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Liu C, Bi Z, Xu H, Zhang R, Wang J, Liang Y, Zhang L, Yu J. Regulatory Mechanism of Peroxisome Number Reduction Caused by FgPex4 and FgPex22-like Deletion in Fusarium graminearum. J Fungi (Basel) 2023; 9:1083. [PMID: 37998888 PMCID: PMC10672079 DOI: 10.3390/jof9111083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
Peroxisomes are single-membrane-bound organelles that play critical roles in eukaryotic cellular functions. Peroxisome quantity is a key factor influencing the homeostasis and pathogenic processes of pathogenic fungi. The aim of the present study was to investigate the underlying mechanisms of the reduction in number of peroxisomes in Fusarium graminearum consequent to FgPex4 and FgPex22-like deletion. The number of peroxisomes decreased by 40.55% and 39.70% when FgPex4 and FgPex22-like, respectively, were absent. Peroxisome biogenesis-related proteins, as well as inheritance- and division-related dynamin-like proteins were reduced at the transcriptional level in the mutant strains. In addition, the degree of pexophagy was intensified and the accumulation of ubiquitinated FgPex5 was also increased in F. graminearum when FgPex4 or FgPex22-like was absent. The findings suggest that FgPex4 and FgPex22-like influence the number of peroxisomes by influencing peroxisome biogenesis and pexophagy.
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Affiliation(s)
| | | | | | | | | | | | - Li Zhang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China; (C.L.); (Z.B.); (H.X.); (R.Z.); (J.W.); (Y.L.)
| | - Jinfeng Yu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China; (C.L.); (Z.B.); (H.X.); (R.Z.); (J.W.); (Y.L.)
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2
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Deori NM, Nagotu S. Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast. Curr Genet 2022; 68:537-550. [PMID: 36242632 DOI: 10.1007/s00294-022-01254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Peroxisomes are highly dynamic organelles present in most eukaryotic cells. They also play an important role in human health and the optimum functioning of cells. An extensive repertoire of proteins is associated with the biogenesis and function of these organelles. Two protein families that are involved in regulating peroxisome number in a cell directly or indirectly are Pex11 and Pex30. Interestingly, these proteins are also reported to regulate the contact sites between peroxisomes and other cell organelles such as mitochondria, endoplasmic reticulum and lipid droplets. In this manuscript, we review our current knowledge of the role of these proteins in peroxisome biogenesis in various yeast species. Further, we also discuss in detail the role of these protein families in the regulation of inter-organelle contacts in yeast.
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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
| | - 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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Farré JC, Mahalingam SS, Proietto M, Subramani S. Peroxisome biogenesis, membrane contact sites, and quality control. EMBO Rep 2018; 20:embr.201846864. [PMID: 30530632 DOI: 10.15252/embr.201846864] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are conserved organelles of eukaryotic cells with important roles in cellular metabolism, human health, redox homeostasis, as well as intracellular metabolite transfer and signaling. We review here the current status of the different co-existing modes of biogenesis of peroxisomal membrane proteins demonstrating the fascinating adaptability in their targeting and sorting pathways. While earlier studies focused on peroxisomes as autonomous organelles, the necessity of the ER and potentially even mitochondria as sources of peroxisomal membrane proteins and lipids has come to light in recent years. Additionally, the intimate physical juxtaposition of peroxisomes with other organelles has transitioned from being viewed as random encounters to a growing appreciation of the expanding roles of such inter-organellar membrane contact sites in metabolic and regulatory functions. Peroxisomal quality control mechanisms have also come of age with a variety of mechanisms operating both during biogenesis and in the cellular response to environmental cues.
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Affiliation(s)
- Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Shanmuga S Mahalingam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Marco Proietto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
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4
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Akşit A, van der Klei IJ. Yeast peroxisomes: How are they formed and how do they grow? Int J Biochem Cell Biol 2018; 105:24-34. [PMID: 30268746 DOI: 10.1016/j.biocel.2018.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
Peroxisomes are single membrane enclosed cell organelles, which are present in almost all eukaryotic cells. In addition to the common peroxisomal pathways such as β-oxidation of fatty acids and decomposition of H2O2, these organelles fulfil a range of metabolic and non-metabolic functions. Peroxisomes are very important since various human disorders exist that are caused by a defect in peroxisome function. Here we describe our current knowledge on the molecular mechanisms of peroxisome biogenesis in yeast, including peroxisomal protein sorting, organelle dynamics and peroxisomal membrane contact sites.
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Affiliation(s)
- Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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5
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Farré JC, Carolino K, Stasyk OV, Stasyk OG, Hodzic Z, Agrawal G, Till A, Proietto M, Cregg J, Sibirny AA, Subramani S. A New Yeast Peroxin, Pex36, a Functional Homolog of Mammalian PEX16, Functions in the ER-to-Peroxisome Traffic of Peroxisomal Membrane Proteins. J Mol Biol 2017; 429:3743-3762. [PMID: 29037759 PMCID: PMC5693695 DOI: 10.1016/j.jmb.2017.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/21/2017] [Accepted: 10/07/2017] [Indexed: 12/17/2022]
Abstract
Peroxisomal membrane proteins (PMPs) traffic to peroxisomes by two mechanisms: direct insertion from the cytosol into the peroxisomal membrane and indirect trafficking to peroxisomes via the endoplasmic reticulum (ER). In mammals and yeast, several PMPs traffic via the ER in a Pex3- and Pex19-dependent manner. In Komagataella phaffii (formerly called Pichia pastoris) specifically, the indirect traffic of Pex2, but not of Pex11 or Pex17, depends on Pex3, but all PMPs tested for indirect trafficking require Pex19. In mammals, the indirect traffic of PMPs also requires PEX16, a protein that is absent in most yeast species. In this study, we isolated PEX36, a new gene in K. phaffii, which encodes a PMP. Pex36 is required for cell growth in conditions that require peroxisomes for the metabolism of certain carbon sources. This growth defect in cells lacking Pex36 can be rescued by the expression of human PEX16, Saccharomyces cerevisiae Pex34, or by overexpression of the endogenous K. phaffii Pex25. Pex36 is not an essential protein for peroxisome proliferation, but in the absence of the functionally redundant protein, Pex25, it becomes essential and less than 20% of these cells show import-incompetent, peroxisome-like structures (peroxisome remnants). In the absence of both proteins, peroxisome biogenesis and the intra-ER sorting of Pex2 and Pex11C are seriously impaired, likely by affecting Pex3 and Pex19 function.
