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Shao X, Zhang Z, Yang F, Yu Y, Guo J, Li J, Xu T, Pan X. Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1390993. [PMID: 38872895 PMCID: PMC11170286 DOI: 10.3389/fpls.2024.1390993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024]
Abstract
Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.
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Affiliation(s)
- Xiuhong Shao
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Zhenchen Zhang
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Faheng Yang
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Yongchao Yu
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Junjie Guo
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Jiqin Li
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Tingyu Xu
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Xiaoying Pan
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
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2
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Fransen M, Lismont C. Peroxisomal hydrogen peroxide signaling: A new chapter in intracellular communication research. Curr Opin Chem Biol 2024; 78:102426. [PMID: 38237354 DOI: 10.1016/j.cbpa.2024.102426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Hydrogen peroxide (H2O2), a natural metabolite commonly found in aerobic organisms, plays a crucial role in numerous cellular signaling processes. One of the key organelles involved in the cell's metabolism of H2O2 is the peroxisome. In this review, we first provide a concise overview of the current understanding of H2O2 as a molecular messenger in thiol redox signaling, along with the role of peroxisomes as guardians and modulators of cellular H2O2 balance. Next, we direct our focus toward the recently identified primary protein targets of H2O2 originating from peroxisomes, emphasizing their importance in unraveling the complex interplay between peroxisomal H2O2 and cell signaling. We specifically focus on three areas: signaling through peroxiredoxin redox relay complexes, calcium signaling, and phospho-signaling. Finally, we highlight key research directions that warrant further investigation to enhance our comprehension of the molecular and biochemical mechanisms linking alterations in peroxisomal H2O2 metabolism with disease.
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Affiliation(s)
- Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Signaling, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Herestraat 49 Box 901, 3000 Leuven, Belgium.
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Signaling, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Herestraat 49 Box 901, 3000 Leuven, Belgium
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3
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Muñoz-Estrada J, Nguyen AV, Goetz SC. TTBK2 mutations associated with spinocerebellar ataxia type 11 disrupt peroxisome dynamics and ciliary localization of SHH signaling proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526333. [PMID: 36778451 PMCID: PMC9915595 DOI: 10.1101/2023.01.31.526333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Frameshift mutations in Tau Tubulin Kinase 2 (TTBK2) cause spinocerebellar ataxia type 11 (SCA11), which is characterized by the progressive loss of Purkinje cells and cerebellar atrophy. Previous work showed that these TTBK2 variants generate truncated proteins that interfere with primary ciliary trafficking and with Sonic Hedgehog (SHH) signaling in mice. Nevertheless, the molecular mechanisms underlying the dominant interference of mutations remain unknown. Herein, we discover that SCA11-associated variants contain a bona fide peroxisomal targeting signal type 1. We find that their expression in RPE1 cells reduces peroxisome numbers within the cell and at the base of the cilia, disrupts peroxisome fission pathways, and impairs trafficking of ciliary SMO upon SHH signaling activation. This work uncovers a neomorphic function of SCA11-causing mutations and identifies requirements for both peroxisomes and cholesterol in trafficking of cilia-localized SHH signaling proteins. In addition, we postulate that molecular mechanisms underlying cellular dysfunction in SCA11 converge on the SHH signaling pathway.
