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Kors S, Schuster M, Maddison DC, Kilaru S, Schrader TA, Costello JL, Islinger M, Smith GA, Schrader M. New insights into the functions of ACBD4/5-like proteins using a combined phylogenetic and experimental approach across model organisms. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119843. [PMID: 39271061 DOI: 10.1016/j.bbamcr.2024.119843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024]
Abstract
Acyl-CoA binding domain-containing proteins (ACBDs) perform diverse but often uncharacterised functions linked to cellular lipid metabolism. Human ACBD4 and ACBD5 are closely related peroxisomal membrane proteins, involved in tethering of peroxisomes to the ER and capturing fatty acids for peroxisomal β-oxidation. ACBD5 deficiency causes neurological abnormalities including ataxia and white matter disease. Peroxisome-ER contacts depend on an ACBD4/5-FFAT motif, which interacts with ER-resident VAP proteins. As ACBD4/5-like proteins are present in most fungi and all animals, we combined phylogenetic analyses with experimental approaches to improve understanding of their evolution and functions. Notably, all vertebrates exhibit gene sequences for both ACBD4 and ACBD5, while invertebrates and fungi possess only a single ACBD4/5-like protein. Our analyses revealed alterations in domain structure and FFAT sequences, which help understanding functional diversification of ACBD4/5-like proteins. We show that the Drosophila melanogaster ACBD4/5-like protein possesses a functional FFAT motif to tether peroxisomes to the ER via Dm_Vap33. Depletion of Dm_Acbd4/5 caused peroxisome redistribution in wing neurons and reduced life expectancy. In contrast, the ACBD4/5-like protein of the filamentous fungus Ustilago maydis lacks a FFAT motif and does not interact with Um_Vap33. Loss of Um_Acbd4/5 resulted in an accumulation of peroxisomes and early endosomes at the hyphal tip. Moreover, lipid droplet numbers increased, and mitochondrial membrane potential declined, implying altered lipid homeostasis. Our findings reveal differences between tethering and metabolic functions of ACBD4/5-like proteins across evolution, improving our understanding of ACBD4/5 function in health and disease. The need for a unifying nomenclature for ACBD proteins is discussed.
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Affiliation(s)
- Suzan Kors
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Martin Schuster
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Daniel C Maddison
- School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Sreedhar Kilaru
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tina A Schrader
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Joseph L Costello
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gaynor A Smith
- School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Michael Schrader
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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2
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Liu M, He L. Dietary cysteine and methionine promote peroxisome elevation and fat loss by induction of CG33474 expression in Drosophila adipose tissue. Cell Mol Life Sci 2024; 81:190. [PMID: 38649521 PMCID: PMC11035426 DOI: 10.1007/s00018-024-05226-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
The high-protein diet (HPD) has emerged as a potent dietary approach to curb obesity. Peroxisome, a highly malleable organelle, adapts to nutritional changes to maintain homeostasis by remodeling its structure, composition, and quantity. However, the impact of HPD on peroxisomes and the underlying mechanism remains elusive. Using Drosophila melanogaster as a model system, we discovered that HPD specifically increases peroxisome levels within the adipose tissues. This HPD-induced peroxisome elevation is attributed to cysteine and methionine by triggering the expression of CG33474, a fly homolog of mammalian PEX11G. Both the overexpression of Drosophila CG33474 and human PEX11G result in increased peroxisome size. In addition, cysteine and methionine diets both reduce lipid contents, a process that depends on the presence of CG33474. Furthermore, CG33474 stimulates the breakdown of neutral lipids in a cell-autonomous manner. Moreover, the expression of CG33474 triggered by cysteine and methionine requires TOR signaling. Finally, we found that CG33474 promotes inter-organelle contacts between peroxisomes and lipid droplets (LDs), which might be a potential mechanism for CG33474-induced fat loss. In summary, our findings demonstrate that CG33474/PEX11G may serve as an essential molecular bridge linking HPD to peroxisome dynamics and lipid metabolism.
