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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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2
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Li JQ, Duan DD, Zhang JQ, Zhou YZ, Qin XM, Du GH, Gao L. Bioinformatic prediction of critical genes and pathways involved in longevity in Drosophila melanogaster. Mol Genet Genomics 2019; 294:1463-1475. [PMID: 31327054 DOI: 10.1007/s00438-019-01589-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/21/2019] [Indexed: 01/08/2023]
Abstract
The pursuit of longevity has been the goal of humanity since ancient times. Genetic alterations have been demonstrated to affect lifespan. As increasing numbers of pro-longevity genes and anti-longevity genes have been discovered in Drosophila, screening for functionally important genes among the large number of genes has become difficult. The aim of the present study was to explore critical genes and pathways affecting longevity in Drosophila melanogaster. In this study, 168 genes associated with longevity in D. melanogaster were collected from the Human Ageing Genomic Resources (HAGR) database. Network clustering analysis, network topological analysis, and pathway analysis were integrated to identify key genes and pathways. Quantitative real-time PCR (qRT-PCR) was applied to verify the expression of genes in representative pathways and of predicted genes derived from the gene-gene sub-network. Our results revealed that six key pathways might be associated with longevity, including the longevity-regulating pathway, the peroxisome pathway, the mTOR-signalling pathway, the FOXO-signalling pathway, the AGE-RAGE-signalling pathway in diabetic complications, and the TGF-beta-signalling pathway. Moreover, the results revealed that six key genes in representative pathways, including Cat, Ry, S6k, Sod, Tor, and Tsc1, and the predicted genes Jra, Kay, and Rheb exhibited significant expression changes in ageing D. melanogaster strain w1118 compared to young ones. Overall, our results revealed that six pathways and six key genes might play pivotal roles in regulating longevity, and three interacting genes might be implicated in longevity. The results will not only provide new insight into the mechanisms of longevity, but also provide novel ideas for network-based approaches for longevity-related research.
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Affiliation(s)
- Jia-Qi Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China.,College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Dan-Dan Duan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China.,College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Jian-Qin Zhang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China
| | - Yu-Zhi Zhou
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China
| | - Guan-Hua Du
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China. .,Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, People's Republic of China.
| | - Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wu Cheng Road, Taiyuan, 030006, People's Republic of China.
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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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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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Nagarkar-Jaiswal S, Lee PT, Campbell ME, Chen K, Anguiano-Zarate S, Gutierrez MC, Busby T, Lin WW, He Y, Schulze KL, Booth BW, Evans-Holm M, Venken KJT, Levis RW, Spradling AC, Hoskins RA, Bellen HJ. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila. eLife 2015; 4. [PMID: 25824290 PMCID: PMC4379497 DOI: 10.7554/elife.05338] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 02/06/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we document a collection of ∼7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstrate reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates. DOI:http://dx.doi.org/10.7554/eLife.05338.001 In the last few decades, technical advances in altering the genes of organisms have led to many discoveries about how genes work. For example, it is now possible to add a specific DNA sequence to a gene so that the protein it makes will carry a ‘tag’ that enables us to track it in cells. One such tag is called green fluorescent protein (GFP) and it is often used to study other proteins in living cells because it produces green fluorescence that can be detected under a microscope. It is labor intensive to add tags to individual genes, so this limits the number of proteins that can be studied in this way. In 2011, researchers developed a new method that can easily tag many genes in fruit flies. It makes use of small sections of DNA called transposons, which are able to move around the genome by ‘cutting’ themselves out of one location and ‘pasting’ themselves in somewhere else. The researchers used a transposon called Minos, which is naturally found in fruit flies. When Minos inserts into a gene, it often disrupts the gene and stops it from working. However, the researchers could swap the inserted transposon for a gene encoding GFP by making use of a natural process that rearranges DNA in cells. This resulted in the protein encoded by the gene containing GFP and so it can be detected under a microscope. This method allowed the researchers to create a collection of fly lines that have the GFP tag on many different proteins. Now, Nagarkar-Jaiswal et al. have greatly expanded this initial collection. More than 75% of GFP-tagged proteins worked normally and the flies producing these altered proteins remain healthy. It is possible to use a technique called RNA interference against the GFP to lower the production of the tagged proteins. Moreover, Nagarkar-Jaiswal et al. show that it is also possible to degrade the tagged proteins so that less protein is present. The removal of proteins is reversible and can be done in specific tissues during any phase in fly development. These techniques allow researchers to directly associate the loss of the protein with the consequences for the fly. This collection of fruit fly lines is a useful resource that can help us understand how genes work. The method for tagging the proteins could also be modified to work in other animals. DOI:http://dx.doi.org/10.7554/eLife.05338.002