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Affiliation(s)
- Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Krypton Carolino
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Oleh V Stasyk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, Lviv 79005, Ukraine
| | - Olena G Stasyk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, Lviv 79005, Ukraine; Department of Biochemistry, Biological Faculty, Ivan Franko National University of Lviv, Hrushevsky Street 4, Lviv 79005, Ukraine
| | - Zlatan Hodzic
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gaurav Agrawal
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andreas Till
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Marco Proietto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - James Cregg
- Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, CA 91711, USA
| | - Andriy A Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, Lviv 79005, Ukraine; University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Joshi AS, Huang X, Choudhary V, Levine TP, Hu J, Prinz WA. A family of membrane-shaping proteins at ER subdomains regulates pre-peroxisomal vesicle biogenesis. J Cell Biol 2016; 215:515-529. [PMID: 27872254 PMCID: PMC5119935 DOI: 10.1083/jcb.201602064] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Saccharomyces cerevisiae contains three conserved reticulon and reticulon-like proteins that help maintain ER structure by stabilizing high membrane curvature in ER tubules and the edges of ER sheets. A mutant lacking all three proteins has dramatically altered ER morphology. We found that ER shape is restored in this mutant when Pex30p or its homologue Pex31p is overexpressed. Pex30p can tubulate membranes both in cells and when reconstituted into proteoliposomes, indicating that Pex30p is a novel ER-shaping protein. In contrast to the reticulons, Pex30p is low abundance, and we found that it localizes to subdomains in the ER. We show that these ER subdomains are the sites where most preperoxisomal vesicles (PPVs) are generated. In addition, overproduction or deletion of Pex30p or Pex31p alters the size, shape, and number of PPVs. Our findings suggest that Pex30p and Pex31p help shape and generate regions of the ER where PPV biogenesis occurs.
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Affiliation(s)
- Amit S Joshi
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xiaofang Huang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China
| | - Vineet Choudhary
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tim P Levine
- University College London Institute of Ophthalmology, London EC1V 9EL, England, UK
| | - Junjie Hu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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7
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Agrawal G, Subramani S. De novo peroxisome biogenesis: Evolving concepts and conundrums. BIOCHIMICA ET BIOPHYSICA 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] [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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8
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Motley AM, Galvin PC, Ekal L, Nuttall JM, Hettema EH. Reevaluation of the role of Pex1 and dynamin-related proteins in peroxisome membrane biogenesis. J Cell Biol 2016; 211:1041-56. [PMID: 26644516 PMCID: PMC4674274 DOI: 10.1083/jcb.201412066] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Analysis of Pex1 and dynamin-related protein function indicates peroxisomes multiply mainly by growth and division in Saccharomyces cerevisiae, whereas no evidence was found for the previously proposed role for Pex1 in peroxisome formation by fusion of ER-derived preperoxisomal vesicles. A recent model for peroxisome biogenesis postulates that peroxisomes form de novo continuously in wild-type cells by heterotypic fusion of endoplasmic reticulum–derived vesicles containing distinct sets of peroxisomal membrane proteins. This model proposes a role in vesicle fusion for the Pex1/Pex6 complex, which has an established role in matrix protein import. The growth and division model proposes that peroxisomes derive from existing peroxisomes. We tested these models by reexamining the role of Pex1/Pex6 and dynamin-related proteins in peroxisome biogenesis. We found that induced depletion of Pex1 blocks the import of matrix proteins but does not affect membrane protein delivery to peroxisomes; markers for the previously reported distinct vesicles colocalize in pex1 and pex6 cells; peroxisomes undergo continued growth if fission is blocked. Our data are compatible with the established primary role of the Pex1/Pex6 complex in matrix protein import and show that peroxisomes in Saccharomyces cerevisiae multiply mainly by growth and division.
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Affiliation(s)
- Alison M Motley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Paul C Galvin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Lakhan Ekal
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - James M Nuttall
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
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9
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Targeting and insertion of peroxisomal membrane proteins: ER trafficking versus direct delivery to peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:870-80. [PMID: 26392202 DOI: 10.1016/j.bbamcr.2015.09.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
The importance of peroxisomes is highlighted by severe inherited human disorders linked to impaired peroxisomal biogenesis. Besides the simple architecture of these ubiquitous and dynamic organelles, their biogenesis is surprisingly complex and involves specialized proteins, termed peroxins, which mediate targeting and insertion of peroxisomal membrane proteins (PMPs) into the peroxisomal bilayer, and the import of soluble proteins into the protein-dense matrix of the organelle. The long-standing paradigm that all peroxisomal proteins are imported directly into preexisting peroxisomes has been challenged by the detection of PMPs inside the endoplasmic reticulum (ER). New models propose that the ER originates peroxisomal biogenesis by mediating PMP trafficking to the peroxisomes via budding vesicles. However, the relative contribution of this ER-derived pathway to the total peroxisome population in vivo, and the detailed mechanisms of ER entry and exit of PMPs are controversially discussed. This review aims to summarize present knowledge about how PMPs are targeted to the ER, instead of being inserted directly into preexisting peroxisomes. Moreover, molecular mechanisms that facilitate bilayer insertion of PMPs among different species are discussed.
