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Colasante C, Chen J, Ahlemeyer B, Bonilla-Martinez R, Karnati S, Baumgart-Vogt E. New insights into the distribution, protein abundance and subcellular localisation of the endogenous peroxisomal biogenesis proteins PEX3 and PEX19 in different organs and cell types of the adult mouse. PLoS One 2017; 12:e0183150. [PMID: 28817674 PMCID: PMC5560687 DOI: 10.1371/journal.pone.0183150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/31/2017] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are ubiquitous organelles mainly involved in ROS and lipid metabolism. Their abundance, protein composition and metabolic function vary depending on the cell type and adjust to different intracellular and environmental factors such as oxidative stress or nutrition. The biogenesis and proliferation of these important organelles are regulated by proteins belonging to the peroxin (PEX) family. PEX3, an integral peroxisomal membrane protein, and the cytosolic shuttling receptor PEX19 are thought to be responsible for the early steps of peroxisome biogenesis and assembly of their matrix protein import machinery. Recently, both peroxins were suggested to be also involved in the autophagy of peroxisomes (pexophagy). Despite the fact that distribution and intracellular abundance of these proteins might regulate the turnover of the peroxisomal compartment in a cell type-specific manner, a comprehensive analysis of the endogenous PEX3 and PEX19 distribution in different organs is still missing. In this study, we have therefore generated antibodies against endogenous mouse PEX3 and PEX19 and analysed their abundance and subcellular localisation in various mouse organs, tissues and cell types and compared it to the one of three commonly used peroxisomal markers (PEX14, ABCD3 and catalase). Our results revealed that the abundance of PEX3, PEX19, PEX14, ABCD3 and catalase strongly varies in the analysed organs and cell types, suggesting that peroxisome abundance, biogenesis and matrix protein import are independently regulated. We further found that in some organs, such as heart and skeletal muscle, the majority of the shuttling receptor PEX19 is bound to the peroxisomal membrane and that a strong variability exists in the cell type-specific ratio of cytosol- and peroxisome-associated PEX19. In conclusion, our results indicate that peroxisomes in various cell types are heterogeneous with regards to their matrix, membrane and biogenesis proteins.
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Affiliation(s)
- Claudia Colasante
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
| | - Jiangping Chen
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
| | - Barbara Ahlemeyer
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
| | - Rocio Bonilla-Martinez
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
| | - Srikanth Karnati
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University of Giessen, Giessen, Germany
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Kinoshita N, Matsuura A, Fujiki Y. Peroxisome biogenesis: a novel inducible PEX19 splicing variant is involved in early stages of peroxisome proliferation. J Biochem 2017; 161:297-308. [PMID: 28391327 DOI: 10.1093/jb/mvw075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/25/2016] [Indexed: 01/23/2023] Open
Abstract
Pex19p harbouring a prenylation CAAX box functions as a chaperone and transporter for peroxisomal membrane proteins in membrane assembly. By functional phenotype-complementation assay using a pex19 Chinese hamster ovary cell mutant ZP119, we herein cloned a rat cDNA encoding a protein similar to Pex19p, but with a C-terminal hydrophobic segment in place of the CAAX box region. The transcript of this gene was highly induced by treatment of rats with a peroxisome proliferator, clofibrate, hence termed PEX19i, while the other three less prominently inducible PEX19 variants encoded authentic Pex19p but differed in the length of 3' non-coding region. Pex19pi restored peroxisomes in ZP119 with slightly lower efficiency than Pex19p, showing apparently weaker interaction with Pex11pβ essential for peroxisome proliferation. However, the C-terminal region of Pex19p was not essential for the association of Pex19p with peroxisomal membrane and interaction with membrane assembly factors, Pex3p and Pex16p. Non-prenylated Pex19p interacted with a membrane protein cargo, Pex14p, but more weakly than Pex19pi and the farnesylated Pex19p. Thus, PEX19i most likely plays important roles involving the membrane formation at early stages, in prompt response to peroxisome proliferation. Similar types of PEX19 mRNA variants were also elevated in mouse regenerating liver.