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Affiliation(s)
- Jesús Muñoz-Estrada
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710
| | - Abraham V Nguyen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710
- Molecular Cancer Biology Program, Duke University School of Medicine, Durham, NC 27710
| | - Sarah C Goetz
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710
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4
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Kataya A, Fedosejevs E, Ye Y. Editorial: Post-translational mechanisms involved in regulating peroxisome biogenesis, functions and organelle-crosstalk. Front Cell Dev Biol 2023; 11:1136992. [PMID: 36711036 PMCID: PMC9877304 DOI: 10.3389/fcell.2023.1136992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Affiliation(s)
- Amr Kataya
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,*Correspondence: Amr Kataya, ,
| | - Eric Fedosejevs
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
| | - Yajin Ye
- College of Forestry, Nanjing Forestry University, Nanjing, China
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Okumoto K, Fujiki Y. Analysis of Peroxisome Biogenesis by Phos-Tag SDS-PAGE. Methods Mol Biol 2023; 2643:207-215. [PMID: 36952188 DOI: 10.1007/978-1-0716-3048-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Phos-tag, a selective phosphate-binding molecule, and Phos-tag-based methodologies have been developed to investigate the phosphoproteome. In various analytical techniques using Phos-tag derivatives, phosphate-affinity electrophoresis using Phos-tag acrylamide, called Phos-tag SDS-PAGE, enables separation of phosphorylated proteins with a slower migration from non-phosphorylated proteins in polyacrylamide gels. The procedures for Phos-tag SDS-PAGE are largely common to those for conventional SDS-PAGE, thus being readily available for all laboratories. Phos-tag SDS-PAGE is widely applied to quantitative analysis of the overall phosphorylation state depending on the number and/or sites of the phosphate group. Phos-tag SDS-PAGE has also been introduced to the field of peroxisome study, including oxidative stress-induced and mitosis-specific phosphorylation of Pex14, a central component of the translocation machinery complex for peroxisomal matrix proteins. Here, we describe a practical protocol for Phos-tag SDS-PAGE and its application to peroxisome biogenesis research.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food-Kyushu University Collaboration Program, Kyushu University, Higashi-ku, Fukuoka, Japan.
- Institute of Rheological Function of Food, Fukuoka, Japan.
- Graduate School of Science, University of Hyogo, Hyogo, Japan.
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Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma. Eur J Med Chem 2022; 243:114778. [DOI: 10.1016/j.ejmech.2022.114778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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Kors S, Hacker C, Bolton C, Maier R, Reimann L, Kitchener EJA, Warscheid B, Costello JL, Schrader M. Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β. J Cell Biol 2022; 221:212956. [PMID: 35019937 DOI: 10.1083/jcb.202003143/212956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 11/12/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023] Open
Abstract
Peroxisomes and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism. They form membrane contacts through interaction of the peroxisomal membrane protein ACBD5 (acyl-coenzyme A-binding domain protein 5) and the ER-resident protein VAPB (vesicle-associated membrane protein-associated protein B). ACBD5 binds to the major sperm protein domain of VAPB via its FFAT-like (two phenylalanines [FF] in an acidic tract) motif. However, molecular mechanisms, which regulate formation of these membrane contact sites, are unknown. Here, we reveal that peroxisome-ER associations via the ACBD5-VAPB tether are regulated by phosphorylation. We show that ACBD5-VAPB binding is phosphatase-sensitive and identify phosphorylation sites in the flanking regions and core of the FFAT-like motif, which alter interaction with VAPB-and thus peroxisome-ER contact sites-differently. Moreover, we demonstrate that GSK3β (glycogen synthase kinase-3 β) regulates this interaction. Our findings reveal for the first time a molecular mechanism for the regulation of peroxisome-ER contacts in mammalian cells and expand the current model of FFAT motifs and VAP interaction.
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Affiliation(s)
- Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Christian Hacker
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Chloe Bolton
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Renate Maier
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lena Reimann
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Emily J A Kitchener
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
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9
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Kors S, Hacker C, Bolton C, Maier R, Reimann L, Kitchener EJA, Warscheid B, Costello JL, Schrader M. Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β. J Cell Biol 2022; 221:212956. [PMID: 35019937 PMCID: PMC8759595 DOI: 10.1083/jcb.202003143] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 11/12/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
Peroxisomes and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism. They form membrane contacts through interaction of the peroxisomal membrane protein ACBD5 (acyl-coenzyme A–binding domain protein 5) and the ER-resident protein VAPB (vesicle-associated membrane protein–associated protein B). ACBD5 binds to the major sperm protein domain of VAPB via its FFAT-like (two phenylalanines [FF] in an acidic tract) motif. However, molecular mechanisms, which regulate formation of these membrane contact sites, are unknown. Here, we reveal that peroxisome–ER associations via the ACBD5-VAPB tether are regulated by phosphorylation. We show that ACBD5-VAPB binding is phosphatase-sensitive and identify phosphorylation sites in the flanking regions and core of the FFAT-like motif, which alter interaction with VAPB—and thus peroxisome–ER contact sites—differently. Moreover, we demonstrate that GSK3β (glycogen synthase kinase-3 β) regulates this interaction. Our findings reveal for the first time a molecular mechanism for the regulation of peroxisome–ER contacts in mammalian cells and expand the current model of FFAT motifs and VAP interaction.
