fphys.2021.729440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/14/2021] [Indexed: 01/13/2023] Open
Abstract
Insect seminal fluid, the non-sperm component of the ejaculate, comprises a variegated set of molecules, including, but not limited to, lipids, proteins, carbohydrates, salts, hormones, nucleic acids, and vitamins. The identity and functional role of seminal fluid proteins (SFPs) have been widely investigated, in multiple species. However, most of the other small molecules in insect ejaculates remain uncharacterized. Metabolomics is currently adopted to deepen our understanding of complex biological processes and in the last 15years has been applied to answer different physiological questions. Technological advances in high-throughput methods for metabolite identification such as mass spectrometry and nuclear magnetic resonance (NMR) are now coupled to an expanded bioinformatics toolbox for large-scale data analysis. These improvements allow for the processing of smaller-sized samples and for the identification of hundreds to thousands of metabolites, not only in Drosophila melanogaster but also in disease vectors, animal, and agricultural pests. In this review, we provide an overview of the studies that adopted metabolomics-based approaches in insects, with a particular focus on the reproductive tract (RT) of both sexes and the ejaculate. Progress in the field of metabolomics will contribute not only to achieve a deeper understanding of the composition of insect ejaculates and how they are affected by endogenous and exogenous factors, but also to provide increasingly powerful tools to decipher the identity and molecular interactions between males and females during and after mating.
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Affiliation(s)
- Francesca Scolari
- Institute of Molecular Genetics (IGM)-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Fathiya M Khamis
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Diana Pérez-Staples
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Mexico
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9
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Proshkina E, Yushkova E, Koval L, Zemskaya N, Shchegoleva E, Solovev I, Yakovleva D, Pakshina N, Ulyasheva N, Shaposhnikov M, Moskalev A. Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster. Int J Mol Sci 2021; 22:2396. [PMID: 33673647 PMCID: PMC7957547 DOI: 10.3390/ijms22052396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Liubov Koval
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Nadezhda Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Evgeniya Shchegoleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Ilya Solovev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Daria Yakovleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Natalya Pakshina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Natalia Ulyasheva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia
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10
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Huck DT, Klein MS, Meuti ME. Determining the effects of nutrition on the reproductive physiology of male mosquitoes. JOURNAL OF INSECT PHYSIOLOGY 2021; 129:104191. [PMID: 33428881 DOI: 10.1016/j.jinsphys.2021.104191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/07/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Nutrition affects multiple aspects of insect physiology such as body size and fecundity, but we lack a detailed understanding of how nutrition influences the reproductive physiology of male insects such as mosquitoes. Given that female mosquitoes are vectors of many deadly diseases and can quickly proliferate, understanding how male nutrition impacts female fecundity could be of critical importance. To uncover the relationship between nutrition in adult male mosquitoes and its impacts on reproductive physiology, we reared larvae of the Northern house mosquito, Culex pipiens, on a standard lab diet and divided adult males among three different dietary treatments: low (3%), moderate (10%), and high (20%) sucrose. We found that although overall body size did not differ among treatments, one-week-old males raised on the 3% sucrose diet had significantly smaller male accessory glands (MAGs) compared to males that consumed the 10% and the 20% sucrose diets. Diet affected whole-body lipid content but did not affect whole-body protein content. Using nuclear magnetic resonance (NMR) spectroscopy, we found that diet altered the metabolic composition of the MAGs, including changes in lactic acid, formic acid, and glucose. We also observed changes in protein and lipid abundance and composition in MAGs. Females who mated with males on the 3% diet were found to produce significantly fewer larvae than females who had mated with males on the 10% diet. Taken together, our results demonstrate that the diet of adult male mosquitoes clearly affects male reproductive physiology and female fecundity.
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Affiliation(s)
- Derek T Huck
- Department of Entomology, The Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, United States.
| | - Matthias S Klein
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Rd, Columbus, OH 43210, United States.
| | - Megan E Meuti
- Department of Entomology, The Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, United States.
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Intracellular Density of Wolbachia Is Mediated by Host Autophagy and the Bacterial Cytoplasmic Incompatibility Gene cifB in a Cell Type-Dependent Manner in Drosophila melanogaster. mBio 2021; 12:mBio.02205-20. [PMID: 33436431 PMCID: PMC7844536 DOI: 10.1128/mbio.02205-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Autophagy is an intracellular degradation pathway involved in innate immunity. Pathogenic bacteria have evolved several mechanisms to escape degradation or exploit autophagy to acquire host nutrients. In the case of endosymbionts, which often have commensal or mutualistic interactions with the host, autophagy is not well characterized. We utilized tissue-specific autophagy mutants to determine if Wolbachia, a vertically transmitted obligate endosymbiont of Drosophila melanogaster, is regulated by autophagy in somatic and germ line cell types. Our analysis revealed core autophagy proteins Atg1 and Atg8 and a selective autophagy-specific protein Ref(2)p negatively regulate Wolbachia in the hub, a male gonad somatic cell type. Furthermore, we determined that the Wolbachia effector protein, CifB, modulates autophagy-Wolbachia interactions, identifying a new host-related pathway which these bacterial proteins interact with. In the female germ line, the cell type necessary for inheritance of Wolbachia through vertical transmission, we discovered that bulk autophagy mediated by Atg1 and Atg8 positively regulates Wolbachia density, whereas Ref(2)p had no effect. Global metabolomics of fly ovaries deficient in germ line autophagy revealed reduced lipid and carbon metabolism, implicating metabolites from these pathways as positive regulators of Wolbachia Our work provides further understanding of how autophagy affects bacteria in a cell type-dependent manner.IMPORTANCE Autophagy is a eukaryotic intracellular degradation pathway which can act as an innate immune response to eliminate pathogens. Conversely, pathogens can evolve proteins which modulate the autophagy pathway to subvert degradation and establish an infection. Wolbachia, a vertically transmitted obligate endosymbiont which infects up to 40% of insect species, is negatively regulated by autophagy in whole animals, but the specific molecular mechanism and tissue which govern this interaction remain unknown. Our studies use cell type-specific autophagy mutants to reveal that Wolbachia is negatively regulated by selective autophagy in the soma, while nonselective autophagy positively regulates Wolbachia in the female germ line. These data provide evidence that cell type can drive different basal autophagy programs which modulate intracellular microbes differently. Additionally, we identified that the Wolbachia effector CifB acts in the selective autophagy pathway to aid in intracellular bacterial survival, providing a new function for CifB beyond its previously identified role in reproductive manipulation.