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Affiliation(s)
- Naohiko Kinoshita
- Department of Biology, Faculty of Sciences Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akira Matsuura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Cross LL, Ebeed HT, Baker A. Peroxisome biogenesis, protein targeting mechanisms and PEX gene functions in plants. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:850-62. [DOI: 10.1016/j.bbamcr.2015.09.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
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The Early-Acting Peroxin PEX19 Is Redundantly Encoded, Farnesylated, and Essential for Viability in Arabidopsis thaliana. PLoS One 2016; 11:e0148335. [PMID: 26824478 PMCID: PMC4733102 DOI: 10.1371/journal.pone.0148335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/15/2016] [Indexed: 11/20/2022] Open
Abstract
Peroxisomes are single-membrane bound organelles that are essential for normal development in plants and animals. In mammals and yeast, the peroxin (PEX) proteins PEX3 and PEX19 facilitate the early steps of peroxisome membrane protein (PMP) insertion and pre-peroxisome budding from the endoplasmic reticulum. The PEX3 membrane protein acts as a docking site for PEX19, a cytosolic chaperone for PMPs that delivers PMPs to the endoplasmic reticulum or peroxisomal membrane. PEX19 is farnesylated in yeast and mammals, and we used immunoblotting with prenylation mutants to show that PEX19 also is fully farnesylated in wild-type Arabidopsis thaliana plants. We examined insertional alleles disrupting either of the two Arabidopsis PEX19 isoforms, PEX19A or PEX19B, and detected similar levels of PEX19 protein in the pex19a-1 mutant and wild type; however, PEX19 protein was nearly undetectable in the pex19b-1 mutant. Despite the reduction in PEX19 levels in pex19b-1, both pex19a-1 and pex19b-1 single mutants lacked notable peroxisomal β-oxidation defects and displayed normal levels and localization of peroxisomal matrix and membrane proteins. The pex19a-1 pex19b-1 double mutant was embryo lethal, indicating a redundantly encoded critical role for PEX19 during embryogenesis. Expressing YFP-tagged versions of either PEX19 isoform rescued this lethality, confirming that PEX19A and PEX19B act redundantly in Arabidopsis. We observed that pex19b-1 enhanced peroxisome-related defects of a subset of peroxin-defective mutants, supporting a role for PEX19 in peroxisome function. Together, our data indicate that Arabidopsis PEX19 promotes peroxisome function and is essential for viability.
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Aghamirzaie D, Batra D, Heath LS, Schneider A, Grene R, Collakova E. Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics 2015; 16:928. [PMID: 26572793 PMCID: PMC4647491 DOI: 10.1186/s12864-015-2108-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 10/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptomics reveals the existence of transcripts of different coding potential and strand orientation. Alternative splicing (AS) can yield proteins with altered number and types of functional domains, suggesting the global occurrence of transcriptional and post-transcriptional events. Many biological processes, including seed maturation and desiccation, are regulated post-transcriptionally (e.g., by AS), leading to the production of more than one coding or noncoding sense transcript from a single locus. RESULTS We present an integrated computational framework to predict isoform-specific functions of plant transcripts. This framework includes a novel plant-specific weighted support vector machine classifier called CodeWise, which predicts the coding potential of transcripts with over 96 % accuracy, and several other tools enabling global sequence similarity, functional domain, and co-expression network analyses. First, this framework was applied to all detected transcripts (103,106), out of which 13 % was predicted by CodeWise to be noncoding RNAs in developing soybean embryos. Second, to investigate the role of AS during soybean embryo development, a population of 2,938 alternatively spliced and differentially expressed splice variants was analyzed and mined with respect to timing of expression. Conserved domain analyses revealed that AS resulted in global changes in the number, types, and extent of truncation of functional domains in protein variants. Isoform-specific co-expression network analysis using ArrayMining and clustering analyses revealed specific sub-networks and potential interactions among the components of selected signaling pathways related to seed maturation and the acquisition of desiccation tolerance. These signaling pathways involved abscisic acid- and FUSCA3-related transcripts, several of which were classified as noncoding and/or antisense transcripts and were co-expressed with corresponding coding transcripts. Noncoding and antisense transcripts likely play important regulatory roles in seed maturation- and desiccation-related signaling in soybean. CONCLUSIONS This work demonstrates how our integrated framework can be implemented to make experimentally testable predictions regarding the coding potential, co-expression, co-regulation, and function of transcripts and proteins related to a biological process of interest.
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Dhruv Batra
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Andrew Schneider
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA.