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Affiliation(s)
- Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Christian Hacker
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Chloe Bolton
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Renate Maier
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lena Reimann
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Emily J A Kitchener
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
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10
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Kataya A, Gautam N, Jamshed M, Muench DG, Samuel MA, Thelen JJ, Moorhead GB. Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals. Front Cell Dev Biol 2022; 10:745883. [PMID: 35242755 PMCID: PMC8886021 DOI: 10.3389/fcell.2022.745883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Peroxisomes are eukaryotic specific organelles that perform diverse metabolic functions including fatty acid β-oxidation, reactive species metabolism, photorespiration, and responses to stress. However, the potential regulation of these functions by post-translational modifications, including protein phosphorylation, has had limited study. Recently, we identified and catalogued a large number of peroxisomal phosphorylated proteins, implicating the presence of protein kinases in this organelle. Here, we employed available prediction models coupled with sequence conservation analysis to identify 31 protein kinases from the Arabidopsis kinome (all protein kinases) that contain a putative, non-canonical peroxisomal targeting signal type 1 (PTS1). From this, twelve C-terminal domain-PTS1s were demonstrated to be functional in vivo, targeting enhanced yellow fluorescent protein to peroxisomes, increasing the list of presumptive peroxisomal protein kinases to nineteen. Of the twelve protein kinases with functional PTS1s, we obtained full length clones for eight and demonstrated that seven target to peroxisomes in vivo. Screening homozygous mutants of the presumptive nineteen protein kinases revealed one candidate (GPK1) that harbors a sugar-dependence phenotype, suggesting it is involved in regulating peroxisomal fatty acid β-oxidation. These results present new opportunities for investigating the regulation of peroxisome functions.
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Affiliation(s)
- Amr Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nitija Gautam
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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11
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Deori NM, Infant T, Sundaravadivelu PK, Thummer RP, Nagotu S. Pex30 undergoes phosphorylation and regulates peroxisome number in Saccharomyces cerevisiae. Mol Genet Genomics 2022; 297:573-590. [PMID: 35218395 DOI: 10.1007/s00438-022-01872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Pex30 is a dysferlin domain-containing protein whose role in peroxisome biogenesis has been studied by several research groups. Notably, recent studies have linked this protein to peroxisomes, endoplasmic reticulum and lipid bodies in Saccharomyces cerevisiae. Phosphoproteome studies of S. cerevisiae have identified several phosphorylation sites in Pex30. In this study we expressed and purified Pex30 from its native host. Analysis of the purified protein by circular dichroism spectroscopy showed that it retained its secondary structure and revealed primarily a helical structure. Further phosphorylation of Pex30 at three residues, Threonine 60, Serine 61 and Serine 511 was identified by mass spectrometry in this study. To understand the importance of this post-translational modification in peroxisome biogenesis, the identified residues were mutated to both non-phosphorylatable (alanine) and phosphomimetic (aspartic acid) variants. Upon analysis of the mutant variants by fluorescence microscopy, no alteration in the localization of the protein to ER and peroxisomes was observed. Interestingly, reduced number of peroxisomes were observed in cells expressing phosphomimetic mutations when cultured in peroxisome-inducing conditions. Our data suggest that phosphorylation and dephosphorylation of Pex30 may promote distinct interactions essential in regulating peroxisome number in a cell.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
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Infant T, Deb R, Ghose S, Nagotu S. Post-translational modifications of proteins associated with yeast peroxisome membrane: An essential mode of regulatory mechanism. Genes Cells 2021; 26:843-860. [PMID: 34472666 PMCID: PMC9291962 DOI: 10.1111/gtc.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
Peroxisomes are single membrane‐bound organelles important for the optimum functioning of eukaryotic cells. Seminal discoveries in the field of peroxisomes are made using yeast as a model. Several proteins required for the biogenesis and function of peroxisomes are identified to date. As with proteins involved in other major cellular pathways, peroxisomal proteins are also subjected to regulatory post‐translational modifications. Identification, characterization and mapping of these modifications to specific amino acid residues on proteins are critical toward understanding their functional significance. Several studies have tried to identify post‐translational modifications of peroxisomal proteins and determine their impact on peroxisome structure and function. In this manuscript, we provide an overview of the various post‐translational modifications that govern the peroxisome dynamics in yeast.