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Knoops K, Manivannan S, Cepinska MN, Krikken AM, Kram AM, Veenhuis M, van der Klei IJ. Preperoxisomal vesicles can form in the absence of Pex3. ACTA ACUST UNITED AC 2014; 204:659-68. [PMID: 24590171 PMCID: PMC3941047 DOI: 10.1083/jcb.201310148] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Contrary to earlier findings, preperoxisomal membrane structures form in yeast cells lacking the peroxin Pex3 and are competent to mature into functional peroxisomes upon Pex3 reintroduction. We demonstrate that the peroxin Pex3 is not required for the formation of peroxisomal membrane structures in yeast pex3 mutant cells. Notably, pex3 mutant cells already contain reticular and vesicular structures that harbor key proteins of the peroxisomal receptor docking complex—Pex13 and Pex14—as well as the matrix proteins Pex8 and alcohol oxidase. Other peroxisomal membrane proteins in these cells are unstable and transiently localized to the cytosol (Pex10, Pmp47) or endoplasmic reticulum (Pex11). These reticular and vesicular structures are more abundant in cells of a pex3 atg1 double deletion strain, as the absence of Pex3 may render them susceptible to autophagic degradation, which is blocked in this double mutant. Contrary to earlier suggestions, peroxisomes are not formed de novo from the endoplasmic reticulum when the PEX3 gene is reintroduced in pex3 cells. Instead, we find that reintroduced Pex3 sorts to the preperoxisomal structures in pex3 cells, after which these structures mature into normal peroxisomes.
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Affiliation(s)
- Kèvin Knoops
- Molecular Cell Biology, University of Groningen, 9747 AG Groningen, Netherlands
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11
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Veenhuis M, van der Klei IJ. A critical reflection on the principles of peroxisome formation in yeast. Front Physiol 2014; 5:110. [PMID: 24688473 PMCID: PMC3960572 DOI: 10.3389/fphys.2014.00110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/04/2014] [Indexed: 11/13/2022] Open
Abstract
We have evaluated the current knowledge on peroxisome proliferation in yeast. In wild-type cells, peroxisomes multiply predominantly by fission at conditions that require peroxisome function(s) for growth. In cells that lack peroxisomes, for instance in pex3 and pex19 mutants or in mutants that display inheritance defects, peroxisomes may form de novo. We propose a novel machinery for the de novo formation of peroxisomes in pex3 cells, in which new peroxisomes do not arise from the endoplasmic reticulum. This machinery is based on the recent observation that membrane vesicles are present in pex3 cells that display peroxisomal characteristics in that they contain specific peroxisomal membrane and matrix proteins. These structures are the source for newly formed peroxisomes upon reintroduction of Pex3. Furthermore, we critically evaluate the principles of sorting of other peroxisomal membrane proteins to their target organelle and the function of the endoplasmic reticulum therein.
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Affiliation(s)
- Marten Veenhuis
- Molecular Cell Biology, University of Groningen Groningen, Netherlands
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12
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Williams C, van der Klei IJ. Pexophagy-linked degradation of the peroxisomal membrane protein Pex3p involves the ubiquitin-proteasome system. Biochem Biophys Res Commun 2013; 438:395-401. [PMID: 23899522 DOI: 10.1016/j.bbrc.2013.07.086] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/20/2013] [Indexed: 11/29/2022]
Abstract
Peroxisome autophagy, also known as pexophagy, describes the wholesale degradation of peroxisomes via the vacuole, when organelles become damaged or redundant. In the methylotrophic yeast Hansenula polymorpha, pexophagy is stimulated when cells growing on methanol are exposed to excess glucose. Degradation of the peroxisomal membrane protein Pex3p, a process that does not involve the vacuole, was shown to trigger pexophagy. In this contribution, we have characterised pexophagy-associated Pex3p degradation further. We show that Pex3p breakdown depends on ubiquitin and confirm that Pex3p is a target for ubiquitination. Furthermore, we identify a role for the peroxisomal E3 ligases Pex2p and Pex10p in Pex3p degradation, suggesting the existence of a ubiquitin-dependent pathway involved in removing proteins from the peroxisomal membrane.
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Affiliation(s)
- Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.
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Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat--store 'em up or burn 'em down. Genetics 2013; 193:1-50. [PMID: 23275493 PMCID: PMC3527239 DOI: 10.1534/genetics.112.143362] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lipid droplets (LDs) and peroxisomes are central players in cellular lipid homeostasis: some of their main functions are to control the metabolic flux and availability of fatty acids (LDs and peroxisomes) as well as of sterols (LDs). Both fatty acids and sterols serve multiple functions in the cell—as membrane stabilizers affecting membrane fluidity, as crucial structural elements of membrane-forming phospholipids and sphingolipids, as protein modifiers and signaling molecules, and last but not least, as a rich carbon and energy source. In addition, peroxisomes harbor enzymes of the malic acid shunt, which is indispensable to regenerate oxaloacetate for gluconeogenesis, thus allowing yeast cells to generate sugars from fatty acids or nonfermentable carbon sources. Therefore, failure of LD and peroxisome biogenesis and function are likely to lead to deregulated lipid fluxes and disrupted energy homeostasis with detrimental consequences for the cell. These pathological consequences of LD and peroxisome failure have indeed sparked great biomedical interest in understanding the biogenesis of these organelles, their functional roles in lipid homeostasis, interaction with cellular metabolism and other organelles, as well as their regulation, turnover, and inheritance. These questions are particularly burning in view of the pandemic development of lipid-associated disorders worldwide.
