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Cells
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Peroxisome Biogenesis and Protein Targeting Mechanisms
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Peroxisome Biogenesis and Protein Targeting Mechanisms

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Intracellular and Plasma Membranes".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 14002

Special Issue Editor

Dr. Harald W. Platta

E-Mail Website
Guest Editor
Biochemie & Pathobiochemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
Interests: biogenesis of peroxisomes; biochemistry of peroxisomes; peroxisomal disorders; intracellular protein transport; protein–protein interactions; ubiquitination; phosphorylation of proteins and lipids; intracellular signaling; autophagy pathways
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Peroxisomes are dynamic organelles that play a central role in lipid metabolism and cellular redox homeostasis. These so-called `multi-purpose’ organelles can undergo a context-dependent metamorphosis in number, size, shape, and function. Specialized forms, which are grouped as a microbody family, have been described as glyoxysomes of plants and certain fungi, glycosomes of parasitic protists like trypanosomes and Woronin bodies in filamentous fungi.

The biogenesis of peroxisomes can be categorized into five sub-networks that facilitate the key aspects of the development of functional peroxisomes: formation of the peroxisomal membrane, the targeting of peroxisomal matrix enzymes, peroxisomal fission, the inheritance of peroxisomes as well as the generation of contact sites to other organelles.

The important physiologic role of peroxisomes in health and disease is highlighted by the occurrence of peroxisomal disorders in humans. The regulation of peroxisomal biogenesis is also linked to age-associated diseases and the molecular process of aging as well as their function as a critical subcellular signaling hub in immune response and inflammation. Moreover, the control of peroxisomal function as a direct regulatory link to peroxisomal degradation via pexophagy is part of current research.

Therefore, this Special Issue aims to provide a platform for researchers around the world to communicate their latest findings and views on the targeting of peroxisomal proteins and low molecular weight factors in the multifaceted context of peroxisomal biogenesis.

Dr. Harald W. Platta
Guest Editor

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Keywords

  • Peroxisome
  • microbody family
  • protein targeting
  • protein import
  • lipid metabolism
  • ubiquitination
  • phosphorylation
  • organelle contact sites
  • organelle dysfunction
  • peroxisomal disorders
  • organelle degradation

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Published Papers (4 papers)