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Giannopoulou EA, Emmanouilidis L, Sattler M, Dodt G, Wilmanns M. Towards the molecular mechanism of the integration of peroxisomal membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:863-9. [PMID: 26434995 PMCID: PMC4819957 DOI: 10.1016/j.bbamcr.2015.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 11/30/2022]
Abstract
The correct topogenesis of peroxisomal membrane proteins is a crucial step for the formation of functioning peroxisomes. Although this process has been widely studied, the exact mechanism with which it occurs has not yet been fully characterized. Nevertheless, it is generally accepted that peroxisomes employ three proteins – Pex3, Pex19 and Pex16 in mammals – for the insertion of peroxisomal membrane proteins into the peroxisomal membrane. Structural biology approaches have been utilized for the elucidation of the mechanistic questions of peroxisome biogenesis, mainly by providing information on the architecture of the proteins significant for this process. This review aims to summarize, compare and put into perspective the structural knowledge that has been generated mainly for Pex3 and Pex19 and their interaction partners in recent years. This article is part of a Special Issue entitled: Peroxisomes edited by Ralf Erdmann. Structures of the PMP insertion factors Pex3 and Pex19 and their interactions with other protein ligands Structural insights provide a mechanistic understanding of the PMP functional network. Functional implications of structural order/disorder transitions
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Affiliation(s)
| | - Leonidas Emmanouilidis
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Gabriele Dodt
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Matthias Wilmanns
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany; University of Hamburg Clinical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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Nyathi Y, Zhang X, Baldwin JM, Bernhardt K, Johnson B, Baldwin SA, Theodoulou FL, Baker A. Pseudo half-molecules of the ABC transporter, COMATOSE, bind Pex19 and target to peroxisomes independently but are both required for activity. FEBS Lett 2012; 586:2280-6. [PMID: 22710125 DOI: 10.1016/j.febslet.2012.05.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 05/30/2012] [Indexed: 11/25/2022]
Abstract
Peroxisomal ABC transporters of animals and fungi are "half-size" proteins which dimerise to form a functional transporter. However, peroxisomal ABC transporters of land plants are synthesised as a single polypeptide which represents a fused heterodimer. The N- and C-terminal pseudo-halves of COMATOSE (CTS; AtABCD1) were expressed as separate polypeptides which bound Pex19 in vitro and targeted independently to the peroxisome membrane in yeast, where they were stable but not functional. When co-expressed, the pseudo-halves were fully functional as indicated by ATPase activity and rescue of the pxa1pxa2Δ mutant for growth on oleate. The functional significance of heterodimer asymmetry is discussed.
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Affiliation(s)
- Yvonne Nyathi
- Centre for Plant Sciences, Irene Manton Building, University of Leeds, Leeds LS2 9JT, UK
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Zhang X, De Marcos Lousa C, Schutte-Lensink N, Ofman R, Wanders RJ, Baldwin SA, Baker A, Kemp S, Theodoulou FL. Conservation of targeting but divergence in function and quality control of peroxisomal ABC transporters: an analysis using cross-kingdom expression. Biochem J 2011; 436:547-57. [PMID: 21476988 DOI: 10.1042/bj20110249] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
ABC (ATP-binding cassette) subfamily D transporters are found in all eukaryotic kingdoms and are known to play essential roles in mammals and plants; however, their number, organization and physiological contexts differ. Via cross-kingdom expression experiments, we have explored the conservation of targeting, protein stability and function between mammalian and plant ABCD transporters. When expressed in tobacco epidermal cells, the mammalian ABCD proteins ALDP (adrenoleukodystrophy protein), ALDR (adrenoleukodystrophy-related protein) and PMP70 (70 kDa peroxisomal membrane protein) targeted faithfully to peroxisomes and P70R (PMP70-related protein) targeted to the ER (endoplasmic reticulum), as in the native host. The Arabidopsis thaliana peroxin AtPex19_1 interacted with human peroxisomal ABC transporters both in vivo and in vitro, providing an explanation for the fidelity of targeting. The fate of X-linked adrenoleukodystrophy disease-related mutants differed between fibroblasts and plant cells. In fibroblasts, levels of ALDP in some 'protein-absent' mutants were increased by low-temperature culture, in some cases restoring function. In contrast, all mutant ALDP proteins examined were stable and correctly targeted in plant cells, regardless of their fate in fibroblasts. ALDR complemented the seed germination defect of the Arabidopsis cts-1 mutant which lacks the peroxisomal ABCD transporter CTS (Comatose), but neither ALDR nor ALDP was able to rescue the defect in fatty acid β-oxidation in establishing seedlings. Taken together, our results indicate that the mechanism for trafficking of peroxisomal membrane proteins is shared between plants and mammals, but suggest differences in the sensing and turnover of mutant ABC transporter proteins and differences in substrate specificity and/or function.
