1
|
Yuan W, Veenhuis M, van der Klei IJ. The birth of yeast peroxisomes. Biochim Biophys Acta 2015; 1863:902-10. [PMID: 26367802 DOI: 10.1016/j.bbamcr.2015.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 11/25/2022]
Abstract
This contribution describes the phenotypic differences of yeast peroxisome-deficient mutants (pex mutants). In some cases different phenotypes were reported for yeast mutants deleted in the same PEX gene. These differences are most likely related to the marker proteins and methods used to detect peroxisomal remnants. This is especially evident for pex3 and pex19 mutants, where the localization of receptor docking proteins (Pex13, Pex14) resulted in the identification of peroxisomal membrane remnants, which do not contain other peroxisomal membrane proteins, such as the ring proteins Pex2, Pex10 and Pex12. These structures in pex3 and pex19 cells are the template for peroxisome formation upon introduction of the missing gene. Taken together, these data suggest that in all yeast pex mutants analyzed so far peroxisomes are not formed de novo but use membrane remnant structures as a template for peroxisome formation upon reintroduction of the missing gene. The relevance of this model for peroxisomal membrane protein and lipid sorting to peroxisomes is discussed.
Collapse
Affiliation(s)
- Wei Yuan
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands.
| |
Collapse
|
2
|
Saraya R, Krikken AM, Veenhuis M, van der Klei IJ. Retraction. Peroxisome reintroduction in Hansenula polymorpha requires Pex25 and Rho1. ACTA ACUST UNITED AC 2015; 210:519. [PMID: 26240187 PMCID: PMC4523605 DOI: 10.1083/jcb.20101208307062015r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Bohnert M, Zerbes RM, Davies KM, Mühleip AW, Rampelt H, Horvath SE, Boenke T, Kram A, Perschil I, Veenhuis M, Kühlbrandt W, van der Klei IJ, Pfanner N, van der Laan M. Central role of Mic10 in the mitochondrial contact site and cristae organizing system. Cell Metab 2015; 21:747-55. [PMID: 25955210 DOI: 10.1016/j.cmet.2015.04.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/09/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
The mitochondrial contact site and cristae organizing system (MICOS) is a conserved multi-subunit complex crucial for maintaining the characteristic architecture of mitochondria. Studies with deletion mutants identified Mic10 and Mic60 as core subunits of MICOS. Mic60 has been studied in detail; however, topogenesis and function of Mic10 are unknown. We report that targeting of Mic10 to the mitochondrial inner membrane requires a positively charged internal loop, but no cleavable presequence. Both transmembrane segments of Mic10 carry a characteristic four-glycine motif, which has been found in the ring-forming rotor subunit of F1Fo-ATP synthases. Overexpression of Mic10 profoundly alters the architecture of the inner membrane independently of other MICOS components. The four-glycine motifs are dispensable for interaction of Mic10 with other MICOS subunits but are crucial for the formation of large Mic10 oligomers. Our studies identify a unique role of Mic10 oligomers in promoting the formation of inner membrane crista junctions.
Collapse
Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Ralf M Zerbes
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Universität Freiburg, 79104 Freiburg, Germany
| | - Karen M Davies
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Alexander W Mühleip
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Heike Rampelt
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thorina Boenke
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Anita Kram
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Inge Perschil
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Marten Veenhuis
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ida J van der Klei
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
4
|
de Vries B, Todde V, Stevens P, Salomons F, van der Klei IJ, Veenhuis M. Pex14p is Not Required for Microautophagy and in Catalytic Amounts for Macropexophagy in Hansenula polymorpha. Autophagy 2014; 2:183-8. [PMID: 16874074 DOI: 10.4161/auto.2549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We showed before that the two oppositely directed processes of peroxisome biogenesis and selective peroxisome degradation (macropexophagy) converge at the peroxisomal membrane protein Pex14p. Here we show that this protein is not required for peroxisome degradation during nitrogen starvation-induced general autophagy, thereby limiting its function to the selective degradation process. Pex14p is present in two forms, namely an unmodified (Pex14p) and a phosphorylated form (Pex14p(Pi)) that are differently induced during peroxisome proliferation. The data suggest that Pex14p is required for peroxisome biogenesis during organelle proliferation and Pex14p(Pi) in macropexophagy. Finally, we show that macropexophagy is not coupled to normal peroxisome assembly, because Pex14p is required in only catalytic amounts to allow initiation of the selective peroxisome degradation process.
Collapse
Affiliation(s)
- Bart de Vries
- Laboratory of Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | | | | | |
Collapse
|
5
|
Meijer WH, van der Klei IJ, Veenhuis M, Kiel JAKW. ATGGenes Involved in Non-Selective Autophagy are Conserved from Yeast to Man, but the Selective Cvt and Pexophagy Pathways also Require Organism-Specific Genes. Autophagy 2014; 3:106-16. [PMID: 17204848 DOI: 10.4161/auto.3595] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
ATG genes encode proteins that are required for macroautophagy, the Cvt pathway and/or pexophagy. Using the published Atg protein sequences, we have screened protein and DNA databases to identify putative functional homologs (orthologs) in 21 fungal species (yeast and filamentous fungi) of which the genome sequences were available. For comparison with Atg proteins in higher eukaryotes, also an analysis of Arabidopsis thaliana and Homo sapiens databases was included. This analysis demonstrated that Atg proteins required for non-selective macroautophagy are conserved from yeast to man, stressing the importance of this process in cell survival and viability. The A. thaliana and human genomes encode multiple proteins highly similar to specific fungal Atg proteins (paralogs), possibly representing cell type-specific isoforms. The Atg proteins specifically involved in the Cvt pathway and/or pexophagy showed poor conservation, and were generally not present in A. thaliana and man. Furthermore, Atg19, the receptor of Cvt cargo, was only detected in Saccharomyces cerevisiae. Nevertheless, Atg11, a protein that links receptor-bound cargo (peroxisomes, the Cvt complex) to the autophagic machinery was identified in all yeast species and filamentous fungi under study. This suggests that in fungi an organism-specific form of selective autophagy may occur, for which specialized Atg proteins have evolved.
Collapse
Affiliation(s)
- Wiebe H Meijer
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | |
Collapse
|
6
|
Aksam EB, Koek A, Kiel JAKW, Jourdan S, Veenhuis M, van der Klei IJ. A Peroxisomal Lon Protease and Peroxisome Degradation by Autophagy Play Key Roles in Vitality ofHansenula polymorphaCells. Autophagy 2014; 3:96-105. [PMID: 17172804 DOI: 10.4161/auto.3534] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In eukaryote cells various mechanisms exist that are responsible for the removal of non-functional proteins. Here we show that in the yeast Hansenula polymorpha (H. polymorpha) a peroxisomal Lon protease, Pln, plays a role in degradation of unfolded and non-assembled peroxisomal matrix proteins. In addition, we demonstrate that whole peroxisomes are constitutively degraded by autophagy during normal vegetative growth of WT cells. Deletion of both H. polymorpha PLN and ATG1, required for autophagy, resulted in a significant increase in peroxisome numbers, paralleled by a decrease in cell viability relative to WT cells. Also, in these cells and in cells of PLN and ATG1 single deletion strains, the intracellular levels of reactive oxygen species had increased relative to WT controls. The enhanced generation of reactive oxygen species may be related to an uneven distribution of peroxisomal catalase activities in the mutant cells, as demonstrated by cytochemistry. We speculate that in the absence of HpPln or autophagy unfolded and non-assembled peroxisomal matrix proteins accumulate, which can form aggregates and lead to an imbalance in hydrogen peroxide production and degradation in some of the organelles.