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Affiliation(s)
- Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suchetana Ghose
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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13
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Yamashita K, Tamura S, Honsho M, Yada H, Yagita Y, Kosako H, Fujiki Y. Mitotic phosphorylation of Pex14p regulates peroxisomal import machinery. J Cell Biol 2021; 219:152047. [PMID: 32854114 PMCID: PMC7659713 DOI: 10.1083/jcb.202001003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/28/2020] [Accepted: 07/13/2020] [Indexed: 01/27/2023] Open
Abstract
Peroxisomal matrix proteins are imported into peroxisomes via membrane-bound docking/translocation machinery. One central component of this machinery is Pex14p, a peroxisomal membrane protein involved in the docking of Pex5p, the receptor for peroxisome targeting signal type 1 (PTS1). Studies in several yeast species have shown that Pex14p is phosphorylated in vivo, whereas no function has been assigned to Pex14p phosphorylation in yeast and mammalian cells. Here, we investigated peroxisomal protein import and its dynamics in mitotic mammalian cells. In mitotically arrested cells, Pex14p is phosphorylated at Ser-232, resulting in a lower import efficiency of catalase, but not the majority of proteins including canonical PTS1 proteins. Conformational change induced by the mitotic phosphorylation of Pex14p more likely increases homomeric interacting affinity and suppresses topological change of its N-terminal part, thereby giving rise to the retardation of Pex5p export in mitotic cells. Taken together, these data show that mitotic phosphorylation of Pex14p and consequent suppression of catalase import are a mechanism of protecting DNA upon nuclear envelope breakdown at mitosis.
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Affiliation(s)
- Koichiro Yamashita
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
| | - Hiroto Yada
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichi Yagita
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
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14
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Bürgi J, Ekal L, Wilmanns M. Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function. Traffic 2021; 22:140-152. [PMID: 33580581 DOI: 10.1111/tra.12785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 01/11/2023]
Abstract
Proteins composed of tetratricopeptide repeat (TPR) arrays belong to the α-solenoid tandem-repeat family that have unique properties in terms of their overall conformational flexibility and ability to bind to multiple protein ligands. The peroxisomal matrix protein import receptor Pex5 comprises two TPR triplets that recognize protein cargos with a specific C-terminal Peroxisomal Targeting Signal (PTS) 1 motif. Import of PTS1-containing protein cargos into peroxisomes through a transient pore is mainly driven by allosteric binding, coupling and release mechanisms, without a need for external energy. A very similar TPR architecture is found in the functionally unrelated TRIP8b, a regulator of the hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel. TRIP8b binds to the HCN ion channel via a C-terminal sequence motif that is nearly identical to the PTS1 motif of Pex5 receptor cargos. Pex5, Pex5-related Pex9, and TRIP8b also share a less conserved N-terminal domain. This domain provides a second protein cargo-binding site and plays a distinct role in allosteric coupling of initial cargo loading by PTS1 motif-mediated interactions and different downstream functional readouts. The data reviewed here highlight the overarching role of molecular allostery in driving the diverse functions of TPR array proteins, which could form a model for other α-solenoid tandem-repeat proteins involved in translocation processes across membranes.
