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Ravindran R, Bacellar IOL, Castellanos-Girouard X, Wahba HM, Zhang Z, Omichinski JG, Kisley L, Michnick SW. Peroxisome biogenesis initiated by protein phase separation. Nature 2023; 617:608-615. [PMID: 37165185 PMCID: PMC10302873 DOI: 10.1038/s41586-023-06044-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Peroxisomes are organelles that carry out β-oxidation of fatty acids and amino acids. Both rare and prevalent diseases are caused by their dysfunction1. Among disease-causing variant genes are those required for protein transport into peroxisomes. The peroxisomal protein import machinery, which also shares similarities with chloroplasts2, is unique in transporting folded and large, up to 10 nm in diameter, protein complexes into peroxisomes3. Current models postulate a large pore formed by transmembrane proteins4; however, so far, no pore structure has been observed. In the budding yeast Saccharomyces cerevisiae, the minimum transport machinery includes the membrane proteins Pex13 and Pex14 and the cargo-protein-binding transport receptor, Pex5. Here we show that Pex13 undergoes liquid-liquid phase separation (LLPS) with Pex5-cargo. Intrinsically disordered regions in Pex13 and Pex5 resemble those found in nuclear pore complex proteins. Peroxisomal protein import depends on both the number and pattern of aromatic residues in these intrinsically disordered regions, consistent with their roles as 'stickers' in associative polymer models of LLPS5,6. Finally, imaging fluorescence cross-correlation spectroscopy shows that cargo import correlates with transient focusing of GFP-Pex13 and GFP-Pex14 on the peroxisome membrane. Pex13 and Pex14 form foci in distinct time frames, suggesting that they may form channels at different saturating concentrations of Pex5-cargo. Our findings lead us to suggest a model in which LLPS of Pex5-cargo with Pex13 and Pex14 results in transient protein transport channels7.
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Affiliation(s)
- Rini Ravindran
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | - Isabel O L Bacellar
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
- Douglas Research Centre, Montreal, Quebec, Canada
| | | | - Haytham M Wahba
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Zhenghao Zhang
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Mitchell Physics Building (MPHY), College Station, TX, USA
| | - James G Omichinski
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada.
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2
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Deori NM, Infant T, Thummer RP, Nagotu S. Characterization of the Multiple Domains of Pex30 Involved in Subcellular Localization of the Protein and Regulation of Peroxisome Number. Cell Biochem Biophys 2023; 81:39-47. [PMID: 36462131 DOI: 10.1007/s12013-022-01122-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Pex30 is a peroxisomal protein whose role in peroxisome biogenesis via the endoplasmic reticulum has been established. It is a 58 KDa multi-domain protein that facilitates contact site formation between various organelles. The present study aimed to investigate the role of various domains of the protein in its sub-cellular localization and regulation of peroxisome number. For this, we created six truncations of the protein (1-87, 1-250, 1-352, 88-523, 251-523 and 353-523) and tagged GFP at the C-terminus. Biochemical methods and fluorescence microscopy were used to characterize the effect of truncation on expression and localization of the protein. Quantitative analysis was performed to determine the effect of truncation on peroxisome number in these cells. Expression of the truncated variants in cells lacking PEX30 did not cause any effect on cell growth. Interestingly, variable expression and localization of the truncated variants in both peroxisome-inducing and non-inducing medium was observed. Truncated variants depicted different distribution patterns such as punctate, reticulate and cytosolic fluorescence. Interestingly, lack of the complete dysferlin domain or C-Dysf resulted in increased peroxisome number similar to as reported for cells lacking Pex30. No contribution of this domain in the reticulate distribution of the proteins was also observed. Our results show an interesting role for the various domains of Pex30 in localization and regulation of peroxisome number.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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3
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Skowyra ML, Rapoport TA. PEX5 translocation into and out of peroxisomes drives matrix protein import. Mol Cell 2022; 82:3209-3225.e7. [PMID: 35931083 PMCID: PMC9444985 DOI: 10.1016/j.molcel.2022.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal enzymes are imported from the cytosol by the receptor PEX5, which interacts with a docking complex in the peroxisomal membrane and then returns to the cytosol after monoubiquitination by a membrane-embedded ubiquitin ligase. The mechanism by which PEX5 shuttles between cytosol and peroxisomes and releases cargo inside the lumen is unclear. Here, we use Xenopus egg extract to demonstrate that PEX5 accompanies cargo completely into the lumen, utilizing WxxxF/Y motifs near its N terminus that bind a lumenal domain of the docking complex. PEX5 recycling is initiated by an amphipathic helix that binds to the lumenal side of the ubiquitin ligase. The N terminus then emerges in the cytosol for monoubiquitination. Finally, PEX5 is extracted from the lumen, resulting in the unfolding of the receptor and cargo release. Our results reveal the unique mechanism by which PEX5 ferries proteins into peroxisomes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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4
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Abstract
Fungal peroxisomes are characterized by a number of specific biological functions. To understand the physiology and biochemistry of these organelles knowledge of the proteome content is crucial. Here, we address different strategies to predict peroxisomal proteins by bioinformatics approaches. These tools range from simple text searches to network based learning strategies. A complication of this analysis is the existence of cryptic peroxisomal proteins, which are overlooked in conventional bioinformatics queries. These include proteins where targeting information results from transcriptional and posttranscriptional alterations. But also proteins with low efficiency targeting motifs that are predominantly localized in the cytosol, and proteins lacking any canonical targeting information, can play important roles within peroxisomes. Many of these proteins are so far unpredictable. Detection and characterization of these cryptic peroxisomal proteins revealed the presence of novel peroxisomal enzymatic reaction networks in fungi.
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Affiliation(s)
- Johannes Freitag
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Alina C Stiebler
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany.
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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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Abstract
Our knowledge of the proteome of plant peroxisomes is far from being complete, and the functional complexity and plasticity of this cell organelle are amazingly high particularly in plants, as exemplified by the model species Arabidopsis thaliana. Plant-specific peroxisome functions that have been uncovered only recently include, for instance, the participation of peroxisomes in phylloquinone and biotin biosynthesis. Experimental proteome studies have been proved very successful in defining the proteome of Arabidopsis peroxisomes but this approach also faces significant challenges and limitations. Complementary to experimental approaches, computational methods have emerged as important powerful tools to define the proteome of soluble matrix proteins of plant peroxisomes. Compared to other cell organelles such as mitochondria, plastids and the ER, the simultaneous operation of two major import pathways for soluble proteins in peroxisomes is rather atypical. Novel machine learning prediction approaches have been developed for peroxisome targeting signals type 1 (PTS1) and revealed high sensitivity and specificity, as validated by in vivo subcellular targeting analyses in diverse transient plant expression systems. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In contrast, the prediction of PTS2 proteins largely remains restricted to genome searches by conserved patterns contrary to more advanced machine learning methods. Here, we summarize and discuss the capabilities and accuracies of available prediction algorithms for PTS1 and PTS2 carrying proteins.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Gopal Chowdhary
- KIIT School of Biotechnology, Campus XI, KIIT University, Bhubaneswar, 751024, India
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7
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Abstract
Plant peroxisomes are required for a number of fundamental physiological processes, such as primary and secondary metabolism, development and stress response. Indexing the dynamic peroxisome proteome is prerequisite to fully understanding the importance of these organelles. Mass Spectrometry (MS)-based proteome analysis has allowed the identification of novel peroxisomal proteins and pathways in a relatively high-throughput fashion and significantly expanded the list of proteins and biochemical reactions in plant peroxisomes. In this chapter, we summarize the experimental proteomic studies performed in plants, compile a list of ~200 confirmed Arabidopsis peroxisomal proteins, and discuss the diverse plant peroxisome functions with an emphasis on the role of Arabidopsis MS-based proteomics in discovering new peroxisome functions. Many plant peroxisome proteins and biochemical pathways are specific to plants, substantiating the complexity, plasticity and uniqueness of plant peroxisomes. Mapping the full plant peroxisome proteome will provide a knowledge base for the improvement of crop production, quality and stress tolerance.
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Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
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Abstract
Autolysosomes are organelles that sequester and degrade a portion of the cytoplasm during autophagy. Although autophagosomes are short lived compared to other organelles such as mitochondria, plastids, and peroxisomes, many autolysosomes accumulate in tobacco BY-2 cells cultured under sucrose starvation conditions in the presence of a cysteine protease inhibitor. We here describe our methodology for isolating autolysosomes from BY-2 cells by conventional cell fractionation using a Percoll gradient. The autolysosome fraction separates clearly from fractions containing mitochondria and peroxisomes. It contains acid phosphatase, vacuolar H+-ATPase, and protease activity. Electron micrographs show that the fraction contains partially degraded cytoplasm seen in autolysosomes before isolation although an autolysosome structure is only partially preserved.
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Affiliation(s)
| | - Yuko Inoue-Aono
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama, 338-8570, Japan
| | - Yuji Moriyasu
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama, 338-8570, Japan.