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Affiliation(s)
- Meng Liu
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Li He
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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3
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Makdissi S, Parsons BD, Di Cara F. Towards early detection of neurodegenerative diseases: A gut feeling. Front Cell Dev Biol 2023; 11:1087091. [PMID: 36824371 PMCID: PMC9941184 DOI: 10.3389/fcell.2023.1087091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The gastrointestinal tract communicates with the nervous system through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the enteric nervous system, the vagus nerve, the immune system, endocrine signals, the microbiota, and its metabolites. Alteration of communications in the gut-brain axis is emerging as an overlooked cause of neuroinflammation. Neuroinflammation is a common feature of the pathogenic mechanisms involved in various neurodegenerative diseases (NDs) that are incurable and debilitating conditions resulting in progressive degeneration and death of neurons, such as in Alzheimer and Parkinson diseases. NDs are a leading cause of global death and disability, and the incidences are expected to increase in the following decades if prevention strategies and successful treatment remain elusive. To date, the etiology of NDs is unclear due to the complexity of the mechanisms of diseases involving genetic and environmental factors, including diet and microbiota. Emerging evidence suggests that changes in diet, alteration of the microbiota, and deregulation of metabolism in the intestinal epithelium influence the inflammatory status of the neurons linked to disease insurgence and progression. This review will describe the leading players of the so-called diet-microbiota-gut-brain (DMGB) axis in the context of NDs. We will report recent findings from studies in model organisms such as rodents and fruit flies that support the role of diets, commensals, and intestinal epithelial functions as an overlooked primary regulator of brain health. We will finish discussing the pivotal role of metabolisms of cellular organelles such as mitochondria and peroxisomes in maintaining the DMGB axis and how alteration of the latter can be used as early disease makers and novel therapeutic targets.
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Affiliation(s)
- Stephanie Makdissi
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
| | - Brendon D. Parsons
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
| | - Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
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4
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Ueda K, Haskins J, Simmonds AJ. Manipulation and Visualization of Peroxisomes in Drosophila. Methods Mol Biol 2023; 2643:455-467. [PMID: 36952206 DOI: 10.1007/978-1-0716-3048-8_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Drosophila melanogaster is a proven metazoan model to investigate the fundamentals of human genetic diseases including peroxisome-related disorders. Drosophila have facile cell and animal culture but with a relatively simpler genome and organ morphology compared to vertebrates. Drosophila Schneider 2 (S2) cells have been used extensively as a platform for investigating peroxisome functions like transport along the cytoskeleton via their amenability to RNA-interference (RNAi)-based gene knockdown. Similarly, novel findings regarding tissue-specific roles for peroxisomes have come from studies in developing flies. Individual organs can be targeted for RNAi or gene mutations affecting a limited group of cells in the context of the entire animal. Here, we provide basic protocols on how to visualize peroxisomes and manipulate expression of the Peroxin or other peroxisome genes in S2 cells and developing Drosophila organs.
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Affiliation(s)
- Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Julie Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew James Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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5
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Ueda K, Anderson-Baron MN, Haskins J, Hughes SC, Simmonds AJ. Recruitment of Peroxin14 to lipid droplets affects lipid storage in Drosophila. J Cell Sci 2022; 135:275042. [PMID: 35274690 DOI: 10.1242/jcs.259092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/20/2022] [Indexed: 10/18/2022] Open
Abstract
Both peroxisomes and lipid droplets regulate cellular lipid homeostasis. Direct inter-organellar contacts as well as novel roles for proteins associated with peroxisome or lipid droplets occur when cells are induced to liberate fatty acids from lipid droplets. We have shown a non-canonical role for as subset of peroxisome-assembly (Peroxin) proteins in this process. Transmembrane proteins Peroxin3, Peroxin13 and Peroxin14 surround newly formed lipid droplets. Trafficking of Peroxin14 to lipid droplets was enhanced by loss of Peroxin19, which directs insertion of transmembrane proteins like Peroxin14 into the peroxisome bilayer membrane. Accumulation of Peroxin14 around lipid droplets did not induce changes to peroxisome size or number, nor was co-recruitment of the remaining Peroxins needed to assemble peroxisomes observed. Increasing the relative level of Peroxin14 surrounding lipid droplets affected recruitment of Hsl lipase. Fat-body specific reduction of these lipid droplet-associated Peroxins causes a unique effect on larval fat body development and affected their survival on lipid-enriched or minimal diets.