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Thoms S, Harms I, Kalies KU, Gärtner J. Peroxisome formation requires the endoplasmic reticulum channel protein Sec61. Traffic 2012; 13:599-609. [PMID: 22212716 DOI: 10.1111/j.1600-0854.2011.01324.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 12/21/2022]
Abstract
In peroxisome formation, models of near-autonomous peroxisome biogenesis with membrane protein integration directly from the cytosol into the peroxisomal membrane are in direct conflict with models whereby peroxisomes bud from the endoplasmic reticulum and receive their membrane proteins through a branch of the secretory pathway. We therefore reinvestigated the role of the Sec61 complex, the protein-conducting channel of the endoplasmic reticulum (ER) in peroxisome formation. We found that depletion or partial inactivation of Sec61 in yeast disables peroxisome formation. The ER entry of the early peroxisomal membrane protein Pex3 engineered with a glycosylation tag is reduced in sec61 mutant cells. Moreover, we were able to reconstitute Pex3 import into ER membranes in vitro, and we identified a variant of a signal anchor sequence for ER translocation at the Pex3 N-terminus. Our findings are consistent with a Sec61 requirement for peroxisome formation and a fundamental role of the ER in peroxisome biogenesis.
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Affiliation(s)
- Sven Thoms
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University of Göttingen, 37075, Göttingen, Germany.
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Huber A, Koch J, Kragler F, Brocard C, Hartig A. A subtle interplay between three Pex11 proteins shapes de novo formation and fission of peroxisomes. Traffic 2011; 13:157-67. [PMID: 21951626 PMCID: PMC3245845 DOI: 10.1111/j.1600-0854.2011.01290.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The organization of eukaryotic cells into membrane-bound compartments must be faithfully sustained for survival of the cell. A subtle equilibrium exists between the degradation and the proliferation of organelles. Commonly, proliferation is initiated by a membrane remodeling process. Here, we dissect the function of proteins driving organelle proliferation in the particular case of peroxisomes. These organelles are formed either through a growth and division process from existing peroxisomes or de novo from the endoplasmic reticulum (ER). Among the proteins involved in the biogenesis of peroxisomes, peroxins, members of the Pex11 protein family participate in peroxisomal membrane alterations. In the yeast Saccharomyces cerevisiae, the Pex11 family consists of three proteins, Pex11p, Pex25p and Pex27p. Here we demonstrate that yeast mutants lacking peroxisomes require the presence of Pex25p to regenerate this organelle de novo. We also provide evidence showing that Pex27p inhibits peroxisomal function and illustrate that Pex25p initiates elongation of the peroxisomal membrane. Our data establish that although structurally conserved each of the three Pex11 protein family members plays a distinct role. While ScPex11p promotes the proliferation of peroxisomes already present in the cell, ScPex25p initiates remodeling at the peroxisomal membrane and ScPex27p acts to counter this activity. In addition, we reveal that ScPex25p acts in concert with Pex3p in the initiation of de novo peroxisome biogenesis from the ER.
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Affiliation(s)
- Anja Huber
- University of Vienna, Max F. Perutz Laboratories, Center for Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, Vienna, Austria
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Saraya R, Krikken AM, Veenhuis M, van der Klei IJ. Peroxisome reintroduction in Hansenula polymorpha requires Pex25 and Rho1. ACTA ACUST UNITED AC 2011; 193:885-900. [PMID: 21606207 PMCID: PMC3105547 DOI: 10.1083/jcb.201012083] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We identified two proteins, Pex25 and Rho1, which are involved in reintroduction of peroxisomes in peroxisome-deficient yeast cells. These are, together with Pex3, the first proteins identified as essential for this process. Of the three members of the Hansenula polymorpha Pex11 protein family-Pex11, Pex25, and Pex11C-only Pex25 was required for reintroduction of peroxisomes into a peroxisome-deficient mutant strain. In peroxisome-deficient pex3 cells, Pex25 localized to structures adjacent to the ER, whereas in wild-type cells it localized to peroxisomes. Pex25 cells were not themselves peroxisome deficient but instead contained a slightly increased number of peroxisomes. Interestingly, pex11 pex25 double deletion cells, in which both peroxisome fission (due to the deletion of PEX11) and reintroduction (due to deletion of PEX25) was blocked, did display a peroxisome-deficient phenotype. Peroxisomes reappeared in pex11 pex25 cells upon synthesis of Pex25, but not of Pex11. Reintroduction in the presence of Pex25 required the function of the GTPase Rho1. These data therefore provide new and detailed insight into factors important for de novo peroxisome formation in yeast.
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Affiliation(s)
- Ruchi Saraya
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, 9700 CC Groningen, Netherlands
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18
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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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19
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Delille HK, Agricola B, Guimaraes SC, Borta H, Lüers GH, Fransen M, Schrader M. Pex11pbeta-mediated growth and division of mammalian peroxisomes follows a maturation pathway. J Cell Sci 2010; 123:2750-62. [PMID: 20647371 DOI: 10.1242/jcs.062109] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Peroxisomes are ubiquitous subcellular organelles, which multiply by growth and division but can also form de novo via the endoplasmic reticulum. Growth and division of peroxisomes in mammalian cells involves elongation, membrane constriction and final fission. Dynamin-like protein (DLP1/Drp1) and its membrane adaptor Fis1 function in the later stages of peroxisome division, whereas the membrane peroxin Pex11pbeta appears to act early in the process. We have discovered that a Pex11pbeta-YFP(m) fusion protein can be used as a specific tool to further dissect peroxisomal growth and division. Pex11pbeta-YFP(m) inhibited peroxisomal segmentation and division, but resulted in the formation of pre-peroxisomal membrane structures composed of globular domains and tubular extensions. Peroxisomal matrix and membrane proteins were targeted to distinct regions of the peroxisomal structures. Pex11pbeta-mediated membrane formation was initiated at pre-existing peroxisomes, indicating that growth and division follows a multistep maturation pathway and that formation of mammalian peroxisomes is more complex than simple division of a pre-existing organelle. The implications of these findings on the mechanisms of peroxisome formation and membrane deformation are discussed.