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Affiliation(s)
- Jérôme Bürgi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
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15
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Wong S, Weisman LS. Roles and regulation of myosin V interaction with cargo. Adv Biol Regul 2021; 79:100787. [PMID: 33541831 PMCID: PMC7920922 DOI: 10.1016/j.jbior.2021.100787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 05/08/2023]
Abstract
A major question in cell biology is, how are organelles and large macromolecular complexes transported within a cell? Myosin V molecular motors play critical roles in the distribution of organelles, vesicles, and mRNA. Mis-localization of organelles that depend on myosin V motors underlie diseases in the skin, gut, and brain. Thus, the delivery of organelles to their proper destination is important for animal physiology and cellular function. Cargoes attach to myosin V motors via cargo specific adaptor proteins, which transiently bridge motors to their cargoes. Regulation of these adaptor proteins play key roles in the regulation of cargo transport. Emerging studies reveal that cargo adaptors play additional essential roles in the activation of myosin V, and the regulation of actin filaments. Here, we review how motor-adaptor interactions are controlled to regulate the proper loading and unloading of cargoes, as well as roles of adaptor proteins in the regulation of myosin V activity and the dynamics of actin filaments.
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Affiliation(s)
- Sara Wong
- Cell and Molecular Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Lois S Weisman
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States.
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16
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Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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17
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Schummer A, Maier R, Gabay-Maskit S, Hansen T, Mühlhäuser WWD, Suppanz I, Fadel A, Schuldiner M, Girzalsky W, Oeljeklaus S, Zalckvar E, Erdmann R, Warscheid B. Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae. Front Cell Dev Biol 2020; 8:549451. [PMID: 33042991 PMCID: PMC7522779 DOI: 10.3389/fcell.2020.549451] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
The peroxisomal biogenesis factor Pex14p is an essential component of the peroxisomal matrix protein import machinery. Together with Pex13p and Pex17p, it is part of the membrane-associated peroxisomal docking complex in yeast, facilitating the binding of cargo-loaded receptor proteins for translocation of cargo proteins into the peroxisome. Furthermore, Pex14p is part of peroxisomal import pores. The central role of Pex14p in peroxisomal matrix protein import processes renders it an obvious target for regulatory mechanisms such as protein phosphorylation. To explore this possibility, we examined the state of Pex14p phosphorylation in Saccharomyces cerevisiae. Phos-tag-SDS-PAGE of Pex14p affinity-purified from solubilized membranes revealed Pex14p as multi-phosphorylated protein. Using mass spectrometry, we identified 16 phosphorylation sites, with phosphorylation hot spots located in the N- and C-terminal regions of Pex14p. Analysis of phosphomimicking and non-phosphorylatable variants of Pex14p revealed a decreased import of GFP carrying a peroxisomal targeting signal type 1, indicating a functional relevance of Pex14p phosphorylation in peroxisomal matrix protein import. We show that this effect can be ascribed to the phosphomimicking mutation at serine 266 of Pex14p (Pex14p-S266D). We further screened the subcellular distribution of 23 native GFP-tagged peroxisomal matrix proteins by high-content fluorescence microscopy. Only Cit2p, the peroxisomal isoform of citrate synthase, was affected in the Pex14p-S266D mutant, showing increased cytosolic localization. Cit2p is part of the glyoxylate cycle, which is required for the production of essential carbohydrates when yeast is grown on non-fermentable carbon sources. Pex14p-S266 phosphosite mutants showed reversed growth phenotypes in oleic acid and ethanol with acetyl-CoA formed in peroxisomes and the cytosol, respectively. Overexpression of Cit2p rescued the growth phenotype of yeast cells expressing Pex14p-S266D in oleic acid. Our data indicate that phosphorylation of Pex14p at S266 provides a mechanism for controlling the peroxisomal import of Cit2p, which helps S. cerevisiae cells to adjust their carbohydrate metabolism according to the nutritional conditions.