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9
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Abstract
Low-density lipoproteins (LDLs) are taken up by the cell mainly through receptor-mediated endocytosis. LDL-derived cholesterol leaves lysosome and further transports to downstream organelles for specific cellular needs. We recently report that cholesterol transfers from lysosome to peroxisome through lysosome-peroxisome membrane contact (LPMC). Here, we use iodixanol density gradient centrifugation to isolate lysosomes and peroxisomes separately for the in vitro reconstitution of LPMC. We also apply 3H-cholesterol-labeled lysosomes and peroxisomes in vitro to measure 3H-cholesterol transfer through LPMC.
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Affiliation(s)
- Jie Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya-Cheng Liao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jian Xiao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Yoon J, Kim YH, Min J. Evaluation of In Vitro Function by Subcellular Distribution of Lysosomal and Peroxisomal Protein in Saccharomyces cerevisiae. J Nanosci Nanotechnol 2017; 17:244-250. [PMID: 29620334 DOI: 10.1166/jnn.2017.12448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lysosomes and peroxisomes, contained in all eukaryote cells, are similar but have completely different function. Lysosomes have three dozen different kinds of hydrolytic enzymes and release lysosomal enzymes to digest intra/extracellular materials. The lysosomal enzymes degrade bacteria cell walls and proteins in cell, exhibiting an antimicrobial and anticancerous effect. Peroxisomes contain oxidative enzymes such as peroxidase, D-amino acid oxidase, and catalase allowing the ability to degrade melanin in hyperpigmentation disorders. Exposure of Saccharomyces cerevisiae and HeLa cells to chemical stress alters lysosomal and peroxisomal enzymes. Chemical stresses such as phenylhydrazine, sodium azide, rolipram, NH4Cl, salicylic acid, H2O2 and 6-hydroxdopamine (6-OHDA) have been suggested to stimulate In Vitro function of lysosome and peroxisome-like organelles (LPO) isolated from S. cerevisiae, and we demonstrate activity of LPO in HeLa cells through chemical analysis. The lysosomes of cells exposed to salicylic acid, 6-OHDA and H2O2 had increased antimicrobial and anticancerous activity, and the peroxisomes of cells exposed to phenylhydrazine and sodium azide had reduced effect of melanin degradation. Therefore, our results suggest that activity of lysosomes and peroxisomes can be regulated by several stimuli, therefore lysosomes may be used as antimicrobial agents, apoptosis-inducing materials, or peroxisomal enzymes to be useful agents for cosmeceutical skin lightening and treatment of hyperpigmentation disorders.
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Nakamura M, Suzuki A, Akada J, Tomiyoshi K, Hoshida H, Akada R. End Joining-Mediated Gene Expression in Mammalian Cells Using PCR-Amplified DNA Constructs that Contain Terminator in Front of Promoter. Mol Biotechnol 2016; 57:1018-29. [PMID: 26350674 DOI: 10.1007/s12033-015-9890-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mammalian gene expression constructs are generally prepared in a plasmid vector, in which a promoter and terminator are located upstream and downstream of a protein-coding sequence, respectively. In this study, we found that front terminator constructs-DNA constructs containing a terminator upstream of a promoter rather than downstream of a coding region-could sufficiently express proteins as a result of end joining of the introduced DNA fragment. By taking advantage of front terminator constructs, FLAG substitutions, and deletions were generated using mutagenesis primers to identify amino acids specifically recognized by commercial FLAG antibodies. A minimal epitope sequence for polyclonal FLAG antibody recognition was also identified. In addition, we analyzed the sequence of a C-terminal Ser-Lys-Leu peroxisome localization signal, and identified the key residues necessary for peroxisome targeting. Moreover, front terminator constructs of hepatitis B surface antigen were used for deletion analysis, leading to the identification of regions required for the particle formation. Collectively, these results indicate that front terminator constructs allow for easy manipulations of C-terminal protein-coding sequences, and suggest that direct gene expression with PCR-amplified DNA is useful for high-throughput protein analysis in mammalian cells.
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Affiliation(s)
- Mikiko Nakamura
- Innovation Center, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan.
- Yamaguchi University Biomedical Engineering Center (YUBEC), Tokiwadai, Ube, 755-8611, Japan.
| | - Ayako Suzuki
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan
| | - Junko Akada
- Innovation Center, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, 879-5503, Japan
| | - Keisuke Tomiyoshi
- Department of Applied Chemistry, Faculty of Engineering, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan
- Yamaguchi University Biomedical Engineering Center (YUBEC), Tokiwadai, Ube, 755-8611, Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan.
- Yamaguchi University Biomedical Engineering Center (YUBEC), Tokiwadai, Ube, 755-8611, Japan.
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12
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). Biochim Biophys Acta 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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Agrawal G, Subramani S. De novo peroxisome biogenesis: Evolving concepts and conundrums. Biochim Biophys Acta 2016; 1863:892-901. [PMID: 26381541 PMCID: PMC4791208 DOI: 10.1016/j.bbamcr.2015.09.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
Peroxisomes proliferate by growth and division of pre-existing peroxisomes or could arise de novo. Though the de novo pathway of peroxisome biogenesis is a more recent discovery, several studies have highlighted key mechanistic details of the pathway. The endoplasmic reticulum (ER) is the primary source of lipids and proteins for the newly-formed peroxisomes. More recently, an intricate sorting process functioning at the ER has been proposed, that segregates specific PMPs first to peroxisome-specific ER domains (pER) and then assembles PMPs selectively into distinct pre-peroxisomal vesicles (ppVs) that later fuse to form import-competent peroxisomes. In addition, plausible roles of the three key peroxins Pex3, Pex16 and Pex19, which are also central to the growth and division pathway, have been suggested in the de novo process. In this review, we discuss key developments and highlight the unexplored avenues in de novo peroxisome biogenesis.
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Affiliation(s)
- Gaurav Agrawal
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA.
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14
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Gao H, Metz J, Teanby NA, Ward AD, Botchway SW, Coles B, Pollard MR, Sparkes I. In Vivo Quantification of Peroxisome Tethering to Chloroplasts in Tobacco Epidermal Cells Using Optical Tweezers. Plant Physiol 2016; 170:263-72. [PMID: 26518344 PMCID: PMC4704594 DOI: 10.1104/pp.15.01529] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/24/2015] [Indexed: 05/19/2023]
Abstract
Peroxisomes are highly motile organelles that display a range of motions within a short time frame. In static snapshots, they can be juxtaposed to chloroplasts, which has led to the hypothesis that they are physically interacting. Here, using optical tweezers, we tested the dynamic physical interaction in vivo. Using near-infrared optical tweezers combined with TIRF microscopy, we were able to trap peroxisomes and approximate the forces involved in chloroplast association in vivo in tobacco (Nicotiana tabacum) and observed weaker tethering to additional unknown structures within the cell. We show that chloroplasts and peroxisomes are physically tethered through peroxules, a poorly described structure in plant cells. We suggest that peroxules have a novel role in maintaining peroxisome-organelle interactions in the dynamic environment. This could be important for fatty acid mobilization and photorespiration through the interaction with oil bodies and chloroplasts, highlighting a fundamentally important role for organelle interactions for essential biochemistry and physiological processes.
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Affiliation(s)
- Hongbo Gao
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Jeremy Metz
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Nick A Teanby
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Andy D Ward
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Stanley W Botchway
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Benjamin Coles
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Mark R Pollard
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
| | - Imogen Sparkes
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom (H.G., J.M., I.S.);School of Earth Sciences, University of Bristol, Clifton, Bristol BS8 1RJ, United Kingdom (N.A.T.); andCentral Laser Facility, Science and Technology Facilities Council, Didcot, Oxon OX11 0FA, United Kingdom (A.D.W., S.W.B., B.C., M.R.P.)
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15
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Chen Y, Pieuchot L, Loh RA, Yang J, Kari TMA, Wong JY, Jedd G. Hydrophobic handoff for direct delivery of peroxisome tail-anchored proteins. Nat Commun 2014; 5:5790. [PMID: 25517356 DOI: 10.1038/ncomms6790] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 11/04/2014] [Indexed: 02/06/2023] Open
Abstract
Tail-anchored (TA) proteins are inserted into membranes post-translationally through a C-terminal transmembrane domain (TMD). The PEX19 protein binds peroxisome TA proteins in the cytoplasm and delivers them to the membrane through the PEX3 receptor protein. An amphipathic segment in PEX19 promotes docking on PEX3. However, how this leads to substrate insertion is unknown. Here we reconstitute peroxisome TA protein biogenesis into two sequential steps of substrate TMD engagement and membrane insertion. We identify a series of previously uncharacterized amphipathic segments in PEX19 and identify one whose hydrophobicity is required for membrane insertion, but not TMD chaperone activity or PEX3 binding. A membrane-proximal hydrophobic surface of PEX3 promotes an unconventional form of membrane intercalation, and is also required for TMD insertion. Together, these data support a mechanism in which hydrophobic moieties in the TMD chaperone and its membrane-associated receptor act in a concerted manner to prompt TMD release and membrane insertion.
