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Lourdes SR, Gurung R, Giri S, Mitchell CA, McGrath MJ. A new role for phosphoinositides in regulating mitochondrial dynamics. Adv Biol Regul 2024; 91:101001. [PMID: 38057188 DOI: 10.1016/j.jbior.2023.101001] [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: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Phosphoinositides are a minor group of membrane-associated phospholipids that are transiently generated on the cytoplasmic leaflet of many organelle membranes and the plasma membrane. There are seven functionally distinct phosphoinositides, each derived via the reversible phosphorylation of phosphatidylinositol in various combinations on the inositol ring. Their generation and termination is tightly regulated by phosphatidylinositol-kinases and -phosphatases. These enzymes can function together in an integrated and coordinated manner, whereby the phosphoinositide product of one enzyme may subsequently serve as a substrate for another to generate a different phosphoinositide species. This regulatory mechanism not only enables the transient generation of phosphoinositides on membranes, but also more complex sequential or bidirectional conversion pathways, and phosphoinositides can also be transferred between organelles via membrane contacts. It is this capacity to fine-tune phosphoinositide signals that makes them ideal regulators of membrane organization and dynamics, through their recruitment of signalling, membrane altering and lipid transfer proteins. Research spanning several decades has provided extensive evidence that phosphoinositides are major gatekeepers of membrane organization, with roles in endocytosis, exocytosis, autophagy, lysosome dynamics, vesicular transport and secretion, cilia, inter-organelle membrane contact, endosome maturation and nuclear function. By contrast, there has been remarkably little known about the role of phosphoinositides at mitochondria - an enigmatic and major knowledge gap, with challenges in reliably detecting phosphoinositides at this site. Here we review recent significant breakthroughs in understanding the role of phosphoinositides in regulating mitochondrial dynamics and metabolic function.
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Affiliation(s)
- Sonia Raveena Lourdes
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Rajendra Gurung
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Saveen Giri
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
| | - Meagan J McGrath
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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2
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Ferreras S, Singh NP, Le Borgne R, Bun P, Binz T, Parton RG, Verbavatz JM, Vannier C, Galli T. A synthetic organelle approach to probe SNARE-mediated membrane fusion in a bacterial host. J Biol Chem 2023; 299:102974. [PMID: 36738791 PMCID: PMC10011478 DOI: 10.1016/j.jbc.2023.102974] [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: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
In vivo and in vitro assays, particularly reconstitution using artificial membranes, have established the role of synaptic soluble N-Ethylmaleimide-sensitive attachment protein receptors (SNAREs) VAMP2, Syntaxin-1A, and SNAP-25 in membrane fusion. However, using artificial membranes requires challenging protein purifications that could be avoided in a cell-based assay. Here, we developed a synthetic biological approach based on the generation of membrane cisternae by the integral membrane protein Caveolin in Escherichia coli and coexpression of SNAREs. Syntaxin-1A/SNAP-25/VAMP-2 complexes were formed and regulated by SNARE partner protein Munc-18a in the presence of Caveolin. Additionally, Syntaxin-1A/SNAP-25/VAMP-2 synthesis provoked increased length of E. coli only in the presence of Caveolin. We found that cell elongation required SNAP-25 and was inhibited by tetanus neurotoxin. This elongation was not a result of cell division arrest. Furthermore, electron and super-resolution microscopies showed that synaptic SNAREs and Caveolin coexpression led to the partial loss of the cisternae, suggesting their fusion with the plasma membrane. In summary, we propose that this assay reconstitutes membrane fusion in a simple organism with an easy-to-observe phenotype and is amenable to structure-function studies of SNAREs.
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Affiliation(s)
- Soledad Ferreras
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Neha Pratap Singh
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Remi Le Borgne
- Université Paris Cité, CNRS, UMR7592, Institut Jacques Monod, Paris, France
| | - Philippe Bun
- Université Paris Cité, NeurImag, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France
| | - Thomas Binz
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, Qld, Brisbane, Australia
| | | | - Christian Vannier
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France.
