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Huber RJ, Kim WD. Trafficking of adhesion and aggregation-modulating proteins during the early stages of Dictyostelium development. Cell Signal 2024; 121:111292. [PMID: 38986731 DOI: 10.1016/j.cellsig.2024.111292] [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: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
The social amoeba Dictyostelium discoideum has been studied for close to a century to better understand conserved cellular and developmental processes. The life cycle of this model eukaryote is composed of a unicellular growth phase and a multicellular developmental phase that is induced by starvation. When starved, individual cells undergo chemotactic aggregation to form multicellular mounds that develop into slugs. Terminal differentiation of cells within slugs forms fruiting bodies, each composed of a stalk that supports a mass of viable spores that germinate and restart the life cycle when nutrients become available. Calcium-dependent cell adhesion protein A (CadA) and countin (CtnA) are two proteins that regulate adhesion and aggregation, respectively, during the early stages of D. discoideum development. While the functions of these proteins have been well-studied, the mechanisms regulating their trafficking are not fully understood. In this study, we reveal pathways and cellular components that regulate the intracellular and extracellular amounts of CadA and CtnA during aggregation. During growth and starvation, CtnA localizes to cytoplasmic vesicles and punctae. We show that CtnA is glycosylated and this post-translational modification is required for its secretion. Upon autophagy induction, a signal peptide for secretion facilitates the release of CtnA from cells via a pathway involving the μ subunit of the AP3 complex (Apm3) and the WASP and SCAR homolog, WshA. Additionally, CtnA secretion is negatively regulated by the D. discoideum orthologs of the human non-selective cation channel mucolipin-1 (Mcln) and sorting receptor sortilin (Sort1). As for CadA, it localizes to the cell periphery in growth-phase and starved cells. The intracellular and extracellular amounts of CadA are modulated by autophagy genes (atg1, atg9), Apm3, WshA, and Mcln. We integrate these data with previously published findings to generate a comprehensive model summarizing the trafficking of CadA and CtnA in D. discoideum. Overall, this study enhances our understanding of protein trafficking during D. discoideum aggregation, and more broadly, provides insight into the multiple pathways that regulate protein trafficking and secretion in all eukaryotes.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada.
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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Li Y, Zhao T, Gao W, Miao B, Fu Z, Zhang Z, Li Q, Sun D. Regulatory mechanisms of autophagy on DHA and carotenoid accumulation in Crypthecodinium sp. SUN. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:50. [PMID: 38566214 PMCID: PMC10985998 DOI: 10.1186/s13068-024-02493-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Autophagy is a crucial process of cellular self-destruction and component reutilization that can affect the accumulation of total fatty acids (TFAs) and carotenoids in microalgae. The regulatory effects of autophagy process in a docosahexaenoic acid (DHA) and carotenoids simultaneously producing microalga, Crypthecodinium sp. SUN, has not been studied. Thus, the autophagy inhibitor (3-methyladenine (MA)) and activator (rapamycin) were used to regulate autophagy in Crypthecodinium sp. SUN. RESULTS The inhibition of autophagy by 3-MA was verified by transmission electron microscopy, with fewer autophagy vacuoles observed. Besides, 3-MA reduced the glucose absorption and intracellular acetyl-CoA level, which resulting in the decrease of TFA and DHA levels by 15.83 and 26.73% respectively; Surprisingly, 3-MA increased intracellular reactive oxygen species level but decreased the carotenoids level. Comparative transcriptome analysis showed that the downregulation of the glycolysis, pentose phosphate pathway and tricarboxylic acid cycle may underlie the decrease of acetyl-CoA, NADPH and ATP supply for fatty acid biosynthesis; the downregulation of PSY and HMGCR may underlie the decreased carotenoids level. In addition, the class I PI3K-AKT signaling pathway may be crucial for the regulation of carbon and energy metabolism. At last, rapamycin was used to activate autophagy, which significantly enhanced the cell growth and TFA level and eventually resulted in 1.70-fold increase in DHA content. CONCLUSIONS Our findings indicate the mechanisms of autophagy in Crypthecodinium sp. SUN and highlight a way to manipulate cell metabolism by regulating autophagy. Overall, this study provides valuable insights to guide further research on autophagy-regulated TFA and carotenoids accumulation in Crypthecodinium sp. SUN.