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Affiliation(s)
- Xuebin Zhang
- Biological Chemistry Department, Rothamsted Research, Harpenden, Herts. AL5 2JQ, UK
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9
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Kaur N, Hu J. Defining the plant peroxisomal proteome: from Arabidopsis to rice. FRONTIERS IN PLANT SCIENCE 2011; 2:103. [PMID: 22645559 PMCID: PMC3355810 DOI: 10.3389/fpls.2011.00103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 12/08/2011] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small subcellular organelles mediating a multitude of processes in plants. Proteomics studies over the last several years have yielded much needed information on the composition of plant peroxisomes. In this review, the status of peroxisome proteomics studies in Arabidopsis and other plant species and the cumulative advances made through these studies are summarized. A reference Arabidopsis peroxisome proteome is generated, and some unique aspects of Arabidopsis peroxisomes that were uncovered through proteomics studies and hint at unanticipated peroxisomal functions are also highlighted. Knowledge gained from Arabidopsis was utilized to compile a tentative list of peroxisome proteins for the model monocot plant, rice. Differences in the peroxisomal proteome between these two model plants were drawn, and novel facets in rice were expounded upon. Finally, we discuss about the current limitations of experimental proteomics in decoding the complete and dynamic makeup of peroxisomes, and complementary and integrated approaches that would be beneficial to defining the peroxisomal metabolic and regulatory roadmaps. The synteny of genomes in the grass family makes rice an ideal model to study peroxisomes in cereal crops, in which these organelles have received much less attention, with the ultimate goal to improve crop yield.
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Affiliation(s)
- Navneet Kaur
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Plant Biology Department, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Jianping Hu, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. e-mail:
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Abstract
Plant peroxisomes are extremely dynamic, moving and undergoing changes of shape in response to metabolic and environmental signals. Matrix proteins are imported via one of two import pathways, depending on the targeting signal within the protein. Each pathway has a specific receptor but utilizes common membrane-bound translocation machinery. Current models invoke receptor recycling, which may involve cycles of ubiquitination. Some components of the import machinery may also play a role in proteolytic turnover of matrix proteins, prompting parallels with the endoplasmic-reticulum-associated degradation pathway. Peroxisome membrane proteins, some of which are imported post-translationally, others of which may traffic to peroxisomes via the endoplasmic reticulum, use distinct proteinaceous machinery. The isolation of mutants defective in peroxisome biogenesis has served to emphasize the important role of peroxisomes at all stages of the plant life cycle.
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Rucktäschel R, Girzalsky W, Erdmann R. Protein import machineries of peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:892-900. [PMID: 20659419 DOI: 10.1016/j.bbamem.2010.07.020] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
Peroxisomes are a class of structurally and functionally related organelles present in almost all eukaryotic cells. The importance of peroxisomes for human life is highlighted by severe inherited diseases which are caused by defects of peroxins, encoded by PEX genes. To date 32 peroxins are known to be involved in different aspects of peroxisome biogenesis. This review addresses two of these aspects, the translocation of soluble proteins into the peroxisomal matrix and the biogenesis of the peroxisomal membrane. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Robert Rucktäschel
- Abteilung für Systembiochemie, Institut für Physiologische Chemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Rucktäschel R, Halbach A, Girzalsky W, Rottensteiner H, Erdmann R. De novo synthesis of peroxisomes upon mitochondrial targeting of Pex3p. Eur J Cell Biol 2010; 89:947-54. [PMID: 20655617 DOI: 10.1016/j.ejcb.2010.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes can form either by growth and division of pre-existing peroxisomes or by de novo synthesis from the endoplasmic reticulum. Pex3p is the key component for both pathways and its targeting to the ER is thought to initiate the de novo formation of peroxisomes. Here, we addressed the question whether Pex3p also can induce peroxisome formation from mitochondrial membranes. Pex3p was targeted to mitochondria by fusion with the mitochondrial targeting signal of Tom20p. The Tom20p-Pex3p-fusion protein was expressed in Pex3p-deficient cells, which are characterized by the lack of peroxisomal membranes. De novo formation of import-competent peroxisomes was observed upon expression of the mitochondrial Pex3p in the mutant cells. This de novo synthesis is independent of the GTPases Vps1p and Dnm1p, two proteins required for peroxisome fission. We conclude that natural or artificial targeting of Pex3p to any endomembrane may initiate peroxisome formation and that also Pex3p-containing mitochondria can serve as source for the de novo synthesis of peroxisomes.