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Affiliation(s)
- Hannah K Delille
- Centre for Cell Biology and Department of Biology, University of Aveiro, Aveiro, Portugal
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20
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Saraya R, Veenhuis M, van der Klei IJ. Peroxisomes as dynamic organelles: peroxisome abundance in yeast. FEBS J 2010; 277:3279-88. [DOI: 10.1111/j.1742-4658.2010.07740.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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van der Zand A, Braakman I, Tabak HF. Peroxisomal membrane proteins insert into the endoplasmic reticulum. Mol Biol Cell 2010; 21:2057-65. [PMID: 20427571 PMCID: PMC2883949 DOI: 10.1091/mbc.e10-02-0082] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We demonstrate that the entry of peroxisomal membrane proteins (PMPs) into the ER is mediated by the general ER import machinery. Within the ER, PMPs attain their correct topology and subsequently travel to peroxisomes. Our results show that the ER forms an obligate requirement to maintain peroxisomes in multiplying cells. We show that a comprehensive set of 16 peroxisomal membrane proteins (PMPs) encompassing all types of membrane topologies first target to the endoplasmic reticulum (ER) in Saccharomyces cerevisiae. These PMPs insert into the ER membrane via the protein import complexes Sec61p and Get3p (for tail-anchored proteins). This trafficking pathway is representative for multiplying wild-type cells in which the peroxisome population needs to be maintained, as well as for mutant cells lacking peroxisomes in which new peroxisomes form after complementation with the wild-type version of the mutant gene. PMPs leave the ER in a Pex3p-Pex19p–dependent manner to end up in metabolically active peroxisomes. These results further extend the new concept that peroxisomes derive their basic framework (membrane and membrane proteins) from the ER and imply a new functional role for Pex3p and Pex19p.
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Affiliation(s)
- Adabella van der Zand
- Cellular Protein Chemistry, Faculty of Science, Utrecht University, NL-3584 CH Utrecht, The Netherlands
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22
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23
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Abstract
With every cell division, peroxisomes duplicate and are segregated between progeny cells. Here, we discuss the different modes of peroxisome multiplication and the machinery that is involved in each case. Peroxisomes have been considered by many to be peripheral to mainstream cell biology. However, this is changing in response to the recent finding that peroxisomes obtain membrane constituents from the endoplasmic reticulum, making them the latest branch of the endomembrane system to be identified. Furthermore, the observations that peroxisome and mitochondrial biogenesis can occur in a coordinated manner, and that these organelles share factors for their multiplication, demonstrate previously unanticipated aspects of cellular organisation.
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Affiliation(s)
- Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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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: 65] [Impact Index Per Article: 4.3] [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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25
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Kurbatova E, Otzen M, van der Klei IJ. p24 proteins play a role in peroxisome proliferation in yeast. FEBS Lett 2009; 583:3175-80. [PMID: 19733569 DOI: 10.1016/j.febslet.2009.08.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 08/27/2009] [Accepted: 08/28/2009] [Indexed: 11/19/2022]
Abstract
Emp24 is a member of the p24 protein family, which was initially localized to the endoplasmic reticulum, Golgi and COP vesicles, but has recently shown to be associated with Saccharomyces cerevisiae peroxisomes as well. Using cell fractionation and electron- and fluorescence microscopy, we show that in the yeast Hansenula polymorpha, Emp24 also associates with peroxisomes. In addition, we show that peroxisome numbers are strongly decreased in H. polymorpha cells lacking two proteins of the p24 complex, Emp24 and Erp3. Detailed fluorescence microscopy analyses suggest that emp24.erp3 cells are disturbed in peroxisome fission and inheritance.
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Affiliation(s)
- Elena Kurbatova
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands
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26
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Abstract
Peroxisomes play an important role in lipid metabolic pathways and are implicated in many human disorders. Their biogenesis has been studied over the last two decades using many uni and multi-cellular model systems and many aspects of the mechanisms and proteins involved in peroxisome biogenesis are conserved from yeast to humans. In this manuscript we review the recent progress made in our understanding of the mechanisms by which matrix and membrane proteins are sorted to and assembled into peroxisomes.
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Affiliation(s)
- Changle Ma
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
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27
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Camões F, Bonekamp NA, Delille HK, Schrader M. Organelle dynamics and dysfunction: A closer link between peroxisomes and mitochondria. J Inherit Metab Dis 2009; 32:163-80. [PMID: 19067229 DOI: 10.1007/s10545-008-1018-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/30/2008] [Accepted: 11/04/2008] [Indexed: 12/23/2022]
Abstract
Mitochondria and peroxisomes are ubiquitous subcellular organelles, which fulfil an indispensable role in the cellular metabolism of higher eukaryotes. Moreover, they are highly dynamic and display large plasticity. There is growing evidence now that both organelles exhibit a closer interrelationship than previously appreciated. This connection includes metabolic cooperations and cross-talk, a novel putative mitochondria-to-peroxisome vesicular trafficking pathway, as well as an overlap in key components of their fission machinery. Thus, peroxisomal alterations in metabolism, biogenesis, dynamics and proliferation can potentially influence mitochondrial functions, and vice versa. In this review, we present the latest progress in the emerging field of peroxisomal and mitochondrial interrelationship with a particular emphasis on organelle dynamics and its implication in diseases.