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Affiliation(s)
- Yiming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- School of Life Sciences, Hebei University, Baoding, 071000, China
| | - Tiantian Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Weizheng Gao
- School of Life Sciences, Hebei University, Baoding, 071000, China
| | - Bowen Miao
- School of Life Sciences, Hebei University, Baoding, 071000, China
| | - Zhongxiang Fu
- School of Life Sciences, Hebei University, Baoding, 071000, China
| | - Zhao Zhang
- School of Life Sciences, Hebei University, Baoding, 071000, China
| | - Qingyang Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Dongzhe Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
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Huber RJ, Kim WD, Wilson-Smillie MLDM. Mechanisms regulating the intracellular trafficking and release of CLN5 and CTSD. Traffic 2024; 25:e12925. [PMID: 38272448 DOI: 10.1111/tra.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/27/2024]
Abstract
Ceroid lipofuscinosis neuronal 5 (CLN5) and cathepsin D (CTSD) are soluble lysosomal enzymes that also localize extracellularly. In humans, homozygous mutations in CLN5 and CTSD cause CLN5 disease and CLN10 disease, respectively, which are two subtypes of neuronal ceroid lipofuscinosis (commonly known as Batten disease). The mechanisms regulating the intracellular trafficking of CLN5 and CTSD and their release from cells are not well understood. Here, we used the social amoeba Dictyostelium discoideum as a model system to examine the pathways and cellular components that regulate the intracellular trafficking and release of the D. discoideum homologs of human CLN5 (Cln5) and CTSD (CtsD). We show that both Cln5 and CtsD contain signal peptides for secretion that facilitate their release from cells. Like Cln5, extracellular CtsD is glycosylated. In addition, Cln5 release is regulated by the amount of extracellular CtsD. Autophagy induction promotes the release of Cln5, and to a lesser extent CtsD. Release of Cln5 requires the autophagy proteins Atg1, Atg5, and Atg9, as well as autophagosomal-lysosomal fusion. Atg1 and Atg5 are required for the release of CtsD. Together, these data support a model where Cln5 and CtsD are actively released from cells via their signal peptides for secretion and pathways linked to autophagy. The release of Cln5 and CtsD from cells also requires microfilaments and the D. discoideum homologs of human AP-3 complex mu subunit, the lysosomal-trafficking regulator LYST, mucopilin-1, and the Wiskott-Aldrich syndrome-associated protein WASH, which all regulate lysosomal exocytosis in this model organism. These findings suggest that lysosomal exocytosis also facilitates the release of Cln5 and CtsD from cells. In addition, we report the roles of ABC transporters, microtubules, osmotic stress, and the putative D. discoideum homologs of human sortilin and cation-independent mannose-6-phosphate receptor in regulating the intracellular/extracellular distribution of Cln5 and CtsD. In total, this study identifies the cellular mechanisms regulating the release of Cln5 and CtsD from D. discoideum cells and provides insight into how altered trafficking of CLN5 and CTSD causes disease in humans.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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Zhang H, Tian Y, Yu W, Tong D, Ji Y, Qu X, Deng T, Li X, Xu Y. TMEM175 downregulation participates in impairment of the autophagy related lysosomal dynamics following neonatal hypoxic-ischemic brain injury. J Cell Physiol 2023; 238:2512-2527. [PMID: 37566721 DOI: 10.1002/jcp.31096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
The mechanism underlying long-term cognitive impairment caused by neonatal hypoxic-ischemic brain injury (HIBI) remains unclear. Autophagy is a closely related mechanism and may play a role in this process. We aimed to investigate the role of lysosomal transmembrane protein 175 (TMEM175) in the autophagy-lysosome pathway in neonatal rats with HIBI. A neonatal rat model of HIBI was established, hypoxia was induced, followed by left common carotid artery ligation. Expression levels of TMEM175 and the corresponding proteins involved in autophagy flux and the endolysosomal system fusion process were measured. Rats were administered TMEM175 plasmid via intracerebroventricular injection to induce overexpression. Brain damage and cognitive function were then assessed. TMEM175 was downregulated in the hippocampal tissue, and the autophagy-lysosome pathway was impaired following HIBI in neonatal rats. Overexpression of TMEM175 significantly mitigated neuronal injury and improved long-term cognitive and memory function in neonatal rats with HIBI. We found that improvement in the autophagy-lysosome pathway and endolysosomal system homeostasis, which are TMEM175 related, occurred via regulation of lysosomal membrane dynamic fusion. TMEM175 plays a critical role in maintaining the autophagy-lysosome pathway and endolysosomal homeostasis, contributing to the amelioration of neuronal injury and impaired long-term cognitive function following neonatal HIBI.