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Affiliation(s)
- Sonal Nagarkar-Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Megan E Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kuchuan Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States
| | | | - Manuel Cantu Gutierrez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Theodore Busby
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Yuchun He
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Karen L Schulze
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Benjamin W Booth
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Martha Evans-Holm
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Robert W Levis
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, United States
| | - Allan C Spradling
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, United States
| | - Roger A Hoskins
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
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Faust JE, Manisundaram A, Ivanova PT, Milne SB, Summerville JB, Brown HA, Wangler M, Stern M, McNew JA. Peroxisomes are required for lipid metabolism and muscle function in Drosophila melanogaster. PLoS One 2014; 9:e100213. [PMID: 24945818 PMCID: PMC4063865 DOI: 10.1371/journal.pone.0100213] [Citation(s) in RCA: 30] [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: 02/27/2014] [Accepted: 05/22/2014] [Indexed: 01/19/2023] Open
Abstract
Peroxisomes are ubiquitous organelles that perform lipid and reactive oxygen species metabolism. Defects in peroxisome biogenesis cause peroxisome biogenesis disorders (PBDs). The most severe PBD, Zellweger syndrome, is characterized in part by neuronal dysfunction, craniofacial malformations, and low muscle tone (hypotonia). These devastating diseases lack effective therapies and the development of animal models may reveal new drug targets. We have generated Drosophila mutants with impaired peroxisome biogenesis by disrupting the early peroxin gene pex3, which participates in budding of pre-peroxisomes from the ER and peroxisomal membrane protein localization. pex3 deletion mutants lack detectible peroxisomes and die before or during pupariation. At earlier stages of development, larvae lacking Pex3 display reduced size and impaired lipid metabolism. Selective loss of peroxisomes in muscles impairs muscle function and results in flightless animals. Although, hypotonia in PBD patients is thought to be a secondary effect of neuronal dysfunction, our results suggest that peroxisome loss directly affects muscle physiology, possibly by disrupting energy metabolism. Understanding the role of peroxisomes in Drosophila physiology, specifically in muscle cells may reveal novel aspects of PBD etiology.
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Affiliation(s)
- Joseph E. Faust
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Arvind Manisundaram
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Pavlina T. Ivanova
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Stephen B. Milne
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - James B. Summerville
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - H. Alex Brown
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Stern
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - James A. McNew
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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8
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Van Veldhoven PP, Baes M. Peroxisome deficient invertebrate and vertebrate animal models. Front Physiol 2013; 4:335. [PMID: 24319432 PMCID: PMC3837297 DOI: 10.3389/fphys.2013.00335] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/01/2013] [Indexed: 11/29/2022] Open
Abstract
Although peroxisomes are ubiquitous organelles in all animal species, their importance for the functioning of tissues and organs remains largely unresolved. Because peroxins are essential for the biogenesis of peroxisomes, an obvious approach to investigate their physiological role is to inactivate a Pex gene or to suppress its translation. This has been performed in mice but also in more primitive organisms including D. melanogaster, C. elegans, and D. rerio, and the major findings and abnormalities in these models will be highlighted. Although peroxisomes are generally not essential for embryonic development and organogenesis, a generalized inactivity of peroxisomes affects lifespan and posthatching/postnatal growth, proving that peroxisomal metabolism is necessary for the normal maturation of these organisms. Strikingly, despite the wide variety of model organisms, corresponding tissues are affected including the central nervous system and the testis. By inactivating peroxisomes in a cell type selective way in the brain of mice, it was also demonstrated that peroxisomes are necessary to prevent neurodegeneration. As these peroxisome deficient model organisms recapitulate pathologies of patients affected with peroxisomal diseases, their further analysis will contribute to the elucidation of still elusive pathogenic mechanisms.