Collapse
Affiliation(s)
- Eda Bener Aksam
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands
| | | | | | | | | | | |
Collapse
|
7
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Kèvin Knoops
- Molecular Cell Biology, University of Groningen, 9747 AG Groningen, Netherlands
| | | | | | | | | | | | | |
Collapse
|
8
|
Veenhuis M, Klei IJVD. De novo peroxisome biogenesis revisited. Microb Cell 2014; 1:128-130. [PMID: 28357233 PMCID: PMC5349201 DOI: 10.15698/mic2014.04.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an alternative peroxisome formation pathway in yeast
pex3 and pex19 cells, which relies on the
existence of small peroxisomal remnants that are present in these cells. This
groundbreaking result challenges current models prescribing that peroxisomes
derive de novo from the ER. Our data also has major
implications for the sorting pathway of specific peroxisomal membrane proteins
(PMPs). We propose a novel sorting pathway for the PMPs Pex13 and Pex14 that is
independent of the known Pex3/Pex19 machinery.
Collapse
Affiliation(s)
- Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Ida J V D Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| |
Collapse
|
9
|
Hettema EH, Erdmann R, van der Klei I, Veenhuis M. Evolving models for peroxisome biogenesis. Curr Opin Cell Biol 2014; 29:25-30. [PMID: 24681485 PMCID: PMC4148619 DOI: 10.1016/j.ceb.2014.02.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 12/11/2022]
Abstract
Significant progress has been made towards our understanding of the mechanism of peroxisome formation, in particular concerning sorting of peroxisomal membrane proteins, matrix protein import and organelle multiplication. Here we evaluate the progress made in recent years. We focus mainly on progress made in yeasts. We indicate the gaps in our knowledge and discuss conflicting models.
Collapse
Affiliation(s)
- Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Ralf Erdmann
- System Biochie, Ruhr Universitat Bochum, Universitatstr. 150, D-44780, Bochum, Germany
| | - Ida van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology institute, University of Groningen, 11 103, 9700CC, Groningen, The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology institute, University of Groningen, 11 103, 9700CC, Groningen, The Netherlands
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Marten Veenhuis
- Molecular Cell Biology, University of Groningen Groningen, Netherlands
| | | |
Collapse
|
11
|
Lehnerer M, Keizer-Gunnik L, Veenhuis M, Gietl C. Functional Analysis of the N-Terminal Prepeptides of Watermelon Mitochondrial and Glyoxysomal Malate Dehydrogenases*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1994.tb00800.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Abstract
Hansenula polymorpha is a methylotrophic yeast species that has favorable properties for heterologous protein production and metabolic engineering. It provides an attractive expression platform with the capability to secrete high levels of commercially important proteins. Over the past few years many efforts have led to advances in the development of this microbial host including the generation of expression vectors containing strong constitutive or inducible promoters and a large array of dominant and auxotrophic markers. Moreover, highly efficient transformation procedures used to generate genetically stable strains are now available. Here, we describe these tools as well as the methods for genetic engineering of H. polymorpha.
Collapse
Affiliation(s)
- Ruchi Saraya
- Molecular Cell Biology, Kluyver Centre for Genomics of Industrial Fermentation, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | | | | |
Collapse
|
13
|
van Zutphen T, Todde V, de Boer R, Kreim M, Hofbauer HF, Wolinski H, Veenhuis M, van der Klei IJ, Kohlwein SD. Lipid droplet autophagy in the yeast Saccharomyces cerevisiae. Mol Biol Cell 2013; 25:290-301. [PMID: 24258026 PMCID: PMC3890349 DOI: 10.1091/mbc.e13-08-0448] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytosolic lipid droplets (LDs) are ubiquitous organelles in prokaryotes and eukaryotes that play a key role in cellular and organismal lipid homeostasis. Triacylglycerols (TAGs) and steryl esters, which are stored in LDs, are typically mobilized in growing cells or upon hormonal stimulation by LD-associated lipases and steryl ester hydrolases. Here we show that in the yeast Saccharomyces cerevisiae, LDs can also be turned over in vacuoles/lysosomes by a process that morphologically resembles microautophagy. A distinct set of proteins involved in LD autophagy is identified, which includes the core autophagic machinery but not Atg11 or Atg20. Thus LD autophagy is distinct from endoplasmic reticulum-autophagy, pexophagy, or mitophagy, despite the close association between these organelles. Atg15 is responsible for TAG breakdown in vacuoles and is required to support growth when de novo fatty acid synthesis is compromised. Furthermore, none of the core autophagy proteins, including Atg1 and Atg8, is required for LD formation in yeast.
Collapse
Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology, University of Groningen, 9747 AG Groningen, Netherlands Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Lefevre SD, Roermund CW, Wanders RJA, Veenhuis M, Klei IJ. The significance of peroxisome function in chronological aging of Saccharomyces cerevisiae. Aging Cell 2013; 12:784-93. [PMID: 23755917 PMCID: PMC3824234 DOI: 10.1111/acel.12113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 12/01/2022] Open
Abstract
We studied the chronological lifespan of glucose-grown Saccharomyces cerevisiae in relation to the function of intact peroxisomes. We analyzed four different peroxisome-deficient (pex) phenotypes. These included Δpex3 cells that lack peroxisomal membranes and in which all peroxisomal proteins are mislocalized together with Δpex6 in which all matrix proteins are mislocalized to the cytosol, whereas membrane proteins are still correctly sorted to peroxisomal ghosts. In addition, we analyzed two mutants in which the peroxisomal location of the β-oxidation machinery is in part disturbed. We analyzed Δpex7 cells that contain virtually normal peroxisomes, except that all matrix proteins that contain a peroxisomal targeting signal type 2 (PTS2, also including thiolase), are mislocalized to the cytosol. In Δpex5 cells, peroxisomes only contain matrix proteins with a PTS2 in conjunction with all proteins containing a peroxisomal targeting signal type 1 (PTS1, including all β-oxidation enzymes except thiolase) are mislocalized to the cytosol. We show that intact peroxisomes are an important factor in yeast chronological aging because all pex mutants showed a reduced chronological lifespan. The strongest reduction was observed in Δpex5 cells. Our data indicate that this is related to the complete inactivation of the peroxisomal β-oxidation pathway in these cells due to the mislocalization of thiolase. Our studies suggest that during chronological aging, peroxisomal β-oxidation contributes to energy generation by the oxidation of fatty acids that are released by degradation of storage materials and recycled cellular components during carbon starvation conditions.