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Affiliation(s)
- Yinxiao Chen
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Laurent Pieuchot
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Rachel Ann Loh
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Jing Yang
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Teuku Mahfuzh Aufar Kari
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Jie Yun Wong
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
| | - Gregory Jedd
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
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16
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Nascimento AFZ, Trindade DM, Tonoli CCC, de Giuseppe PO, Assis LHP, Honorato RV, de Oliveira PSL, Mahajan P, Burgess-Brown NA, von Delft F, Larson RE, Murakami MT. Structural insights into functional overlapping and differentiation among myosin V motors. J Biol Chem 2013; 288:34131-34145. [PMID: 24097982 PMCID: PMC3837155 DOI: 10.1074/jbc.m113.507202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/27/2013] [Indexed: 11/06/2022] Open
Abstract
Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.
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Affiliation(s)
- Andrey F Z Nascimento
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Daniel M Trindade
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Priscila O de Giuseppe
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Leandro H P Assis
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Rodrigo V Honorato
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Paulo S L de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Pravin Mahajan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Roy E Larson
- Department of Cellular & Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, São Paulo 14049-900, Brazil
| | - Mario T Murakami
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil.
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17
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Planas-Portell J, Gallart M, Tiburcio AF, Altabella T. Copper-containing amine oxidases contribute to terminal polyamine oxidation in peroxisomes and apoplast of Arabidopsis thaliana. BMC Plant Biol 2013; 13:109. [PMID: 23915037 PMCID: PMC3751259 DOI: 10.1186/1471-2229-13-109] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyamines (PAs) are oxidatively deaminated at their primary or secondary amino-groups by copper-containing amine oxidases (CuAOs) or FAD-dependent amine oxidases (PAOs), respectively. Both enzymes have long been considered to be apoplastic proteins. However, three out of five PAO isoforms in Arabidopsis thaliana are localized in peroxisomes, while the other two PAOs are predicted to be cytosolic. Interestingly, most of these PAOs do not contribute to terminal PA oxidation, but instead are involved in the back-conversion pathway, producing spermidine from spermine and putrescine from spermidine, which in turn is inhibited by putrescine. This opens the question as to whether PAs are catabolized in the apoplast of Arabidopsis and if the terminal oxidation occurs in the peroxisomes. The main objective of this study was to know if these catabolic processes are mediated by CuAOs. RESULTS A. thaliana contains ten genes annotated as CuAOs, but only one (ATAO1) has been characterized at the protein level. Reported herein is the characterization of three genes encoding putative Arabidopsis CuAOs (AtCuAO1, AtCuAO2 and AtCuAO3). These genes encode functional CuAOs that use putrescine and spermidine as substrates. AtCuAO1, like ATAO1, is an extracellular protein, while AtCuAO2 and AtCuAO3 are localized in peroxisomes. The three genes present a different expression profile in response to exogenous treatments, such as application of abcisic acid, methyl jasmonate, salycilic acid, flagellin 22 and wounding. CONCLUSIONS PA catabolism in the Arabidopsis apoplast is mediated predominantly by CuAOs, while in peroxisomes the co-localization of CuAO-dependent terminal catabolism with PAO-back-conversion machineries might contribute to modulating putrescine-mediated inhibition of the back-conversion, suggesting the occurrence of a tight coordination between both catabolic pathways. The expression profile of AtCuAO1-3 in response to different exogenous treatments, together with the different localization of the corresponding proteins, provides evidence for the functional diversification of Arabidopsis CuAO proteins.
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Affiliation(s)
- Joan Planas-Portell
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Marta Gallart
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Antonio F Tiburcio
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Teresa Altabella
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Laboratory of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
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18
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Heyneke E, Luschin-Ebengreuth N, Krajcer I, Wolkinger V, Müller M, Zechmann B. Dynamic compartment specific changes in glutathione and ascorbate levels in Arabidopsis plants exposed to different light intensities. BMC Plant Biol 2013; 13:104. [PMID: 23865417 PMCID: PMC3728233 DOI: 10.1186/1471-2229-13-104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 07/16/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Excess light conditions induce the generation of reactive oxygen species (ROS) directly in the chloroplasts but also cause an accumulation and production of ROS in peroxisomes, cytosol and vacuoles. Antioxidants such as ascorbate and glutathione occur in all cell compartments where they detoxify ROS. In this study compartment specific changes in antioxidant levels and related enzymes were monitored among Arabidopsis wildtype plants and ascorbate and glutathione deficient mutants (vtc2-1 and pad2-1, respectively) exposed to different light intensities (50, 150 which was considered as control condition, 300, 700 and 1,500 μmol m(-2) s(-1)) for 4 h and 14 d. RESULTS The results revealed that wildtype plants reacted to short term exposure to excess light conditions with the accumulation of ascorbate and glutathione in chloroplasts, peroxisomes and the cytosol and an increased activity of catalase in the leaves. Long term exposure led to an accumulation of ascorbate and glutathione mainly in chloroplasts. In wildtype plants an accumulation of ascorbate and hydrogen peroxide (H2O2) could be observed in vacuoles when exposed to high light conditions. The pad2-1 mutant reacted to long term excess light exposure with an accumulation of ascorbate in peroxisomes whereas the vtc2-1 mutant reacted with an accumulation of glutathione in the chloroplasts (relative to the wildtype) and nuclei during long term high light conditions indicating an important role of these antioxidants in these cell compartments for the protection of the mutants against high light stress. CONCLUSION The results obtained in this study demonstrate that the accumulation of ascorbate and glutathione in chloroplasts, peroxisomes and the cytosol is an important reaction of plants to short term high light stress. The accumulation of ascorbate and H2O2 along the tonoplast and in vacuoles during these conditions indicates an important route for H2O2 detoxification under these conditions.
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Affiliation(s)
- Elmien Heyneke
- Department of Lothar Willmitzer, Max-Planck-Institute of Molecular Plant Physiology, Golm, 14476, Germany
| | - Nora Luschin-Ebengreuth
- Institute for Electron Microscopy and Fine Structure Research, Graz University of Technology, Steyrergasse 17, Graz, 8010, Austria
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, Graz, 8010, Austria
| | - Iztok Krajcer
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, Graz, 8010, Austria
| | - Volker Wolkinger
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, Graz, 8010, Austria
| | - Maria Müller
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, Graz, 8010, Austria
| | - Bernd Zechmann
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, Graz, 8010, Austria
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19
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Hartwig S, Knebel B, Goeddeke S, Koellmer C, Jacob S, Nitzgen U, Passlack W, Schiller M, Dicken HD, Haas J, Muller-Wieland D, Lehr S, Kotzka J. So close and yet so far: mitochondria and peroxisomes are one but with specific talents. Arch Physiol Biochem 2013; 119:126-35. [PMID: 23705958 DOI: 10.3109/13813455.2013.796994] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cellular compartmentalization of central metabolic pathways as lipid metabolism to mitochondria and peroxisomes enables high efficient control processes. The basis to understand mitochondrial or peroxisomal function is exactly to determine proteins physically present. For proteomic investigations of mouse liver organelles, we developed 2-DE reference maps covering the range pH 4-9, available under ( www.diabesityprot.org ). MALDI-TOF-MS/MS analyses identified a total of 799 (mitochondria) and 681 (peroxisome) protein spots resembling 323 and 293 unique proteins, respectively. Direct comparison of mitochondrial and peroxisomal proteins indicated an approximate overlap of 2/3 of identified proteins. Gene Ontologies (GO) of the identified proteins in respect to physical presence confirmed functional specifications within the organelles. The 2-DE organelle reference maps will aid to point out functional differences and similarities. Our observations suggest that for functional analyses metabolic alterations focusing on one organelle are not sufficient and parallel comparison of both organelles is to be preferred.
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Affiliation(s)
- Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Deusseldorf, Leibniz Center for Diabetes Research, 40225 Düsseldorf, Germany
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20
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Bonekamp NA, Grille S, Cardoso MJ, Almeida M, Aroso M, Gomes S, Magalhaes AC, Ribeiro D, Islinger M, Schrader M. Self-interaction of human Pex11pβ during peroxisomal growth and division. PLoS One 2013; 8:e53424. [PMID: 23308220 PMCID: PMC3538539 DOI: 10.1371/journal.pone.0053424] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/28/2012] [Indexed: 12/15/2022] Open
Abstract
Pex11 proteins are involved in membrane elongation and division processes associated with the multiplication of peroxisomes. Human Pex11pβ has recently been linked to a new disorder affecting peroxisome morphology and dynamics. Here, we have analyzed the exact membrane topology of Pex11pβ. Studies with an epitope-specific antibody and protease protection assays show that Pex11pβ is an integral membrane protein with two transmembrane domains flanking an internal region exposed to the peroxisomal matrix and N- and C-termini facing the cytosol. A glycine-rich internal region within Pex11pβ is dispensable for peroxisome membrane elongation and division. However, we demonstrate that an amphipathic helix (Helix 2) within the first N-terminal 40 amino acids is crucial for membrane elongation and self-interaction of Pex11pβ. Interestingly, we find that Pex11pβ self-interaction strongly depends on the detergent used for solubilization. We also show that N-terminal cysteines are not essential for membrane elongation, and that putative N-terminal phosphorylation sites are dispensable for Pex11pβ function. We propose that self-interaction of Pex11pβ regulates its membrane deforming activity in conjunction with membrane lipids.