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12
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Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
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13
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Onyango MG, Attardo GM, Kelly ET, Bialosuknia SM, Stout J, Banker E, Kuo L, Ciota AT, Kramer LD. Zika Virus Infection Results in Biochemical Changes Associated With RNA Editing, Inflammatory and Antiviral Responses in Aedes albopictus. Front Microbiol 2020; 11:559035. [PMID: 33133033 PMCID: PMC7561680 DOI: 10.3389/fmicb.2020.559035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
Rapid and significant range expansion of both the Zika virus (ZIKV) and its Aedes vector species has resulted in the declaration of ZIKV as a global health threat. Successful transmission of ZIKV by its vector requires a complex series of interactions between these entities including the establishment, replication and dissemination of the virus within the mosquito. The metabolic conditions within the mosquito tissues play a critical role in mediating the crucial processes of viral infection and replication and represent targets for prevention of virus transmission. In this study, we carried out a comprehensive metabolomic phenotyping of ZIKV infected and uninfected Ae. albopictus by untargeted analysis of primary metabolites, lipids and biogenic amines. We performed a comparative metabolomic study of infection state with the aim of understanding the biochemical changes resulting from the interaction between the ZIKV and its vector. We have demonstrated that ZIKV infection results in changes to the cellular metabolic environment including a significant enrichment of inosine and pseudo-uridine (Ψ) levels which may be associated with RNA editing activity. In addition, infected mosquitoes demonstrate a hypoglycemic phenotype and show significant increases in the abundance of metabolites such as prostaglandin H2, leukotriene D4 and protoporphyrinogen IX which are associated with antiviral activity. These provide a basis for understanding the biochemical response to ZIKV infection and pathology in the vector. Future mechanistic studies targeting these ZIKV infection responsive metabolites and their associated biosynthetic pathways can provide inroads to identification of mosquito antiviral responses with infection blocking potential.
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Affiliation(s)
- Maria G. Onyango
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
| | - Geoffrey M. Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Erin Taylor Kelly
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Sean M. Bialosuknia
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
- School of Public Health, State University of New York, Albany, NY, United States
| | - Jessica Stout
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
| | - Elyse Banker
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
| | - Lili Kuo
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
| | - Alexander T. Ciota
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
- School of Public Health, State University of New York, Albany, NY, United States
| | - Laura D. Kramer
- Wadsworth Center, New York State Department of Health, Slingerlands, NY, United States
- School of Public Health, State University of New York, Albany, NY, United States
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14
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Sun SJ, Catherall AM, Pascoal S, Jarrett BJM, Miller SE, Sheehan MJ, Kilner RM. Rapid local adaptation linked with phenotypic plasticity. Evol Lett 2020; 4:345-359. [PMID: 32774883 PMCID: PMC7403679 DOI: 10.1002/evl3.176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 11/05/2022] Open
Abstract
Models of "plasticity-first" evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can facilitate rapid microevolutionary change between diverging populations. Here, we show how plasticity may have generated adaptive differences in fecundity between neighboring wild populations of burying beetles Nicrophorus vespilloides. These populations occupy distinct Cambridgeshire woodlands that are just 2.5 km apart and that probably originated from a common ancestral population about 1000-4000 years ago. We find that populations are divergently adapted to breed on differently sized carrion. Adaptive differences in clutch size and egg size are associated with divergence at loci connected with oogenesis. The populations differ specifically in the elevation of the reaction norm linking clutch size to carrion size (i.e., genetic accommodation), and in the likelihood that surplus offspring will be lost after hatching. We suggest that these two processes may have facilitated rapid local adaptation on a fine-grained spatial scale.
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Affiliation(s)
- Syuan-Jyun Sun
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Andrew M Catherall
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Benjamin J M Jarrett
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom.,Department of Entomology Michigan State University East Lansing Michigan 48824
| | - Sara E Miller
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Michael J Sheehan
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Rebecca M Kilner
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
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15
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Tuthill BF, Searcy LA, Yost RA, Musselman LP. Tissue-specific analysis of lipid species in Drosophila during overnutrition by UHPLC-MS/MS and MALDI-MSI. J Lipid Res 2020; 61:275-290. [PMID: 31900315 PMCID: PMC7053833 DOI: 10.1194/jlr.ra119000198] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Diets high in calories can be used to model metabolic diseases, including obesity and its associated comorbidities, in animals. Drosophila melanogaster fed high-sugar diets (HSDs) exhibit complications of human obesity including hyperglycemia, hyperlipidemia, insulin resistance, cardiomyopathy, increased susceptibility to infection, and reduced longevity. We hypothesize that lipid storage in the high-sugar-fed fly's fat body (FB) reaches a maximum capacity, resulting in the accumulation of toxic lipids in other tissues or lipotoxicity. We took two approaches to characterize tissue-specific lipotoxicity. Ultra-HPLC-MS/MS and MALDI-MS imaging enabled spatial and temporal localization of lipid species in the FB, heart, and hemolymph. Substituent chain length was diet dependent, with fewer odd chain esterified FAs on HSDs in all sample types. By contrast, dietary effects on double bond content differed among organs, consistent with a model where some substituent pools are shared and others are spatially restricted. Both di- and triglycerides increased on HSDs in all sample types, similar to observations in obese humans. Interestingly, there were dramatic effects of sugar feeding on lipid ethers, which have not been previously associated with lipotoxicity. Taken together, we have identified candidate endocrine mechanisms and molecular targets that may be involved in metabolic disease and lipotoxicity.
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Affiliation(s)
- Bryon F. Tuthill
- Department of Biological Sciences,Binghamton University, Binghamton, NY
| | - Louis A. Searcy
- Department of Chemistry,University of Florida, Gainesville, FL
| | - Richard A. Yost
- Department of Chemistry,University of Florida, Gainesville, FL
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16
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Zhou S, Morgante F, Geisz MS, Ma J, Anholt RRH, Mackay TFC. Systems genetics of the Drosophila metabolome. Genome Res 2020; 30:392-405. [PMID: 31694867 PMCID: PMC7111526 DOI: 10.1101/gr.243030.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/11/2019] [Indexed: 02/06/2023]
Abstract
How effects of DNA sequence variants are transmitted through intermediate endophenotypes to modulate organismal traits remains a central question in quantitative genetics. This problem can be addressed through a systems approach in a population in which genetic polymorphisms, gene expression traits, metabolites, and complex phenotypes can be evaluated on the same genotypes. Here, we focused on the metabolome, which represents the most proximal link between genetic variation and organismal phenotype, and quantified metabolite levels in 40 lines of the Drosophila melanogaster Genetic Reference Panel. We identified sex-specific modules of genetically correlated metabolites and constructed networks that integrate DNA sequence variation and variation in gene expression with variation in metabolites and organismal traits, including starvation stress resistance and male aggression. Finally, we asked to what extent SNPs and metabolites can predict trait phenotypes and generated trait- and sex-specific prediction models that provide novel insights about the metabolomic underpinnings of complex phenotypes.