Collapse
Affiliation(s)
- Sophie D. Lefevre
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
| | - Carlo W. Roermund
- Departments of Pediatrics and Clinical Chemistry Laboratory of Genetic Metabolic Diseases Academic Medical Centre University of Amsterdam 1105 AZ Amsterdam The Netherlands
| | - Ronald J. A. Wanders
- Departments of Pediatrics and Clinical Chemistry Laboratory of Genetic Metabolic Diseases Academic Medical Centre University of Amsterdam 1105 AZ Amsterdam The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
| | - Ida J. Klei
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
| |
Collapse
|
15
|
Abstract
We studied the role of peroxisomal catalase in chronological aging of the yeastHansenula polymorpha in relation to various growth substrates. Catalase-deficient (cat) cells showed a similar chronological life span (CLS) relative to the wild-type control upon growth on carbon and nitrogen sources that are not oxidized by peroxisomal enzymes. However, when media contained methylamine, which is oxidized by peroxisomal amine oxidase, the CLS of cat cells was significantly reduced. Conversely, the CLS of cat cells was enhanced relative to the wild-type control, when cells were grown on methanol, which is oxidized by peroxisomal alcohol oxidase. At these conditions strongly enhanced ROS levels were observed during the exponential growth phase of cat cells. This was paralleled by activation of the transcription factor Yap1, as well as an increase in the levels of the antioxidant enzymes cytochrome c peroxidase and superoxide dismutase. Upon deletion of the genes encoding Yap1 or cytochrome c peroxidase, the CLS extension of cat cells on methanol was abolished. These findings reveal for the first time an important role of enhanced cytochrome c peroxidase levels in yeast CLS extension.
Collapse
Affiliation(s)
- Adam Kawałek
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | | | | | | |
Collapse
|
16
|
Scheckhuber CQ, Veenhuis M, van der Klei IJ. Improving penicillin biosynthesis in Penicillium chrysogenum by glyoxalase overproduction. Metab Eng 2013; 18:36-43. [DOI: 10.1016/j.ymben.2013.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/25/2022]
|
17
|
Manivannan S, de Boer R, Veenhuis M, van der Klei IJ. Lumenal peroxisomal protein aggregates are removed by concerted fission and autophagy events. Autophagy 2013; 9:1044-56. [PMID: 23614977 DOI: 10.4161/auto.24543] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We demonstrated that in the yeast Hansenula polymorpha peroxisome fission and degradation are coupled processes that are important to remove intra-organellar protein aggregates. Protein aggregates were formed in peroxisomes upon synthesis of a mutant catalase variant. We showed that the introduction of these aggregates in the peroxisomal lumen had physiological disadvantages as it affected growth and caused enhanced levels of reactive oxygen species. Formation of the protein aggregates was followed by asymmetric peroxisome fission to separate the aggregate from the mother organelle. Subsequently, these small, protein aggregate-containing organelles were degraded by autophagy. In line with this observation we showed that the degradation of the protein aggregates was strongly reduced in dnm1 and pex11 cells in which peroxisome fission is reduced. Moreover, this process was dependent on Atg1 and Atg11.
Collapse
|
18
|
Abstract
Peroxisomes are ubiquitous and versatile cell organelles. They consist of a single membrane that encloses a proteinaceous matrix. Conserved functions are fatty acid β-oxidation and hydrogen peroxide metabolism. In filamentous fungi, many other metabolic functions have been identified. Also, they contain highly specialized peroxisome-derived structures termed Woronin bodies, which have a structural function in plugging septal pores in order to prevent cytoplasmic bleeding of damaged hyphae.In filamentous fungi peroxisomes play key roles in the production of a range of secondary metabolites such as antibiotics. Most likely the atlas of fungal peroxisomal metabolic pathways is still far from complete. Relative recently discovered functions include their role in biotin biosynthesis as well as in the production of several toxins, among which polyketides. Finally, in filamentous fungi peroxisomes are important for development and pathogenesis.In this contribution we present an overview of our current knowledge on fungal peroxisome formation as well as on their functional diversity.
Collapse
Affiliation(s)
- Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 11103, 9700CC, Groningen, The Netherlands,
| | | |
Collapse
|
19
|
Abstract
Background Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast Hansenula polymorpha grown at conditions that require primary peroxisome metabolism for growth. Methodology/Principal Findings The chronological lifespan of H. polymorpha is strongly enhanced when cells are grown on methanol or ethanol, metabolized by peroxisome enzymes, relative to growth on glucose that does not require peroxisomes. The short lifespan of H. polymorpha on glucose is mainly due to medium acidification, whereas most likely ROS do not play an important role. Growth of cells on methanol/methylamine instead of methanol/ammonium sulphate resulted in further lifespan enhancement. This was unrelated to medium acidification. We show that oxidation of methylamine by peroxisomal amine oxidase at carbon starvation conditions is responsible for lifespan extension. The methylamine oxidation product formaldehyde is further oxidized resulting in NADH generation, which contributes to increased ATP generation and reduction of ROS levels in the stationary phase. Conclusion/Significance We conclude that primary peroxisome metabolism enhanced chronological lifespan of H. polymorpha. Moreover, the possibility to generate NADH at carbon starvation conditions by an organic nitrogen source supports further extension of the lifespan of the cell. Consequently, the interpretation of CLS analyses in yeast should include possible effects on the energy status of the cell.
Collapse
Affiliation(s)
- Sanjeev Kumar
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
| | | | | | | |
Collapse
|
20
|
Zerbes RM, van der Klei IJ, Veenhuis M, Pfanner N, van der Laan M, Bohnert M. Mitofilin complexes: conserved organizers of mitochondrial membrane architecture. Biol Chem 2012; 393:1247-61. [DOI: 10.1515/hsz-2012-0239] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/09/2012] [Indexed: 11/15/2022]
Abstract
Abstract
Mitofilin proteins are crucial organizers of mitochondrial architecture. They are located in the inner mitochondrial membrane and interact with several protein complexes of the outer membrane, thereby generating contact sites between the two membrane systems of mitochondria. Within the inner membrane, mitofilins are part of hetero-oligomeric protein complexes that have been termed the mitochondrial inner membrane organizing system (MINOS). MINOS integrity is required for the maintenance of the characteristic morphology of the inner mitochondrial membrane, with an inner boundary region closely apposed to the outer membrane and cristae membranes, which form large tubular invaginations that protrude into the mitochondrial matrix and harbor the enzyme complexes of the oxidative phosphorylation machinery. MINOS deficiency comes along with a loss of crista junction structures and the detachment of cristae from the inner boundary membrane. MINOS has been conserved in evolution from unicellular eukaryotes to humans, where alterations of MINOS subunits are associated with multiple pathological conditions.