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Affiliation(s)
| | - Myriam Baes
- Laboratory of Cellular Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU LeuvenLeuven, Belgium
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Faust JE, Verma A, Peng C, McNew JA. An inventory of peroxisomal proteins and pathways in Drosophila melanogaster. Traffic 2012; 13:1378-92. [PMID: 22758915 PMCID: PMC3443258 DOI: 10.1111/j.1600-0854.2012.01393.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 06/28/2012] [Accepted: 07/03/2012] [Indexed: 11/29/2022]
Abstract
Peroxisomes are ubiquitous organelles housing a variety of essential biochemical pathways. Peroxisome dysfunction causes a spectrum of human diseases known as peroxisome biogenesis disorders (PBD). Although much is known regarding the mechanism of peroxisome biogenesis, it is still unclear how peroxisome dysfunction leads to the disease state. Several recent studies have shown that mutations in Drosophila peroxin genes cause phenotypes similar to those seen in humans with PBDs suggesting that Drosophila might be a useful system to model PBDs. We have analyzed the proteome of Drosophila to identify the proteins involved in peroxisomal biogenesis and homeostasis as well as metabolic enzymes that function within the organelle. The subcellular localization of five of these predicted peroxisomal proteins was confirmed. Similar to Caenorhabditis elegans, Drosophila appears to only utilize the peroxisome targeting signal type 1 system for matrix protein import. This work will further our understanding of peroxisomes in Drosophila and add to the usefulness of this emerging model system.
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Affiliation(s)
- Joseph E. Faust
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street MS601, Houston, TX 77005
| | - Avani Verma
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street MS601, Houston, TX 77005
| | - Chengwei Peng
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street MS601, Houston, TX 77005
| | - James A. McNew
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street MS601, Houston, TX 77005
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Drosophila melanogaster larvae fed by glucose and fructose demonstrate difference in oxidative stress markers and antioxidant enzymes of adult flies. Comp Biochem Physiol A Mol Integr Physiol 2011; 160:27-34. [DOI: 10.1016/j.cbpa.2011.04.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/27/2011] [Accepted: 04/27/2011] [Indexed: 01/05/2023]
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Nakayama M, Sato H, Okuda T, Fujisawa N, Kono N, Arai H, Suzuki E, Umeda M, Ishikawa HO, Matsuno K. Drosophila carrying pex3 or pex16 mutations are models of Zellweger syndrome that reflect its symptoms associated with the absence of peroxisomes. PLoS One 2011; 6:e22984. [PMID: 21826223 PMCID: PMC3149631 DOI: 10.1371/journal.pone.0022984] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 07/10/2011] [Indexed: 11/19/2022] Open
Abstract
The peroxisome biogenesis disorders (PBDs) are currently difficult-to-treat multiple-organ dysfunction disorders that result from the defective biogenesis of peroxisomes. Genes encoding Peroxins, which are required for peroxisome biogenesis or functions, are known causative genes of PBDs. The human peroxin genes PEX3 or PEX16 are required for peroxisomal membrane protein targeting, and their mutations cause Zellweger syndrome, a class of PBDs. Lack of understanding about the pathogenesis of Zellweger syndrome has hindered the development of effective treatments. Here, we developed potential Drosophila models for Zellweger syndrome, in which the Drosophila pex3 or pex16 gene was disrupted. As found in Zellweger syndrome patients, peroxisomes were not observed in the homozygous Drosophila pex3 mutant, which was larval lethal. However, the pex16 homozygote lacking its maternal contribution was viable and still maintained a small number of peroxisome-like granules, even though PEX16 is essential for the biosynthesis of peroxisomes in humans. These results suggest that the requirements for pex3 and pex16 in peroxisome biosynthesis in Drosophila are different, and the role of PEX16 orthologs may have diverged between mammals and Drosophila. The phenotypes of our Zellweger syndrome model flies, such as larval lethality in pex3, and reduced size, shortened longevity, locomotion defects, and abnormal lipid metabolisms in pex16, were reminiscent of symptoms of this disorder, although the Drosophila pex16 mutant does not recapitulate the infant death of Zellweger syndrome. Furthermore, pex16 mutants showed male-specific sterility that resulted from the arrest of spermatocyte maturation. pex16 expressed in somatic cyst cells but not germline cells had an essential role in the maturation of male germline cells, suggesting that peroxisome-dependent signals in somatic cyst cells could contribute to the progression of male germ-cell maturation. These potential Drosophila models for Zellweger syndrome should contribute to our understanding of its pathology.