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Affiliation(s)
- Shanshan Zhou
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Fabio Morgante
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Matthew S Geisz
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, JiangXi Agricultural University, JiangXi, China
| | - Robert R H Anholt
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Trudy F C Mackay
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
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17
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Reisdorph NA, Walmsley S, Reisdorph R. A Perspective and Framework for Developing Sample Type Specific Databases for LC/MS-Based Clinical Metabolomics. Metabolites 2019; 10:metabo10010008. [PMID: 31877765 PMCID: PMC7023092 DOI: 10.3390/metabo10010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics has the potential to greatly impact biomedical research in areas such as biomarker discovery and understanding molecular mechanisms of disease. However, compound identification (ID) remains a major challenge in liquid chromatography mass spectrometry-based metabolomics. This is partly due to a lack of specificity in metabolomics databases. Though impressive in depth and breadth, the sheer magnitude of currently available databases is in part what makes them ineffective for many metabolomics studies. While still in pilot phases, our experience suggests that custom-built databases, developed using empirical data from specific sample types, can significantly improve confidence in IDs. While the concept of sample type specific databases (STSDBs) and spectral libraries is not entirely new, inclusion of unique descriptors such as detection frequency and quality scores, can be used to increase confidence in results. These features can be used alone to judge the quality of a database entry, or together to provide filtering capabilities. STSDBs rely on and build upon several available tools for compound ID and are therefore compatible with current compound ID strategies. Overall, STSDBs can potentially result in a new paradigm for translational metabolomics, whereby investigators confidently know the identity of compounds following a simple, single STSDB search.
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Affiliation(s)
- Nichole A. Reisdorph
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, CO 80045, USA;
- Correspondence: ; Tel.: +1-303-724-9234
| | - Scott Walmsley
- Masonic Cancer Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA;
- Institute for Health Informatics, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Rick Reisdorph
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, CO 80045, USA;
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18
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Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. Nat Commun 2019; 10:4052. [PMID: 31492856 PMCID: PMC6731244 DOI: 10.1038/s41467-019-11933-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolites are active controllers of cellular physiology, but their role in complex behaviors is less clear. Here we report metabolic changes that occur during the transition between hunger and satiety in Drosophila melanogaster. To analyze these data in the context of fruit fly metabolic networks, we developed Flyscape, an open-access tool. We show that in response to eating, metabolic profiles change in quick, but distinct ways in the heads and bodies. Consumption of a high sugar diet dulls the metabolic and behavioral differences between the fasted and fed state, and reshapes the way nutrients are utilized upon eating. Specifically, we found that high dietary sugar increases TCA cycle activity, alters neurochemicals, and depletes 1-carbon metabolism and brain health metabolites N-acetyl-aspartate and kynurenine. Together, our work identifies the metabolic transitions that occur during hunger and satiation, and provides a platform to study the role of metabolites and diet in complex behavior. The relationship between metabolomic and behavioral changes is not well understood. Here, the authors analyze metabolome changes in D. melanogaster heads and bodies during hunger and satiety, and develop the Flyscape tool to visualize the resulting metabolic networks and integrate them with other omics data.
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19
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Yang E, Gamberi C, Chaurand P. Mapping the fly Malpighian tubule lipidome by imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:557-566. [PMID: 31038251 DOI: 10.1002/jms.4366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 05/20/2023]
Abstract
Matrix-assisted laser/desorption ionization imaging mass spectrometry (MALDI IMS) is an analytical technique for understanding the spatial distribution of biomolecules across a sample surface. Originally employed for mammalian tissues, this technology has been adapted to study specimens as diverse as microbes and cell cultures, food such as strawberries, and invertebrates including the vinegar fly Drosophila melanogaster. As an ideal model organism, Drosophila has brought greater understanding about conserved biological processes, organism development, and diseased states and even informed management practices of agriculturally and environmentally important species. Drosophila displays anatomically separated renal (Malpighian) tubules that are the physiological equivalent to the vertebrate nephron. Insect Malpighian tubules are also responsible for pesticide detoxification. In this article, we first describe an effective workflow and sample preparation method to study the phospholipid distribution of the Malpighian tubules that initially involves the manual microdissection of the tubules in saline buffer followed by a series of washes to remove excess salt and enhances the phospholipid signals prior to matrix deposition and IMS at 25-μm spatial resolution. We also established a complementary methodology for lipid IMS analysis of whole-body fly sections using a dual-polarity data acquisition approach at the same spatial resolution after matrix deposition by sublimation. Both procedures yield rich signal profiles from the major phospholipid classes. The reproducibility and high-quality results offered by these methodologies enable cohort studies of Drosophila through MALDI IMS.
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Affiliation(s)
- Ethan Yang
- Department of Chemistry, University of Montreal, Pavillon Roger-Gaudry, 2900, boul. Édouard-Montpetit, Montreal, QC, Canada, H3C 3J7
| | - Chiara Gamberi
- Biology Department, Concordia University, Montreal, QC, Canada, H4B 1R6
| | - Pierre Chaurand
- Department of Chemistry, University of Montreal, Pavillon Roger-Gaudry, 2900, boul. Édouard-Montpetit, Montreal, QC, Canada, H3C 3J7
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20
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Oza VH, Aicher JK, Reed LK. Random Forest Analysis of Untargeted Metabolomics Data Suggests Increased Use of Omega Fatty Acid Oxidation Pathway in Drosophila Melanogaster Larvae Fed a Medium Chain Fatty Acid Rich High-Fat Diet. Metabolites 2018; 9:metabo9010005. [PMID: 30602659 PMCID: PMC6359074 DOI: 10.3390/metabo9010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/27/2018] [Accepted: 12/27/2018] [Indexed: 12/27/2022] Open
Abstract
Obesity is a complex disease, shaped by both genetic and environmental factors such as diet. In this study, we use untargeted metabolomics and Drosophila melanogaster to model how diet and genotype shape the metabolome of obese phenotypes. We used 16 distinct outbred genotypes of Drosophila larvae raised on normal (ND) and high-fat (HFD) diets, to produce three distinct phenotypic classes; genotypes that stored more triglycerides on a ND relative to the HFD, genotypes that stored more triglycerides on a HFD relative to ND, and genotypes that showed no change in triglyceride storage on either of the two diets. Using untargeted metabolomics we characterized 350 metabolites: 270 with definitive chemical IDs and 80 that were chemically unidentified. Using random forests, we determined metabolites that were important in discriminating between the HFD and ND larvae as well as between the triglyceride phenotypic classes. We found that flies fed on a HFD showed evidence of an increased use of omega fatty acid oxidation pathway, an alternative to the more commonly used beta fatty acid oxidation pathway. Additionally, we observed no correlation between the triglyceride storage phenotype and free fatty acid levels (laurate, caprate, caprylate, caproate), indicating that the distinct metabolic profile of fatty acids in high-fat diet fed Drosophila larvae does not propagate into triglyceride storage differences. However, dipeptides did show moderate differences between the phenotypic classes. We fit Gaussian graphical models (GGMs) of the metabolic profiles for HFD and ND flies to characterize changes in metabolic network structure between the two diets, finding the HFD to have a greater number of edges indicating that metabolome varies more across samples on a HFD. Taken together, these results show that, in the context of obesity, metabolomic profiles under distinct dietary conditions may not be reliable predictors of phenotypic outcomes in a genetically diverse population.