Collapse
|
21
|
Zerbes RM, Bohnert M, Stroud DA, von der Malsburg K, Kram A, Oeljeklaus S, Warscheid B, Becker T, Wiedemann N, Veenhuis M, van der Klei IJ, Pfanner N, van der Laan M. Role of MINOS in Mitochondrial Membrane Architecture: Cristae Morphology and Outer Membrane Interactions Differentially Depend on Mitofilin Domains. J Mol Biol 2012; 422:183-91. [DOI: 10.1016/j.jmb.2012.05.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/01/2012] [Accepted: 05/01/2012] [Indexed: 12/26/2022]
|
22
|
Bohnert M, Wenz LS, Zerbes RM, Horvath SE, Stroud DA, von der Malsburg K, Müller JM, Oeljeklaus S, Perschil I, Warscheid B, Chacinska A, Veenhuis M, van der Klei IJ, Daum G, Wiedemann N, Becker T, Pfanner N, van der Laan M. Role of mitochondrial inner membrane organizing system in protein biogenesis of the mitochondrial outer membrane. Mol Biol Cell 2012; 23:3948-56. [PMID: 22918945 PMCID: PMC3469511 DOI: 10.1091/mbc.e12-04-0295] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. We report that MINOS independently interacts with both preprotein translocases of the outer mitochondrial membrane and plays a role in the biogenesis of β-barrel proteins of the outer membrane. Mitochondria contain two membranes, the outer membrane and the inner membrane with folded cristae. The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. MINOS interacts with both preprotein transport machineries of the outer membrane, the translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). It is unknown, however, whether MINOS plays a role in the biogenesis of outer membrane proteins. We have dissected the interaction of MINOS with TOM and SAM and report that MINOS binds to both translocases independently. MINOS binds to the SAM complex via the conserved polypeptide transport–associated domain of Sam50. Mitochondria lacking mitofilin, the large core subunit of MINOS, are impaired in the biogenesis of β-barrel proteins of the outer membrane, whereas mutant mitochondria lacking any of the other five MINOS subunits import β-barrel proteins in a manner similar to wild-type mitochondria. We show that mitofilin is required at an early stage of β-barrel biogenesis that includes the initial translocation through the TOM complex. We conclude that MINOS interacts with TOM and SAM independently and that the core subunit mitofilin is involved in biogenesis of outer membrane β-barrel proteins.
Collapse
Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Bartoszewska M, Williams C, Kikhney A, Opaliński Ł, van Roermund CWT, de Boer R, Veenhuis M, van der Klei IJ. Peroxisomal proteostasis involves a Lon family protein that functions as protease and chaperone. J Biol Chem 2012; 287:27380-95. [PMID: 22733816 DOI: 10.1074/jbc.m112.381566] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins are subject to continuous quality control for optimal proteostasis. The knowledge of peroxisome quality control systems is still in its infancy. Here we show that peroxisomes contain a member of the Lon family of proteases (Pln). We show that Pln is a heptameric protein and acts as an ATP-fueled protease and chaperone. Hence, Pln is the first chaperone identified in fungal peroxisomes. In cells of a PLN deletion strain peroxisomes contain protein aggregates, a major component of which is catalase-peroxidase. We show that this enzyme is sensitive to oxidative damage. The oxidatively damaged, but not the native protein, is a substrate of the Pln protease. Cells of the pln strain contain enhanced levels of catalase-peroxidase protein but reduced catalase-peroxidase enzyme activities. Together with the observation that Pln has chaperone activity in vitro, our data suggest that catalase-peroxidase aggregates accumulate in peroxisomes of pln cells due to the combined absence of Pln protease and chaperone activities.
Collapse
Affiliation(s)
- Magdalena Bartoszewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, P. O. Box 11103, 9700CC Groningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Manivannan S, Scheckhuber CQ, Veenhuis M, van der Klei IJ. The impact of peroxisomes on cellular aging and death. Front Oncol 2012; 2:50. [PMID: 22662318 PMCID: PMC3356858 DOI: 10.3389/fonc.2012.00050] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 05/01/2012] [Indexed: 01/27/2023] Open
Abstract
Peroxisomes are ubiquitous eukaryotic organelles, which perform a plethora of functions including hydrogen peroxide metabolism and β-oxidation of fatty acids. Reactive oxygen species produced by peroxisomes are a major contributing factor to cellular oxidative stress, which is supposed to significantly accelerate aging and cell death according to the free radical theory of aging. However, relative to mitochondria, the role of the other oxidative organelles, the peroxisomes, in these degenerative pathways has not been extensively investigated. In this contribution we discuss our current knowledge on the role of peroxisomes in aging and cell death, with focus on studies performed in yeast.
Collapse
Affiliation(s)
- Selvambigai Manivannan
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen Groningen, Netherlands
| | | | | | | |
Collapse
|
25
|
Opaliński Ł, Bartoszewska M, Fekken S, Liu H, de Boer R, van der Klei I, Veenhuis M, Kiel JAKW. De novo peroxisome biogenesis in Penicillium chrysogenum is not dependent on the Pex11 family members or Pex16. PLoS One 2012; 7:e35490. [PMID: 22536392 PMCID: PMC3334907 DOI: 10.1371/journal.pone.0035490] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 03/16/2012] [Indexed: 11/18/2022] Open
Abstract
We have analyzed the role of the three members of the Pex11 protein family in peroxisome formation in the filamentous fungus Penicillium chrysogenum. Two of these, Pex11 and Pex11C, are components of the peroxisomal membrane, while Pex11B is present at the endoplasmic reticulum. We show that Pex11 is a major factor involved in peroxisome proliferation. We also demonstrate that P. chrysogenum cells deleted for known peroxisome fission factors (all Pex11 family proteins and Vps1) still contain peroxisomes. Interestingly, we find that, unlike in mammals, Pex16 is not essential for peroxisome biogenesis in P. chrysogenum, as partially functional peroxisomes are present in a pex16 deletion strain. We also show that Pex16 is not involved in de novo biogenesis of peroxisomes, as peroxisomes were still present in quadruple Δpex11 Δpex11B Δpex11C Δpex16 mutant cells. By contrast, pex3 deletion in P. chrysogenum led to cells devoid of peroxisomes, suggesting that Pex3 may function independently of Pex16. Finally, we demonstrate that the presence of intact peroxisomes is important for the efficiency of ß-lactam antibiotics production by P. chrysogenum. Remarkably, distinct from earlier results with low penicillin producing laboratory strains, upregulation of peroxisome numbers in a high producing P. chrysogenum strain had no significant effect on penicillin production.