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Affiliation(s)
- Andreas Schummer
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Renate Maier
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tobias Hansen
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Wignand W D Mühlhäuser
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Ida Suppanz
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Wolfgang Girzalsky
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Silke Oeljeklaus
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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18
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Okumoto K, El Shermely M, Natsui M, Kosako H, Natsuyama R, Marutani T, Fujiki Y. The peroxisome counteracts oxidative stresses by suppressing catalase import via Pex14 phosphorylation. eLife 2020; 9:55896. [PMID: 32831175 PMCID: PMC7498260 DOI: 10.7554/elife.55896] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Most of peroxisomal matrix proteins including a hydrogen peroxide (H2O2)-decomposing enzyme, catalase, are imported in a peroxisome-targeting signal type-1 (PTS1)-dependent manner. However, little is known about regulation of the membrane-bound protein import machinery. Here, we report that Pex14, a central component of the protein translocation complex in peroxisomal membrane, is phosphorylated in response to oxidative stresses such as H2O2 in mammalian cells. The H2O2-induced phosphorylation of Pex14 at Ser232 suppresses peroxisomal import of catalase in vivo and selectively impairs in vitro the interaction of catalase with the Pex14-Pex5 complex. A phosphomimetic mutant Pex14-S232D elevates the level of cytosolic catalase, but not canonical PTS1-proteins, conferring higher cell resistance to H2O2. We thus suggest that the H2O2-induced phosphorylation of Pex14 spatiotemporally regulates peroxisomal import of catalase, functioning in counteracting action against oxidative stress by the increase of cytosolic catalase.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Mahmoud El Shermely
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Masanao Natsui
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Ryuichi Natsuyama
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Toshihiro Marutani
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Hisayama-machi, Fukuoka, Japan
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19
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Peroxisomal Cofactor Transport. Biomolecules 2020; 10:biom10081174. [PMID: 32806597 PMCID: PMC7463629 DOI: 10.3390/biom10081174] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Peroxisomes are eukaryotic organelles that are essential for growth and development. They are highly metabolically active and house many biochemical reactions, including lipid metabolism and synthesis of signaling molecules. Most of these metabolic pathways are shared with other compartments, such as Endoplasmic reticulum (ER), mitochondria, and plastids. Peroxisomes, in common with all other cellular organelles are dependent on a wide range of cofactors, such as adenosine 5′-triphosphate (ATP), Coenzyme A (CoA), and nicotinamide adenine dinucleotide (NAD). The availability of the peroxisomal cofactor pool controls peroxisome function. The levels of these cofactors available for peroxisomal metabolism is determined by the balance between synthesis, import, export, binding, and degradation. Since the final steps of cofactor synthesis are thought to be located in the cytosol, cofactors must be imported into peroxisomes. This review gives an overview about our current knowledge of the permeability of the peroxisomal membrane with the focus on ATP, CoA, and NAD. Several members of the mitochondrial carrier family are located in peroxisomes, catalyzing the transfer of these organic cofactors across the peroxisomal membrane. Most of the functions of these peroxisomal cofactor transporters are known from studies in yeast, humans, and plants. Parallels and differences between the transporters in the different organisms are discussed here.
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20
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Sandalio LM, Gotor C, Romero LC, Romero-Puertas MC. Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications. Int J Mol Sci 2019; 20:E4881. [PMID: 31581473 PMCID: PMC6801620 DOI: 10.3390/ijms20194881] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Peroxisomes, which are ubiquitous organelles in all eukaryotes, are highly dynamic organelles that are essential for development and stress responses. Plant peroxisomes are involved in major metabolic pathways, such as fatty acid β-oxidation, photorespiration, ureide and polyamine metabolism, in the biosynthesis of jasmonic, indolacetic, and salicylic acid hormones, as well as in signaling molecules such as reactive oxygen and nitrogen species (ROS/RNS). Peroxisomes are involved in the perception of environmental changes, which is a complex process involving the regulation of gene expression and protein functionality by protein post-translational modifications (PTMs). Although there has been a growing interest in individual PTMs in peroxisomes over the last ten years, their role and cross-talk in the whole peroxisomal proteome remain unclear. This review provides up-to-date information on the function and crosstalk of the main peroxisomal PTMs. Analysis of whole peroxisomal proteomes shows that a very large number of peroxisomal proteins are targeted by multiple PTMs, which affect redox balance, photorespiration, the glyoxylate cycle, and lipid metabolism. This multilevel PTM regulation could boost the plasticity of peroxisomes and their capacity to regulate metabolism in response to environmental changes.