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Affiliation(s)
- Huiyi Zhang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ye Tian
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Weiwei Yu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dongyi Tong
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yichen Ji
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinrui Qu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianjiao Deng
- The First Clinical College, China Medical University, Shenyang, China
| | - Xinsheng Li
- The First Clinical College, China Medical University, Shenyang, China
| | - Ying Xu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
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Xiong Q, Feng R, Fischer S, Karow M, Stumpf M, Meßling S, Nitz L, Müller S, Clemen CS, Song N, Li P, Wu C, Eichinger L. Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity. Cells 2023; 12:1514. [PMID: 37296637 PMCID: PMC10252828 DOI: 10.3390/cells12111514] [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: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Autophagy and the ubiquitin proteasome system are the two major processes for the clearance and recycling of proteins and organelles in eukaryotic cells. Evidence is accumulating that there is extensive crosstalk between the two pathways, but the underlying mechanisms are still unclear. We previously found that autophagy 9 (ATG9) and 16 (ATG16) proteins are crucial for full proteasomal activity in the unicellular amoeba Dictyostelium discoideum. In comparison to AX2 wild-type cells, ATG9-and ATG16- cells displayed a 60%, and ATG9-/16- cells a 90%, decrease in proteasomal activity. Mutant cells also showed a significant increase in poly-ubiquitinated proteins and contained large ubiquitin-positive protein aggregates. Here, we focus on possible reasons for these results. Reanalysis of published tandem mass tag-based quantitative proteomic results of AX2, ATG9-, ATG16-, and ATG9-/16- cells revealed no change in the abundance of proteasomal subunits. To identify possible differences in proteasome-associated proteins, we generated AX2 wild-type and ATG16- cells expressing the 20S proteasomal subunit PSMA4 as GFP-tagged fusion protein, and performed co-immunoprecipitation experiments followed by mass spectrometric analysis. The results revealed no significant differences in the abundance of proteasomes between the two strains. However, we found enrichment as well as depletion of proteasomal regulators and differences in the ubiquitination of associated proteins for ATG16-, as compared to AX2 cells. Recently, proteaphagy has been described as a means to replace non-functional proteasomes. We propose that autophagy-deficient D. discoideum mutants suffer from inefficient proteaphagy, which results in the accumulation of modified, less-active, and also of inactive, proteasomes. As a consequence, these cells exhibit a dramatic decrease in proteasomal activity and deranged protein homeostasis.