Collapse
Affiliation(s)
- Łukasz Opaliński
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Magdalena Bartoszewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Susan Fekken
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Haiyin Liu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Ida van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Jan A. K. W. Kiel
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
- * E-mail:
| |
Collapse
|
26
|
Saraya R, Krikken AM, Kiel JA, Baerends RJ, Veenhuis M, Klei IJ. Novel genetic tools for Hansenula polymorpha. FEMS Yeast Res 2011; 12:271-8. [DOI: 10.1111/j.1567-1364.2011.00772.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ruchi Saraya
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| | - Arjen M. Krikken
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| | - Jan A.K.W. Kiel
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| | - Richard J.S. Baerends
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| | - Ida J. Klei
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute; Kluyver Centre for Genomics of Industrial Fermentation; University of Groningen; Groningen; The Netherlands
| |
Collapse
|
27
|
Boender LGM, Maris AJA, Hulster EAF, Almering MJH, Klei IJ, Veenhuis M, Winde JH, Pronk JT, Daran-Lapujade P. Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures. FEMS Yeast Res 2011; 11:603-20. [PMID: 22093745 PMCID: PMC3498732 DOI: 10.1111/j.1567-1364.2011.00750.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/09/2011] [Accepted: 08/16/2011] [Indexed: 11/30/2022] Open
Abstract
Extremely low specific growth rates (below 0.01 h(-1) ) represent a largely unexplored area of microbial physiology. In this study, anaerobic, glucose-limited retentostats were used to analyse physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to cultivation at near-zero specific growth rates. While quiescence is typically investigated as a result of carbon starvation, cells in retentostat are fed by small, but continuous carbon and energy supply. Yeast cells cultivated near-zero specific growth rates, while metabolically active, exhibited characteristics previously associated with quiescence, including accumulation of storage polymers and an increased expression of genes involved in exit from the cell cycle into G(0) . Unexpectedly, analysis of transcriptome data from retentostat and chemostat cultures showed, as specific growth rate was decreased, that quiescence-related transcriptional responses were already set in at specific growth rates above 0.025 h(-1) . These observations stress the need for systematic dissection of physiological responses to slow growth, quiescence, ageing and starvation and indicate that controlled cultivation systems such as retentostats can contribute to this goal. Furthermore, cells in retentostat do not (or hardly) divide while remaining metabolically active, which emulates the physiological status of metazoan post-mitotic cells. We propose retentostat as a powerful cultivation tool to investigate chronological ageing-related processes.
Collapse
Affiliation(s)
- Léonie GM Boender
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Antonius JA Maris
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Erik AF Hulster
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Marinka JH Almering
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Ida J Klei
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Molecular Cell Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenHaren, The Netherlands
| | - Marten Veenhuis
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Molecular Cell Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenHaren, The Netherlands
| | - Johannes H Winde
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Jack T Pronk
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Pascale Daran-Lapujade
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| |
Collapse
|
28
|
von der Malsburg K, Müller J, Bohnert M, Oeljeklaus S, Kwiatkowska P, Becker T, Loniewska-Lwowska A, Wiese S, Rao S, Milenkovic D, Hutu D, Zerbes R, Schulze-Specking A, Meyer H, Martinou JC, Rospert S, Rehling P, Meisinger C, Veenhuis M, Warscheid B, van der Klei I, Pfanner N, Chacinska A, van der Laan M. Dual Role of Mitofilin in Mitochondrial Membrane Organization and Protein Biogenesis. Dev Cell 2011; 21:694-707. [DOI: 10.1016/j.devcel.2011.08.026] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Revised: 08/25/2011] [Accepted: 08/29/2011] [Indexed: 11/28/2022]
|
29
|
van Zutphen T, Veenhuis M, van der Klei IJ. Damaged peroxisomes are subject to rapid autophagic degradation in the yeast Hansenula polymorpha. Autophagy 2011; 7:863-72. [PMID: 21490428 DOI: 10.4161/auto.7.8.15697] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Evidence is accumulating that damaged components of eukaryotic cells are removed by autophagic degradation (e.g., mitophagy). Here we show that peroxisomes that are damaged by the abrupt removal of the membrane protein Pex3 are massively and rapidly degraded even when the cells are placed at peroxisome-inducing conditions and hence need the organelles for growth. Pex3 degradation was induced by a temperature shift using Hansenula polymorpha pex3Δ cells producing a Pex3 fusion protein containing an N-terminal temperature sensitive degron sequence. The massive peroxisome degradation process, associated with Pex3 degradation, showed properties of both micro- and macropexophagy and was dependent on Atg1 and Ypt7. This mode of peroxisome degradation is of physiological significance as it was also observed at conditions that excessive ROS is formed from peroxisome metabolism, i.e., when methanol-grown wild-type cells are exposed to methanol excess conditions.
Collapse
Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology; Groningen Biomolecular Sciences and Biotechnology Institute, Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, Groningen, The Netherlands
| | | | | |
Collapse
|
30
|
Bartoszewska M, Opaliński L, Veenhuis M, van der Klei IJ. The significance of peroxisomes in secondary metabolite biosynthesis in filamentous fungi. Biotechnol Lett 2011; 33:1921-31. [PMID: 21660569 PMCID: PMC3173629 DOI: 10.1007/s10529-011-0664-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/24/2011] [Indexed: 01/08/2023]
Abstract
Peroxisomes are ubiquitous organelles characterized by a protein-rich matrix surrounded by a single membrane. In filamentous fungi, peroxisomes are crucial for the primary metabolism of several unusual carbon sources used for growth (e.g. fatty acids), but increasing evidence is presented that emphasize the crucial role of these organelles in the formation of a variety of secondary metabolites. In filamentous fungi, peroxisomes also play a role in development and differentiation whereas specialized peroxisomes, the Woronin bodies, play a structural role in plugging septal pores. The biogenesis of peroxisomes in filamentous fungi involves the function of conserved PEX genes, as well as genes that are unique for these organisms. Peroxisomes are also subject to autophagic degradation, a process that involves ATG genes. The interplay between organelle biogenesis and degradation may serve a quality control function, thereby allowing a continuous rejuvenation of the organelle population in the cells.
Collapse
Affiliation(s)
- Magdalena Bartoszewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 11103, 9700 CC Groningen, The Netherlands
| | | | | | | |
Collapse
|
31
|
Opaliński Ł, Veenhuis M, van der Klei IJ. Peroxisomes: Membrane events accompanying peroxisome proliferation. Int J Biochem Cell Biol 2011; 43:847-51. [DOI: 10.1016/j.biocel.2011.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/03/2011] [Accepted: 03/07/2011] [Indexed: 10/18/2022]
|
32
|
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.
Collapse
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
| | | | | | | |
Collapse
|
33
|
Cepińska MN, Veenhuis M, van der Klei IJ, Nagotu S. Peroxisome Fission is Associated with Reorganization of Specific Membrane Proteins. Traffic 2011; 12:925-37. [DOI: 10.1111/j.1600-0854.2011.01198.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
34
|
Opaliński Ł, Kiel JAKW, Williams C, Veenhuis M, van der Klei IJ. Membrane curvature during peroxisome fission requires Pex11. EMBO J 2010; 30:5-16. [PMID: 21113128 PMCID: PMC3020119 DOI: 10.1038/emboj.2010.299] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 11/03/2010] [Indexed: 01/25/2023] Open
Abstract
Pex11p is required for peroxisome proliferation. This study demonstrates that the N-terminus of Pex11p forms an amphipathic helix that generates membrane curvature required for peroxisome fission. Pex11 is a key player in peroxisome proliferation, but the molecular mechanisms of its function are still unknown. Here, we show that Pex11 contains a conserved sequence at the N-terminus that can adopt the structure of an amphipathic helix. Using Penicillium chrysogenum Pex11, we show that this amphipathic helix, termed Pex11-Amph, associates with liposomes in vitro. This interaction is especially evident when negatively charged liposomes are used with a phospholipid content resembling that of peroxisomal membranes. Binding of Pex11-Amph to negatively charged membrane vesicles resulted in strong tubulation. This tubulation of vesicles was also observed when the entire soluble N-terminal domain of Pex11 was used. Using mutant peptides, we demonstrate that maintaining the amphipathic properties of Pex11-Amph in conjunction with retaining its α-helical structure are crucial for its function. We show that the membrane remodelling capacity of the amphipathic helix in Pex11 is conserved from yeast to man. Finally, we demonstrate that mutations abolishing the membrane remodelling activity of the Pex11-Amph domain also hamper the function of full-length Pex11 in peroxisome fission in vivo.