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Research

20 pages, 3274 KiB  
Article
Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulating Lysine Biosynthesis
by Yotam David, Inês Gomes Castro, Eden Yifrach, Chen Bibi, Enas Katawi, Dekel Yahav Har-Shai, Sagie Brodsky, Naama Barkai, Tommer Ravid, Miriam Eisenstein, Shmuel Pietrokovski, Maya Schuldiner and Einat Zalckvar
Cells 2022, 11(9), 1426; https://doi.org/10.3390/cells11091426 - 22 Apr 2022
Cited by 5 | Viewed by 3218
Abstract
Peroxisomes host essential metabolic enzymes and are crucial for human health and survival. Although peroxisomes were first described over 60 years ago, their entire proteome has not yet been identified. As a basis for understanding the variety of peroxisomal functions, we used a [...] Read more.
Peroxisomes host essential metabolic enzymes and are crucial for human health and survival. Although peroxisomes were first described over 60 years ago, their entire proteome has not yet been identified. As a basis for understanding the variety of peroxisomal functions, we used a high-throughput screen to discover peroxisomal proteins in yeast. To visualize low abundance proteins, we utilized a collection of strains containing a peroxisomal marker in which each protein is expressed from the constitutive and strong TEF2 promoter. Using this approach, we uncovered 18 proteins that were not observed in peroxisomes before and could show their metabolic and targeting factor dependence for peroxisomal localization. We focus on one newly identified and uncharacterized matrix protein, Ynl097c-b, and show that it localizes to peroxisomes upon lysine deprivation and that its localization to peroxisomes depends on the lysine biosynthesis enzyme, Lys1. We demonstrate that Ynl097c-b affects the abundance of Lys1 and the lysine biosynthesis pathway. We have therefore renamed this protein Pls1 for Peroxisomal Lys1 Stabilizing 1. Our work uncovers an additional layer of regulation on the central lysine biosynthesis pathway. More generally it highlights how the discovery of peroxisomal proteins can expand our understanding of cellular metabolism. Full article
(This article belongs to the Special Issue Peroxisome Biogenesis and Protein Targeting Mechanisms)
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22 pages, 7188 KiB  
Article
Cell Type-Selective Loss of Peroxisomal β-Oxidation Impairs Bipolar Cell but Not Photoreceptor Survival in the Retina
by Daniëlle Swinkels, Yannick Das, Sai Kocherlakota, Stefan Vinckier, Eric Wever, Antoine H.C. van Kampen, Frédéric M. Vaz and Myriam Baes
Cells 2022, 11(1), 161; https://doi.org/10.3390/cells11010161 - 4 Jan 2022
Cited by 13 | Viewed by 3975
Abstract
Retinal degeneration is a common feature in peroxisomal disorders leading to blindness. Peroxisomes are present in the different cell types of the retina; however, their precise contribution to retinal integrity is still unclear. We previously showed that mice lacking the central peroxisomal β-oxidation [...] Read more.
Retinal degeneration is a common feature in peroxisomal disorders leading to blindness. Peroxisomes are present in the different cell types of the retina; however, their precise contribution to retinal integrity is still unclear. We previously showed that mice lacking the central peroxisomal β-oxidation enzyme, multifunctional protein 2 (MFP2), develop an early onset retinal decay including photoreceptor cell death. To decipher the function of peroxisomal β-oxidation in photoreceptors, we generated cell type selective Mfp2 knockout mice, using the Crx promotor targeting photoreceptors and bipolar cells. Surprisingly, Crx-Mfp2−/− mice maintained photoreceptor length and number until the age of 1 year. A negative electroretinogram was indicative of preserved photoreceptor phototransduction, but impaired downstream bipolar cell signaling from the age of 6 months. The photoreceptor ribbon synapse was affected, containing free-floating ribbons and vesicles with altered size and density. The bipolar cell interneurons sprouted into the ONL and died. Whereas docosahexaenoic acid levels were normal in the neural retina, levels of lipids containing very long chain polyunsaturated fatty acids were highly increased. Crx-Pex5−/− mice, in which all peroxisomal functions are inactivated in photoreceptors and bipolar cells, developed the same phenotype as Crx-Mfp2−/− mice. In conclusion, the early photoreceptor death in global Mfp2−/− mice is not driven cell autonomously. However, peroxisomal β-oxidation is essential for the integrity of photoreceptor ribbon synapses and of bipolar cells. Full article
(This article belongs to the Special Issue Peroxisome Biogenesis and Protein Targeting Mechanisms)
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26 pages, 6589 KiB  
Article
Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11
by Katarzyna M. Zientara-Rytter, Shanmuga S. Mahalingam, Jean-Claude Farré, Krypton Carolino and Suresh Subramani
Cells 2022, 11(1), 157; https://doi.org/10.3390/cells11010157 - 4 Jan 2022
Cited by 5 | Viewed by 3151
Abstract
Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the Pichia pastoris Pex11 is recognized and chaperoned by Pex19, targeted to peroxisome membranes and inserted [...] Read more.
Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the Pichia pastoris Pex11 is recognized and chaperoned by Pex19, targeted to peroxisome membranes and inserted therein. We demonstrate that Pex11 contains one Pex19-binding site (Pex19-BS) that is required for Pex11 insertion into peroxisomal membranes by Pex19, but is non-essential for peroxisomal trafficking. We provide extensive mutational analyses regarding the recognition of Pex19-BS in Pex11 by Pex19. Pex11 also has a second, Pex19-independent membrane peroxisome-targeting signal (mPTS) that is preserved among Pex11-family proteins and anchors the human HsPex11γ to the outer leaflet of the peroxisomal membrane. Thus, unlike most PMPs, Pex11 can use two mechanisms of transport to peroxisomes, where only one of them depends on its direct interaction with Pex19, but the other does not. However, Pex19 is necessary for membrane insertion of Pex11. We show that Pex11 can self-interact, using both homo- and/or heterotypic interactions involving its N-terminal helical domains. We demonstrate that Pex19 acts as a chaperone by interacting with the Pex19-BS in Pex11, thereby protecting Pex11 from spontaneous oligomerization that would otherwise cause its aggregation and subsequent degradation. Full article
(This article belongs to the Special Issue Peroxisome Biogenesis and Protein Targeting Mechanisms)
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22 pages, 16466 KiB  
Article
Hypothyroidism Intensifies Both Canonic and the De Novo Pathway of Peroxisomal Biogenesis in Rat Brown Adipocytes in a Time-Dependent Manner
by Marija Aleksic, Igor Golic, Andjelika Kalezic, Aleksandra Jankovic, Bato Korac and Aleksandra Korac
Cells 2021, 10(9), 2248; https://doi.org/10.3390/cells10092248 - 30 Aug 2021
Cited by 2 | Viewed by 2630
Abstract
Despite peroxisomes being important partners of mitochondria by carrying out fatty acid oxidation in brown adipocytes, no clear evidence concerning peroxisome origin and way(s) of biogenesis exists. Herein we used methimazole-induced hypothyroidism for 7, 15, and 21 days to study peroxisomal remodeling and [...] Read more.
Despite peroxisomes being important partners of mitochondria by carrying out fatty acid oxidation in brown adipocytes, no clear evidence concerning peroxisome origin and way(s) of biogenesis exists. Herein we used methimazole-induced hypothyroidism for 7, 15, and 21 days to study peroxisomal remodeling and origin in rat brown adipocytes. We found that peroxisomes originated via both canonic, and de novo pathways. Each pathway operates in euthyroid control and over the course of hypothyroidism, in a time-dependent manner. Hypothyroidism increased the peroxisomal number by 1.8-, 3.6- and 5.8-fold on days 7, 15, and 21. Peroxisomal presence, their distribution, and their degree of maturation were heterogeneous in brown adipocytes in a Harlequin-like manner, reflecting differences in their origin. The canonic pathway, through numerous dumbbell-like and “pearls on strings” structures, supported by high levels of Pex11β and Drp1, prevailed on day 7. The de novo pathway of peroxisomal biogenesis started on day 15 and became dominant by day 21. The transition of peroxisomal biogenesis from canonic to the de novo pathway was driven by increased levels of Pex19, PMP70, Pex5S, and Pex26 and characterized by numerous tubular structures. Furthermore, specific peroxisomal origin from mitochondria, regardless of thyroid status, indicates their mutual regulation in rat brown adipocytes. Full article
(This article belongs to the Special Issue Peroxisome Biogenesis and Protein Targeting Mechanisms)
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