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Affiliation(s)
- Vishal H Oza
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Joseph K Aicher
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
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21
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Dow JA, Pandit A, Davies SA. New views on the Malpighian tubule from post-genomic technologies. CURRENT OPINION IN INSECT SCIENCE 2018; 29:7-11. [PMID: 30551828 DOI: 10.1016/j.cois.2018.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 06/09/2023]
Abstract
Successful insect diversification depends at least in part on the ability to osmoregulate successfully across a broad range of ecological niches. First described in the 17th Century, and Malpighian tubules have been studied physiologically for 70 years. However, our understanding has been revolutionized by the advent of genomics, transcriptomics, proteomics and metabolomics. Such technologies are natural partners with (though do not obligatorily require) model organisms and transgenic technologies. This review describes the recent impact of multi-omic technologies on our understanding or renal function and control in insects.
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Affiliation(s)
- Julian At Dow
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - Aniruddha Pandit
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Shireen A Davies
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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22
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Perry T, Batterham P. Harnessing model organisms to study insecticide resistance. CURRENT OPINION IN INSECT SCIENCE 2018; 27:61-67. [PMID: 30025636 DOI: 10.1016/j.cois.2018.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
The vinegar fly, Drosophila melanogaster, has made an enormous contribution to our understanding of insecticide targets, metabolism and transport. This contribution has been enabled by the unmatched capacity to manipulate genes in D. melanogaster and the fact that lessons learn in this system have been applicable to pests, because of the evolutionary conservation of key genes, particularly those encoding targets. With the advent of the CRISPR-Cas9 gene editing technology, genes can now be manipulated in pest species, but this review points to advantages that are likely to keep D. melanogaster at the forefront of insecticide research.
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Affiliation(s)
- Trent Perry
- School of BioSciences/Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Philip Batterham
- School of BioSciences/Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.
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23
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Bienkowski RS, Banerjee A, Rounds JC, Rha J, Omotade OF, Gross C, Morris KJ, Leung SW, Pak C, Jones SK, Santoro MR, Warren ST, Zheng JQ, Bassell GJ, Corbett AH, Moberg KH. The Conserved, Disease-Associated RNA Binding Protein dNab2 Interacts with the Fragile X Protein Ortholog in Drosophila Neurons. Cell Rep 2018; 20:1372-1384. [PMID: 28793261 DOI: 10.1016/j.celrep.2017.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/28/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A) RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII, but not futsch, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A) tail length, similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. Altogether, these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14.
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Affiliation(s)
- Rick S Bienkowski
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ayan Banerjee
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jennifer Rha
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Omotola F Omotade
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christina Gross
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Kevin J Morris
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara W Leung
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - ChangHui Pak
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephanie K Jones
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael R Santoro
- Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
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24
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The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster. Sci Rep 2018; 8:6215. [PMID: 29670218 PMCID: PMC5906449 DOI: 10.1038/s41598-018-24542-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Abstract
The metabolic phenotype of an organism depends on a complex regulatory network, which integrates the plethora of intrinsic and external information and prioritizes the flow of nutrients accordingly. Given the rise of metabolic disorders including obesity, a detailed understanding of this regulatory network is in urgent need. Yet, our level of understanding is far from completeness and complicated by the discovery of additional layers in metabolic regulation, such as the impact of the microbial community present in the gut on the hosts’ energy storage levels. Here, we investigate the interplay between genome variation, diet and the gut microbiome in the shaping of a metabolic phenotype. For this purpose, we reared a set of fully sequenced wild type Drosophila melanogaster flies under basal and nutritionally challenged conditions and performed metabolic and microbiome profiling experiments. Our results introduce the fly as a model system to investigate the impact of genome variation on the metabolic response to diet alterations and reveal candidate single nucleotide polymorphisms associated with different metabolic traits, as well as metabolite-metabolite and metabolite-microbe correlations. Intriguingly, the dietary changes affected the microbiome composition less than anticipated. These results challenge the current view of a rapidly changing microbiome in response to environmental fluctuations.
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25
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Walmsley S, Cruickshank-Quinn C, Quinn K, Zhang X, Petrache I, Bowler RP, Reisdorph R, Reisdorph N. A prototypic small molecule database for bronchoalveolar lavage-based metabolomics. Sci Data 2018; 5:180060. [PMID: 29664467 PMCID: PMC5903367 DOI: 10.1038/sdata.2018.60] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 02/06/2023] Open
Abstract
The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we describe prototypic, small molecule databases derived from human BALF samples (n=117). Human BALF was extracted into lipid and aqueous fractions and analyzed using liquid chromatography mass spectrometry. Following filtering to reduce contaminants and artifacts, the resulting BALF databases (BALF-DBs) contain 11,736 lipid and 658 aqueous compounds. Over 10% of these were found in 100% of samples. Testing the BALF-DBs using nested test sets produced a 99% match rate for lipids and 47% match rate for aqueous molecules. Searching an independent dataset resulted in 45% matching to the lipid BALF-DB compared to<25% when general databases are searched. The BALF-DBs are available for download from MetaboLights. Overall, the BALF-DBs can reduce false positives and improve confidence in compound identification compared to when general databases are used.
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Affiliation(s)
- Scott Walmsley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Charmion Cruickshank-Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Xing Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Irina Petrache
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Russell P Bowler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Richard Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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26
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Abstract
Excess adipose fat accumulation, or obesity, is a growing problem worldwide in terms of both the rate of incidence and the severity of obesity-associated metabolic disease. Adipose tissue evolved in animals as a specialized dynamic lipid storage depot: adipose cells synthesize fat (a process called lipogenesis) when energy is plentiful and mobilize stored fat (a process called lipolysis) when energy is needed. When a disruption of lipid homeostasis favors increased fat synthesis and storage with little turnover owing to genetic predisposition, overnutrition or sedentary living, complications such as diabetes and cardiovascular disease are more likely to arise. The vinegar fly Drosophila melanogaster (Diptera: Drosophilidae) is used as a model to better understand the mechanisms governing fat metabolism and distribution. Flies offer a wealth of paradigms with which to study the regulation and physiological effects of fat accumulation. Obese flies accumulate triacylglycerols in the fat body, an organ similar to mammalian adipose tissue, which specializes in lipid storage and catabolism. Discoveries in Drosophila have ranged from endocrine hormones that control obesity to subcellular mechanisms that regulate lipogenesis and lipolysis, many of which are evolutionarily conserved. Furthermore, obese flies exhibit pathophysiological complications, including hyperglycemia, reduced longevity and cardiovascular function - similar to those observed in obese humans. Here, we review some of the salient features of the fly that enable researchers to study the contributions of feeding, absorption, distribution and the metabolism of lipids to systemic physiology.