Collapse
Affiliation(s)
- Łukasz Opaliński
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, Haren, The Netherlands
| | | | | | | | | |
Collapse
|
35
|
|
36
|
Cavanaugh CM, Abbott MS, Veenhuis M. Immunochemical localization of ribulose-1,5-bisphosphate carboxylase in the symbiont-containing gills of Solemya velum (Bivalvia: Mollusca). Proc Natl Acad Sci U S A 2010; 85:7786-9. [PMID: 16593987 PMCID: PMC282278 DOI: 10.1073/pnas.85.20.7786] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The distribution of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase (RbuP(2)Case; EC 4.1.1.39) was examined by using two immunological methods in tissues of Solemya velum, an Atlantic coast bivalve containing putative chemoautotrophic symbionts. Antibodies elicited by the purified large subunit of RbuP(2)Case from tobacco (Nicotiana tabacum) cross-reacted on immunoblots with a protein of similar molecular mass occurring in extracts of the symbiont-containing gill tissue of S. velum. No cross-reactivity was detected in symbiont-free tissue extracts. The antiserum also cross-reacted in immunoblots with proteins of Thiobacillus neapolitanus, a free-living sulfuroxidizing chemoautotroph whose RbuP(2)Case has been well characterized. In protein A-gold immunoelectron microscopy studies, this antiserum consistently labeled the symbionts but not surrounding host gill tissue, indicating that the symbionts are responsible for the RbuP(2)Case activity.
Collapse
Affiliation(s)
- C M Cavanaugh
- Harvard University, The Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138
| | | | | |
Collapse
|
37
|
Opaliński L, Kiel JAKW, Homan TG, Veenhuis M, van der Klei IJ. Penicillium chrysogenum Pex14/17p--a novel component of the peroxisomal membrane that is important for penicillin production. FEBS J 2010; 277:3203-18. [PMID: 20597979 DOI: 10.1111/j.1742-4658.2010.07726.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By genome analysis, we previously identified Pex14/17p as a putative novel peroxin of Penicillium chrysogenum. Here, we show that Pex14/17p is a component of the peroxisomal membrane that is essential for efficient peroxisomal targeting signal 1 and peroxisomal targeting signal 2 matrix protein import, implying that the protein is indeed a genuine peroxin. Additionally, a PEX14/17 deletion strain is affected in conidiospore formation. Pex14/17p has properties of both Pex14p and Pex17p, in that the N-terminus of this protein is similar to the highly conserved Pex5p-binding region present in the N-termini of Pex14p proteins, whereas its C-terminus shows weak similarity to yeast Pex17p proteins. We have identified a novel motif in both Pex17p and Pex14/17p that is absent in Pex14p. We show that an N-terminally truncated, but not a C-terminally truncated, Pex14/17p is able to complement both the matrix protein import and sporulation defects of a Delta pex14/17 strain, implying that it is the Pex17p-related portion of the protein that is crucial for its function as a peroxin. Possibly, this compensates for the fact that P. chrysogenum lacks an authenthic Pex17p. We also show that, in P. chrysogenum, Pex14/17p plays a role in making the penicillin biosynthesis process more efficient.
Collapse
Affiliation(s)
- Lukasz Opaliński
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | | | |
Collapse
|
38
|
Abstract
A study was performed to gain insight into the mechanism of acid-tolerant, chemolithotrophic nitrification. Microorganisms that nitrified at pH 4 were enriched from two Dutch acid soils. Nitrate production in the enrichment cultures was indicated to be of a chemolithoautotrophic nature as it was (i) completely inhibited by acetylene at a concentration as low as 1 mumol/liter and (ii) strongly retarded under conditions of carbon dioxide limitation. Electron microscopy of the enrichment cultures showed the presence of bacteria that were morphologically similar to strains of known chemolithotrophic nitrifying genera. Many of the enriched bacteria, in particular those that were identified as ammonium oxidizers, were aggregated. Filtration experiments indicated that aggregated cells were able to nitrify at low pH, whereas single cells were not. It is hypothesized that cells inside the aggregates are protected against the toxicity of nitrous acid. Nitrification by aggregated chemolithoautotrophic bacteria may be the dominating process of nitrate formation in many acid soils as it does not appear to depend on the existence of microsites of high pH (acid-sensitive autotrophic nitrification) or on the availability of organic carbon (heterotrophic nitrification).
Collapse
Affiliation(s)
- W De Boer
- Institute for Ecological Research, P.O. Box 40, 6666 ZG Heteren, and Laboratory for Electron Microscopy, Biological Centre, University of Groningen, 9751 NN Haren, The Netherlands, and Abteilung für Mikrobiologie, Institut für Allgemeine Botanik der Universität Hamburg, D-2000 Hamburg 52, Germany
| | | | | | | | | |
Collapse
|
39
|
Klompmaker SH, Kilic A, Baerends RJ, Veenhuis M, van der Klei IJ. Activation of a peroxisomal Pichia pastoris D-amino acid oxidase, which uses d-alanine as a preferred substrate, depends on pyruvate carboxylase. FEMS Yeast Res 2010; 10:708-16. [PMID: 20550580 DOI: 10.1111/j.1567-1364.2010.00647.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
d-Amino acid oxidase (DAO) is an important flavo-enzyme that catalyzes the oxidative deamination of d-amino acids into the corresponding alpha-keto acid, ammonia and H(2)O(2). We identified two amino acid oxidases in the methylotrophic yeast Pichia pastoris: Dao1p, which preferentially uses d-alanine as a substrate, and Dao2p, which uses d-aspartate as a preferred substrate. Dao1p has a molecular mass of 38.2 kDa and a pH optimum of 9.6. This enzyme was localized to peroxisomes, albeit a typical peroxisomal targeting signal is lacking. Interestingly, P. pastoris mutant strains, defective in the enzyme pyruvate carboxylase, showed a pronounced growth defect on d-alanine, concomitant with a significant reduction in Dao1p activity relative to the wild-type control. This indicates that pyruvate carboxylase functions in import and/or activation of P. pastoris Dao1p.