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France; GHU Paris psychiatrie neurosciences, Paris, France.
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The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. MEMBRANES 2022; 12:membranes12070696. [PMID: 35877899 PMCID: PMC9324892 DOI: 10.3390/membranes12070696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023]
Abstract
Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key roles in membrane binding, whereas the C-terminal poly aspartic acid (polyD) motif specifically autoinhibits the PH domain binding to the membrane phosphatidylinositol 3-phosphate (PtdIns3P). Since the Phafin2 FYVE domain also binds PtdIns3P, the role of the polyD motif remains unclear. In this study, bioinformatics tools and resources were employed to determine the concurrence of the PH-FYVE module with the polyD motif among Phafin2 and PH-, FYVE-, or polyD-containing proteins from bacteria to humans. FYVE was found to be an ancient domain of Phafin2 and is related to proteins that are present in both prokaryotes and eukaryotes. Interestingly, the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals. PolyD motifs are absent in PH domain-free FYVE-containing proteins, which usually display cellular trafficking or autophagic functions. Moreover, the prediction of the Phafin2-interacting network indicates that Phafin2 primarily cross-talks with proteins involved in autophagy, protein trafficking, and neuronal function. Taken together, the concurrence of the polyD motif with the PH domain may be associated with complex cellular functions that evolved specifically in animals.
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Designer phospholipids – structural retrieval, chemo-/bio- synthesis and isotopic labeling. Biotechnol Adv 2022; 60:108025. [DOI: 10.1016/j.biotechadv.2022.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022]
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Lu J, Dong W, Hammond GR, Hong Y. Hypoxia controls plasma membrane targeting of polarity proteins by dynamic turnover of PI4P and PI(4,5)P2. eLife 2022; 11:79582. [PMID: 35678383 PMCID: PMC9242647 DOI: 10.7554/elife.79582] [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: 04/20/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-biphosphate (PIP2) are key phosphoinositides that determine the identity of the plasma membrane (PM) and regulate numerous key biological events there. To date, mechanisms regulating the homeostasis and dynamic turnover of PM PI4P and PIP2 in response to various physiological conditions and stresses remain to be fully elucidated. Here, we report that hypoxia in Drosophila induces acute and reversible depletion of PM PI4P and PIP2 that severely disrupts the electrostatic PM targeting of multiple polybasic polarity proteins. Genetically encoded ATP sensors confirmed that hypoxia induces acute and reversible reduction of cellular ATP levels which showed a strong real-time correlation with the levels of PM PI4P and PIP2 in cultured cells. By combining genetic manipulations with quantitative imaging assays we showed that PI4KIIIα, as well as Rbo/EFR3 and TTC7 that are essential for targeting PI4KIIIα to PM, are required for maintaining the homeostasis and dynamic turnover of PM PI4P and PIP2 under normoxia and hypoxia. Our results revealed that in cells challenged by energetic stresses triggered by hypoxia, ATP inhibition and possibly ischemia, dramatic turnover of PM PI4P and PIP2 could have profound impact on many cellular processes including electrostatic PM targeting of numerous polybasic proteins.
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Affiliation(s)
- Juan Lu
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, China [CN]
| | - Wei Dong
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
| | - Gerald R Hammond
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
| | - Yang Hong
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, United States
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Moore WM, Milshteyn D, Tsai YT, Budin I. Engineering the bilayer: Emerging genetic tool kits for mechanistic lipid biology. Curr Opin Chem Biol 2021; 65:66-73. [PMID: 34218059 DOI: 10.1016/j.cbpa.2021.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/19/2022]
Abstract
The structural diversity of lipids underpins the biophysical properties of cellular membranes, which vary across all scales of biological organization. Because lipid composition results from complex metabolic and transport pathways, its experimental control has been a major goal of mechanistic membrane biology. Here, we argue that in the wake of synthetic biology, similar metabolic engineering strategies can be applied to control the composition, physicochemical properties, and function of cell membranes. In one emerging area, titratable expression platforms allow for specific and genome-wide alterations in lipid biosynthetic genes, providing analog control over lipidome stoichiometry in membranes. Simultaneously, heterologous expression of biosynthetic genes and pathways has allowed for gain-of-function experiments with diverse lipids in non-native systems. Finally, we highlight future directions for tool development, including recently discovered lipid transport pathways to intracellular lipid pools. Further tool development providing synthetic control of membrane properties can allow biologists to untangle membrane lipid structure-associated functions.