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Affiliation(s)
- Minoru Nakayama
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyasu Sato
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Takayuki Okuda
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Nao Fujisawa
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Nozomu Kono
- Graduate School of Pharmaceutical Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Arai
- Graduate School of Pharmaceutical Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Emiko Suzuki
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, Japan
| | - Masato Umeda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hiroyuki O. Ishikawa
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Kenji Matsuno
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
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Mast FD, Li J, Virk MK, Hughes SC, Simmonds AJ, Rachubinski RA. A Drosophila model for the Zellweger spectrum of peroxisome biogenesis disorders. Dis Model Mech 2011; 4:659-72. [PMID: 21669930 PMCID: PMC3180231 DOI: 10.1242/dmm.007419] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human peroxisome biogenesis disorders are lethal genetic diseases in which abnormal peroxisome assembly compromises overall peroxisome and cellular function. Peroxisomes are ubiquitous membrane-bound organelles involved in several important biochemical processes, notably lipid metabolism and the use of reactive oxygen species for detoxification. Using cultured cells, we systematically characterized the peroxisome assembly phenotypes associated with dsRNA-mediated knockdown of 14 predicted Drosophila homologs of PEX genes (encoding peroxins; required for peroxisome assembly and linked to peroxisome biogenesis disorders), and confirmed that at least 13 of them are required for normal peroxisome assembly. We also demonstrate the relevance of Drosophila as a genetic model for the early developmental defects associated with the human peroxisome biogenesis disorders. Mutation of the PEX1 gene is the most common cause of peroxisome biogenesis disorders and is one of the causes of the most severe form of the disease, Zellweger syndrome. Inherited mutations in Drosophila Pex1 correlate with reproducible defects during early development. Notably, Pex1 mutant larvae exhibit abnormalities that are analogous to those exhibited by Zellweger syndrome patients, including developmental delay, poor feeding, severe structural abnormalities in the peripheral and central nervous systems, and early death. Finally, microarray analysis defined several clusters of genes whose expression varied significantly between wild-type and mutant larvae, implicating peroxisomal function in neuronal development, innate immunity, lipid and protein metabolism, gamete formation, and meiosis.
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Affiliation(s)
- Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Islinger M, Cardoso MJR, Schrader M. Be different--the diversity of peroxisomes in the animal kingdom. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:881-97. [PMID: 20347886 DOI: 10.1016/j.bbamcr.2010.03.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/15/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
Peroxisomes represent so-called "multipurpose organelles" as they contribute to various anabolic as well as catabolic pathways. Thus, with respect to the physiological specialization of an individual organ or animal species, peroxisomes exhibit a functional diversity, which is documented by significant variations in their proteome. These differences are usually regarded as an adaptational response to the nutritional and environmental life conditions of a specific organism. Thus, human peroxisomes can be regarded as an in part physiologically unique organellar entity fulfilling metabolic functions that differ from our animal model systems. In line with this, a profound understanding on how peroxisomes acquired functional heterogeneity in terms of an evolutionary and mechanistic background is required. This review summarizes our current knowledge on the heterogeneity of peroxisomal physiology, providing insights into the genetic and cell biological mechanisms, which lead to the differential localization or expression of peroxisomal proteins and further gives an overview on peroxisomal biochemical pathways, which are specialized in different animal species and organs. Moreover, it addresses the impact of proteome studies on our understanding of differential peroxisome function describing the utility of mass spectrometry and computer-assisted algorithms to identify peroxisomal target sequences for the detection of new organ- or species-specific peroxisomal proteins.
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Affiliation(s)
- M Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karls University, 69120 Heidelberg, Germany
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Palanker L, Tennessen JM, Lam G, Thummel CS. Drosophila HNF4 regulates lipid mobilization and beta-oxidation. Cell Metab 2009; 9:228-39. [PMID: 19254568 PMCID: PMC2673486 DOI: 10.1016/j.cmet.2009.01.009] [Citation(s) in RCA: 201] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 12/15/2008] [Accepted: 01/28/2009] [Indexed: 11/17/2022]
Abstract
Drosophila HNF4 (dHNF4) is the single ancestral ortholog of a highly conserved subfamily of nuclear receptors that includes two mammalian receptors, HNFalpha and HNFgamma, and 269 members in C. elegans. We show here that dHNF4 null mutant larvae are sensitive to starvation. Starved mutant larvae consume glycogen normally but retain lipids in their midgut and fat body and have increased levels of long-chain fatty acids, suggesting that they are unable to efficiently mobilize stored fat for energy. Microarray studies support this model, indicating reduced expression of genes that control lipid catabolism and beta-oxidation. A GAL4-dHNF4;UAS-lacZ ligand sensor can be activated by starvation or exogenous long-chain fatty acids, suggesting that dHNF4 is responsive to dietary signals. Taken together, our results support a feed-forward model for dHNF4, in which fatty acids released from triglycerides activate the receptor, inducing enzymes that drive fatty acid oxidation for energy production.