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Affiliation(s)
- Laura Palanker Musselman
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Ronald P Kühnlein
- Department of Biochemistry 1, Institute of Molecular Biosciences, University of Graz, Humboldtstraβe 50/II, A-8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
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27
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Metabolomics: State-of-the-Art Technologies and Applications on Drosophila melanogaster. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:257-276. [PMID: 29951824 DOI: 10.1007/978-981-13-0529-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metabolomics is one of the latest "omics" technology concerned with the high-throughput identification and quantification of metabolites, the final products of cellular processes. The revealed data provide an instantaneous snapshot of an organism's metabolic pathways, which can be used to explain its phenotype or physiology. On the other hand, Drosophila has shown its power in studying metabolism and related diseases. At this stage, we have the state-of-the-art knowledge in place: a potential candidate to study cellular metabolism (Drosophila melanogaster) and a powerful methodology for metabolic network decipherer (metabolomics). Yet missing is advanced metabolomics technologies like isotope-assisted metabolomics optimized for Drosophila. In this chapter, we will discuss on the current status and future perspectives in technologies and applications of Drosophila metabolomics.
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28
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Zampieri M, Sauer U. Metabolomics-driven understanding of genotype-phenotype relations in model organisms. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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Arnés M, Casas-Tintó S, Malmendal A, Ferrús A. Amyloid β42 peptide is toxic to non-neural cells in Drosophila yielding a characteristic metabolite profile and the effect can be suppressed by PI3K. Biol Open 2017; 6:1664-1671. [PMID: 29141953 PMCID: PMC5703620 DOI: 10.1242/bio.029991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human Aβ42 peptide is associated with Alzheimer's disease through its deleterious effects in neurons. Expressing the human peptide in adult Drosophila in a tissue- and time-controlled manner, we show that Aβ42 is also toxic in non-neural cells, neurosecretory and epithelial cell types in particular. This form of toxicity includes the aberrant signaling by Wingless morphogen leading to the eventual activation of Caspase 3. Preventing Caspase 3 activation by means of p53 keeps epithelial cells from elimination but maintains the Aβ42 toxicity yielding more severe deleterious effects to the organism. Metabolic profiling by nuclear magnetic resonance (NMR) of adult flies at selected ages post Aβ42 expression onset reveals characteristic changes in metabolites as early markers of the pathological process. All morphological and most metabolic features of Aβ42 toxicity can be suppressed by the joint overexpression of PI3K. Summary: The Alzheimer's disease-related Aβ42 peptide is toxic for non-neural cells. This toxicity can be detected by specific metabolite changes and suppressed by the overexpression of the enzyme PI3K.
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Affiliation(s)
- Mercedes Arnés
- Dept. of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal, Avda. Doctor Arce, 37, 28002 Madrid, Spain
| | - Sergio Casas-Tintó
- Dept. of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal, Avda. Doctor Arce, 37, 28002 Madrid, Spain
| | - Anders Malmendal
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Alberto Ferrús
- Dept. of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal, Avda. Doctor Arce, 37, 28002 Madrid, Spain
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30
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Li H, Tennessen JM. Methods for studying the metabolic basis of Drosophila development. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2017; 6:10.1002/wdev.280. [PMID: 28556549 PMCID: PMC5561480 DOI: 10.1002/wdev.280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/03/2017] [Accepted: 04/14/2017] [Indexed: 01/06/2023]
Abstract
The field of metabolic research has experienced an unexpected renaissance. While this renewed interest in metabolism largely originated in response to the global increase in diabetes and obesity, studies of metabolic regulation now represent the frontier of many biomedical fields. This trend is especially apparent in developmental biology, where metabolism influences processes ranging from stem cell differentiation and tissue growth to sexual maturation and reproduction. In this regard, the fruit fly Drosophila melanogaster has emerged as a powerful tool for dissecting conserved mechanisms that underlie developmental metabolism, often with a level of detail that is simply not possible in other animals. Here we describe why the fly is an ideal system for exploring the relationship between metabolism and development, and outline a basic experimental strategy for conducting these studies. WIREs Dev Biol 2017, 6:e280. doi: 10.1002/wdev.280 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hongde Li
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405
| | - Jason M. Tennessen
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405
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31
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Cox JE, Thummel CS, Tennessen JM. Metabolomic Studies in Drosophila. Genetics 2017; 206:1169-1185. [PMID: 28684601 PMCID: PMC5500124 DOI: 10.1534/genetics.117.200014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.
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Affiliation(s)
- James E Cox
- Department of Biochemistry and
- The Metabolomics Core Research Facility, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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32
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Viant MR, Kurland IJ, Jones MR, Dunn WB. How close are we to complete annotation of metabolomes? Curr Opin Chem Biol 2017; 36:64-69. [PMID: 28113135 PMCID: PMC5337156 DOI: 10.1016/j.cbpa.2017.01.001] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/28/2016] [Accepted: 01/02/2017] [Indexed: 01/04/2023]
Abstract
The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here, we review the status of metabolome annotation and describe advances in the analytical methodologies being applied. In part through new international coordination, we conclude that we are now entering a new era of metabolome annotation.
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Affiliation(s)
- Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Irwin J Kurland
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Martin R Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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33
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Considerations when choosing a genetic model organism for metabolomics studies. Curr Opin Chem Biol 2016; 36:7-14. [PMID: 28025166 DOI: 10.1016/j.cbpa.2016.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023]
Abstract
Model organisms are important in many areas of chemical biology. In metabolomics, model organisms can provide excellent samples for methods development as well as the foundation of comparative phylometabolomics, which will become possible as metabolomics applications expand. Comparative studies of conserved and unique metabolic pathways will help in the annotation of metabolites as well as provide important new targets of investigation in biology and biomedicine. However, most chemical biologists are not familiar with genetics, which needs to be considered when choosing a model organism. In this review we summarize the strengths and weaknesses of several genetic systems, including natural isolates, recombinant inbred lines, and genetic mutations. We also discuss methods to detect targets of selection on the metabolome.
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34
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Schou MF, Kristensen TN, Pedersen A, Karlsson BG, Loeschcke V, Malmendal A. Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster. Am J Physiol Regul Integr Comp Physiol 2016; 312:R211-R222. [PMID: 27927623 PMCID: PMC5336569 DOI: 10.1152/ajpregu.00268.2016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022]
Abstract
The ability of ectotherms to respond to changes in their thermal environment through plastic mechanisms is central to their adaptive capability. However, we still lack knowledge on the physiological and functional responses by which ectotherms acclimate to temperatures during development, and in particular, how physiological stress at extreme temperatures may counteract beneficial acclimation responses at benign temperatures. We exposed Drosophila melanogaster to 10 developmental temperatures covering their entire permissible temperature range. We obtained metabolic profiles and reaction norms for several functional traits: egg-to-adult viability, developmental time, and heat and cold tolerance. Females were more heat tolerant than males, whereas no sexual dimorphism was found in cold tolerance. A group of metabolites, mainly free amino acids, had linear reaction norms. Several energy-carrying molecules, as well as some sugars, showed distinct inverted U-shaped norms of reaction across the thermal range, resulting in a positive correlation between metabolite intensities and egg-to-adult viability. At extreme temperatures, low levels of these metabolites were interpreted as a response characteristic of costs of homeostatic perturbations. Our results provide novel insights into a range of metabolites reported to be central for the acclimation response and suggest several new candidate metabolites. Low and high temperatures result in different adaptive physiological responses, but they also have commonalities likely to be a result of the failure to compensate for the physiological stress. We suggest that the regulation of metabolites that are tightly connected to the performance curve is important for the ability of ectotherms to cope with variation in temperature.
