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Tang L, Chu T, Shang J, Yang R, Song C, Bao D, Tan Q, Jian H. Oxidative Stress and Autophagy Are Important Processes in Post Ripeness and Brown Film Formation in Mycelium of Lentinula edodes. Front Microbiol 2022; 13:811673. [PMID: 35283832 PMCID: PMC8908433 DOI: 10.3389/fmicb.2022.811673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Lentinula edodes (Berk.) Pegler, the shiitake mushroom, is one of the most important mushrooms in the global mushroom industry. Although mycelium post ripeness and brown film (BF) formation are crucial for fruiting body initiation, the underlying molecular mechanisms of BF formation are largely unknown. In this study, proteomic quantification (relative and absolute) and metabolomic profiling of L. edodes were performed using isobaric tags and gas chromatography-mass spectroscopy, respectively. A total of 2,474 proteins were identified, which included 239 differentially expressed proteins. Notably, several proteins associated with autophagy were upregulated, including RPD3, TOR1, VAC8, VPS1, and VPS27. Transmission electron microscopy also indicated that autophagy occurred in post ripeness and BF formation. In time-dependent analysis of the metabolome, metabolites associated with oxidative stress and autophagy changed significantly, including mannitol, trehalose, myo-inositol, glucose, leucine, valine, glutamine, and 4-aminobutyric acid. Thus, oxidative stress and autophagy were important processes in post ripeness and BF formation in L. edodes, and new insights were gained into molecular mechanisms at proteome and metabolome levels.
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Affiliation(s)
- Lihua Tang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Ting Chu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China.,School of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Junjun Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Ruiheng Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Chunyan Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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2
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Dmytruk O, Bulbotka N, Zazulya A, Semkiv M, Dmytruk K, Sibirny A. Fructose-1,6-bisphosphatase degradation in the methylotrophic yeast Komagataella phaffii occurs in autophagy pathway. Cell Biol Int 2020; 45:528-535. [PMID: 31903651 DOI: 10.1002/cbin.11304] [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: 10/02/2019] [Accepted: 01/04/2020] [Indexed: 11/11/2022]
Abstract
Many enzymes of methanol metabolism of methylotrophic yeasts are located in peroxisomes whereas some of them have the cytosolic localization. After shift of methanol-grown cells of methylotrophic yeasts to glucose medium, a decrease in the activity of cytosolic (formaldehyde dehydrogenase, formate dehydrogenase, and fructose-1,6-bisphosphatase [FBP]) along with peroxisomal enzymes of methanol metabolism is observed. Mechanisms of inactivation of cytosolic enzymes remain unknown. To study the mechanism of FBP inactivation, the changes in its specific activity of the wild type strain GS200, the strain with the deletion of the GSS1 hexose sensor gene and strain defected in autophagy pathway SMD1163 of Komagataella phaffii with or without the addition of the MG132 (proteasome degradation inhibitor) were investigated after shift of methanol-grown cells in glucose medium. Western blot analysis showed that inactivation of FBP in GS200 occurred due to protein degradation whereas inactivation in the strains SMD1163 and gss1Δ was negligible in such conditions. The effect of the proteasome inhibitor MG132 on FBP inactivation was insignificant. To confirm FBP degradation pathway, the recombinant strains with GFP-labeled Fbp1 of K. phaffii and red fluorescent protein-labeled peroxisomes were constructed on the background of GS200 and SMD1163. The fluorescent microscopy analysis of the constructed strains was performed using the vacuolar membrane dye FM4-64. Microscopic data confirmed that Fbp1 degrades by autophagy pathway in K. phaffii. K. phaffii transformants, which express heterologous β-galactosidase under FLD promoter, have been constructed.
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Affiliation(s)
- Olena Dmytruk
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Nina Bulbotka
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Anastasya Zazulya
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Marta Semkiv
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Kostyantyn Dmytruk
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Street 14/16, 79005, Lviv, Ukraine.,Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
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3
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Hou J, Rao M, Zheng W, Fan J, Law BYK. Advances on Cell Autophagy and Its Potential Regulatory Factors in Renal Ischemia-Reperfusion Injury. DNA Cell Biol 2019; 38:895-904. [PMID: 31347925 DOI: 10.1089/dna.2019.4767] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ischemia-reperfusion injury is a major reason for acute kidney injury and various kidney diseases. Autophagy plays an important role during renal ischemia-reperfusion injury (RIRI), but it remains controversial whether autophagy contributes to cell survival or ischemia-reperfusion-induced cell death. In the review, we summarized the function of autophagy in the progression of acute ischemic kidney injury, as well as its related molecular mechanisms. While analyzing the opposite roles of autophagy in RIRI, it was concluded that the protective or detrimental function of autophagy was depending on the timing and amount of the activation of cell autophagy. We also summarized the regulatory agents, including active compounds, proteins, or microRNAs (miRNAs), which regulated the cell autophagy during renal acute ischemic kidney injury process. This explained why the opposite conclusion occurred when cell autophagy was studied in the RIRI models from different researchers. Therefore, the article provided a hypothesis to control cell autophagy at the appropriate timing and intensity so as to alleviate renal injury and sustain cell survival of the renal cell.