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Affiliation(s)
- Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Matthew N Anderson-Baron
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada.,Future Fields, 11130 105 Ave NW, Edmonton, AB T5H 0L5, Canada
| | - Julie Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Sarah C Hughes
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
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6
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Liu Y, Weaver CM, Sen Y, Eitzen G, Simmonds AJ, Linchieh L, Lurette O, Hebert-Chatelain E, Rachubinski RA, Di Cara F. The Nitric Oxide Donor, S-Nitrosoglutathione, Rescues Peroxisome Number and Activity Defects in PEX1G843D Mild Zellweger Syndrome Fibroblasts. Front Cell Dev Biol 2021; 9:714710. [PMID: 34434934 PMCID: PMC8382563 DOI: 10.3389/fcell.2021.714710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
Peroxisome biogenesis disorders (PBDs) are a group of metabolic developmental diseases caused by mutations in one or more genes encoding peroxisomal proteins. Zellweger syndrome spectrum (PBD-ZSS) results from metabolic dysfunction caused by damaged or non-functional peroxisomes and manifests as a multi-organ syndrome with significant morbidity and mortality for which there is no current drug therapy. Mild PBD-ZSS patients can exhibit a more progressive disease course and could benefit from the identification of drugs to improve the quality of life and extend the lifespan of affected individuals. Our study used a high-throughput screen of FDA-approved compounds to identify compounds that improve peroxisome function and biogenesis in human fibroblast cells carrying the mild PBD-ZSS variant, PEX1G843D. Our screen identified the nitrogen oxide donor, S-nitrosoglutathione (GSNO), as a potential therapeutic for this mild form of PBD-ZSS. Further biochemical characterization showed that GSNO enhances both peroxisome number and function in PEX1G843D mutant fibroblasts and leads to increased survival and longer lifespan in an in vivo humanized Drosophila model carrying the PEX1G843D mutation. GSNO is therefore a strong candidate to be translated to clinical trials as a potential therapeutic for mild PBD-ZSS.
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Affiliation(s)
- Yidi Liu
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Ceileigh M Weaver
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
| | - Yarina Sen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Gary Eitzen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Lilliana Linchieh
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Olivier Lurette
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | | | | | - Francesca Di Cara
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
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7
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Chornyi S, IJlst L, van Roermund CWT, Wanders RJA, Waterham HR. Peroxisomal Metabolite and Cofactor Transport in Humans. Front Cell Dev Biol 2021; 8:613892. [PMID: 33505966 PMCID: PMC7829553 DOI: 10.3389/fcell.2020.613892] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Peroxisomes are membrane-bound organelles involved in many metabolic pathways and essential for human health. They harbor a large number of enzymes involved in the different pathways, thus requiring transport of substrates, products and cofactors involved across the peroxisomal membrane. Although much progress has been made in understanding the permeability properties of peroxisomes, there are still important gaps in our knowledge about the peroxisomal transport of metabolites and cofactors. In this review, we discuss the different modes of transport of metabolites and essential cofactors, including CoA, NAD+, NADP+, FAD, FMN, ATP, heme, pyridoxal phosphate, and thiamine pyrophosphate across the peroxisomal membrane. This transport can be mediated by non-selective pore-forming proteins, selective transport proteins, membrane contact sites between organelles, and co-import of cofactors with proteins. We also discuss modes of transport mediated by shuttle systems described for NAD+/NADH and NADP+/NADPH. We mainly focus on current knowledge on human peroxisomal metabolite and cofactor transport, but also include knowledge from studies in plants, yeast, fruit fly, zebrafish, and mice, which has been exemplary in understanding peroxisomal transport mechanisms in general.