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Affiliation(s)
- Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - Torsten N Kristensen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Anders Pedersen
- The Swedish NMR-Centre, University of Gothenburg, Gothenburg, Sweden; and
| | - B Göran Karlsson
- The Swedish NMR-Centre, University of Gothenburg, Gothenburg, Sweden; and
| | | | - Anders Malmendal
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark
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35
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Vedelek V, Laurinyecz B, Kovács AL, Juhász G, Sinka R. Testis-Specific Bb8 Is Essential in the Development of Spermatid Mitochondria. PLoS One 2016; 11:e0161289. [PMID: 27529784 PMCID: PMC4986964 DOI: 10.1371/journal.pone.0161289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Mitochondria are essential organelles of developing spermatids in Drosophila, which undergo dramatic changes in size and shape after meiotic division, where mitochondria localized in the cytoplasm, migrate near the nucleus, aggregate, fuse and create the Nebenkern. During spermatid elongation the two similar mitochondrial derivatives of the Nebenkern start to elongate parallel to the axoneme. One of the elongated mitochondrial derivatives starts to lose volume and becomes the minor mitochondrial derivative, while the other one accumulates paracrystalline and becomes the major mitochondrial derivative. Proteins and intracellular environment that are responsible for cyst elongation and paracrystalline formation in the major mitochondrial derivative need to be identified. In this work we investigate the function of the testis specific big bubble 8 (bb8) gene during spermatogenesis. We show that a Minos element insertion in bb8 gene, a predicted glutamate dehydrogenase, causes recessive male sterility. We demonstrate bb8 mRNA enrichment in spermatids and the mitochondrial localisation of Bb8 protein during spermatogenesis. We report that megamitochondria develop in the homozygous mutant testes, in elongating spermatids. Ultrastructural analysis of the cross section of elongated spermatids shows enlarged mitochondria and the production of paracrystalline in both major and minor mitochondrial derivatives. Our results suggest that the Bb8 protein and presumably glutamate metabolism has a crucial role in the normal development and establishment of the identity of the mitochondrial derivatives during spermatid elongation.
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Affiliation(s)
- Viktor Vedelek
- Department of Genetics, University of Szeged, Szeged, Hungary
| | | | - Attila L Kovács
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged, Hungary
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36
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Wang H, Xu J, Chen Y, Zhang R, He J, Wang Z, Zang Q, Wei J, Song X, Abliz Z. Optimization and Evaluation Strategy of Esophageal Tissue Preparation Protocols for Metabolomics by LC–MS. Anal Chem 2016; 88:3459-64. [DOI: 10.1021/acs.analchem.5b04709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Huiqing Wang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jing Xu
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Yanhua Chen
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Ruiping Zhang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jiuming He
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Zhonghua Wang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Qingce Zang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jinfeng Wei
- New
Drug Safety Evaluation Center, Institute of Materia Medica, Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Xiaowei Song
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Zeper Abliz
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
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37
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Ott S, Vishnivetskaya A, Malmendal A, Crowther DC. Metabolic changes may precede proteostatic dysfunction in a Drosophila model of amyloid beta peptide toxicity. Neurobiol Aging 2016; 41:39-52. [PMID: 27103517 PMCID: PMC4869574 DOI: 10.1016/j.neurobiolaging.2016.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/21/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
Abstract
Amyloid beta (Aβ) peptide aggregation is linked to the initiation of Alzheimer's disease; accordingly, aggregation-prone isoforms of Aβ, expressed in the brain, shorten the lifespan of Drosophila melanogaster. However, the lethal effects of Aβ are not apparent until after day 15. We used shibireTS flies that exhibit a temperature-sensitive paralysis phenotype as a reporter of proteostatic robustness. In this model, we found that increasing age but not Aβ expression lowered the flies' permissive temperature, suggesting that Aβ did not exert its lethal effects by proteostatic disruption. Instead, we observed that chemical challenges, in particular oxidative stressors, discriminated clearly between young (robust) and old (sensitive) flies. Using nuclear magnetic resonance spectroscopy in combination with multivariate analysis, we compared water-soluble metabolite profiles at various ages in flies expressing Aβ in their brains. We observed 2 genotype-linked metabolomic signals, the first reported the presence of any Aβ isoform and the second the effects of the lethal Arctic Aβ. Lethality was specifically associated with signs of oxidative respiration dysfunction and oxidative stress.
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Affiliation(s)
- Stanislav Ott
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Anders Malmendal
- Faculty of Health and Medical Sciences, Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark.
| | - Damian C Crowther
- Department of Genetics, University of Cambridge, Cambridge, UK; Neuroscience IMED, MedImmune Limited, Granta Park, Cambridge, UK.
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38
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Brinzer RA, Henderson L, Marchiondo AA, Woods DJ, Davies SA, Dow JAT. Metabolomic profiling of permethrin-treated Drosophila melanogaster identifies a role for tryptophan catabolism in insecticide survival. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 67:74-86. [PMID: 26474926 DOI: 10.1016/j.ibmb.2015.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/08/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
Insecticides and associated synergists are rapidly losing efficacy in target insect pest populations making the discovery of alternatives a priority. To discover novel targets for permethrin synergists, metabolomics was performed on permethrin-treated Drosophila melanogaster. Changes were observed in several metabolic pathways including those for amino acids, glycogen, glycolysis, energy, nitrogen, NAD(+), purine, pyrimidine, lipids and carnitine. Markers for acidosis, ammonia stress, oxidative stress and detoxification responses were also observed. Many of these changes had not been previously characterized after permethrin exposure. From the altered pathways, tryptophan catabolism was selected for further investigation. The knockdown of some tryptophan catabolism genes (vermilion, cinnabar and CG6950) in the whole fly and in specific tissues including fat body, midgut and Malpighian tubules using targeted RNAi resulted in altered survival phenotypes against acute topical permethrin exposure. The knockdown of vermilion, cinnabar and CG6950 in the whole fly also altered survival phenotypes against chronic oral permethrin, fenvalerate, DDT, chlorpyriphos and hydramethylnon exposure. Thus tryptophan catabolism has a previously uncharacterized role in defence against insecticides, and shows that metabolomics is a powerful tool for target identification in pesticide research.