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15
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Southall TD, Terhzaz S, Cabrero P, Chintapalli VR, Evans JM, Dow JAT, Davies SA. Novel subcellular locations and functions for secretory pathway Ca2+/Mn2+-ATPases. Physiol Genomics 2006; 26:35-45. [PMID: 16609144 DOI: 10.1152/physiolgenomics.00038.2006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Secretory pathway Ca2+/Mn2+-ATPases (SPCAs) are important for maintenance of cellular Ca2+and Mn2+homeostasis, and, to date, all SPCAs have been found to localize to the Golgi apparatus. The single Drosophila SPCA gene ( SPoCk) was identified by an in silico screen for novel Ca2+-ATPases. It encoded three SPoCk isoforms with novel, distinct subcellular specificities in the endoplasmic reticulum (ER) and peroxisomes in addition to the Golgi. Furthermore, expression of the peroxisome-associated SPoCk isoform was sexually dimorphic. Overexpression of organelle-specific SPoCk isoforms impacted on cytosolic Ca2+handling in both cultured Drosophila cells and a transporting epithelium, the Drosophila Malpighian (renal) tubule. Specifically, the ER isoform impacted on inositol ( 1 , 4 , 5 )-trisphosphate-mediated Ca2+signaling and the Golgi isoform impacted on diuresis, whereas the peroxisome isoform colocalized with Ca2+“spherites” and impacted on calcium storage and transport. Interfering RNA directed against the common exons of the three SPoCk isoforms resulted in aberrant Ca2+signaling and abolished neuropeptide-stimulated diuresis by the tubule. SPoCk thus contributed to both of the contrasting requirements for Ca2+in transporting epithelia: to transport or store Ca2+in bulk without compromising its use as a signal.
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Affiliation(s)
- Tony D Southall
- Division of Molecular Genetics, Anderson College Complex, University of Glasgow, Glasgow, United Kingdom
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16
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Carter C, Thornburg RW. Tobacco nectarin I. Purification and characterization as a germin-like, manganese superoxide dismutase implicated in the defensE of floral reproductive tissues. J Biol Chem 2000; 275:36726-33. [PMID: 10952990 DOI: 10.1074/jbc.m006461200] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nectarin I, a protein that accumulates in the nectar of Nicotiana sp. , was determined to contain superoxide dismutase activity by colorimetric and in-gel assays. This activity was found to be remarkably thermostable. Extended incubations at temperatures up to 90 degrees C did not diminish the superoxide dismutase activity of nectarin I. This attribute allowed nectarin I to be purified to homogeneity by heat denaturation of the other nectar proteins. By SDS-polyacrylamide gel electrophoresis, nectarin I appeared as a 29-kDa monomer. If the protein sample was not boiled prior to loading the gel, then nectarin I migrated as 165-kDa oligomeric protein. By matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, the protomer subunit was found to be a 22.5-kDa protein. Purified nectarin I contained 0.5 atoms of manganese/monomer, and the superoxide dismutase activity of nectarin I was not inhibited by either H(2)O(2) or NaCN. Following denaturation, the superoxide dismutase activity was restored after Mn(2+) addition. Addition of Fe(2+), Cu(2+), Zn(2+), and Cu(2+)/Zn(2+) did not restore superoxide dismutase activity. The quaternary structure of the reconstituted enzyme was examined, and only tetrameric and pentameric aggregates were enzymatically active. The reconstituted enzyme was also shown to generate H(2)O(2). Putative nectarin I homologues were found in the nectars of several other plant species.