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Affiliation(s)
- Nina A. Bonekamp
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Sandra Grille
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Maria Joao Cardoso
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Monica Almeida
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Miguel Aroso
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Silvia Gomes
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Ana Cristina Magalhaes
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Daniela Ribeiro
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Markus Islinger
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Michael Schrader
- Centre for Cell Biology and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, Devon, United Kingdom
- * E-mail:
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21
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Abstract
Because of its ability to study specifically labeled structures, fluorescence microscopy is the most widely used technique for investigating live cell dynamics and function. Fluorescence correlation spectroscopy is an established method for studying molecular transport and diffusion coefficients at a fixed spatial scale. We propose a new approach, dispersion-relation fluorescence spectroscopy (DFS), to study the transport dynamics over a broad range of spatial and temporal scales. The molecules of interest are labeled with a fluorophore whose motion gives rise to spontaneous fluorescence intensity fluctuations that are analyzed to quantify the governing mass transport dynamics. These data are characterized by the effective dispersion relation. We report on experiments demonstrating that DFS can distinguish diffusive from advection motion in a model system, where we obtain quantitatively accurate values of both diffusivities and advection velocities. Because of its spatially resolved information, DFS can distinguish between directed and diffusive transport in living cells. Our data indicate that the fluorescently labeled actin cytoskeleton exhibits active transport motion along a direction parallel to the fibers and diffusive in the perpendicular direction.
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Affiliation(s)
- Ru Wang
- Quantitative Light Imaging Laboratory, Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Abstract
In Chlorophycean algal cells, these organelles are generally called microbodies because they lack the enzymes found in the peroxisomes of higher plants. Microbodies in some algae contain fewer enzymes than the peroxisomes of higher plants, and some unicellular green algae in Chlorophyceae such as Chlamydomonas reinhardtii do not possess catalase, an enzyme commonly found in peroxisomes. Thus, whether microbodies in Chlorophycean algae are similar to the peroxisomes of higher plants, and whether they use a similar transport mechanism for the peroxisomal targeting signal (PTS), remain unclear. To determine whether the PTS is present in the microbodies of Chlorophycean algae, and to visualize the microbodies in Chlamydomonas cells, we examined the sub-cellular localization of green fluorescent proteins (GFP) fused to several PTS-like sequences. We detected GFP compartments that were spherical with a diameter of 0.3-1.0 μm in transgenic Chlamydomonas. Comparative analysis of the character of GFP-compartments observed by fluorescence microscopy and that of microbodies by electron microscopy indicated that the compartments were one and the same. The result also showed that the microbodies in Chlorophycean cells have a similar transport mechanism to that of peroxisomes of higher plants.
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Affiliation(s)
- Yasuko Hayashi
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi, Ninotyou, Niigata, Niigata 950-2181, Japan.
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24
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von Reuss SH, Bose N, Srinivasan J, Yim JJ, Judkins JC, Sternberg PW, Schroeder FC. Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C. elegans. J Am Chem Soc 2012; 134:1817-24. [PMID: 22239548 PMCID: PMC3269134 DOI: 10.1021/ja210202y] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the model organism Caenorhabditis elegans, a family of endogenous small molecules, the ascarosides function as key regulators of developmental timing and behavior that act upstream of conserved signaling pathways. The ascarosides are based on the dideoxysugar ascarylose, which is linked to fatty-acid-like side chains of varying lengths derived from peroxisomal β-oxidation. Despite the importance of ascarosides for many aspects of C. elegans biology, knowledge of their structures, biosynthesis, and homeostasis remains incomplete. We used an MS/MS-based screen to profile ascarosides in C. elegans wild-type and mutant metabolomes, which revealed a much greater structural diversity of ascaroside derivatives than previously reported. Comparison of the metabolomes from wild-type and a series of peroxisomal β-oxidation mutants showed that the enoyl CoA-hydratase MAOC-1 serves an important role in ascaroside biosynthesis and clarified the functions of two other enzymes, ACOX-1 and DHS-28. We show that, following peroxisomal β-oxidation, the ascarosides are selectively derivatized with moieties of varied biogenetic origin and that such modifications can dramatically affect biological activity, producing signaling molecules active at low femtomolar concentrations. Based on these results, the ascarosides appear as a modular library of small-molecule signals, integrating building blocks from three major metabolic pathways: carbohydrate metabolism, peroxisomal β-oxidation of fatty acids, and amino acid catabolism. Our screen further demonstrates that ascaroside biosynthesis is directly affected by nutritional status and that excretion of the final products is highly selective.
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Affiliation(s)
- Stephan H. von Reuss
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jagan Srinivasan
- Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Joshua J. Yim
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Joshua C. Judkins
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul W. Sternberg
- Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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25
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Kriechbaumer V, von Löffelholz O, Abell BM. Chaperone receptors: guiding proteins to intracellular compartments. Protoplasma 2012; 249:21-30. [PMID: 21461941 DOI: 10.1007/s00709-011-0270-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 03/02/2011] [Indexed: 05/04/2023]
Abstract
Despite mitochondria and chloroplasts having their own genome, 99% of mitochondrial proteins (Rehling et al., Nat Rev Mol Cell Biol 5:519-530, 2004) and more than 95% of chloroplast proteins (Soll, Curr Opin Plant Biol 5:529-535, 2002) are encoded by nuclear DNA, synthesised in the cytosol and imported post-translationally. Protein targeting to these organelles depends on cytosolic targeting factors, which bind to the precursor, and then interact with membrane receptors to deliver the precursor into a translocase. The molecular chaperones Hsp70 and Hsp90 have been widely implicated in protein targeting to mitochondria and chloroplasts, and receptors capable of recognising these chaperones have been identified at the surface of both these organelles (Schlegel et al., Mol Biol Evol 24:2763-2774, 2007). The role of these chaperone receptors is not fully understood, but they have been shown to increase the efficiency of protein targeting (Young et al., Cell 112:41-50, 2003; Qbadou et al., EMBO J 25:1836-1847, 2006). Whether these receptors contribute to the specificity of targeting is less clear. A class of chaperone receptors bearing tetratricopeptide repeat domains is able to specifically bind the highly conserved C terminus of Hsp70 and/or Hsp90. Interestingly, at least of one these chaperone receptors can be found on each organelle (Schlegel et al., Mol Biol Evol 24:2763-2774, 2007), which suggests a universal role in protein targeting for these chaperone receptors. This review will investigate the role that chaperone receptors play in targeting efficiency and specificity, as well as examining recent in silico approaches to find novel chaperone receptors.
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26
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Holth TF, Beckius J, Zorita I, Cajaraville MP, Hylland K. Assessment of lysosomal membrane stability and peroxisome proliferation in the head kidney of Atlantic cod (Gadus morhua) following long-term exposure to produced water components. Mar Environ Res 2011; 72:127-134. [PMID: 21821279 DOI: 10.1016/j.marenvres.2011.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/05/2011] [Accepted: 07/11/2011] [Indexed: 05/31/2023]
Abstract
There is a need for sensitive biological effect methods by which to detect impacts of chronic exposure to low concentrations of contaminants. Two methods shown to be potentially useful for monitoring purposes in fish include lysosomal membrane stability and peroxisome proliferation. These biological endpoints were assessed in Atlantic cod (Gadus morhua) head kidney following exposure to a mixture of produced water components including polycyclic aromatic hydrocarbons, phenol, and alkylphenols. Lysosomal damage of head kidney cells occurred within the first two weeks and did not recover during the entire exposure period (32 weeks). Lysosomal membrane stability was not affected by gender and was responsive at low concentrations of contamination, indicating that lysosomal membrane stability measured in the head kidney could be a useful biomarker for effects of offshore pollution. Peroxisome proliferation, measured as acyl-CoA oxidase activity in the head kidney, appeared to be a potential biomarker in male cod exposed less than 16 weeks.
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Affiliation(s)
- T F Holth
- University of Oslo, Department of Biology, Norway.
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Arent S, Christensen CE, Pye VE, Nørgaard A, Henriksen A. The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J Biol Chem 2010; 285:24066-77. [PMID: 20463021 PMCID: PMC2911295 DOI: 10.1074/jbc.m110.106005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/12/2010] [Indexed: 11/06/2022] Open
Abstract
Plant fatty acids can be completely degraded within the peroxisomes. Fatty acid degradation plays a role in several plant processes including plant hormone synthesis and seed germination. Two multifunctional peroxisomal isozymes, MFP2 and AIM1, both with 2-trans-enoyl-CoA hydratase and l-3-hydroxyacyl-CoA dehydrogenase activities, function in mouse ear cress (Arabidopsis thaliana) peroxisomal beta-oxidation, where fatty acids are degraded by the sequential removal of two carbon units. A deficiency in either of the two isozymes gives rise to a different phenotype; the biochemical and molecular background for these differences is not known. Structure determination of Arabidopsis MFP2 revealed that plant peroxisomal MFPs can be grouped into two families, as defined by a specific pattern of amino acid residues in the flexible loop of the acyl-binding pocket of the 2-trans-enoyl-CoA hydratase domain. This could explain the differences in substrate preferences and specific biological functions of the two isozymes. The in vitro substrate preference profiles illustrate that the Arabidopsis AIM1 hydratase has a preference for short chain acyl-CoAs compared with the Arabidopsis MFP2 hydratase. Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes.