Collapse
|
40
|
Huberts DHEW, Venselaar H, Vriend G, Veenhuis M, van der Klei IJ. The moonlighting function of pyruvate carboxylase resides in the non-catalytic end of the TIM barrel. Biochim Biophys Acta 2010; 1803:1038-42. [PMID: 20359504 DOI: 10.1016/j.bbamcr.2010.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 03/21/2010] [Accepted: 03/23/2010] [Indexed: 02/03/2023]
Abstract
Pyruvate carboxylase is a highly conserved enzyme that functions in replenishing the tricarboxylic acid cycle with oxaloacetate. In the yeast Hansenulapolymorpha, the pyruvate carboxylase protein is also required for import and assembly of the peroxisomal enzyme alcohol oxidase. This additional role, which is unrelated to the enzyme activity, represents an example of a special form of multifunctionality called moonlighting. We have performed a detailed site-directed mutagenesis approach to elucidate which region(s) of H. polymorpha pyruvate carboxylase are involved in its second function. This resulted in the identification of three amino acids that are essential for the moonlighting function. Mutating these residues in a single mutant protein fully inactivated the moonlighting function, but not the enzyme activity of pyruvate carboxylase because the strain was prototrophic. A 3D homology model revealed that all three residues are positioned at the side of a TIM barrel where the N-terminal ends of the beta-strands are located. This is a novel observation as the TIM barrel proteins invariably are enzymes and have their catalytic side at the C-terminal end of the beta-sheets. Our finding implies that a TIM barrel fold can also fulfill a non-enzymatic function and that this function can reside at the N-terminal end of the barrel.
Collapse
Affiliation(s)
- Daphne H E W Huberts
- Department of Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, NL-9750 AA Haren, The Netherlands
| | | | | | | | | |
Collapse
|
41
|
Saraya R, Cepińska MN, Kiel JAKW, Veenhuis M, van der Klei IJ. A conserved function for Inp2 in peroxisome inheritance. Biochim Biophys Acta 2010; 1803:617-22. [PMID: 20153784 DOI: 10.1016/j.bbamcr.2010.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/05/2010] [Accepted: 02/05/2010] [Indexed: 10/19/2022]
Abstract
In budding yeast Saccharomyces cerevisiae, the peroxisomal protein Inp2 is required for inheritance of peroxisomes to the bud, by connecting the organelles to the motor protein Myo2 and the actin cytoskeleton. Recent data suggested that the function of Inp2 may not be conserved in other yeast species. Using in silico analyses we have identified a weakly conserved Inp2-related protein in 18 species of budding yeast and analyzed the role of the identified protein in the methylotrophic yeast Hansenula polymorpha in peroxisome inheritance. Our data show that H. polymorpha Inp2 locates to peroxisomes, interacts with Myo2, and is essential for peroxisome inheritance.
Collapse
Affiliation(s)
- Ruchi Saraya
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AA Haren, The Netherlands
| | | | | | | | | |
Collapse
|
42
|
Abstract
Peroxisomes are unique organelles which display properties of autonomous organelles, as they can multiply by fission of pre-existing ones. Peroxisomes, however, can also develop from the endoplasmic reticulum (ER). This process has convincingly been shown in peroxisome-deficient yeast cells, upon reintroduction of the corresponding gene. Whether peroxisomes also are formed from the ER in wild-type cells that contain peroxisomes is still under debate. Also, the existence of vesicular transport pathways between peroxisomes and the ER is still unresolved. Several new proteins and pathways that play a role in peroxisome proliferation have been identified in the last few years. A surprising finding was that proteins well known for their function in mitochondrial fission (Fis1, Dnm1) are responsible for peroxisome fission as well. In this contribution we discuss recent advancements in research on peroxisome proliferation.
Collapse
Affiliation(s)
- Shirisha Nagotu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, PO Box 14, 9750 AA Haren, The Netherlands
| | | | | |
Collapse
|
43
|
|
44
|
van Zutphen T, Baerends RJS, Susanna KA, de Jong A, Kuipers OP, Veenhuis M, van der Klei IJ. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis. BMC Genomics 2010; 11:1. [PMID: 20044946 PMCID: PMC2827406 DOI: 10.1186/1471-2164-11-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 01/04/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant proteins, but are also used in fundamental research as model organisms to study peroxisome biology. During exponential growth on glucose, cells of H. polymorpha typically contain a single, small peroxisome that is redundant for growth while on methanol multiple, enlarged peroxisomes are present. These organelles are crucial to support growth on methanol, as they contain key enzymes of methanol metabolism.In this study, changes in the transcriptional profiles during adaptation of H. polymorpha cells from glucose- to methanol-containing media were investigated using DNA-microarray analyses. RESULTS Two hours after the shift of cells from glucose to methanol nearly 20% (1184 genes) of the approximately 6000 annotated H. polymorpha genes were significantly upregulated with at least a two-fold differential expression. Highest upregulation (> 300-fold) was observed for the genes encoding the transcription factor Mpp1 and formate dehydrogenase, an enzyme of the methanol dissimilation pathway. Upregulated genes also included genes encoding other enzymes of methanol metabolism as well as of peroxisomal beta-oxidation.A moderate increase in transcriptional levels (up to 4-fold) was observed for several PEX genes, which are involved in peroxisome biogenesis. Only PEX11 and PEX32 were higher upregulated. In addition, an increase was observed in expression of the several ATG genes, which encode proteins involved in autophagy and autophagy processes. The strongest upregulation was observed for ATG8 and ATG11.Approximately 20% (1246 genes) of the genes were downregulated. These included glycolytic genes as well as genes involved in transcription and translation. CONCLUSION Transcriptional profiling of H. polymorpha cells shifted from glucose to methanol showed the expected downregulation of glycolytic genes together with upregulation of the methanol utilisation pathway. This serves as a confirmation and validation of the array data obtained. Consistent with this, also various PEX genes were upregulated. The strong upregulation of ATG genes is possibly due to induction of autophagy processes related to remodeling of the cell architecture required to support growth on methanol. These processes may also be responsible for the enhanced peroxisomal beta-oxidation, as autophagy leads to recycling of membrane lipids. The prominent downregulation of transcription and translation may be explained by the reduced growth rate on methanol (td glucose 1 h vs td methanol 4.5 h).
Collapse
Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology, University of Groningen, Haren, the Netherlands
| | | | | | | | | | | | | |
Collapse
|
45
|
Gidijala L, Kiel JAKW, Douma RD, Seifar RM, van Gulik WM, Bovenberg RAL, Veenhuis M, van der Klei IJ. An engineered yeast efficiently secreting penicillin. PLoS One 2009; 4:e8317. [PMID: 20016817 PMCID: PMC2789386 DOI: 10.1371/journal.pone.0008317] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 11/24/2009] [Indexed: 11/18/2022] Open
Abstract
This study aimed at developing an alternative host for the production of penicillin (PEN). As yet, the industrial production of this beta-lactam antibiotic is confined to the filamentous fungus Penicillium chrysogenum. As such, the yeast Hansenula polymorpha, a recognized producer of pharmaceuticals, represents an attractive alternative. Introduction of the P. chrysogenum gene encoding the non-ribosomal peptide synthetase (NRPS) delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) in H. polymorpha, resulted in the production of active ACVS enzyme, when co-expressed with the Bacillus subtilis sfp gene encoding a phosphopantetheinyl transferase that activated ACVS. This represents the first example of the functional expression of a non-ribosomal peptide synthetase in yeast. Co-expression with the P. chrysogenum genes encoding the cytosolic enzyme isopenicillin N synthase as well as the two peroxisomal enzymes isopenicillin N acyl transferase (IAT) and phenylacetyl CoA ligase (PCL) resulted in production of biologically active PEN, which was efficiently secreted. The amount of secreted PEN was similar to that produced by the original P. chrysogenum NRRL1951 strain (approx. 1 mg/L). PEN production was decreased over two-fold in a yeast strain lacking peroxisomes, indicating that the peroxisomal localization of IAT and PCL is important for efficient PEN production. The breakthroughs of this work enable exploration of new yeast-based cell factories for the production of (novel) beta-lactam antibiotics as well as other natural and semi-synthetic peptides (e.g. immunosuppressive and cytostatic agents), whose production involves NRPS's.