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Affiliation(s)
- F Camões
- Centre for Cell Biology & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
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28
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Titorenko VI, Rachubinski RA. Spatiotemporal dynamics of the ER-derived peroxisomal endomembrane system. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 272:191-244. [PMID: 19121819 DOI: 10.1016/s1937-6448(08)01605-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Recent studies have provided evidence that peroxisomes constitute a multicompartmental endomembrane system. The system begins to form with the targeting of certain peroxisomal membrane proteins to the ER and their exit from the ER via preperoxisomal carriers. These carriers undergo a multistep maturation into metabolically active peroxisomes containing the entire complement of peroxisomal membrane and matrix proteins. At each step, the import of a subset of proteins and the uptake of certain membrane lipids result in the formation of a distinct, more mature compartment of the peroxisomal endomembrane system. Individual peroxisomal compartments proliferate by undergoing one or several rounds of division. Herein, we discuss various strategies that evolutionarily diverse organisms use to coordinate compartment formation, maturation, and division in the peroxisomal endomembrane system. We also critically evaluate the molecular and cellular mechanisms governing these processes, outline the most important unanswered questions, and suggest directions for future research.
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29
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Biogenesis of peroxisomes and mitochondria: linked by division. Histochem Cell Biol 2009; 131:441-6. [PMID: 19219450 DOI: 10.1007/s00418-009-0561-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
Peroxisomes and mitochondria are metabolically linked organelles, which are crucial to human health and development. The search for components involved in their dynamics and maintenance led to the interesting finding that mitochondria and peroxisomes share components of their division machinery. Recently, it became clear that this is a common strategy used by mammals, fungi and plants. Furthermore, a closer interrelationship between peroxisomes and mitochondria has been proposed, which might have an impact on functionality and disease conditions. Here, we briefly highlight the major findings, views and open questions concerning peroxisomal formation, division, and interrelationship with mitochondria.
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30
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Krikken AM, Veenhuis M, van der Klei IJ. Hansenula polymorpha pex11 cells are affected in peroxisome retention. FEBS J 2009; 276:1429-39. [DOI: 10.1111/j.1742-4658.2009.06883.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Nagotu S, Krikken AM, Otzen M, Kiel JAKW, Veenhuis M, van der Klei IJ. Peroxisome Fission inHansenula polymorphaRequires Mdv1 and Fis1, Two Proteins Also Involved in Mitochondrial Fission. Traffic 2008; 9:1471-84. [DOI: 10.1111/j.1600-0854.2008.00772.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Tabak HF, van der Zand A, Braakman I. Peroxisomes: minted by the ER. Curr Opin Cell Biol 2008; 20:393-400. [PMID: 18619829 DOI: 10.1016/j.ceb.2008.05.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/23/2008] [Accepted: 05/23/2008] [Indexed: 11/16/2022]
Abstract
Peroxisomes are one of numerous organelles in a eukaryotic cell; they are small, single-membrane-bound vesicles involved in cellular metabolism, particularly fatty acid degradation. Transport of metabolites and co-factors in and across the membrane is taken care of by specific transporters. Peroxisome formation and maintenance has been debated for a long time: opinions swinging from autonomous to ER-derived organelles. Only recently it has been established firmly that the site of origin of peroxisomes is the ER. It implies that a new branch of the endomembrane system is open to further characterization.
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Affiliation(s)
- Henk F Tabak
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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33
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Lingard MJ, Gidda SK, Bingham S, Rothstein SJ, Mullen RT, Trelease RN. Arabidopsis PEROXIN11c-e, FISSION1b, and DYNAMIN-RELATED PROTEIN3A cooperate in cell cycle-associated replication of peroxisomes. THE PLANT CELL 2008; 20:1567-85. [PMID: 18539750 PMCID: PMC2483373 DOI: 10.1105/tpc.107.057679] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Although participation of PEROXIN11 (PEX11), FISSION1 (FISl), and DYNAMIN-RELATED PROTEIN (DRP) has been well established during induced peroxisome proliferation in response to external stimuli, their roles in cell cycle-associated constitutive replication/duplication have not been fully explored. Herein, bimolecular fluorescence complementation experiments with Arabidopsis thaliana suspension cells revealed homooligomerization of all five PEX11 isoforms (PEX11a-e) and heterooligomerizations of all five PEX11 isoforms with FIS1b, but not FIS1a nor DRP3A. Intracellular protein targeting experiments demonstrated that FIS1b, but not FIS1a nor DRP3A, targeted to peroxisomes only when coexpressed with PEX11d or PEX11e. Simultaneous silencing of PEX11c-e or individual silencing of DRP3A, but not FIS1a nor FIS1b, resulted in approximately 40% reductions in peroxisome number. During G2 in synchronized cell cultures, peroxisomes sequentially enlarged, elongated, and then doubled in number, which correlated with peaks in PEX11, FIS1, and DRP3A expression. Overall, these data support a model for the replication of preexisting peroxisomes wherein PEX11c, PEX11d, and PEX11e act cooperatively during G2 to promote peroxisome elongation and recruitment of FIS1b to the peroxisome membrane, where DRP3A stimulates fission of elongated peroxisomes into daughter peroxisomes, which are then distributed between daughter cells.
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Affiliation(s)
- Matthew J Lingard
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
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34
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Abstract
More than half a century of research on peroxisomes has revealed unique features of this ubiquitous subcellular organelle, which have often been in disagreement with existing dogmas in cell biology. About 50 peroxisomal enzymes have so far been identified, which contribute to several crucial metabolic processes such as β-oxidation of fatty acids, biosynthesis of ether phospholipids and metabolism of reactive oxygen species, and render peroxisomes indispensable for human health and development. It became obvious that peroxisomes are highly dynamic organelles that rapidly assemble, multiply and degrade in response to metabolic needs. However, many aspects of peroxisome biology are still mysterious. This review addresses recent exciting discoveries on the biogenesis, formation and degradation of peroxisomes, on peroxisomal dynamics and division, as well as on the interaction and cross talk of peroxisomes with other subcellular compartments. Furthermore, recent advances on the role of peroxisomes in medicine and in the identification of novel peroxisomal proteins are discussed.