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Affiliation(s)
- Serhii Chornyi
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
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8
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Kechasov D, de Grahl I, Endries P, Reumann S. Evolutionary Maintenance of the PTS2 Protein Import Pathway in the Stramenopile Alga Nannochloropsis. Front Cell Dev Biol 2020; 8:593922. [PMID: 33330478 PMCID: PMC7710942 DOI: 10.3389/fcell.2020.593922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The stramenopile alga Nannochloropsis evolved by secondary endosymbiosis of a red alga by a heterotrophic host cell and emerged as a promising organism for biotechnological applications, such as the production of polyunsaturated fatty acids and biodiesel. Peroxisomes play major roles in fatty acid metabolism but experimental analyses of peroxisome biogenesis and metabolism in Nannochloropsis are not reported yet. In fungi, animals, and land plants, soluble proteins of peroxisomes are targeted to the matrix by one of two peroxisome targeting signals (type 1, PTS1, or type 2, PTS2), which are generally conserved across kingdoms and allow the prediction of peroxisomal matrix proteins from nuclear genome sequences. Because diatoms lost the PTS2 pathway secondarily, we investigated its presence in the stramenopile sister group of diatoms, the Eustigmatophyceae, represented by Nannochloropsis. We detected a full-length gene of a putative PEX7 ortholog coding for the cytosolic receptor of PTS2 proteins and demonstrated its expression in Nannochloropsis gaditana. The search for predicted PTS2 cargo proteins in N. gaditana yielded several candidates. In vivo subcellular targeting analyses of representative fusion proteins in different plant expression systems demonstrated that two predicted PTS2 domains were indeed functional and sufficient to direct a reporter protein to peroxisomes. Peroxisome targeting of the predicted PTS2 cargo proteins was further confirmed in Nannochloropsis oceanica by confocal and transmission electron microscopy. Taken together, the results demonstrate for the first time that one group of stramenopile algae maintained the import pathway for PTS2 cargo proteins. To comprehensively map and model the metabolic capabilities of Nannochloropsis peroxisomes, in silico predictions needs to encompass both the PTS1 and the PTS2 matrix proteome.
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Affiliation(s)
- Dmitry Kechasov
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Pierre Endries
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
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9
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Pridie C, Ueda K, Simmonds AJ. Rosy Beginnings: Studying Peroxisomes in Drosophila. Front Cell Dev Biol 2020; 8:835. [PMID: 32984330 PMCID: PMC7477296 DOI: 10.3389/fcell.2020.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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10
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Abstract
Peroxisomes are organelles in eukaryotic cells responsible for processing several types of lipids and management of reactive oxygen species. A conserved family of peroxisome biogenesis (Peroxin, Pex) genes encode proteins essential to peroxisome biogenesis or function. In yeast and mammals, PEROXIN7 (PEX7) acts as a cytosolic receptor protein that targets enzymes containing a peroxisome targeting signal 2 (PTS2) motif for peroxisome matrix import. The PTS2 motif is not present in the Drosophila melanogaster homologs of these enzymes. However, the fly genome contains a Pex7 gene (CG6486) that is very similar to yeast and human PEX7. We find that Pex7 is expressed in tissue-specific patterns analogous to differentiating neuroblasts in D. melanogaster embryos. This is correlated with a requirement for Pex7 in this cell lineage as targeted somatic Pex7 knockout in embryonic neuroblasts reduced survival. We also found that Pex7 over-expression in the same cell lineages caused lethality during the larval stage. Targeted somatic over-expression of a Pex7 transgene in neuroblasts of Pex7 homozygous null mutants resulted in a semi-lethal phenotype similar to targeted Pex7 knockout. These findings suggest that D. melanogaster has tissue-specific requirements for Pex7 during embryo development.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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11