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Affiliation(s)
- C Carter
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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17
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Yagi S, Ogawa H. Effect of tryptophan metabolites on fluorescent granules in the Malpighian tubules of eye color mutants of Drosophila melanogaster. Zoolog Sci 1996; 13:97-104. [PMID: 8688814 DOI: 10.2108/zsj.13.97] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fluorescent granules that are stained with Nile blue sulfate are present in larval Malpighian tubules in the wild type strain of Drosophila melanogaster, Oregon-R. These granules emit a weak blue fluorescence and most of them are about 2 microns or more in diameter. The ommochrome precursor 3-hydroxy-kynurenine (3-HK) is actively transferred into the tubules of Oregon-R. Changes in the fluorescent granules in the Malpighian tubules on administration of ommochrome precursors were investigated in eye color mutants of Drosophila. The fluorescent granules in the tubules of the nonautonomous mutants v;bw and cn bw emit a strong blue fluorescence and most of them are about 1 micron or less in diameter. When v;bw and cn bw larvae were cultured on medium supplemented with kynurenine or 3-HK, respectively, the fluorescence intensity of their granules decreased, and their size increased. These additions resulted in almost equal accumulation of 3-HK to that in Oregon-R. On the other hand, no 3-HK accumulated in the tubules of larvae of the autonomous mutants bw;st, ltd bw and w, which lack the fluorescent granules. These findings indicate that the fluorescent granules are an important intracellular site for uptake or storage of ommochrome precursors in larval Malpighian tubules of Drosophila.
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Affiliation(s)
- S Yagi
- Department of Life Sciences, Faculty of Integrated Arts and Sciences, University of Tokushima, Japan
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18
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Glatigny A, Scazzocchio C. Cloning and molecular characterization of hxA, the gene coding for the xanthine dehydrogenase (purine hydroxylase I) of Aspergillus nidulans. J Biol Chem 1995; 270:3534-50. [PMID: 7876088 DOI: 10.1074/jbc.270.8.3534] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have cloned and sequenced the hxA gene coding for the xanthine dehydrogenase (purine hydroxylase I) of Aspergillus nidulans. The gene codes for a polypeptide of 1363 amino acids. The sequencing of a nonsense mutation, hxA5, proves formally that the clones isolated correspond to the hxA gene. The gene sequence is interrupted by three introns. Similarity searches reveal two iron-sulfur centers and a NAD/FAD-binding domain and have enabled a consensus sequence to be determined for the molybdenum cofactor-binding domain. The A. nidulans sequence is a useful outclass for the other known sequences, which are all from metazoans. In particular, it gives added significance to the missense mutations sequenced in Drosophila melanogaster and leads to the conclusion that while one of the recently sequenced human genes codes for a xanthine dehydrogenase, the other one must code for a different molybdenum-containing hydroxylase, possibly an aldehyde oxidase. The transcription of the hxA gene is induced by the uric acid analogue 2-thiouric acid and repressed by ammonium. Induction necessitates the product of the uaY regulatory gene.
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Affiliation(s)
- A Glatigny
- Institut de Génétique et Microbiologie, Unité Associtée au CNRS 1354, Université Paris-Sud, Centre d'Orsay, France
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19
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Affiliation(s)
- M J de Hoop
- Laboratory of Biochemistry, Groningen University, The Netherlands
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Reaume AG, Knecht DA, Chovnick A. The rosy locus in Drosophila melanogaster: xanthine dehydrogenase and eye pigments. Genetics 1991; 129:1099-109. [PMID: 1783294 PMCID: PMC1204774 DOI: 10.1093/genetics/129.4.1099] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The rosy gene in Drosophila melanogaster codes for the enzyme xanthine dehydrogenase (XDH). Mutants that have no enzyme activity are characterized by a brownish eye color phenotype reflecting a deficiency in the red eye pigment. Xanthine dehydrogenase is not synthesized in the eye, but rather is transported there. The present report describes the ultrastructural localization of XDH in the Drosophila eye. Three lines of evidence are presented demonstrating that XDH is sequestered within specific vacuoles, the type II pigment granules. Histochemical and antibody staining of frozen sections, as well as thin layer chromatography studies of several adult genotypes serve to examine some of the factors and genic interactions that may be involved in transport of XDH, and in eye pigment formation. While a specific function for XDH in the synthesis of the red, pteridine eye pigments remains unknown, these studies present evidence that: (1) the incorporation of XDH into the pigment granules requires specific interaction between a normal XDH molecule and one or more transport proteins; (2) the structural integrity of the pigment granule itself is dependent upon the presence of a normal balance of eye pigments, a notion advanced earlier.