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Affiliation(s)
- Qiuhong Xiong
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China
| | - Rong Feng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China
| | - Sarah Fischer
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Malte Karow
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Maria Stumpf
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Susanne Meßling
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Leonie Nitz
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Stefan Müller
- CECAD Proteomics Facility, Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Christoph S. Clemen
- Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
- Institute of Vegetative Physiology, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ning Song
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China
| | - Ping Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China
| | - Ludwig Eichinger
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
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Zhao X, Wang J, Wang Y, Zhang M, Zhao W, Zhang H, Zhao L. Interferon‑stimulated gene 15 promotes progression of endometrial carcinoma and weakens antitumor immune response. Oncol Rep 2022; 47:110. [PMID: 35445736 PMCID: PMC9073416 DOI: 10.3892/or.2022.8321] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/14/2021] [Indexed: 11/24/2022] Open
Abstract
Endometrial carcinoma (EC) is one of the most common gynecological cancers with a poor prognosis. Therefore, clarifying the details of the molecular mechanisms is of great importance for EC diagnosis and clinical management. Interferon-stimulated gene 15 (ISG15) plays an important role in the development of various cancers. However, its role in EC remains unclear. High ISG15 expression was observed in EC, which was associated with poor clinical outcomes and pathological stage of patients with EC, thus representing a promising marker for EC progression. Further exploratory analysis revealed that the elevated ISG15 levels in EC were driven by aberrant DNA methylation, independent of copy number variation and specific transcription factor aberrations. Accordingly, knockdown of ISG15 by small interfering RNA attenuated the malignant cellular phenotype of EC cell lines, including proliferation and colony formation in vitro. Finally, investigation of the molecular mechanisms indicated that ISG15 promoted the cell cycle G1/S transition in EC. Furthermore, ISG15 promoted EC progression by activating the MYC proto-oncogene protein signaling pathway. Moreover, ECs with high levels of ISG15 harbored a more vital immune escape ability, evidenced not only by significantly less invasive CD8+ T cells, but also higher expression of T cell inhibitory factors, such as programmed death-ligand 1. These results suggest a tumor-promoting role of ISG15 in EC, which may be a promising marker for diagnosis, prognosis and therapeutic immunity.
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Affiliation(s)
- Xiwa Zhao
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Jingjing Wang
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yaojie Wang
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Mengmeng Zhang
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Wei Zhao
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Hui Zhang
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Lianmei Zhao
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
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Ren Y, Zhang Q, Yan X, Hou D, Huang H, Li C, Rao D, Li Y. Genomic insights into the evolution of the critically endangered soft‐shelled turtle
Rafetus swinhoei. Mol Ecol Resour 2022; 22:1972-1985. [DOI: 10.1111/1755-0998.13596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Qiang Zhang
- Changsha Ecological Zoo Changsha 410002 China
| | - Xiahui Yan
- Changsha Ecological Zoo Changsha 410002 China
| | - Dongmin Hou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | | | - Chunhui Li
- Changsha Ecological Zoo Changsha 410002 China
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
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Vincent O, Antón-Esteban L, Bueno-Arribas M, Tornero-Écija A, Navas MÁ, Escalante R. The WIPI Gene Family and Neurodegenerative Diseases: Insights From Yeast and Dictyostelium Models. Front Cell Dev Biol 2021; 9:737071. [PMID: 34540850 PMCID: PMC8442847 DOI: 10.3389/fcell.2021.737071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/12/2021] [Indexed: 02/01/2023] Open
Abstract
WIPIs are a conserved family of proteins with a characteristic 7-bladed β-propeller structure. They play a prominent role in autophagy, but also in other membrane trafficking processes. Mutations in human WIPI4 cause several neurodegenerative diseases. One of them is BPAN, a rare disease characterized by developmental delay, motor disorders, and seizures. Autophagy dysfunction is thought to play an important role in this disease but the precise pathological consequences of the mutations are not well established. The use of simple models such as the yeast Saccharomyces cerevisiae and the social amoeba Dictyostelium discoideum provides valuable information on the molecular and cellular function of these proteins, but also sheds light on possible pathways that may be relevant in the search for potential therapies. Here, we review the function of WIPIs as well as disease-causing mutations with a special focus on the information provided by these simple models.