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Graves HK, Jangam S, Tan KL, Pignata A, Seto ES, Yamamoto S, Wangler MF. A Genetic Screen for Genes That Impact Peroxisomes in Drosophila Identifies Candidate Genes for Human Disease. G3 (BETHESDA, MD.) 2020; 10:69-77. [PMID: 31767637 PMCID: PMC6945042 DOI: 10.1534/g3.119.400803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
Peroxisomes are subcellular organelles that are essential for proper function of eukaryotic cells. In addition to being the sites of a variety of oxidative reactions, they are crucial regulators of lipid metabolism. Peroxisome loss or dysfunction leads to multi-system diseases in humans that strongly affect the nervous system. In order to identify previously unidentified genes and mechanisms that impact peroxisomes, we conducted a genetic screen on a collection of lethal mutations on the X chromosome in Drosophila Using the number, size and morphology of GFP tagged peroxisomes as a readout, we screened for mutations that altered peroxisomes based on clonal analysis and confocal microscopy. From this screen, we identified eighteen genes that cause increases in peroxisome number or altered morphology when mutated. We examined the human homologs of these genes and found that they are involved in a diverse array of cellular processes. Interestingly, the human homologs from the X-chromosome collection are under selective constraint in human populations and are good candidate genes particularly for dominant genetic disease. This in vivo screening approach for peroxisome defects allows identification of novel genes that impact peroxisomes in vivo in a multicellular organism and is a valuable platform to discover genes potentially involved in dominant disease that could affect peroxisomes.
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Affiliation(s)
| | | | - Kai Li Tan
- Department of Molecular and Human Genetics
| | | | | | - Shinya Yamamoto
- Department of Molecular and Human Genetics,
- Department of Neuroscience
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, and
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX 77030
| | - Michael F Wangler
- Department of Molecular and Human Genetics,
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, and
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX 77030
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12
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Hughes SC, Simmonds AJ. Drosophila mRNA Localization During Later Development: Past, Present, and Future. Front Genet 2019; 10:135. [PMID: 30899273 PMCID: PMC6416162 DOI: 10.3389/fgene.2019.00135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple mechanisms tightly regulate mRNAs during their transcription, translation, and degradation. Of these, the physical localization of mRNAs to specific cytoplasmic regions is relatively easy to detect; however, linking localization to functional regulatory roles has been more difficult to establish. Historically, Drosophila melanogaster is a highly effective model to identify localized mRNAs and has helped identify roles for this process by regulating various cell activities. The majority of the well-characterized functional roles for localizing mRNAs to sub-regions of the cytoplasm have come from the Drosophila oocyte and early syncytial embryo. At present, relatively few functional roles have been established for mRNA localization within the relatively smaller, differentiated somatic cell lineages characteristic of later development, beginning with the cellular blastoderm, and the multiple cell lineages that make up the gastrulating embryo, larva, and adult. This review is divided into three parts—the first outlines past evidence for cytoplasmic mRNA localization affecting aspects of cellular activity post-blastoderm development in Drosophila. The majority of these known examples come from highly polarized cell lineages such as differentiating neurons. The second part considers the present state of affairs where we now know that many, if not most mRNAs are localized to discrete cytoplasmic regions in one or more somatic cell lineages of cellularized embryos, larvae or adults. Assuming that the phenomenon of cytoplasmic mRNA localization represents an underlying functional activity, and correlation with the encoded proteins suggests that mRNA localization is involved in far more than neuronal differentiation. Thus, it seems highly likely that past-identified examples represent only a small fraction of localization-based mRNA regulation in somatic cells. The last part highlights recent technological advances that now provide an opportunity for probing the role of mRNA localization in Drosophila, moving beyond cataloging the diversity of localized mRNAs to a similar understanding of how localization affects mRNA activity.