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Affiliation(s)
- Robert A Brinzer
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Louise Henderson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | | | | | - Shireen A Davies
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Julian A T Dow
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK.
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39
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Metabolomic and Gene Expression Profiles Exhibit Modular Genetic and Dietary Structure Linking Metabolic Syndrome Phenotypes in Drosophila. G3-GENES GENOMES GENETICS 2015; 5:2817-29. [PMID: 26530416 PMCID: PMC4683653 DOI: 10.1534/g3.115.023564] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genetic and environmental factors influence complex disease in humans, such as metabolic syndrome, and Drosophila melanogaster serves as an excellent model in which to test these factors experimentally. Here we explore the modularity of endophenotypes with an in-depth reanalysis of a previous study by Reed et al. (2014), where we raised 20 wild-type genetic lines of Drosophila larvae on four diets and measured gross phenotypes of body weight, total sugar, and total triglycerides, as well as the endophenotypes of metabolomic and whole-genome expression profiles. We then perform new gene expression experiments to test for conservation of phenotype-expression correlations across different diets and populations. We find that transcript levels correlated with gross phenotypes were enriched for puparial adhesion, metamorphosis, and central energy metabolism functions. The specific metabolites L-DOPA and N-arachidonoyl dopamine make physiological links between the gross phenotypes across diets, whereas leucine and isoleucine thus exhibit genotype-by-diet interactions. Between diets, we find low conservation of the endophenotypes that correlate with the gross phenotypes. Through the follow-up expression study, we found that transcript-trait correlations are well conserved across populations raised on a familiar diet, but on a novel diet, the transcript-trait correlations are no longer conserved. Thus, physiological canalization of metabolic phenotypes breaks down in a novel environment exposing cryptic variation. We cannot predict the physiological basis of disease in a perturbing environment from profiles observed in the ancestral environment. This study demonstrates that variation for disease traits within a population is acquired through a multitude of physiological mechanisms, some of which transcend genetic and environmental influences, and others that are specific to an individual’s genetic and environmental context.
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40
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Khalil SM, Römpp A, Pretzel J, Becker K, Spengler B. Phospholipid Topography of Whole-Body Sections of the Anopheles stephensi Mosquito, Characterized by High-Resolution Atmospheric-Pressure Scanning Microprobe Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2015; 87:11309-16. [PMID: 26491885 DOI: 10.1021/acs.analchem.5b02781] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
High-resolution atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) has been employed to study the molecular anatomical structure of rodent malaria vector Anopheles stephensi mosquitoes. A dedicated sample preparation method was developed which suits both, the special tissue properties of the sample and the requirements of high-resolution MALDI imaging. Embedding in 5% carboxymethylcellulose (CMC) was used to maintain the tissue integrity of the whole mosquitoes, being very soft, fragile, and difficult to handle. Individual lipid compounds, specifically representing certain cell types, tissue areas, or organs, were detected and imaged in 20 μm-thick whole-body tissue sections at a spatial resolution of 12 μm per image pixel. Mass spectrometric data and information quality were based on a mass resolution of 70,000 (at m/z 200) and a mass accuracy of better than 2 ppm in positive-ion mode on an orbital trapping mass spectrometer. A total of 67 imaged lipids were assigned by database search and, in a number of cases, identified via additional MS/MS fragmentation studies directly from tissue. This is the first MSI study at 12 μm spatial resolution of the malaria vector Anopheles. The study provides insights into the molecular anatomy of Anopheles stephensi and the distribution and localization of major classes of glycerophospholipids and sphingolipids. These data can be a basis for future experiments, investigating, e.g., the metabolism of Plasmodium-infected and -uninfected Anopheles mosquitoes.
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Affiliation(s)
- Saleh M Khalil
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Jette Pretzel
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen , 35392 Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen , 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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41
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Moghadam NN, Holmstrup M, Manenti T, Loeschcke V. Phospholipid fatty acid composition linking larval-density to lifespan of adult Drosophila melanogaster. Exp Gerontol 2015; 72:177-83. [PMID: 26481768 DOI: 10.1016/j.exger.2015.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 10/05/2015] [Accepted: 10/16/2015] [Indexed: 12/30/2022]
Abstract
Pre-adult density-associated alterations in the composition of storage lipids may affect the cell membrane fatty acid profile (mainly phospholipids), membrane integrity, and cell function. The present study evaluated the impact of pre-adult density conditions, sex, and the selection regime on the composition of phospholipid fatty acids and lifespan of Drosophila melanogaster. The phospholipid profile of adult flies developed under larval crowding contained a higher proportion of polyunsaturated fatty acids, lower proportion of monounsaturated fatty acids, and greater risk of peroxidation. There was also a negative correlation between the peroxidation index (PI) and longevity. The longevity-selected females showed a lower PI compared with control lines under both densities. The present results indicate that pre-adult density may play a significant role in the lifespan of adult flies by altering the composition of phospholipids and shaping cell membrane bilayers with different susceptibilities to peroxidation.
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Affiliation(s)
- Neda Nasiri Moghadam
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Martin Holmstrup
- Department of Bioscience, Aarhus University, Vejlsøvej 25, PO Box 314, DK-8600 Silkeborg, Denmark
| | - Tommaso Manenti
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| | - Volker Loeschcke
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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42
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Laye MJ, Tran V, Jones DP, Kapahi P, Promislow DEL. The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila. Aging Cell 2015; 14:797-808. [PMID: 26085309 PMCID: PMC4568967 DOI: 10.1111/acel.12358] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2015] [Indexed: 11/28/2022] Open
Abstract
Dietary restriction (DR) is a robust intervention that extends lifespan and slows the onset of age-related diseases in diverse organisms. While significant progress has been made in attempts to uncover the genetic mechanisms of DR, there are few studies on the effects of DR on the metabolome. In recent years, metabolomic profiling has emerged as a powerful technology to understand the molecular causes and consequences of natural aging and disease-associated phenotypes. Here, we use high-resolution mass spectroscopy and novel computational approaches to examine changes in the metabolome from the head, thorax, abdomen, and whole body at multiple ages in Drosophila fed either a nutrient-rich ad libitum (AL) or nutrient-restricted (DR) diet. Multivariate analysis clearly separates the metabolome by diet in different tissues and different ages. DR significantly altered the metabolome and, in particular, slowed age-related changes in the metabolome. Interestingly, we observed interacting metabolites whose correlation coefficients, but not mean levels, differed significantly between AL and DR. The number and magnitude of positively correlated metabolites was greater under a DR diet. Furthermore, there was a decrease in positive metabolite correlations as flies aged on an AL diet. Conversely, DR enhanced these correlations with age. Metabolic set enrichment analysis identified several known (e.g., amino acid and NAD metabolism) and novel metabolic pathways that may affect how DR effects aging. Our results suggest that network structure of metabolites is altered upon DR and may play an important role in preventing the decline of homeostasis with age.