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Affiliation(s)
- Susan Arent
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Caspar E. Christensen
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Valerie E. Pye
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Allan Nørgaard
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Anette Henriksen
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
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Hanson ML, Peer CJ, Brundage R, Callery PS, Brundage K, Schafer R, Eremin S, Barnett JB. Subcellular localization of the amide class herbicide 3,4-dichloropropionanilide (DCPA) in T cells and hepatocytes. J Toxicol Environ Health A 2010; 73:1-4. [PMID: 19953415 PMCID: PMC2888467 DOI: 10.1080/15287390903249131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
3,4-Dichloropropionanilide (DCPA), or propanil, a post-emergent herbicide used on rice and wheat crops in the United States, is immunotoxic in vivo and in vitro. Although it has been documented that DCPA exerts differential effects on specific immune cell types and is toxic to the liver, the way in which DCPA modulates intracellular functions leading to these effects is less understood. In this study, Jurkat T cells and hepatocytes from C57Bl/6 mice were exposed to 100 microM DCPA for 1.5 h. Following incubation, subcellular fractions of each cell type were isolated. DCPA, when present, was removed from each cell fraction by liquid-liquid extraction. The extraction product was then analyzed for the presence of DCPA using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The cellular uptake of DCPA was monitored by detection of the molecular ion and product ion of DCPA. The analyses demonstrate that DCPA, a lipophilic compound, localizes primarily in the cytosol of T cells and hepatocytes. These results indicate that DCPA is able to cross the plasma membrane and is accessible to intracellular immunomodulatory effectors.
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Affiliation(s)
- Miranda L. Hanson
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Cody J. Peer
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Rodney Brundage
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Patrick S. Callery
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Kathleen Brundage
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Rosana Schafer
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Sergei Eremin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russian Federation
| | - John B. Barnett
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia
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29
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Wang RYL, Stork J, Nagy PD. A key role for heat shock protein 70 in the localization and insertion of tombusvirus replication proteins to intracellular membranes. J Virol 2009; 83:3276-87. [PMID: 19153242 PMCID: PMC2655559 DOI: 10.1128/jvi.02313-08] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 01/09/2009] [Indexed: 01/18/2023] Open
Abstract
Plus-stranded RNA viruses coopt host proteins to promote their robust replication in infected hosts. Tomato bushy stunt tombusvirus (TBSV) is a model virus that can replicate a small replicon RNA in Saccharomyces cerevisiae and in plants. The tombusvirus replicase complex contains heat shock protein 70 (Hsp70), an abundant cytosolic chaperone, which is required for TBSV replication. To dissect the function of Hsp70 in TBSV replication, in this paper we use an Hsp70 mutant (ssa1 ssa2) yeast strain that supports a low level of TBSV replication. Using confocal laser microscopy and cellular fractionation experiments, we find that the localization of the viral replication proteins changes to the cytosol in the mutant cells from the peroxisomal membranes in wild-type cells. An in vitro membrane insertion assay shows that Hsp70 promotes the integration of the viral replication proteins into subcellular membranes. This step seems to be critical for the assembly of the viral replicase complex. Using a gene-silencing approach and quercetin as a chemical inhibitor to downregulate Hsp70 levels, we also confirm the significance of cytosolic Hsp70 in the replication of TBSV and other plant viruses in a plant host. Taken together, our results suggest that cytosolic Hsp70 plays multiple roles in TBSV replication, such as affecting the subcellular localization and membrane insertion of the viral replication proteins as well as the assembly of the viral replicase.
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30
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Steinberg SJ, Snowden A, Braverman NE, Chen L, Watkins PA, Clayton PT, Setchell KDR, Heubi JE, Raymond GV, Moser AB, Moser HW. A PEX10 defect in a patient with no detectable defect in peroxisome assembly or metabolism in cultured fibroblasts. J Inherit Metab Dis 2009; 32:109-19. [PMID: 19127411 DOI: 10.1007/s10545-008-0969-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/10/2008] [Accepted: 10/09/2008] [Indexed: 11/28/2022]
Abstract
Zellweger spectrum disorders (ZSD) are diagnosed by biochemical assay in blood, urine and cultured fibroblasts and PEX gene mutation identification. In most cases studies in fibroblasts corroborate results obtained in body fluids. In 1996 Clayton and colleagues described a 10-year old girl with evidence of a peroxisome disorder, based on elevated bile acid metabolites and phytanate. At the time it was not possible to distinguish whether she had a ZSD or a single peroxisomal protein defect. Studies in our laboratory showed that she also had elevated plasma pipecolate, supporting the former diagnosis. Despite the abnormal metabolites detected in blood (phytanate, bile acid intermediates and pipecolate), analysis of multiple peroxisomal pathways in fibroblasts yielded normal results. In addition, she had a milder clinical phenotype than usually associated with ZSD. Since complementation analysis to determine the gene defect was not possible, we screened this patient following the PEX Gene Screen algorithm (PGS). The PGS provides a template for sequencing PEX gene exons independent of complementation analysis. Two mutations in PEX10 were identified, a frameshift mutation inherited from her father and a de novo missense mutation in a conserved functional domain on the other allele. This case highlights that molecular analysis may be essential to the diagnosis of patients at the milder end of the ZSD spectrum. Furthermore, it supports the concept that some tissues are less affected by certain PEX gene defects than brain and liver.
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Affiliation(s)
- S J Steinberg
- Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.
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31
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Abstract
Peroxisomes are single-membraned organelles ubiquitous to eukaryotic cells that house metabolic reactions that generate and destroy harmful oxidative intermediates. They are dynamic structures whose morphology, abundance, composition, and function depend on the cell type and environment. Perhaps due to the potentially damaging and protective metabolic roles of peroxisomes and their dynamic presence in the cell, peroxisome biogenesis is emerging as a process that involves complex underlying mechanisms of regulated formation and maintenance. There are roughly 30 known peroxins, proteins involved in peroxisome biogenesis, many of which have been conserved from yeast to mammals. This review focuses on the biogenesis of peroxisomes with an emphasis on the regulation of peroxisome formation and the import of peroxisomal matrix proteins in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Jennifer J Smith
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.
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32
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Abstract
Peroxisomal proteomic protein profiles of exposure to marine pollution have been recently introduced in biomonitoring experiments. However, laboratory experiments to study the independent effect of common pollutants are needed to define a minimal protein expression signature (PES) of exposure to a specific pollutant. The aim of this study was to obtain PESs in blue mussels (Mytilus edulis) exposed to two different crude oil mixtures for future application in biomonitoring areas affected by oil spills. In the study, peroxisome-enriched fractions from digestive gland of M. edulis (L., 1758) were analysed by two-dimensional fluorescence difference electrophoresis (DIGE) and mass spectrometry (MS) after 3 weeks of exposure to crude oil mixtures: crude oil or crude oil spiked with alkylated phenols (AP) and extra polycyclic aromatic hydrocarbons (PAH) in a laboratory flow-through system. A minimal PES composed by 13 protein spots and unique PESs of exposure to the two different mixtures were identified. A total of 22 spots from the two-dimensional maps that had shown a significant increase or decrease in abundance in each of the exposed groups exposed were analysed. The hierarchical clustering analysis succeeded in discriminating the exposed groups from the control groups based on the unique PES. The PESs obtained were consistent with protein patterns obtained in previous field experiments. The results suggest that the protein profiles obtained by peroxisomal proteomics could be used to assess oil exposure in marine pollution assessments.
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Affiliation(s)
- J Mi
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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Zolman BK, Martinez N, Millius A, Adham AR, Bartel B. Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes. Genetics 2008; 180:237-51. [PMID: 18725356 PMCID: PMC2535678 DOI: 10.1534/genetics.108.090399] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 07/08/2008] [Indexed: 01/04/2023] Open
Abstract
Genetic evidence suggests that indole-3-butyric acid (IBA) is converted to the active auxin indole-3-acetic acid (IAA) by removal of two side-chain methylene units in a process similar to fatty acid beta-oxidation. Previous studies implicate peroxisomes as the site of IBA metabolism, although the enzymes that act in this process are still being identified. Here, we describe two IBA-response mutants, ibr1 and ibr10. Like the previously described ibr3 mutant, which disrupts a putative peroxisomal acyl-CoA oxidase/dehydrogenase, ibr1 and ibr10 display normal IAA responses and defective IBA responses. These defects include reduced root elongation inhibition, decreased lateral root initiation, and reduced IBA-responsive gene expression. However, peroxisomal energy-generating pathways necessary during early seedling development are unaffected in the mutants. Positional cloning of the genes responsible for the mutant defects reveals that IBR1 encodes a member of the short-chain dehydrogenase/reductase family and that IBR10 resembles enoyl-CoA hydratases/isomerases. Both enzymes contain C-terminal peroxisomal-targeting signals, consistent with IBA metabolism occurring in peroxisomes. We present a model in which IBR3, IBR10, and IBR1 may act sequentially in peroxisomal IBA beta-oxidation to IAA.
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Affiliation(s)
- Bethany K Zolman
- Department of Biology, University of Missouri, St. Louis, Missouri 63121, USA.