Collapse
Affiliation(s)
- Loknath Gidijala
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Jan A. K. W. Kiel
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Rutger D. Douma
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Reza M. Seifar
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Walter M. van Gulik
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Centre, Delft, The Netherlands
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Ida J. van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- * E-mail:
| |
Collapse
|
46
|
Sagt CMJ, ten Haaft PJ, Minneboo IM, Hartog MP, Damveld RA, van der Laan JM, Akeroyd M, Wenzel TJ, Luesken FA, Veenhuis M, van der Klei I, de Winde JH. Peroxicretion: a novel secretion pathway in the eukaryotic cell. BMC Biotechnol 2009; 9:48. [PMID: 19457257 PMCID: PMC2693430 DOI: 10.1186/1472-6750-9-48] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 05/20/2009] [Indexed: 11/21/2022] Open
Abstract
Background Enzyme production in microbial cells has been limited to secreted enzymes or intracellular enzymes followed by expensive down stream processing. Extracellular enzymes consists mainly of hydrolases while intracellular enzymes exhibit a much broader diversity. If these intracellular enzymes could be secreted by the cell the potential of industrial applications of enzymes would be enlarged. Therefore a novel secretion pathway for intracellular proteins was developed, using peroxisomes as secretion vesicles. Results Peroxisomes were decorated with a Golgi derived v-SNARE using a peroxisomal membrane protein as an anchor. This allowed the peroxisomes to fuse with the plasma membrane. Intracellular proteins were transported into the peroxisomes by adding a peroxisomal import signal (SKL tag). The proteins which were imported in the peroxisomes, were released into the extra-cellular space through this artificial secretion pathway which was designated peroxicretion. This concept was supported by electron microscopy studies. Conclusion Our results demonstrate that it is possible to reroute the intracellular trafficking of vesicles by changing the localisation of SNARE molecules, this approach can be used in in vivo biological studies to clarify the different control mechanisms regulating intracellular membrane trafficking. In addition we demonstrate peroxicretion of a diverse set of intracellular proteins. Therefore, we anticipate that the concept of peroxicretion may revolutionize the production of intracellular proteins from fungi and other microbial cells, as well as from mammalian cells.
Collapse
Affiliation(s)
- Cees M J Sagt
- DSM Biotechnology Center, Beijerinck Laboratory, PO Box 1, 2600MA Delft, the Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
|
48
|
Kiel JAKW, van den Berg MA, Fusetti F, Poolman B, Bovenberg RAL, Veenhuis M, van der Klei IJ. Matching the proteome to the genome: the microbody of penicillin-producing Penicillium chrysogenum cells. Funct Integr Genomics 2009; 9:167-84. [PMID: 19156454 DOI: 10.1007/s10142-009-0110-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 01/05/2009] [Accepted: 01/05/2009] [Indexed: 10/21/2022]
Abstract
In the filamentous fungus Penicillium chrysogenum, microbodies are essential for penicillin biosynthesis. To better understand the role of these organelles in antibiotics production, we determined the matrix enzyme contents of P. chrysogenum microbodies. Using a novel in silico approach, we first obtained a catalogue of 200 P. chrysogenum proteins with putative microbody targeting signals (PTSs). This included two orthologs of proteins involved in cephalosporin biosynthesis, which we demonstrate to be bona fide microbody matrix constituents. Subsequently, we performed a proteomics based inventory of P. chrysogenum microbody matrix proteins using nano-LC-MS/MS analysis. We identified 89 microbody proteins, 79 with a PTS, including the two known microbody-borne penicillin biosynthesis enzymes, isopenicillin N:acyl CoA acyltransferase and phenylacetyl-CoA ligase. Comparative analysis revealed that 69 out of 79 PTS proteins identified experimentally were in the reference list. A prominent microbody protein was identified as a novel fumarate reductase-cytochrome b5 fusion protein, which contains an internal PTS2 between the two functional domains. We show that this protein indeed localizes to P. chrysogenum microbodies.
Collapse
Affiliation(s)
- Jan A K W Kiel
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, AA Haren, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
49
|
Bener Aksam E, Jungwirth H, Kohlwein SD, Ring J, Madeo F, Veenhuis M, van der Klei IJ. Absence of the peroxiredoxin Pmp20 causes peroxisomal protein leakage and necrotic cell death. Free Radic Biol Med 2008; 45:1115-24. [PMID: 18694816 DOI: 10.1016/j.freeradbiomed.2008.07.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 07/01/2008] [Accepted: 07/08/2008] [Indexed: 11/30/2022]
Abstract
We analyzed the role of the peroxisomal peroxiredoxin Pmp20 of the yeast Hansenula polymorpha. Cells of a PMP20 disruption strain (pmp20) grew normally on substrates that are not metabolized by peroxisomal enzymes, but showed a severe growth defect on methanol, the metabolism of which involves a hydrogen peroxide producing peroxisomal oxidase. This growth defect was paralleled by leakage of peroxisomal matrix proteins into the cytosol. Methanol-induced pmp20 cells accumulated enhanced levels of reactive oxygen species and lipid peroxidation products. Moreover, the fatty acid composition of methanol-induced pmp20 cells differed relative to WT controls, suggesting an effect on fatty acid homeostasis. Plating assays and FACS-based analysis of cell death markers revealed that pmp20 cells show loss of clonogenic efficiency and membrane integrity, when cultured on methanol. We conclude that the absence of the peroxisomal peroxiredoxin leads to loss of peroxisome membrane integrity and necrotic cell death.
Collapse
Affiliation(s)
- Eda Bener Aksam
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
50
|
van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJM, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WHM, Joardar V, Kiel JAKW, Kovalchuk A, Martín JF, Nierman WC, Nijland JG, Pronk JT, Roubos JA, van der Klei IJ, van Peij NNME, Veenhuis M, von Döhren H, Wagner C, Wortman J, Bovenberg RAL. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol 2008; 26:1161-8. [PMID: 18820685 DOI: 10.1038/nbt.1498] [Citation(s) in RCA: 344] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 08/27/2008] [Indexed: 11/09/2022]
Abstract
Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
Collapse
|