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Affiliation(s)
- Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC/UAM, Madrid, Spain
| | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC/UAM, Madrid, Spain
| | | | - Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC/UAM, Madrid, Spain
| | - María-Ángeles Navas
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC/UAM, Madrid, Spain
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Tornero-Écija A, Tábara LC, Bueno-Arribas M, Antón-Esteban L, Navarro-Gómez C, Sánchez I, Vincent O, Escalante R. A Dictyostelium model for BPAN disease reveals a functional relationship between the WDR45/WIPI4 homolog Wdr45l and Vmp1 in the regulation of autophagy-associated PtdIns3P and ER stress. Autophagy 2021; 18:661-677. [PMID: 34328055 PMCID: PMC9037511 DOI: 10.1080/15548627.2021.1953262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PROPPINs are conserved PtdIns3P-binding proteins required for autophagosome biogenesis that fold into a characteristic group of seven-bladed beta-propellers. Mutations in WDR45/WIPI4, a human member of this family, lead to BPAN, a rare form of neurodegeneration. We have generated mutants for the two PROPPIN proteins present in the model system Dictyostelium discoideum (Atg18 and Wdr45l) and characterized their function. Lack of Wdr45l greatly impairs autophagy, while Atg18 only causes subtle defects in the maturation of autolysosomes. The strong phenotype of the Wdr45l mutant is strikingly similar to that observed in Dictyostelium cells lacking Vmp1, an ER protein required for omegasome formation. Common phenotypes include impaired growth in axenic medium, lack of aggregation, and local enrichment of PtdIns3P as determined by the use of lipid reporters. In addition, Vmp1 and Wdr45l mutants show a chronically active response to ER stress. For both mutants, this altered PtdIns3P localization can be prevented by the additional mutation of the upstream regulator Atg1, which also leads to recovery of axenic growth and reduction of ER stress. We propose that, in addition to an autophagy defect, local autophagy-associated PtdIns3P accumulation might contribute to the pathogenesis of BPAN by disrupting ER homeostasis. The introduction of BPAN-associated mutations in Dictyostelium Wdr45l reveals the impact of pathogenic residues on the function and localization of the protein.
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Affiliation(s)
- Alba Tornero-Écija
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Luis-Carlos Tábara
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Miranda Bueno-Arribas
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Laura Antón-Esteban
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | | | - Irene Sánchez
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Olivier Vincent
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Ricardo Escalante
- C.S.I.C./U.A.M., Instituto De Investigaciones Biomédicas Alberto Sols, Madrid, Spain
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Lin NX, He RZ, Xu Y, Yu XW. Augmented peroxisomal ROS buffering capacity renders oxidative and thermal stress cross-tolerance in yeast. Microb Cell Fact 2021; 20:131. [PMID: 34247591 PMCID: PMC8273976 DOI: 10.1186/s12934-021-01623-1] [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: 02/23/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
Background Thermotolerant yeast has outstanding potential in industrial applications. Komagataella phaffii (Pichia pastoris) is a common cell factory for industrial production of heterologous proteins. Results Herein, we obtained a thermotolerant K. phaffii mutant G14 by mutagenesis and adaptive evolution. G14 exhibited oxidative and thermal stress cross-tolerance and high heterologous protein production efficiency. The reactive oxygen species (ROS) level and lipid peroxidation in G14 were reduced compared to the parent. Oxidative stress response (OSR) and heat shock response (HSR) are two major responses to thermal stress, but the activation of them was different in G14 and its parent. Compared with the parent, G14 acquired the better performance owing to its stronger OSR. Peroxisomes, as the main cellular site for cellular ROS generation and detoxification, had larger volume in G14 than the parent. And, the peroxisomal catalase activity and expression level in G14 was also higher than that of the parent. Excitingly, the gene knockdown of CAT encoding peroxisomal catalase by dCas9 severely reduced the oxidative and thermal stress cross-tolerance of G14. These results suggested that the augmented OSR was responsible for the oxidative and thermal stress cross-tolerance of G14. Nevertheless, OSR was not strong enough to protect the parent from thermal stress, even when HSR was initiated. Therefore, the parent cannot recover, thereby inducing the autophagy pathway and resulting in severe cell death. Conclusions Our findings indicate the importance of peroxisome and the significance of redox balance in thermotolerance of yeasts. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01623-1.