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Affiliation(s)
- Sarah C Hughes
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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13
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Distinct Roles for Peroxisomal Targeting Signal Receptors Pex5 and Pex7 in Drosophila. Genetics 2018; 211:141-149. [PMID: 30389805 DOI: 10.1534/genetics.118.301628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/26/2018] [Indexed: 12/26/2022] Open
Abstract
Peroxisomes are ubiquitous membrane-enclosed organelles involved in lipid processing and reactive oxygen detoxification. Mutations in human peroxisome biogenesis genes (Peroxin, PEX, or Pex) cause developmental disabilities and often early death. Pex5 and Pex7 are receptors that recognize different peroxisomal targeting signals called PTS1 and PTS2, respectively, and traffic proteins to the peroxisomal matrix. We characterized mutants of Drosophila melanogaster Pex5 and Pex7 and found that adult animals are affected in lipid processing. Pex5 mutants exhibited severe developmental defects in the embryonic nervous system and muscle, similar to what is observed in humans with PEX5 mutations, while Pex7 fly mutants were weakly affected in brain development, suggesting different roles for fly Pex7 and human PEX7. Of note, although no PTS2-containing protein has been identified in Drosophila, Pex7 from Drosophila can function as a bona fide PTS2 receptor because it can rescue targeting of the PTS2-containing protein thiolase to peroxisomes in PEX7 mutant human fibroblasts.
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Di Cara F, Bülow MH, Simmonds AJ, Rachubinski RA. Dysfunctional peroxisomes compromise gut structure and host defense by increased cell death and Tor-dependent autophagy. Mol Biol Cell 2018; 29:2766-2783. [PMID: 30188767 PMCID: PMC6249834 DOI: 10.1091/mbc.e18-07-0434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The gut has a central role in digestion and nutrient absorption, but it also serves in defending against pathogens, engages in mutually beneficial interactions with commensals, and is a major source of endocrine signals. Gut homeostasis is necessary for organismal health and changes to the gut are associated with conditions like obesity and diabetes and inflammatory illnesses like Crohn's disease. We report that peroxisomes, organelles involved in lipid metabolism and redox balance, are required to maintain gut epithelium homeostasis and renewal in Drosophila and for survival and development of the organism. Dysfunctional peroxisomes in gut epithelial cells activate Tor kinase-dependent autophagy that increases cell death and epithelial instability, which ultimately alter the composition of the intestinal microbiota, compromise immune pathways in the gut in response to infection, and affect organismal survival. Peroxisomes in the gut effectively function as hubs that coordinate responses from stress, metabolic, and immune signaling pathways to maintain enteric health and the functionality of the gut-microbe interface.
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Affiliation(s)
- Francesca Di Cara
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Margret H Bülow
- Development, Genetics and Molecular Physiology, LIMES (Life and Medical Sciences), University of Bonn, D-53115 Bonn, Germany
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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15
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Dietary rescue of lipotoxicity-induced mitochondrial damage in Peroxin19 mutants. PLoS Biol 2018; 16:e2004893. [PMID: 29920513 PMCID: PMC6025876 DOI: 10.1371/journal.pbio.2004893] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 06/29/2018] [Accepted: 06/01/2018] [Indexed: 11/19/2022] Open
Abstract
Mutations in peroxin (PEX) genes lead to loss of peroxisomes, resulting in the formation of peroxisomal biogenesis disorders (PBDs) and early lethality. Studying PBDs and their animal models has greatly contributed to our current knowledge about peroxisomal functions. Very-long-chain fatty acid (VLCFA) accumulation has long been suggested as a major disease-mediating factor, although the exact pathological consequences are unclear. Here, we show that a Drosophila Pex19 mutant is lethal due to a deficit in medium-chain fatty acids (MCFAs). Increased lipolysis mediated by Lipase 3 (Lip3) leads to accumulation of free fatty acids and lipotoxicity. Administration of MCFAs prevents lipolysis and decreases the free fatty acid load. This drastically increases the survival rate of Pex19 mutants without reducing VLCFA accumulation. We identified a mediator of MCFA-induced lipolysis repression, the ceramide synthase Schlank, which reacts to MCFA supplementation by increasing its repressive action on