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Affiliation(s)
- Luisa M Sandalio
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
| | - Cecilia Gotor
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Luis C Romero
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Maria C Romero-Puertas
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
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21
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Kataya ARA, Muench DG, Moorhead GB. A Framework to Investigate Peroxisomal Protein Phosphorylation in Arabidopsis. TRENDS IN PLANT SCIENCE 2019; 24:366-381. [PMID: 30683463 DOI: 10.1016/j.tplants.2018.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Peroxisomes perform essential roles in a range of cellular processes, highlighted by lipid metabolism, reactive species detoxification, and response to a variety of stimuli. The ability of peroxisomes to grow, divide, respond to changing cellular needs, interact with other organelles, and adjust their proteome as required, suggest that, like other organelles, their specialized roles are highly regulated. Similar to most other cellular processes, there is an emerging role for protein phosphorylation to regulate these events. In this review, we establish a knowledge framework of key players that control protein phosphorylation events in the plant peroxisome (i.e., the protein kinases and phosphatases), and highlight a vastly expanded set of (phospho)substrates.
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Affiliation(s)
- Amr R A Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, 4036, Norway; Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada; www.katayaproject.com.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
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22
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Abstract
Microbial synthesis represents an alternative approach for the sustainable production of chemicals, fuels, and medicines. However, construction of biosynthetic pathways always suffers from side reactions, toxicity of intermediates, or low efficiency of substrate channeling. Subcellular compartmentalization may contribute to a more efficient production of target products by reducing side reactions and toxic effects within a compact insular space. The peroxisome, a type of organelle that is involved in catabolism of fatty acids and reactive oxygen species, has attracted a great deal of attention in the construction of eukaryotic cell factories with little impact on essential cellular function. In this chapter, we will systematically review recent advances in peroxisomal compartmentalization for microbial production of valuable biomolecules. Additionally, detailed experimental designs and protocols are also described. We hope a comprehensive understanding of peroxisomes will promote their application in metabolic engineering and synthetic biology.
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Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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23
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Kalel VC, Erdmann R. Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries. Subcell Biochem 2018; 89:299-321. [PMID: 30378029 DOI: 10.1007/978-981-13-2233-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxisomes are dynamic organelles of eukaryotic cells performing a wide range of functions including fatty acid oxidation, peroxide detoxification and ether-lipid synthesis in mammals. Peroxisomes lack their own DNA and therefore have to import proteins post-translationally. Peroxisomes can import folded, co-factor bound and even oligomeric proteins. The involvement of cycling receptors is a special feature of peroxisomal protein import. Complex machineries of peroxin (PEX) proteins mediate peroxisomal matrix and membrane protein import. Identification of PEX genes was dominated by forward genetic techniques in the early 90s. However, recent developments in proteomic techniques has revolutionized the detailed characterization of peroxisomal protein import. Here, we summarize the current knowledge on peroxisomal protein import with emphasis on the contribution of proteomic approaches to our understanding of the composition and function of the peroxisomal protein import machineries.