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Affiliation(s)
- Nai-Xin Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Rui-Zhen He
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, People's Republic of China.
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RNA seq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16. BMC Genomics 2021; 22:444. [PMID: 34126926 PMCID: PMC8204557 DOI: 10.1186/s12864-021-07756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 and ATG16. However, the functions of these two core ATG proteins still need further elucidation. Here, we applied RNAseq and tandem mass tag (TMT) proteomic approaches to identify differentially expressed genes (DEGs) and proteins (DEPs) in Dictyostelium discoideum ATG9‾, ATG16‾ and ATG9‾/16‾ strains in comparison to AX2 wild-type cells. RESULT In total, we identified 332 (279 up and 53 down), 639 (487 up and 152 down) and 260 (114 up and 146 down) DEGs and 124 (83 up and 41 down), 431 (238 up and 193 down) and 677 (347 up and 330 down) DEPs in ATG9‾, ATG16‾ and ATG9‾/16‾ strains, respectively. Thus, in the single knock-out strains, the number of DEGs was higher than the number of DEPs while in the double knock-out strain the number of DEPs was higher. Comparison of RNAseq and proteomic data further revealed, that only a small proportion of the transcriptional changes were reflected on the protein level. Gene ontology (GO) analysis revealed an enrichment of DEPs involved in lipid metabolism and oxidative phosphorylation. Furthermore, we found increased expression of the anti-oxidant enzymes glutathione reductase (gsr) and catalase A (catA) in ATG16‾ and ATG9‾/16‾ cells, respectively, indicating adaptation to excess reactive oxygen species (ROS). CONCLUSIONS Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells. Our results suggest, that most changes in protein abundance were not caused by transcriptional changes, but were rather due to changes in protein homeostasis. In particular, knock-out of atg9 and/or atg16 appears to cause dysregulation of lipid metabolism and oxidative phosphorylation.
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Hou J, Wang JJ, Lin HY, Feng MG, Ying SH. Roles of autophagy-related genes in conidiogenesis and blastospore formation, virulence, and stress response of Beauveria bassiana. Fungal Biol 2020; 124:1052-1057. [PMID: 33213785 DOI: 10.1016/j.funbio.2020.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 10/23/2022]
Abstract
Autophagy is a conserved intracellular recycling mechanism, in which autophagy-related genes 12 and 16 (ATG12 and ATG16) function in a complex controlling the ubiquitin-like conjugation system. In the insect-pathogenic fungus Beauveria bassiana, ATG12 and ATG16 were functionally characterized. Disruption of BbATG12 or BbATG16 resulted in the absence of autophagic bodies under starvation stress. ΔBbATG12 and ΔBbATG16 mutant strains displayed similar defects in asexual development (conidiation and blastospore formation) and tolerance to oxidative stress. ΔBbATG16 strain exhibited the impaired growth on the media with gelatin or chitin as a single nitrogen source, and ΔBbATG12 displayed decreased growth on the media with sucrose, fructose or maltose as a single carbon source. Both BbATG12 and BbATG16 were required for fungal virulence. BbATG16 mutation had more effects on fungal virulence than BbATG12 in topical infection assay, although both genes had similar contributions to fungal virulence in intrahemocoel injection assay. This study indicates that BbATG12 and BbATG16 mediate diverse biological functions in addition to their convergent roles in autophagy.