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34
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Abstract
To identify previously unknown peroxisomal proteins, we established an optimized method for isolating highly purified peroxisomes from etiolated soybean cotyledons using Percoll density gradient centrifugation followed by iodixanol density gradient centrifugation. Proteins in highly purified peroxisomes were separated by two-dimensional PAGE. We performed peptide mass fingerprinting of proteins separated in the gel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry and used the peptide mass fingerprints to search a non-redundant soybean expressed sequence tag database. We succeeded in assigning 92 proteins to 70 sequences in the database. Among them, proteins encoded by 30 sequences were judged to be located in peroxisomes. These included enzymes for fatty acid beta-oxidation, the glyoxylate cycle, photorespiratory glycolate metabolism, stress response and metabolite transport. We also show experimental evidence that plant peroxisomes contain a short-chain dehydrogenase/reductase family protein, enoyl-CoA hydratase/isomerase family protein, 3-hydroxyacyl-CoA dehydrogenase-like protein and a voltage-dependent anion-selective channel protein.
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Affiliation(s)
- Yuko Arai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585 Japan
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35
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Wang RYL, Nagy PD. Tomato bushy stunt virus co-opts the RNA-binding function of a host metabolic enzyme for viral genomic RNA synthesis. Cell Host Microbe 2008; 3:178-87. [PMID: 18329617 DOI: 10.1016/j.chom.2008.02.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 12/31/2007] [Accepted: 02/14/2008] [Indexed: 02/03/2023]
Abstract
Tomato bushy stunt virus (TBSV), a plus-stranded [(+)] RNA plant virus, incorporates the host metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) into the viral replicase complex. Here, we show that, during TBSV replication in yeast, the yeast GAPDH Tdh2p moves from the cytosol to the peroxisomal membrane surface, the site of viral RNA synthesis. In yeast cells lacking Tdh2p, decreasing the levels of its functionally redundant homolog Tdh3p inhibited TBSV replication and resulted in equivalent levels of (+) and minus-stranded [(-)] viral RNA, in contrast to the hallmark excess of (+)RNA. Tdh2p specifically bound an AU pentamer sequence in the (-)RNA, suggesting that GAPDH promotes asymmetric RNA synthesis by selectively retaining the (-)RNA template in the replicase complex. Downregulation of GAPDH in a natural plant host decreased TBSV genomic RNA accumulation. Thus, TBSV co-opts the RNA-binding function of a metabolic protein, helping convert the host cell into a viral factory.
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36
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Hashimoto K, Igarashi H, Mano S, Takenaka C, Shiina T, Yamaguchi M, Demura T, Nishimura M, Shimmen T, Yokota E. An isoform of Arabidopsis myosin XI interacts with small GTPases in its C-terminal tail region. J Exp Bot 2008; 59:3523-31. [PMID: 18703495 PMCID: PMC2561144 DOI: 10.1093/jxb/ern202] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 05/18/2023]
Abstract
Myosin XI, a class of myosins expressed in plants is believed to be responsible for cytoplasmic streaming and the translocation of organelles and vesicles. To gain further insight into the translocation of organelles and vesicles by myosin XI, an isoform of Arabidopsis myosin XI, MYA2, was chosen and its role in peroxisome targeting was examined. Using the yeast two-hybrid screening method, two small GTPases, AtRabD1 and AtRabC2a, were identified as factors that interact with the C-terminal tail region of MYA2. Both recombinant AtRabs tagged with His bound to the recombinant C-terminal tail region of MYA2 tagged with GST in a GTP-dependent manner. Furthermore, AtRabC2a was localized on peroxisomes, when its CFP-tagged form was expressed transiently in protoplasts prepared from Arabidopsis leaf tissue. It is suggested that MYA2 targets the peroxisome through an interaction with AtRabC2a.
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Affiliation(s)
- Kohsuke Hashimoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1279, Japan
| | - Hisako Igarashi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho Turumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Chikako Takenaka
- Graduate School of Human Environmental Sciences, Kyoto Prefectural University, Nakaragi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takashi Shiina
- Graduate School of Human Environmental Sciences, Kyoto Prefectural University, Nakaragi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Masatoshi Yamaguchi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho Turumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Demura
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho Turumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Teruo Shimmen
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1279, Japan
| | - Etsuo Yokota
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1279, Japan
- To whom correspondence should be addressed: E-mail:
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37
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De Azevedo Souza C, Barbazuk B, Ralph SG, Bohlmann J, Hamberger B, Douglas CJ. Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella. New Phytol 2008; 179:987-1003. [PMID: 18627494 DOI: 10.1111/j.1469-8137.2008.02534.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The plant enzyme 4-coumarate:coenzyme A ligase (4CL) is part of a family of adenylate-forming enzymes present in all organisms. Analysis of genome sequences shows the presence of '4CL-like' enzymes in plants and other organisms, but their evolutionary relationships and functions remain largely unknown. 4CL and 4CL-like genes were identified by BLAST searches in Arabidopsis, Populus, rice, Physcomitrella, Chlamydomonas and microbial genomes. Evolutionary relationships were inferred by phylogenetic analysis of aligned amino acid sequences. Expression patterns of a conserved set of Arabidopsis and poplar 4CL-like acyl-CoA synthetase (ACS) genes were assayed. The conserved ACS genes form a land plant-specific class. Angiosperm ACS genes grouped into five clades, each of which contained representatives in three fully sequenced genomes. Expression analysis revealed conserved developmental and stress-induced expression patterns of Arabidopsis and poplar genes in some clades. Evolution of plant ACS enzymes occurred early in land plants. Differential gene expansion of angiosperm ACS clades has occurred in some lineages. Evolutionary and gene expression data, combined with in vitro and limited in vivo protein function data, suggest that angiosperm ACS enzymes play conserved roles in octadecanoid and fatty acid metabolism, and play roles in organ development, for example in anthers.
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Affiliation(s)
| | - Brad Barbazuk
- Donald Danforth Plant Science Center, St Louis MO 63132, USA
| | - Steven G Ralph
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Bjoern Hamberger
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Ma C, Reumann S. Improved prediction of peroxisomal PTS1 proteins from genome sequences based on experimental subcellular targeting analyses as exemplified for protein kinases from Arabidopsis. J Exp Bot 2008; 59:3767-79. [PMID: 18836189 DOI: 10.1093/jxb/ern221] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Due to current experimental limitations in peroxisome proteome research, the identification of low-abundance regulatory proteins such as protein kinases largely relies on computational protein prediction. To test and improve the identification of regulatory proteins by such a prediction-based approach, the Arabidopsis genome was screened for genes that encode protein kinases with predicted type 1 or type 2 peroxisome targeting signals (PTS1 or PTS2). Upon transient expression in onion epidermal cells, the predicted PTS1 domains of four of the seven protein kinases re-directed the reporter protein, enhanced yellow green fluorescent (EYFP), to peroxisomes and were thus verified as functional PTS1 domains. The full-length fusions, however, remained cytosolic, suggesting that PTS1 exposure is induced by specific signals. To investigate why peroxisome targeting of three other kinases was incorrectly predicted and ultimately to improve the prediction algorithms, selected amino acid residues located upstream of PTS1 tripeptides were mutated and the effect on subcellular targeting of the reporter protein was analysed. Acidic residues in close proximity to major PTS1 tripeptides were demonstrated to inhibit protein targeting to plant peroxisomes even in the case of the prototypical PTS1 tripeptide SKL>, whereas basic residues function as essential auxiliary targeting elements in front of weak PTS1 tripeptides such as SHL>. The functional characterization of these inhibitory and essential enhancer-targeting elements allows their consideration in predictive algorithms to improve the prediction accuracy of PTS1 proteins from genome sequences.
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Affiliation(s)
- Changle Ma
- Department of Plant Biochemistry, Georg-August-University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig-Weg 11, D-37077 Goettingen, Germany
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39
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Abstract
Peroxisomes are small subcellular compartments responsible for a range of essential metabolic processes. Efforts in predicting peroxisomal protein import are challenged by species variation and sparse sequence data sets with experimentally confirmed localization. We present a predictor of peroxisomal import based on the presence of the dominant peroxisomal targeting signal one (PTS1), a seemingly wellconserved but highly unspecific motif. The signal appears to rely on subtle dependencies with the preceding residues. We evaluate prediction accuracies against two alternative predictor services, PEROXIP and the PTS1 PREDICTOR. We test the integrity of prediction on a range of prokaryotic and eukaryotic proteomes lacking peroxisomes. Similarly we test the accuracy on peroxisomal proteins known to not overlap with training data. The model identified a number of proteins within the RIKEN IPS7 mouse protein dataset as potentially novel peroxisomal proteins. Three were confirmed in vitro using immunofluorescent detection of myc-epitope-tagged proteins in transiently transfected BHK-21 cells (Dhrs2, Serhl, and Ehhadh). The final model has a superior specificity to both alternatives, and an accuracy better than PEROXIP and on par with PTS1 PREDICTOR. Thus, the model we present should prove invaluable for labeling PTS1 targeted proteins with high confidence. We use the predictor to screen several additional eukaryotic genomes to revise previously estimated numbers of peroxisomal proteins. Available at http://pprowler.itee.uq.edu.au.