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Affiliation(s)
- Robert Rucktäschel
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
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Girzalsky W, Saffian D, Erdmann R. Peroxisomal protein translocation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:724-31. [DOI: 10.1016/j.bbamcr.2010.01.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 12/22/2009] [Accepted: 01/04/2010] [Indexed: 11/30/2022]
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14
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Shen G, Kuppu S, Venkataramani S, Wang J, Yan J, Qiu X, Zhang H. ANKYRIN REPEAT-CONTAINING PROTEIN 2A is an essential molecular chaperone for peroxisomal membrane-bound ASCORBATE PEROXIDASE3 in Arabidopsis. THE PLANT CELL 2010; 22:811-31. [PMID: 20215589 PMCID: PMC2861468 DOI: 10.1105/tpc.109.065979] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/07/2010] [Accepted: 02/19/2010] [Indexed: 05/21/2023]
Abstract
Arabidopsis thaliana ANKYRIN REPEAT-CONTAINING PROTEIN 2A (AKR2A) interacts with peroxisomal membrane-bound ASCORBATE PEROXIDASE3 (APX3). This interaction involves the C-terminal sequence of APX3 (i.e., a transmembrane domain plus a few basic amino acid residues). The specificity of the AKR2A-APX3 interaction suggests that AKR2A may function as a molecular chaperone for APX3 because binding of AKR2A to the transmembrane domain can prevent APX3 from forming aggregates after translation. Analysis of three akr2a mutants indicates that these mutant plants have reduced steady state levels of APX3. Reduced expression of AKR2A using RNA interference also leads to reduced steady state levels of APX3 and reduced targeting of APX3 to peroxisomes in plant cells. Since AKR2A also binds specifically to the chloroplast OUTER ENVELOPE PROTEIN7 (OEP7) and is required for the biogenesis of OEP7, AKR2A may serve as a molecular chaperone for OEP7 as well. The pleiotropic phenotype of akr2a mutants indicates that AKR2A plays many important roles in plant cellular metabolism and is essential for plant growth and development.
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Kaur N, Reumann S, Hu J. Peroxisome biogenesis and function. THE ARABIDOPSIS BOOK 2009; 7:e0123. [PMID: 22303249 PMCID: PMC3243405 DOI: 10.1199/tab.0123] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small and single membrane-delimited organelles that execute numerous metabolic reactions and have pivotal roles in plant growth and development. In recent years, forward and reverse genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to identify many peroxisome proteins and elucidate their functions. This review focuses on the advances in our understanding of peroxisome biogenesis and metabolism, and further explores the contribution of large-scale analysis, such as in sillco predictions and proteomics, in augmenting our knowledge of peroxisome function In Arabidopsis.
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Affiliation(s)
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory and
- Plant Biology Department, Michigan State University, East Lansing, MI 48824
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16
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Nito K, Kamigaki A, Kondo M, Hayashi M, Nishimura M. Functional classification of Arabidopsis peroxisome biogenesis factors proposed from analyses of knockdown mutants. PLANT & CELL PHYSIOLOGY 2007; 48:763-74. [PMID: 17478547 DOI: 10.1093/pcp/pcm053] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In higher plants, peroxisomes accomplish a variety of physiological functions such as lipid catabolism, photorespiration and hormone biosynthesis. Recently, many factors regulating peroxisomal biogenesis, so-called PEX genes, have been identified not only in plants but also in yeasts and mammals. In the Arabidopsis genome, the presence of at least 22 PEX genes has been proposed. Here, we clarify the physiological functions of 18 PEX genes for peroxisomal biogenesis by analyzing transgenic Arabidopsis plants that suppressed the PEX gene expression using RNA interference. The results indicated that the function of these PEX genes could be divided into two groups. One group involves PEX1, PEX2, PEX4, PEX6, PEX10, PEX12 and PEX13 together with previously characterized PEX5, PEX7 and PEX14. Defects in these genes caused loss of peroxisomal function due to misdistribution of peroxisomal matrix proteins in the cytosol. Of these, the pex10 mutant showed pleiotropic phenotypes that were not observed in any other pex mutants. In contrast, reduced peroxisomal function of the second group, including PEX3, PEX11, PEX16 and PEX19, was induced by morphological changes of the peroxisomes. Cells of the pex16 mutant in particular possessed reduced numbers of large peroxisome(s) that contained unknown vesicles. These results provide experimental evidence indicating that all of these PEX genes play pivotal roles in regulating peroxisomal biogenesis. We conclude that PEX genes belonging to the former group are involved in regulating peroxisomal protein import, whereas those of the latter group are important in maintaining the structure of peroxisome.