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Affiliation(s)
- William M Moore
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Daniel Milshteyn
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yi-Ting Tsai
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Itay Budin
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Ding Q, Ma D, Liu GQ, Li Y, Guo L, Gao C, Hu G, Ye C, Liu J, Liu L, Chen X. Light-powered Escherichia coli cell division for chemical production. Nat Commun 2020; 11:2262. [PMID: 32385264 PMCID: PMC7210317 DOI: 10.1038/s41467-020-16154-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/19/2020] [Indexed: 12/17/2022] Open
Abstract
Cell division can perturb the metabolic performance of industrial microbes. The C period of cell division starts from the initiation to the termination of DNA replication, whereas the D period is the bacterial division process. Here, we first shorten the C and D periods of E. coli by controlling the expression of the ribonucleotide reductase NrdAB and division proteins FtsZA through blue light and near-infrared light activation, respectively. It increases the specific surface area to 3.7 μm−1 and acetoin titer to 67.2 g·L−1. Next, we prolong the C and D periods of E. coli by regulating the expression of the ribonucleotide reductase NrdA and division protein inhibitor SulA through blue light activation-repression and near-infrared (NIR) light activation, respectively. It improves the cell volume to 52.6 μm3 and poly(lactate-co-3-hydroxybutyrate) titer to 14.31 g·L−1. Thus, the optogenetic-based cell division regulation strategy can improve the efficiency of microbial cell factories. Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Danlei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, 410004, Changsha, China
| | - Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 214122, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China.
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8
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Yin N, Zhu G, Luo Q, Liu J, Chen X, Liu L. Engineering of membrane phospholipid component enhances salt stress tolerance in
Saccharomyces cerevisiae. Biotechnol Bioeng 2020; 117:710-720. [DOI: 10.1002/bit.27244] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Nannan Yin
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Guoxing Zhu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Qiuling Luo
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Jia Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Xiulai Chen
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Liming Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University Wuxi China
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Clarke BP, Logeman BL, Hale AT, Luka Z, York JD. A synthetic biological approach to reconstitution of inositide signaling pathways in bacteria. Adv Biol Regul 2019; 73:100637. [PMID: 31378699 DOI: 10.1016/j.jbior.2019.100637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/19/2022]
Abstract
Inositide lipid (PIP) and soluble (IP) signaling pathways produce essential cellular codes conserved in eukaryotes. In many cases, deconvoluting metabolic and functional aspects of individual pathways are confounded by promiscuity and multiplicity of PIP and IP kinases and phosphatases. We report a molecular genetic approach that reconstitutes eukaryotic inositide lipid and soluble pathways in a prokaryotic cell which inherently lack inositide kinases and phosphatases in their genome. By expressing synthetic cassettes of eukaryotic genes, we have reconstructed the heterologous formation of a range of inositide lipids, including PI(3)P, PI(4,5)P2 and PIP3. In addition, we report the reconstruction of lipid-dependent production of inositol hexakisphosphate (IP6). Our synthetic system is scalable, reduces confounding metabolic issues, for example it is devoid of inositide phosphatases and orthologous kinases, and enables accurate characterization gene product enzymatic activity and substrate selectivity. This genetically engineered tool is designed to help interpret metabolic pathways and may facilitate in vivo testing of regulators and small molecule inhibitors. In summary, heterologous expression of inositide pathways in bacteria provide a malleable experimental platform for aiding signaling biologists and offers new insights into metabolism of these essential pathways.
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Affiliation(s)
- Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brandon L Logeman
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Andrew T Hale
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John D York
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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