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Affiliation(s)
- John Hawkins
- ARC Centre for Complex Systems, The University of Queensland, St. Lucia, Queensland 4072, Australia
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40
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Cáceres AJ, Quiñones W, Gualdrón M, Cordeiro A, Avilán L, Michels PAM, Concepción JL. Molecular and biochemical characterization of novel glucokinases from Trypanosoma cruzi and Leishmania spp. Mol Biochem Parasitol 2007; 156:235-45. [PMID: 17904661 DOI: 10.1016/j.molbiopara.2007.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2007] [Revised: 08/17/2007] [Accepted: 08/22/2007] [Indexed: 10/22/2022]
Abstract
Glucokinase genes, found in the genome databases of Trypanosoma cruzi and Leishmania major, were cloned and sequenced. Their expression in Escherichia coli resulted in the synthesis of soluble and active enzymes, TcGlcK and LmjGlcK, with a molecular mass of 43 kDa and 46 kDa, respectively. The enzymes were purified, and values of their kinetic parameters determined. The K(m) values for glucose were 1.0 mM for TcGlcK and 3.3 mM for LmjGlcK. For ATP, the K(m) values were 0.36 mM (TcGlcK) and 0.35 mM (LmjGlcK). A lower K(m) value for glucose (2.55 mM) was found when the (His)(6)-tag was removed from the recombinant LmjGlcK, whereas the TcGlcK retained the same value. The V(max)'s of the T. cruzi and L. major GlcKs were 36.3 and 30.9 U/mg of protein, respectively. No inhibition was exerted by glucose-6-phosphate. Similarly, no inhibition by inorganic pyrophosphate was found in contrast to previous observations made for the T. cruzi and L. mexicana hexokinases. Both trypanosomatid enzymes were only able to phosphorylate glucose indicating that they are true glucokinases. Gel-filtration chromatography showed that the GlcK of both trypanosomatids may occur as a monomer or dimer, dependent on the protein concentration. Both GlcK sequences have a type-1 peroxisome-targeting signal. Indeed, they were shown to be present inside glycosomes using three different methods. These glucokinases present highest, albeit still a moderate 24% sequence identity with their counterpart from Trichomonas vaginalis, which has been classified into group A of the hexokinase family. This group comprises mainly eubacterial and cyanobacterial glucokinases. Indeed, multiple sequence comparisons, as well as kinetic properties, strongly support the notion that these trypanosomatid enzymes belong to group A of the hexokinases, in which they, according to a phylogenetic analysis, form a separate cluster.
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Affiliation(s)
- Ana Judith Cáceres
- Unidad de Bioquímica de Parásitos, Centro de Ingeniería Genética, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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41
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Abstract
In a recent study, we performed a systematic genome analysis for the conservation of genes involved in peroxisome biogenesis (PEX genes) in various fungi. We have now performed a systematic study of the morphology of peroxisome remnants ('ghosts') in Hansenula polymorpha pex mutants (pex1-pex20) and the level of peroxins and matrix proteins in these strains. To this end, all available H. polymorpha pex strains were grown under identical cultivation conditions in glucose-limited chemostat cultures and analyzed in detail. The H. polymorpha pex mutants could be categorized into four distinct groups, namely pex mutants containing: (1) virtually normal peroxisomal structures (pex7, pex17, pex20); (2) small peroxisomal membrane structures with a distinct lumen (pex2, pex4, pex5, pex10, pex12, pex14); (3) multilayered membrane structures lacking apparent matrix protein content (pex1, pex6, pex8, pex13); and (4) no peroxisomal structures (pex3, pex19).
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Affiliation(s)
- Anne Koek
- Laboratory of Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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42
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Abstract
The peroxisome plays a central role in the catabolic and anabolic pathways that contribute to the lipid homeostasis. Besides this main function, this organelle has gained functional diversity. Although several approaches have been used for peroxisomal proteome analysis, a quantitative protein expression analysis of peroxisomes from different tissues has not been elucidated yet. Here, we applied a 2-DE-based method on mouse liver and kidney peroxisomal enriched fractions to study the tissue-dependent protein expression. Ninety-one spots were identified from the 2-DE maps from pH 3.0-10.0 and 51 spots from the basic range corresponding to 31 peroxisomal proteins, 10 putative peroxisomal, 6 cytosolic, 17 mitochondrial and 1 protein from endoplasmic reticulum. Based on the identification and on the equivalent quality of both tissue preparations, the differences emerging from the comparison could be quantified. In liver, proteins involved in pathways such as alpha- and beta-oxidation, isoprenoid biosynthesis, amino acid metabolism and purine and pyrimidine metabolism were more abundant whereas in kidney, proteins from the straight-chain fatty acid beta-oxidation were highly expressed. These results indicate that tissue-specific functional classes of peroxisomal proteins could be relevant to study peroxisomal cellular responses or pathologies. Finally, a web-based peroxisomal proteomic database was built.
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Affiliation(s)
- Jia Mi
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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43
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Guo T, Gregg C, Boukh-Viner T, Kyryakov P, Goldberg A, Bourque S, Banu F, Haile S, Milijevic S, San KHY, Solomon J, Wong V, Titorenko VI. A signal from inside the peroxisome initiates its division by promoting the remodeling of the peroxisomal membrane. J Cell Biol 2007; 177:289-303. [PMID: 17438077 PMCID: PMC2064137 DOI: 10.1083/jcb.200609072] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 03/19/2007] [Indexed: 12/21/2022] Open
Abstract
We define the dynamics of spatial and temporal reorganization of the team of proteins and lipids serving peroxisome division. The peroxisome becomes competent for division only after it acquires the complete set of matrix proteins involved in lipid metabolism. Overloading the peroxisome with matrix proteins promotes the relocation of acyl-CoA oxidase (Aox), an enzyme of fatty acid beta-oxidation, from the matrix to the membrane. The binding of Aox to Pex16p, a membrane-associated peroxin required for peroxisome biogenesis, initiates the biosynthesis of phosphatidic acid and diacylglycerol (DAG) in the membrane. The formation of these two lipids and the subsequent transbilayer movement of DAG initiate the assembly of a complex between the peroxins Pex10p and Pex19p, the dynamin-like GTPase Vps1p, and several actin cytoskeletal proteins on the peroxisomal surface. This protein team promotes membrane fission, thereby executing the terminal step of peroxisome division.
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Affiliation(s)
- Tong Guo
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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44
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Abstract
In this review, we describe the current state of knowledge about the biochemistry of mammalian peroxisomes, especially human peroxisomes. The identification and characterization of yeast mutants defective either in the biogenesis of peroxisomes or in one of its metabolic functions, notably fatty acid beta-oxidation, combined with the recognition of a group of genetic diseases in man, wherein these processes are also defective, have provided new insights in all aspects of peroxisomes. As a result of these and other studies, the indispensable role of peroxisomes in multiple metabolic pathways has been clarified, and many of the enzymes involved in these pathways have been characterized, purified, and cloned. One aspect of peroxisomes, which has remained ill defined, is the transport of metabolites across the peroxisomal membrane. Although it is clear that mammalian peroxisomes under in vivo conditions are closed structures, which require the active presence of metabolite transporter proteins, much remains to be learned about the permeability properties of mammalian peroxisomes and the role of the four half ATP-binding cassette (ABC) transporters therein.
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Affiliation(s)
- Ronald J A Wanders
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Disease, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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45
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Wriessnegger T, Gübitz G, Leitner E, Ingolic E, Cregg J, de la Cruz BJ, Daum G. Lipid composition of peroxisomes from the yeast Pichia pastoris grown on different carbon sources. Biochim Biophys Acta Mol Cell Biol Lipids 2007; 1771:455-61. [PMID: 17293161 DOI: 10.1016/j.bbalip.2007.01.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 01/03/2007] [Accepted: 01/05/2007] [Indexed: 11/28/2022]
Abstract
Highly purified peroxisomes from the yeast Pichia pastoris grown on methanol or oleic acid, respectively, were used to characterize the lipid composition of this organelle. For this purpose, an isolation procedure had to be adapted which yielded highly purified P. pastoris peroxisomes. When peroxisome proliferation was induced by growth on methanol, alcohol oxidase was the predominant peroxisomal protein. Cultivation of P. pastoris on oleic acid led to induction of a family of peroxisomal enzymes catalyzing fatty acid beta-oxidation, whose most prominent members were identified by mass spectrometry. On either carbon source, phosphatidylcholine and phosphatidylethanolamine were the major peroxisomal phospholipids, and cardiolipin was present in peroxisomal membranes at a substantial amount, indicating that this phospholipid is a true peroxisomal component. Ergosterol was the most abundant sterol of P. pastoris peroxisomal membranes irrespective of the culture conditions. The fatty acid composition of whole cells and peroxisomes was highly affected by cultivation of P. pastoris on oleic acid. Under these conditions, oleic acid became the predominant fatty acid in phospholipids from total cell and peroxisomal extracts. Thus, oleic acid was not only utilized as an appropriate carbon source but also as a building block for complex membrane lipids. In summary, our data provide first insight into biochemical properties of P. pastoris peroxisomal membranes, which may become important for the biotechnological use of this yeast.