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Affiliation(s)
- Michael Schrader
- Centre for Cell Biology and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
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35
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Nagotu S, Saraya R, Otzen M, Veenhuis M, van der Klei IJ. Peroxisome proliferation in Hansenula polymorpha requires Dnm1p which mediates fission but not de novo formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1783:760-9. [PMID: 18060881 DOI: 10.1016/j.bbamcr.2007.10.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/26/2007] [Accepted: 10/29/2007] [Indexed: 11/28/2022]
Abstract
We show that the dynamin-like proteins Dnm1p and Vps1p are not required for re-introduction of peroxisomes in Hansenula polymorpha pex3 cells upon complementation with PEX3-GFP. Instead, Dnm1p, but not Vps1p, plays a crucial role in organelle proliferation via fission. In H. polymorpha DNM1 deletion cells (dnm1) a single peroxisome is present that forms long extensions, which protrude into developing buds and divide during cytokinesis. Budding pex11.dnm1 double deletion cells lack these peroxisomal extensions, suggesting that the peroxisomal membrane protein Pex11p is required for their formation. Life cell imaging revealed that fluorescent Dnm1p-GFP spots fluctuate between peroxisomes and mitochondria. On the other hand Pex11p is present over the entire organelle surface, but concentrates during fission at the basis of the organelle extension in dnm1 cells. Our data indicate that peroxisome fission is the major pathway for peroxisome multiplication in H. polymorpha.
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Affiliation(s)
- Shirisha Nagotu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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36
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Platta HW, Erdmann R. Peroxisomal dynamics. Trends Cell Biol 2007; 17:474-84. [PMID: 17913497 DOI: 10.1016/j.tcb.2007.06.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 06/08/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022]
Abstract
Peroxisomes are a dynamic compartment in almost all eukaryotic cells and have diverse metabolic roles in response to environmental changes and cellular demands. The accompanying changes in enzyme content or abundance of peroxisomes are accomplished by dynamically operating membrane- and matrix-protein transport machineries. This review discusses recent progress in understanding peroxisomal proliferation and maintenance, insertion of peroxisomal membrane proteins, compartmentalization of peroxisomal matrix proteins and selective degradation of peroxisomes via pexophagy.
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Affiliation(s)
- Harald W Platta
- Ruhr-Universität Bochum, Medizinische Fakultät, Institut für Physiologische Chemie, Abteilung für Systembiochemie, Universitätsstr. 150, D-44780 Bochum, Germany
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37
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Managadze D, Würtz C, Sichting M, Niehaus G, Veenhuis M, Rottensteiner H. The peroxin PEX14 of Neurospora crassa is essential for the biogenesis of both glyoxysomes and Woronin bodies. Traffic 2007; 8:687-701. [PMID: 17461798 DOI: 10.1111/j.1600-0854.2007.00560.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the filamentous fungus Neurospora crassa, glyoxysomes and Woronin bodies coexist in the same cell. Because several glyoxysomal matrix proteins and also HEX1, the dominant protein of Woronin bodies, possess typical peroxisomal targeting signals, the question arises as to how protein targeting to these distinct yet related types of microbodies is achieved. Here we analyzed the function of the Neurospora ortholog of PEX14, an essential component of the peroxisomal import machinery. PEX14 interacted with both targeting signal receptors and was localized to glyoxysomes but was virtually absent from Woronin bodies. Nonetheless, a pex14Delta mutant not only failed to grow on fatty acids because of a defect in glyoxysomal beta-oxidation but also suffered from cytoplasmic bleeding, indicative of a defect in Woronin body-dependent septal pore plugging. Inspection of pex14Delta mutant hyphae by fluorescence and electron microscopy indeed revealed the absence of Woronin bodies. When these cells were subjected to subcellular fractionation, HEX1 was completely mislocalized to the cytosol. Expression of GFP-HEX1 in wild-type mycelia caused the staining of Woronin bodies and also of glyoxysomes in a targeting signal-dependent manner. Our data support the view that Woronin bodies emerge from glyoxysomes through import of HEX1 and subsequent fission.
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Affiliation(s)
- David Managadze
- Institut für Physiologische Chemie, Abt. Systembiochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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38
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Abstract
Peroxisomes are important organelles of eukaryote cells. Although these structures are of relatively small size, they display an unprecedented functional versatility. The principles of their biogenesis and function are strongly conserved from very simple eukaryotes to humans. Peroxisome-borne proteins are synthesized in the cytosol and posttranslationally incorporated into the organelle. The protein-sorting signal for matrix proteins, peroxisomal targeting signal (PTS), and for membrane proteins (mPTS), are also conserved. Several genes involved in peroxisomal matrix protein import have been identified (PEX genes), but the details of the molecular mechanisms of this translocation process are still unclear. Here we describe procedures to study the subcellular location of peroxisomal matrix and membrane proteins in yeast and fungi. Emphasis is placed on protocols developed for the methylotrophic yeast Hansenula polymorpha, but very similar protocols can be applied for other yeast species and filamentous fungi. The described methods include cell fractionation procedures and subcellular localization studies using fluorescence microscopy and immunolabeling techniques.