lip3. This shifts our understanding of the key defects in peroxisome-deficient cells away from elevated VLCFA levels toward elevated lipolysis and shows that loss of this important organelle can be compensated by a dietary adjustment. Peroxisomes are organelles that contain several enzymes and fatty acids required for many metabolic tasks in the cell, and upon peroxisome loss, their educts accumulate. One example is the accumulation of very-long-chain fatty acids (VLCFAs) with a chain length of more than 20 carbons. These fatty acids cannot be oxidized in mitochondria but are exclusively degraded in peroxisomes. Lowering increased VLCFA levels is sometimes attempted as a treatment option for human disorders with peroxisomal dysfunction, although its effectiveness remains unclear. Here, we have analyzed this process in Drosophila melanogaster and found that peroxisomal loss results not only in VLCFA accumulation but also in a reduction of medium-chain fatty acids (MCFAs). We could show that this is due to a state of high lipolysis and increased mitochondrial activity. By supplementation with MCFAs from coconut oil, we were able to rescue mitochondrial damage and lethality observed in peroxisome-deficient flies. We found that this process is mediated by the ceramide synthase Schlank, which acts as a transcription factor and shuttles between nuclear membrane and endoplasmic reticulum (ER) in response to MCFA availability. We conclude that peroxisome loss triggers the accumulation of free fatty acids and mitochondrial damage in flies and that these effects can be rescued by a diet rich in MCFAs.
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16
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Abstract
As a laboratory animal, Drosophila melanogaster has made extensive contributions to understanding many areas of fundamental biology as well as being an effective model for human disease. Until recently, there was relatively little known about fly peroxisomes. There were early studies that examined the role of peroxisome enzymes during development of organs like the eye. However, with the advent of a well-annotated, sequenced genome, several groups have collectively determined, first by sequence homology and increasingly by functional studies, Drosophila Peroxins and related peroxisome proteins. Notably, it was shown that Drosophila peroxisome biogenesis is mediated via a well-conserved PTS1 import system. Although the fly genome encodes a Pex7 homologue, a canonical PTS2 import system does not seem to be conserved in Drosophila. Given the homology between Drosophila and Saccharomyces cerevisiae or Homo sapiens peroxisome biogenesis and function, Drosophila has emerged as an effective multicellular system to model human Peroxisome Biogenesis Disorders. Finally, Drosophila peroxisome research has recently come into its own, facilitating new discoveries into the role of peroxisomes within specific tissues, such as testes or immune cells.
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Affiliation(s)
- Matthew Anderson-Baron
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-14 Medical Sciences, Edmonton, AB, T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-14 Medical Sciences, Edmonton, AB, T6G 2H7, Canada.
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17
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Di Cara F, Sheshachalam A, Braverman NE, Rachubinski RA, Simmonds AJ. Peroxisome-Mediated Metabolism Is Required for Immune Response to Microbial Infection. Immunity 2017; 47:93-106.e7. [PMID: 28723556 DOI: 10.1016/j.immuni.2017.06.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/20/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022]
Abstract
The innate immune response is critical for animal homeostasis and is conserved from invertebrates to vertebrates. This response depends on specialized cells that recognize, internalize, and destroy microbial invaders through phagocytosis. This is coupled to autonomous or non-autonomous cellular signaling via reactive oxygen species (ROS) and cytokine production. Lipids are known signaling factors in this process, as the acute phase response of macrophages is accompanied by systemic lipid changes that help resolve inflammation. We found that peroxisomes, membrane-enclosed organelles central to lipid metabolism and ROS turnover, were necessary for the engulfment of bacteria by Drosophila and mouse macrophages. Peroxisomes were also required for resolution of bacterial infection through canonical innate immune signaling. Reduced peroxisome function impaired the turnover of the oxidative burst necessary to fight infection. This impaired response to bacterial challenge affected cell and organism survival and revealed a previously unknown requirement for peroxisomes in phagocytosis and innate immunity.