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Affiliation(s)
| | - ViLinh Tran
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA USA
| | - Dean P. Jones
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA USA
| | | | - Daniel E. L. Promislow
- Department of Pathology University of Washington Seattle WA USA
- Department of Biology University of Washington Seattle WA USA
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43
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Abstract
Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.
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Affiliation(s)
- Constanze Kuhlisch
- Friedrich Schiller University, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743 Jena, Germany.
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44
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Abstract
Many organisms have developed a robust ability to adapt and survive in the face of environmental perturbations that threaten the integrity of their genome, proteome, or metabolome. Studies in multiple model organisms have shown that, in general, when exposed to stress, cells activate a complex prosurvival signaling network that includes immune and DNA damage response genes, chaperones, antioxidant enzymes, structural proteins, metabolic enzymes, and noncoding RNAs. The manner of activation runs the gamut from transcriptional induction of genes to increased stability of transcripts to posttranslational modification of important biosynthetic proteins within the stressed tissue. Superimposed on these largely autonomous effects are nonautonomous responses in which the stressed tissue secretes peptides and other factors that stimulate tissues in different organs to embark on processes that ultimately help the organism as a whole cope with stress. This review focuses on the mechanisms by which tissues in one organ adapt to environmental challenges by regulating stress responses in tissues of different organs.
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Affiliation(s)
- Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032;
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45
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Analytical protocols based on LC-MS, GC-MS and CE-MS for nontargeted metabolomics of biological tissues. Bioanalysis 2015; 6:1657-77. [PMID: 25077626 DOI: 10.4155/bio.14.119] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Invasive, site-specific metabolite information could be better obtained from tissues. Hence, highly sensitive mass spectrometry-based metabolomics coupled with separation techniques are increasingly in demand in clinical research for tissue metabolomics application. Applying these techniques to nontargeted tissue metabolomics provides identification of distinct metabolites. These findings could help us to understand alterations at the molecular level, which can also be applied in clinical practice as screening markers for early disease diagnosis. However, tissues as solid and heterogeneous samples pose an additional analytical challenge that should be considered in obtaining broad, reproducible and representative analytical profiles. This manuscript summarizes the state of the art in tissue (human and animal) treatment (quenching, homogenization and extraction) for nontargeted metabolomics with mass spectrometry.
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46
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Bhandari DR, Wang Q, Friedt W, Spengler B, Gottwald S, Römpp A. High resolution mass spectrometry imaging of plant tissues: towards a plant metabolite atlas. Analyst 2015; 140:7696-709. [DOI: 10.1039/c5an01065a] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Label-free chemical imaging of a wide range of metabolites in all major plant organs acquired at high spatial resolution.
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Affiliation(s)
- Dhaka Ram Bhandari
- Justus Liebig University Giessen
- Institute of Inorganic and Analytical Chemistry
- 35392 Giessen
- Germany
| | - Qing Wang
- Justus Liebig University Giessen
- Department of Plant Breeding
- IFZ
- Justus Liebig University Giessen
- 35392 Giessen
| | - Wolfgang Friedt
- Justus Liebig University Giessen
- Department of Plant Breeding
- IFZ
- Justus Liebig University Giessen
- 35392 Giessen
| | - Bernhard Spengler
- Justus Liebig University Giessen
- Institute of Inorganic and Analytical Chemistry
- 35392 Giessen
- Germany
| | - Sven Gottwald
- Justus Liebig University Giessen
- Department of Plant Breeding
- IFZ
- Justus Liebig University Giessen
- 35392 Giessen
| | - Andreas Römpp
- Justus Liebig University Giessen
- Institute of Inorganic and Analytical Chemistry
- 35392 Giessen
- Germany
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47
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Majdi S, Ren L, Fathali H, Li X, Ewing AG. Selected recent in vivo studies on chemical measurements in invertebrates. Analyst 2015; 140:3676-86. [DOI: 10.1039/c4an02172j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Review ofin vivoanalysis of brain chemicals in invertebrates.
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Affiliation(s)
- S. Majdi
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - L. Ren
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - H. Fathali
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - X. Li
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - A. G. Ewing
- Department of Chemistry and Chemical Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
- Department of Chemistry and Molecular Biology
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48
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Hoffman JM, Soltow QA, Li S, Sidik A, Jones DP, Promislow DEL. Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Aging Cell 2014; 13:596-604. [PMID: 24636523 PMCID: PMC4116462 DOI: 10.1111/acel.12215] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2014] [Indexed: 12/24/2022] Open
Abstract
Researchers have used whole-genome sequencing and gene expression profiling to identify genes associated with age, in the hope of understanding the underlying mechanisms of senescence. But there is a substantial gap from variation in gene sequences and expression levels to variation in age or life expectancy. In an attempt to bridge this gap, here we describe the effects of age, sex, genotype, and their interactions on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Among the 6800 features analyzed, we found that over one-quarter of all metabolites were significantly associated with age, sex, genotype, or their interactions, and multivariate analysis shows that individual metabolomic profiles are highly predictive of these traits. Using a metabolomic equivalent of gene set enrichment analysis, we identified numerous metabolic pathways that were enriched among metabolites associated with age, sex, and genotype, including pathways involving sugar and glycerophospholipid metabolism, neurotransmitters, amino acids, and the carnitine shuttle. Our results suggest that high-sensitivity metabolomic studies have excellent potential not only to reveal mechanisms that lead to senescence, but also to help us understand differences in patterns of aging among genotypes and between males and females.
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Affiliation(s)
| | - Quinlyn A. Soltow
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA 30322USA
- ClinMet Inc. 3210 Merryfield Row San Diego CA 92121USA
| | - Shuzhao Li
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
| | - Alfire Sidik
- Department of Genetics University of Georgia Athens GA 30602USA
| | - Dean P. Jones
- Division of Pulmonary Allergy & Critical Care Medicine Department of Medicine Emory University Atlanta GA 30322USA
- Department of Medicine Clinical Biomarkers Laboratory Emory University Atlanta GA 30322USA
- Center for Health Discovery & Well Being Emory University Atlanta GA 30322 USA
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49
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Tennessen JM, Barry WE, Cox J, Thummel CS. Methods for studying metabolism in Drosophila. Methods 2014; 68:105-15. [PMID: 24631891 PMCID: PMC4048761 DOI: 10.1016/j.ymeth.2014.02.034] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 01/17/2023] Open
Abstract
Recent research using Drosophila melanogaster has seen a resurgence in studies of metabolism and physiology. This review focuses on major methods used to conduct this work. These include protocols for dietary interventions, measurements of triglycerides, cholesterol, glucose, trehalose, and glycogen, stains for lipid detection, and the use of gas chromatography-mass spectrometry (GC-MS) to detect major polar metabolites. It is our hope that this will provide a useful framework for both new and current researchers in the field.
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Affiliation(s)
- Jason M Tennessen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - William E Barry
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - James Cox
- Department of Biochemistry and the Metabolomics Core Research Facility, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA.
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