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Affiliation(s)
- Jia Hou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jia-Jia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hai-Yan Lin
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Karow M, Fischer S, Meßling S, Konertz R, Riehl J, Xiong Q, Rijal R, Wagle P, S. Clemen C, Eichinger L. Functional Characterisation of the Autophagy ATG12~5/16 Complex in Dictyostelium discoideum. Cells 2020; 9:cells9051179. [PMID: 32397394 PMCID: PMC7290328 DOI: 10.3390/cells9051179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Macroautophagy, a highly conserved and complex intracellular degradative pathway, involves more than 20 core autophagy (ATG) proteins, among them the hexameric ATG12~5/16 complex, which is part of the essential ubiquitin-like conjugation systems in autophagy. Dictyostelium discoideumatg5 single, atg5/12 double, and atg5/12/16 triple gene knock-out mutant strains displayed similar defects in the conjugation of ATG8 to phosphatidylethanolamine, development, and cell viability upon nitrogen starvation. This implies that ATG5, 12 and 16 act as a functional unit in canonical autophagy. Macropinocytosis of TRITC dextran and phagocytosis of yeast were significantly decreased in ATG5¯ and ATG5¯/12¯ and even further in ATG5¯/12¯/16¯ cells. In contrast, plaque growth on Klebsiella aerogenes was about twice as fast for ATG5¯ and ATG5¯/12¯/16¯ cells in comparison to AX2, but strongly decreased for ATG5¯/12¯ cells. Along this line, phagocytic uptake of Escherichia coli was significantly reduced in ATG5¯/12¯ cells, while no difference in uptake, but a strong increase in membrane association of E. coli, was seen for ATG5¯ and ATG5¯/12¯/16¯ cells. Proteasomal activity was also disturbed in a complex fashion, consistent with an inhibitory activity of ATG16 in the absence of ATG5 and/or ATG12. Our results confirm the essential function of the ATG12~5/16 complex in canonical autophagy, and furthermore are consistent with autophagy-independent functions of the complex and its individual components. They also strongly support the placement of autophagy upstream of the ubiquitin-proteasome system (UPS), as a fully functional UPS depends on autophagy.
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Affiliation(s)
- Malte Karow
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Sarah Fischer
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Susanne Meßling
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Roman Konertz
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Jana Riehl
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Qiuhong Xiong
- Institute of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China;
| | - Ramesh Rijal
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA;
| | - Prerana Wagle
- Bioinformatics Core Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany;
| | - Christoph S. Clemen
- Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany;
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, 50931 Cologne, Germany
- Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
- Correspondence: ; Tel.: +49-221-478-6928; Fax: +49-221-478-97524
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Yamada Y, Schaap P. Cyclic AMP induction of Dictyostelium prespore gene expression requires autophagy. Dev Biol 2019; 452:114-126. [PMID: 31051160 PMCID: PMC6598861 DOI: 10.1016/j.ydbio.2019.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/06/2019] [Accepted: 04/25/2019] [Indexed: 12/27/2022]
Abstract
Dictyostelium discoideum amoebas display colonial multicellularity where starving amoebas aggregate to form migrating slugs and fruiting bodies consisting of spores and three supporting cell types. To resolve the cell signalling mechanism that control sporulation, we use insertional mutagenesis of amoebas transformed with fusion constructs of spore genes and red fluorescent protein. We identified the defective gene in a mutant lacking spore gene expression as the autophagy gene Atg7. Directed knock-out of atg7 and of autophagy genes like atg5 and atg9 yielded a similar phenotype, with lack of viable spores and excessive differentiation of stalk cells. The atg7-, atg5- and atg9- cells were specifically defective in cAMP induction of prespore genes, but showed enhanced cAMP stimulation of prestalk genes at the same developmental stage. The lack of prespore gene induction in the autophagy mutants was not due to deleterious effects of loss of autophagy on known components of the cAMP pathway, such as cAMP receptors and their cAMP-induced phosphorylation and internalization, PKA and the transcription factors SpaA and GbfA, or to lack of NH3 production by proteolysis, which was previously suggested to stimulate the spore pathway. Our continued mutagenesis approach is the most likely to yield the intriguing link between autophagy and prespore gene induction.
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Affiliation(s)
- Yoko Yamada
- School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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15
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Special Issue on "Proteostasis and Autophagy". Cells 2019; 8:cells8070642. [PMID: 31247988 PMCID: PMC6678587 DOI: 10.3390/cells8070642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022] Open
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