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Affiliation(s)
- A G Reaume
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-2131
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Keller GA, Warner TG, Steimer KS, Hallewell RA. Cu,Zn superoxide dismutase is a peroxisomal enzyme in human fibroblasts and hepatoma cells. Proc Natl Acad Sci U S A 1991; 88:7381-5. [PMID: 1651504 PMCID: PMC52299 DOI: 10.1073/pnas.88.16.7381] [Citation(s) in RCA: 145] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The intracellular localization of Cu,Zn superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) has been examined by immunofluorescence using four monoclonal anti-Cu,Zn superoxide dismutase antibodies raised against a recombinant human Cu,Zn superoxide dismutase derivative produced and purified from Escherichia coli. Colocalization with catalase, a peroxisomal matrix enzyme, was used to demonstrate the peroxisomal localization of Cu,Zn superoxide dismutase in human fibroblasts and hepatoma cells. In the fibroblasts of Zellweger syndrome patients, the enzyme is not transported to the peroxisomal ghosts but, like catalase, remains in the cytoplasm. In addition, immunocryoelectron microscopy of yeast cells expressing human Cu,Zn superoxide dismutase showed that the enzyme is translocated to the peroxisomes.
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Affiliation(s)
- G A Keller
- Genentech Inc., South San Francisco, CA 94080
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22
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Abstract
The rosy (ry) locus in Drosophila melanogaster codes for the enzyme xanthine dehydrogenase. Mutants that have no enzyme activity are characterized by a brownish eye color phenotype reflecting a deficiency in the red eye pigment. This report demonstrates that enzyme which is synthesized in some tissue other than the eye is transported and sequestered at the eye. Previous studies find that no leader sequence is associated with this molecule but a peroxisomal targeting sequence has been noted, and the enzyme has been localized to peroxisomes. This represents a rare example of an enzyme involved in intermediary metabolism being transported from one tissue to another and may also be the first example of a peroxisomal protein being secreted from a cell.
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Affiliation(s)
- A G Reaume
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06268
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Angermüller S. Peroxisomal oxidases: cytochemical localization and biological relevance. PROGRESS IN HISTOCHEMISTRY AND CYTOCHEMISTRY 1989; 20:1-65. [PMID: 2574900 DOI: 10.1016/s0079-6336(89)80008-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
(1) alpha-HAOX has a broad substrate specificity. In rat kidney, the enzyme reacts with aliphatic and aromatic alpha-hydroxy acids, in rat liver, however, only with aliphatic ones. (2) The best substrate for the demonstration of alpha-HAOX activity in rat and human liver is glycolate. (3) alpha-hydroxy butyric acid is the best substrate in the luminometric assay for the demonstration of alpha-HAOX activity in the rat kidney, whereas glycolate is not catalysed by the enzyme. (4) In the proximal tubulus epithelial cells of the rat kidney alpha-HAOX is concentrated in the peripheral matrix of the peroxisomes.
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Affiliation(s)
- S Angermüller
- Department of Anatomy and Cell Biology, University of Heidelberg
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Wilson GN, Holmes RD, Hajra AK. Peroxisomal disorders: clinical commentary and future prospects. AMERICAN JOURNAL OF MEDICAL GENETICS 1988; 30:771-92. [PMID: 2461077 DOI: 10.1002/ajmg.1320300311] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent progress in the classification, biochemistry, and molecular biology of peroxisomal disorders is reviewed from a clinical perspective. Diseases such as Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum disease, hyperpipecolic acidemia, chondrodysplasia punctata, and Leber amaurosis share a common phenotype and involve deficiency of multiple peroxisomal enzymes. These disorders are associated with diverse metabolic abnormalities which are useful in pre- or postnatal diagnosis and distinguish these disorders from others such as X-linked adrenoleukodystrophy, adult Refsum disease, hyperoxaluria type I, and acatalasemia. Peroxisome structure is difficult to quantify histologically, since recent studies emphasize its developmental variability and tissue heterogeneity. The ability to manipulate this structure by dietary or pharmaceutical means provides a novel approach to therapy. At the molecular level, deficiency of peroxisomal enzymes responsible for fatty acid beta-oxidation or ether lipid synthesis reflects enhanced protein degradation due to abnormal peroxisomes; messenger RNA for the beta-oxidation enzymes is transcribed normally in peroxisomal disorders and can be increased by peroxisome proliferators. At least one integral structural protein of the peroxisome is synthesized normally in Zellweger syndrome. Hypotheses for the basic defect include defective regulation, uptake, or coenzyme stimulation of imported proteins, as well as defective biosynthesis. One clue to this defect may be a similar evolutionary history of peroxisomes and mitochondria which would explain their common alteration in Zellweger syndrome.
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Affiliation(s)
- G N Wilson
- Department of Pediatrics, William Beaumont Hospital, Royal Oak, Michigan
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