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Affiliation(s)
- Francesca Di Cara
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| | - Avinash Sheshachalam
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nancy E Braverman
- Research Institute of the McGill University Children's Hospital, Montreal, Quebec H4A 3J1, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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18
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Hussain R, Shaukat Z, Khan M, Saint R, Gregory SL. Phosphoenolpyruvate Carboxykinase Maintains Glycolysis-driven Growth in Drosophila Tumors. Sci Rep 2017; 7:11531. [PMID: 28912546 PMCID: PMC5599506 DOI: 10.1038/s41598-017-11613-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/25/2017] [Indexed: 12/27/2022] Open
Abstract
Tumors frequently fail to pass on all their chromosomes correctly during cell division, and this chromosomal instability (CIN) causes irregular aneuploidy and oxidative stress in cancer cells. Our objective was to test knockdowns of metabolic enzymes in Drosophila to find interventions that could exploit the differences between normal and CIN cells to block CIN tumor growth without harming the host animal. We found that depleting by RNAi or feeding the host inhibitors against phosphoenolpyruvate carboxykinase (PEPCK) was able to block the growth of CIN tissue in a brat tumor explant model. Increasing NAD+ or oxidising cytoplasmic NADH was able to rescue the growth of PEPCK depleted tumors, suggesting a problem in clearing cytoplasmic NADH. Consistent with this, blocking the glycerol-3-phosphate shuttle blocked tumor growth, as well as lowering ROS levels. This work suggests that proliferating CIN cells are particularly vulnerable to inhibition of PEPCK, or its metabolic network, because of their compromised redox status.
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Affiliation(s)
- Rashid Hussain
- Department of Genetics and Evolution, University of Adelaide, Adelaide, 5006, Australia
| | - Zeeshan Shaukat
- Department of Genetics and Evolution, University of Adelaide, Adelaide, 5006, Australia
| | - Mahwish Khan
- Department of Genetics and Evolution, University of Adelaide, Adelaide, 5006, Australia
| | | | - Stephen L Gregory
- Department of Genetics and Evolution, University of Adelaide, Adelaide, 5006, Australia.
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Adipocyte Metabolic Pathways Regulated by Diet Control the Female Germline Stem Cell Lineage in Drosophila melanogaster. Genetics 2017; 206:953-971. [PMID: 28396508 DOI: 10.1534/genetics.117.201921] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 12/29/2022] Open
Abstract
Nutrients affect adult stem cells through complex mechanisms involving multiple organs. Adipocytes are highly sensitive to diet and have key metabolic roles, and obesity increases the risk for many cancers. How diet-regulated adipocyte metabolic pathways influence normal stem cell lineages, however, remains unclear. Drosophila melanogaster has highly conserved adipocyte metabolism and a well-characterized female germline stem cell (GSC) lineage response to diet. Here, we conducted an isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis to identify diet-regulated adipocyte metabolic pathways that control the female GSC lineage. On a rich (relative to poor) diet, adipocyte Hexokinase-C and metabolic enzymes involved in pyruvate/acetyl-CoA production are upregulated, promoting a shift of glucose metabolism toward macromolecule biosynthesis. Adipocyte-specific knockdown shows that these enzymes support early GSC progeny survival. Further, enzymes catalyzing fatty acid oxidation and phosphatidylethanolamine synthesis in adipocytes promote GSC maintenance, whereas lipid and iron transport from adipocytes controls vitellogenesis and GSC number, respectively. These results show a functional relationship between specific metabolic pathways in adipocytes and distinct processes in the GSC lineage, suggesting the adipocyte metabolism-stem cell link as an important area of investigation in other stem cell systems.
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