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Affiliation(s)
- Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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24
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Weir HJ, Yao P, Huynh FK, Escoubas CC, Goncalves RL, Burkewitz K, Laboy R, Hirschey MD, Mair WB. Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling. Cell Metab 2017; 26:884-896.e5. [PMID: 29107506 PMCID: PMC5718936 DOI: 10.1016/j.cmet.2017.09.024] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/18/2017] [Accepted: 09/27/2017] [Indexed: 01/01/2023]
Abstract
Mitochondrial network remodeling between fused and fragmented states facilitates mitophagy, interaction with other organelles, and metabolic flexibility. Aging is associated with a loss of mitochondrial network homeostasis, but cellular processes causally linking these changes to organismal senescence remain unclear. Here, we show that AMP-activated protein kinase (AMPK) and dietary restriction (DR) promote longevity in C. elegans via maintaining mitochondrial network homeostasis and functional coordination with peroxisomes to increase fatty acid oxidation (FAO). Inhibiting fusion or fission specifically blocks AMPK- and DR-mediated longevity. Strikingly, however, preserving mitochondrial network homeostasis during aging by co-inhibition of fusion and fission is sufficient itself to increase lifespan, while dynamic network remodeling is required for intermittent fasting-mediated longevity. Finally, we show that increasing lifespan via maintaining mitochondrial network homeostasis requires FAO and peroxisomal function. Together, these data demonstrate that mechanisms that promote mitochondrial homeostasis and plasticity can be targeted to promote healthy aging.
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Affiliation(s)
- Heather J Weir
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Pallas Yao
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Caroline C Escoubas
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Renata L Goncalves
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kristopher Burkewitz
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Raymond Laboy
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - William B Mair
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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25
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Schummer A, Fischer S, Oeljeklaus S, Warscheid B. Study of Peroxisomal Protein Phosphorylation by Functional Proteomics. Methods Mol Biol 2017; 1595:267-289. [PMID: 28409471 DOI: 10.1007/978-1-4939-6937-1_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reversible protein phosphorylation is a frequently occurring posttranslational modification mediated by protein kinases and phosphatases that plays an essential role in the regulation of a large number of cellular processes. Evidence is accumulating that protein phosphorylation is also an important mechanism governing processes associated with peroxisome biology. For an improved and detailed understanding of these processes and their regulation it is therefore crucial to study phosphorylation of peroxisome-associated proteins and to determine the phosphorylated amino acid(s). To place peroxisome-related processes into a larger, cellular context, it is further required to identify the kinases and phosphatases catalyzing phosphorylation and dephosphorylation events in peroxisomal proteins. We here provide a strategy for the targeted analysis of peroxisomal phosphoproteins of Saccharomyces cerevisiae combining affinity purification of epitope-tagged peroxisomal proteins with Phos-tag SDS-PAGE and high-resolution mass spectrometry (MS) for the identification and precise localization of in vivo phosphosites. Furthermore, we describe a protocol for an MS-based in vitro kinase assay using recombinant peroxisomal proteins and a selected kinase facilitating the site-resolved analysis of kinase-substrate relationships.
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Affiliation(s)
- Andreas Schummer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Sven Fischer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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26
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Erdmann R. Assembly, maintenance and dynamics of peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:787-9. [PMID: 26851075 DOI: 10.1016/j.bbamcr.2016.01.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Peroxisomes are ubiquitous organelles of eukaryotic cells, and it is becoming increasingly clear that the biogenesis of these multi-purpose organelles is more complex than initially anticipated. Along this line, peroxisomes exhibit features, which clearly distinguish them from other cellular organelles, like their ability to import folded proteins or their capability to form de novo. However, further insight into the cellular life of peroxisomes also revealed features that they share with other organelles, such as organelle fission or regulated degradation by autophagy, that are similar for peroxisomes, mitochondria and chloroplasts. This special issue highlights recent progress in the understanding of the biogenesis of peroxisomes with emphasis on the assembly, maintenance and dynamics of the organelles. In particular, it focuses on the following areas: (i) topogenesis of peroxisomal matrix proteins as well as the structure and function of peroxisomal protein import machineries. (ii) Peroxisomal targeting of membrane proteins and de novo formation of peroxisomes. (iii) Maintenance of peroxisomes in health and disease. (iv) Proliferation and regulated degradation of peroxisomes. (v) Motility and inheritance of peroxisomes. (vi) Role of peroxisomes in the cellular context.
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Affiliation(s)
- Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University Bochum, D-44780 Bochum, Germany..
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