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Affiliation(s)
- Kazumasa Nito
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
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Manfield IW, Devlin PF, Jen CH, Westhead DR, Gilmartin PM. Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. PLANT PHYSIOLOGY 2007; 143:941-58. [PMID: 17208962 PMCID: PMC1803723 DOI: 10.1104/pp.106.090761] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.
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Affiliation(s)
- Iain W Manfield
- Centre for Plant Sciences, Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
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Fujiki Y, Matsuzono Y, Matsuzaki T, Fransen M. Import of peroxisomal membrane proteins: The interplay of Pex3p- and Pex19p-mediated interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1639-46. [PMID: 17069900 DOI: 10.1016/j.bbamcr.2006.09.030] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 09/07/2006] [Accepted: 09/20/2006] [Indexed: 02/01/2023]
Abstract
In contrast to the molecular mechanisms underlying import of peroxisomal matrix proteins, those involving the transport of membrane proteins remain rather elusive. At present, two targeting routes for peroxisomal membrane proteins (PMPs) have been depicted: class I PMPs are targeted from the cytoplasm directly to the peroxisome membrane, and class II PMPs are sorted indirectly to peroxisomes via the endoplasmic reticulum (ER). In addition, three peroxins--Pex3p, Pex16p, and Pex19p - have been identified as essential factors for PMP assembly in several species including humans: Pex19p is a predominantly cytoplasmic protein that shows a broad PMP-binding specificity; Pex3p serves as the membrane-anchoring site for Pex19p; and Pex16p - a protein absent in most yeasts--is thought to provide the initial scaffold for recruiting the protein import machinery required for peroxisome membrane biogenesis. Remarkably, the function of Pex16p does not appear to be conserved between different species. In addition, significant disagreement exists about whether Pex19p has a chaperone-like role in the cytosol or at the peroxisome membrane and/or functions as a cycling import receptor for newly synthesized PMPs. Here we review the recent progress made in our understanding of the role of two key players in PMP biogenesis, Pex3p and Pex19p.
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Affiliation(s)
- Yukio Fujiki
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan.
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Pinto MP, Grou CP, Alencastre IS, Oliveira ME, Sá-Miranda C, Fransen M, Azevedo JE. The import competence of a peroxisomal membrane protein is determined by Pex19p before the docking step. J Biol Chem 2006; 281:34492-502. [PMID: 16980692 DOI: 10.1074/jbc.m607183200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biogenesis of the mammalian peroxisomal membrane requires the action of Pex3p and Pex16p, two proteins present in the organelle membrane, and Pex19p, a protein that displays a dual subcellular distribution (peroxisomal and cytosolic). Pex19p interacts with most peroxisomal intrinsic membrane proteins, but whether this property reflects its role as an import receptor for this class of proteins or a chaperone-like function in the assembly/disassembly of peroxisomal membrane proteins has been the subject of much controversy. Here, we describe an in vitro system particularly suited to address this issue. It is shown that insertion of a reporter protein into the peroxisomal membrane is a Pex3p-dependent process that does not require ATP/GTP hydrolysis. The system can be programmed with recombinant versions of Pex19p, allowing us to demonstrate that Pex19p-cargo protein complexes formed in the absence of peroxisomes are the substrates for the peroxisomal docking/insertion machinery. Data suggesting that cargo-loaded Pex19p displays a much higher affinity for Pex3p than Pex19p alone are also provided. These results suggest that soluble Pex19p participates in the targeting of newly synthesized peroxisomal membrane proteins to the organelle membrane and support the existence of a cargo-induced peroxisomal targeting mechanism for Pex19p.
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Affiliation(s)
- Manuel P Pinto
- Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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Hayashi M, Nishimura M. Arabidopsis thaliana--a model organism to study plant peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1382-91. [PMID: 17005266 DOI: 10.1016/j.bbamcr.2006.08.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 07/28/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
In higher plants, peroxisomes have been believed to play a pivotal role in three metabolic pathways, which are lipid breakdown, photorespiration and H2O2-detoxificaton. Recently, significant progress in the study of plant peroxisomes was established by forward-/reverse-genetics and post-genomic approaches using Arabidopsis thaliana, the first higher plant to have its entire genome sequenced. These studies illustrated that plant peroxisomes have more diverse functions than we previously thought. Research using Arabidopsis thaliana is improving our understanding of the function of plant peroxisomes.
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Affiliation(s)
- Makoto Hayashi
- National Institute for Basic Biology, Okazaki 444-8585, Japan
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