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Affiliation(s)
- Jing Hou
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, People's Republic of China.,State Key Laboratory of Quality Research in Chinese Medicines (Macau University of Science and Technology), Taipa, People's Republic of China.,Department of Nephrology, the Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Mingyue Rao
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, People's Republic of China.,State Key Laboratory of Quality Research in Chinese Medicines (Macau University of Science and Technology), Taipa, People's Republic of China.,Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Wenlu Zheng
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, People's Republic of China.,State Key Laboratory of Quality Research in Chinese Medicines (Macau University of Science and Technology), Taipa, People's Republic of China.,Department of Nuclear Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Junming Fan
- Chengdu Medical College, Chengdu City, People's Republic of China.,Southwest Medical University, Luzhou, People's Republic of China
| | - Betty Yuen Kwan Law
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, People's Republic of China.,State Key Laboratory of Quality Research in Chinese Medicines (Macau University of Science and Technology), Taipa, People's Republic of China
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4
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Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD. Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw155. [PMID: 28025345 PMCID: PMC5199145 DOI: 10.1093/database/baw155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/10/2016] [Accepted: 11/01/2016] [Indexed: 01/30/2023]
Abstract
We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo.
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Affiliation(s)
| | - Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Switzerland 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Huaiyu Mi
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA and
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA, USA
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA and
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5
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Li J, Yang Z, Li Y, Xia J, Li D, Li H, Ren M, Liao Y, Yu S, Chen Y, Yang Y, Zhang Y. Cell apoptosis, autophagy and necroptosis in osteosarcoma treatment. Oncotarget 2016; 7:44763-44778. [PMID: 27007056 PMCID: PMC5190133 DOI: 10.18632/oncotarget.8206] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 03/07/2016] [Indexed: 12/23/2022] Open
Abstract
Osteosarcoma is the most common primary bone tumor in children and adolescents. Although combined therapy including surgery and multi-agent chemotherapy have resulted in great improvements in the overall survival of patients, chemoresistance remains an obstacle for the treatment of osteosarcoma. Molecular targets or effective agents that are actively involved in cell death including apoptosis, autophagy and necroptosis have been studied. We summarized how these agents (novel compounds, miRNAs, or proteins) regulate apoptotic, autophagic and necroptotic pathways; and discussed the current knowledge on the role of these new agents in chemotherapy resistance in osteosarcoma.
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Affiliation(s)
- Jing Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Zuozhang Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Yi Li
- Department of Oncology, Kunming General Hospital of Chengdu Military Command, Kunming, Yunnan, China
| | - Junfeng Xia
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Dongqi Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Huiling Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Mingyan Ren
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Yedan Liao
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Shunling Yu
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Yanjin Chen
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Yihao Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
| | - Ya Zhang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, the Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, China
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6
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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7
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Choudhry SK, Kawałek A, van der Klei IJ. Peroxisomal quality control mechanisms. Curr Opin Microbiol 2014; 22:30-7. [PMID: 25305535 DOI: 10.1016/j.mib.2014.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
Peroxisomes are ubiquitous organelles that harbor diverse metabolic pathways, which are essential for normal cell performance. Conserved functions of these organelles are hydrogen peroxide metabolism and β-oxidation. Cells employ multiple quality control mechanisms to ensure proper peroxisome function and to protect peroxisomes from damage. These involve the function of molecular chaperones, a peroxisomal Lon protease and autophagic removal of dysfunctional organelles. In addition, multiple mechanisms exist to combat peroxisomal oxidative stress. Here, we outline recent advances in our understanding of peroxisomal quality control, focussing on yeast and filamentous fungi.
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Affiliation(s)
- Sanjeev K Choudhry
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Adam Kawałek
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands.
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8
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Williams C. Going against the flow: A case for peroxisomal protein export. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1386-92. [DOI: 10.1016/j.bbamcr.2014.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
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9
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Sibirny AA. Sensing and signaling for peroxisome autophagic degradation (pexophagy) in yeasts. UKRAINIAN BIOCHEMICAL JOURNAL 2013. [DOI: 10.15407/ubj85.06.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics 2013; 14:837. [PMID: 24279325 PMCID: PMC3866509 DOI: 10.1186/1471-2164-14-837] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/15/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. RESULTS We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole-genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. CONCLUSIONS Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.
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Affiliation(s)
- Nikolai V Ravin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Michael A Eldarov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Vitaly V Kadnikov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Alexey V Beletsky
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Jessica Schneider
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Eugenia S Mardanova
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Elena M Smekalova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Andrey V Mardanov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Konstantin G Skryabin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
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11
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Williams C, van der Klei IJ. Pexophagy-linked degradation of the peroxisomal membrane protein Pex3p involves the ubiquitin-proteasome system. Biochem Biophys Res Commun 2013; 438:395-401. [PMID: 23899522 DOI: 10.1016/j.bbrc.2013.07.086] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/20/2013] [Indexed: 11/29/2022]
Abstract
Peroxisome autophagy, also known as pexophagy, describes the wholesale degradation of peroxisomes via the vacuole, when organelles become damaged or redundant. In the methylotrophic yeast Hansenula polymorpha, pexophagy is stimulated when cells growing on methanol are exposed to excess glucose. Degradation of the peroxisomal membrane protein Pex3p, a process that does not involve the vacuole, was shown to trigger pexophagy. In this contribution, we have characterised pexophagy-associated Pex3p degradation further. We show that Pex3p breakdown depends on ubiquitin and confirm that Pex3p is a target for ubiquitination. Furthermore, we identify a role for the peroxisomal E3 ligases Pex2p and Pex10p in Pex3p degradation, suggesting the existence of a ubiquitin-dependent pathway involved in removing proteins from the peroxisomal membrane.
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Affiliation(s)
- Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.
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12
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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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