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Affiliation(s)
- Ida van der Klei
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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Mullen RT, Trelease RN. The ER-peroxisome connection in plants: Development of the “ER semi-autonomous peroxisome maturation and replication” model for plant peroxisome biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1655-68. [PMID: 17049631 DOI: 10.1016/j.bbamcr.2006.09.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 08/25/2006] [Accepted: 09/06/2006] [Indexed: 10/24/2022]
Abstract
The perceived role of the ER in the biogenesis of plant peroxisomes has evolved significantly from the original "ER vesiculation" model, which portrayed co-translational import of proteins into peroxisomes originating from the ER, to the "ER semi-autonomous peroxisome" model wherein membrane lipids and post-translationally acquired peroxisomal membrane proteins (PMPs) were derived from the ER. Results from more recent studies of various plant PMPs including ascorbate peroxidase, PEX10 and PEX16, as well as a viral replication protein, have since led to the formulation of a more elaborate "ER semi-autonomous peroxisome maturation and replication" model. Herein we review these results in the context of this newly proposed model and its predecessor models. We discuss also key distinct features of the new model pertaining to its central premise that the ER defines the semi-autonomous maturation (maintenance/assembly/differentiation) and duplication (division) features of specialized classes of pre-existing plant peroxisomes. This model also includes a novel peroxisome-to-ER retrograde sorting pathway that may serve as a constitutive protein retrieval/regulatory system. In addition, new plant peroxisomes are envisaged to arise primarily by duplication of the pre-existing peroxisomes that receive essential membrane components from the ER.
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Affiliation(s)
- Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1.
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Boukh-Viner T, Titorenko VI. Lipids and lipid domains in the peroxisomal membrane of the yeast Yarrowia lipolytica. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1688-96. [PMID: 17023063 DOI: 10.1016/j.bbamcr.2006.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/10/2006] [Accepted: 08/18/2006] [Indexed: 11/26/2022]
Abstract
Biological membranes have unique and highly diverse compositions of their lipid constituents. At present, we have only partial understanding of how membrane lipids and lipid domains regulate the structural integrity and functionality of cellular organelles, maintain the unique molecular composition of each organellar membrane by orchestrating the intracellular trafficking of membrane-bound proteins and lipids, and control the steady-state levels of numerous signaling molecules generated in biological membranes. Similar to other organellar membranes, a single lipid bilayer enclosing the peroxisome, an organelle known for its essential role in lipid metabolism, has a unique lipid composition and organizes some of its lipid and protein components into distinctive assemblies. This review highlights recent advances in our knowledge of how lipids and lipid domains of the peroxisomal membrane regulate the processes of peroxisome assembly and maintenance in the yeast Yarrowia lipolytica. We critically evaluate the molecular mechanisms through which lipid constituents of the peroxisomal membrane control these multistep processes and outline directions for future research in this field.
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Affiliation(s)
- Tatiana Boukh-Viner
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-9, Montreal, Quebec, Canada H4B 1R6
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kuravi K, Nagotu S, Krikken AM, Sjollema K, Deckers M, Erdmann R, Veenhuis M, van der Klei IJ. Dynamin-related proteins Vps1p and Dnm1p control peroxisome abundance in Saccharomyces cerevisiae. J Cell Sci 2006; 119:3994-4001. [PMID: 16968746 DOI: 10.1242/jcs.03166] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae contains three dynamin-related-proteins, Vps1p, Dnm1p and Mgm1p. Previous data from glucose-grown VPS1 and DNM1 null mutants suggested that Vps1p, but not Dnm1p, plays a role in regulating peroxisome abundance. Here we show that deletion of DNM1 also results in reduction of peroxisome numbers. This was not observed in glucose-grown dnm1 cells, but was evident in cells grown in the presence of oleate. Similar observations were made in cells lacking Fis1p, a protein involved in Dnm1p function. Fluorescence microscopy of cells producing Dnm1-GFP or GFP-Fis1p demonstrated that both proteins had a dual localization on mitochondria and peroxisomes. Quantitative analysis revealed a greater reduction in peroxisome number in oleate-induced vps1 cells relative to dnm1 or fis1 cells. A significant fraction of oleate-induced vps1 cells still contained two or more peroxisomes. Conversely, almost all cells of a dnm1 vps1 double-deletion strain contained only one, enlarged peroxisome. This suggests that deletion of DNM1 reinforces the vps1 peroxisome phenotype. Time-lapse imaging indicated that during budding of dnm1 vps1 cells, the single peroxisome present in the mother cell formed long protrusions into the developing bud. This organelle divided at a very late stage of the budding process, possibly during cytokinesis.
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Affiliation(s)
- Kasinath Kuravi
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, NL-9750 AA Haren, The Netherlands
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Titorenko VI, Mullen RT. Peroxisome biogenesis: the peroxisomal endomembrane system and the role of the ER. ACTA ACUST UNITED AC 2006; 174:11-7. [PMID: 16801391 PMCID: PMC2064154 DOI: 10.1083/jcb.200604036] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisomes have long been viewed as semiautonomous, static, and homogenous organelles that exist outside the secretory and endocytic pathways of vesicular flow. However, growing evidence supports the view that peroxisomes actually constitute a dynamic endomembrane system that originates from the endoplasmic reticulum. This review highlights the various strategies used by evolutionarily diverse organisms for coordinating the flow of membrane-enclosed carriers through the peroxisomal endomembrane system and critically evaluates the dynamics and molecular mechanisms of this multistep process.
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Abstract
Peroxisomes are ubiquitous subcellular organelles, which are highly dynamic and display large plasticity in response to cellular and environmental conditions. Novel proteins and pathways that mediate and control peroxisome formation, growth, and division continue to be discovered, and the cellular machineries that act together to regulate peroxisome number and size are under active investigation. Here, advances in the field of peroxisomal dynamics and proliferation in mammals and yeast are reviewed. The authors address the signals, conditions, and proteins that affect, regulate, and control the number and size of this essential organelle, especially the components involved in the division of peroxisomes. Special emphasis is on the function of dynamin-related proteins (DRPs), on Fis1, a putative adaptor for DRPs, on the role of the Pex11 family of peroxisomal membrane proteins, and the cytoskeleton.
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Affiliation(s)
- Michael Schrader
- Department of Cell Biology and Cell Pathology, University of Marburg, 35037 Marburg, Germany
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