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Affiliation(s)
- Tamara Wriessnegger
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, Graz, Austria
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46
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Stanley WA, Filipp FV, Kursula P, Schüller N, Erdmann R, Schliebs W, Sattler M, Wilmanns M. Recognition of a functional peroxisome type 1 target by the dynamic import receptor pex5p. Mol Cell 2007; 24:653-663. [PMID: 17157249 PMCID: PMC5030714 DOI: 10.1016/j.molcel.2006.10.024] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 08/16/2006] [Accepted: 10/16/2006] [Indexed: 10/23/2022]
Abstract
Peroxisomes require the translocation of folded and functional target proteins of various sizes across the peroxisomal membrane. We have investigated the structure and function of the principal import receptor Pex5p, which recognizes targets bearing a C-terminal peroxisomal targeting signal type 1. Crystal structures of the receptor in the presence and absence of a peroxisomal target, sterol carrier protein 2, reveal major structural changes from an open, snail-like conformation into a closed, circular conformation. These changes are caused by a long loop C terminal to the 7-fold tetratricopeptide repeat segments. Mutations in residues of this loop lead to defects in peroxisomal import in human fibroblasts. The structure of the receptor/cargo complex demonstrates that the primary receptor-binding site of the cargo is structurally and topologically autonomous, enabling the cargo to retain its native structure and function.
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Affiliation(s)
- Will A Stanley
- European Molecular Biology Laboratory-Hamburg Outstation, Notkestrasse 85, 22603 Hamburg
| | - Fabian V Filipp
- Structural and Computational Biology Unit, European Molecular Biology Laboratory-Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Petri Kursula
- European Molecular Biology Laboratory-Hamburg Outstation, Notkestrasse 85, 22603 Hamburg
| | - Nicole Schüller
- European Molecular Biology Laboratory-Hamburg Outstation, Notkestrasse 85, 22603 Hamburg
| | - Ralf Erdmann
- Department of Systems Biology, Institute for Physiological Chemistry, Faculty of Medicine, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Wolfgang Schliebs
- Department of Systems Biology, Institute for Physiological Chemistry, Faculty of Medicine, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Michael Sattler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory-Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Matthias Wilmanns
- European Molecular Biology Laboratory-Hamburg Outstation, Notkestrasse 85, 22603 Hamburg.
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47
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Abstract
It is widely recognized that much of the information for determining the final subcellular localization of proteins is found in their amino acid sequences. Thus the prediction of protein localization sites is of both theoretical and practical interest. In most cases, the prediction has been attempted in two ways: one is based on the knowledge of experimentally characterized targeting signals, while the other utilizes the statistical differences of general sequence characteristics, such as amino acid composition, between localization sites. Both approaches have limitations, and it is recommended to check the results of various prediction methods based on different principles as well as training data. Recently, increased proteomic analyses of localization sites have provided new data to assess the current status of predictive methods. In this chapter we discuss these issues and close with an example illustrating the use of the WoLF PSORT web server for localization prediction.
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Affiliation(s)
- Kenta Nakai
- Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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48
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Zechmann B, Zellnig G, Urbanek-Krajnc A, Müller M. Artificial elevation of glutathione affects symptom development in ZYMV-infected Cucurbita pepo L. plants. Arch Virol 2006; 152:747-62. [PMID: 17143780 DOI: 10.1007/s00705-006-0880-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 10/20/2006] [Indexed: 12/20/2022]
Abstract
Styrian oil pumpkin seedlings (Cucurbita pepo L. subsp. pepo var. styriaca GREB: .) were treated for 48 h with 1 mM OTC (L-2-oxothiazolidine-4-carboxylic acid) in order to artificially increase cellular glutathione content. They were inoculated with zucchini yellow mosaic virus (ZYMV) 10 days later. The effects of OTC treatment and ZYMV infection on glutathione levels were examined at the subcellular level by immunogold labeling of glutathione using a transmission electron microscope (TEM). These effects were further tested at the whole-tissue level by high performance liquid chromatography (HPLC). Such tests were carried out a) on roots, cotyledons and the first true leaves immediately after OTC treatment in order to analyze to which extent OTC increases glutathione levels in different cell compartments as well as in the whole organ; and b) in older and younger leaves and in roots three weeks after ZYMV inoculation in order to study how possible effects of OTC on symptom development would correlate with glutathione levels at the subcellular level and in the whole organ. Immunocytological and biochemical investigations revealed that, 48 h after OTC treatment, glutathione content had increased in all investigated organs, up to 144% in peroxisomes of cotyledons. Three weeks after ZYMV inoculation, glutathione labeling density had significantly increased within intact cells of infected leaves, up to 124% in the cytosol of younger leaves. Roots showed decreased amounts of glutathione in the TEM. Biochemical studies revealed that OTC treatment resulted in 41 and 51% higher glutathione content in older and younger ZYMV-infected leaves, respectively, in comparison to untreated and ZYMV-infected plants. Evaluation of symptom development at this point revealed that all untreated ZYMV-infected plants had symptoms, whereas only 42% of OTC-treated ZYMV-infected plants showed signs of symptoms. Quantification of ZYMV particles revealed that all organs of OTC-treated and ZYMV-infected plants contained significantly decreased amounts of ZYMV particles over a period of five weeks when compared to the same organs of untreated ZYMV-infected plants. We can conclude that OTC treatment and subsequently elevated glutathione contents within Styrian oil pumpkin plants led to a strong decrease in virus content, which was accompanied by a suppression of ZYMV-induced symptoms as well as reduced and delayed symptom development within plants exhibiting symptoms.
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Affiliation(s)
- B Zechmann
- Institute of Plant Sciences, University of Graz, Graz, Austria.
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49
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Goepfert S, Hiltunen JK, Poirier Y. Identification and functional characterization of a monofunctional peroxisomal enoyl-CoA hydratase 2 that participates in the degradation of even cis-unsaturated fatty acids in Arabidopsis thaliana. J Biol Chem 2006; 281:35894-903. [PMID: 16982622 DOI: 10.1074/jbc.m606383200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A gene, named AtECH2, has been identified in Arabidopsis thaliana to encode a monofunctional peroxisomal enoyl-CoA hydratase 2. Homologues of AtECH2 are present in several angiosperms belonging to the Monocotyledon and Dicotyledon classes, as well as in a gymnosperm. In vitro enzyme assays demonstrated that AtECH2 catalyzed the reversible conversion of 2E-enoyl-CoA to 3R-hydroxyacyl-CoA. AtECH2 was also demonstrated to have enoyl-CoA hydratase 2 activity in an in vivo assay relying on the synthesis of polyhydroxyalkanoate from the polymerization of 3R-hydroxyacyl-CoA in the peroxisomes of Saccharomyces cerevisiae. AtECH2 contained a peroxisome targeting signal at the C-terminal end, was addressed to the peroxisome in S. cerevisiae, and a fusion protein between AtECH2 and a fluorescent protein was targeted to peroxisomes in onion cells. AtECH2 gene expression was strongest in tissues with high beta-oxidation activity, such as germinating seedlings and senescing leaves. The contribution of AtECH2 to the degradation of unsaturated fatty acids was assessed by analyzing the carbon flux through the beta-oxidation cycle in plants that synthesize peroxisomal polyhydroxyalkanoate and that were over- or underexpressing the AtECH2 gene. These studies revealed that AtECH2 participates in vivo to the conversion of the intermediate 3R-hydroxyacyl-CoA, generated by the metabolism of fatty acids with a cis (Z)-unsaturated bond on an even-numbered carbon, to the 2E-enoyl-CoA for further degradation through the core beta-oxidation cycle.
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Affiliation(s)
- Simon Goepfert
- Département de Biologie Moléculaire Végétale, Biophore Building, Université de Lausanne, CH-1015, Switzerland
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50
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Tamura S, Yasutake S, Matsumoto N, Fujiki Y. Dynamic and functional assembly of the AAA peroxins, Pex1p and Pex6p, and their membrane receptor Pex26p. J Biol Chem 2006; 281:27693-704. [PMID: 16854980 DOI: 10.1074/jbc.m605159200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two AAA peroxins, Pex1p and Pex6p, are encoded by PEX1 and PEX6, the causal genes for peroxisome biogenesis disorders of complementation group 1 (CG1) and CG4, respectively. PEX26 responsible for peroxisome biogenesis disorders of CG8 encodes Pex26p, the recruiter of Pex1p.Pex6p complexes to peroxisomes. We herein assigned the binding regions between human Pex1p and Pex6p and elucidated pivotal roles of the AAA cassettes, called D1 and D2 domains, in Pex1p-Pex6p interaction and peroxisome biogenesis. ATP binding in both AAA cassettes but not ATP hydrolysis in D2 of both Pex1p and Pex6p was prerequisite for Pex1p-Pex6p interaction and their peroxisomal localization. The AAA cassettes, D1 and D2, were essential for peroxisome-restoring activity of Pex1p and Pex6p. In HEK293 cells, endogenous Pex1p was partly localized likely as a homo-oligomer in the cytoplasm, while Pex6p and Pex26p were predominantly localized on peroxisomes. Interaction of Pex1p with Pex6p conferred a conformational change and dissociation of the Pex1p oligomer. These results suggested that Pex1p possesses two distinct oligomeric forms, a homo-oligomer in the cytosol and a hetero-oligomer on peroxisome membranes, possibly playing distinct functions in peroxisome biogenesis.
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Affiliation(s)
- Shigehiko Tamura
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan
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