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Parihar K, Ko SHB, Bradley RP, Taylor P, Ramakrishnan N, Baumgart T, Guo W, Weaver VM, Janmey PA, Radhakrishnan R. Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology. MECHANOBIOLOGY IN MEDICINE 2024; 2:100071. [PMID: 38899029 PMCID: PMC11185830 DOI: 10.1016/j.mbm.2024.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A definitive understanding of the interplay between protein binding/migration and membrane curvature evolution is emerging but needs further study. The mechanisms defining such phenomena are critical to intracellular transport and trafficking of proteins. Among trafficking modalities, exosomes have drawn attention in cancer research as these nano-sized naturally occurring vehicles are implicated in intercellular communication in the tumor microenvironment, suppressing anti-tumor immunity and preparing the metastatic niche for progression. A significant question in the field is how the release and composition of tumor exosomes are regulated. In this perspective article, we explore how physical factors such as geometry and tissue mechanics regulate cell cortical tension to influence exosome production by co-opting the biophysics as well as the signaling dynamics of intracellular trafficking pathways and how these exosomes contribute to the suppression of anti-tumor immunity and promote metastasis. We describe a multiscale modeling approach whose impact goes beyond the fundamental investigation of specific cellular processes toward actual clinical translation. Exosomal mechanisms are critical to developing and approving liquid biopsy technologies, poised to transform future non-invasive, longitudinal profiling of evolving tumors and resistance to cancer therapies to bring us one step closer to the promise of personalized medicine.
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Affiliation(s)
- Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Seung-Hyun B. Ko
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan P. Bradley
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Taylor
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - N. Ramakrishnan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Tobias Baumgart
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie M. Weaver
- Department of Surgery, Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA, USA
| | - Paul A. Janmey
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
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2
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Prever L, Squillero G, Hirsch E, Gulluni F. Linking phosphoinositide function to mitosis. Cell Rep 2024; 43:114273. [PMID: 38843397 DOI: 10.1016/j.celrep.2024.114273] [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: 03/18/2024] [Revised: 04/12/2024] [Accepted: 05/09/2024] [Indexed: 07/02/2024] Open
Abstract
Phosphoinositides (PtdIns) are a family of differentially phosphorylated lipid second messengers localized to the cytoplasmic leaflet of both plasma and intracellular membranes. Kinases and phosphatases can selectively modify the PtdIns composition of different cellular compartments, leading to the recruitment of specific binding proteins, which control cellular homeostasis and proliferation. Thus, while PtdIns affect cell growth and survival during interphase, they are also emerging as key drivers in multiple temporally defined membrane remodeling events of mitosis, like cell rounding, spindle orientation, cytokinesis, and abscission. In this review, we summarize and discuss what is known about PtdIns function during mitosis and how alterations in the production and removal of PtdIns can interfere with proper cell division.
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Affiliation(s)
- Lorenzo Prever
- University of Turin, Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", Via Nizza 52, 10126 Turin, Italy
| | - Gabriele Squillero
- University of Turin, Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", Via Nizza 52, 10126 Turin, Italy
| | - Emilio Hirsch
- University of Turin, Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", Via Nizza 52, 10126 Turin, Italy.
| | - Federico Gulluni
- University of Turin, Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", Via Nizza 52, 10126 Turin, Italy.
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3
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Zhang Y, Cui X, Lin S, Lu T, Li H, Lu Y, Cao M, Lin X, Ling X. Knockout of a PLD gene in Schizochytrium limacinum SR21 enhances docosahexaenoic acid accumulation by modulation of the phospholipid profile. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:16. [PMID: 38291531 PMCID: PMC10826259 DOI: 10.1186/s13068-024-02465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND The hydrolysis and transphosphatidylation of phospholipase D (PLD) play important roles in the interconversion of phospholipids (PLs), which has been shown to profoundly impact lipid metabolism in plants. In this study, the effect of the PLD1 gene of Schizochytrium limacinum SR21 (S. limacinum SR21) on lipid metabolism was investigated. RESULTS PLD1 knockout had little impact on cell growth and lipid production, but it significantly improved the percentage of polyunsaturated fatty acids in lipids, of which docosahexaenoic acid (DHA) content increased by 13.3% compared to the wild-type strain. Phospholipomics and real-time quantitative PCR analysis revealed the knockout of PLD1 reduced the interexchange and increased de novo synthesis of PLs, which altered the composition of PLs, accompanied by a final decrease in phosphatidylcholine (PC) and an increase in phosphatidylinositol, lysophosphatidylcholine, and phosphatidic acid levels. PLD1 knockout also increased DHA content in triglycerides (TAGs) and decreased it in PLs. CONCLUSIONS These results indicate that PLD1 mainly performs the transphosphatidylation activity in S. limacinum SR21, and its knockout promotes the migration of DHA from PLs to TAGs, which is conducive to DHA accumulation and storage in TAGs via an acyl CoA-independent pathway. This study provides a novel approach for identifying the mechanism of DHA accumulation and metabolic regulation strategies for DHA production in S. limacinum SR21.
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Affiliation(s)
- Yiting Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Xiaowen Cui
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Shuizhi Lin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Tao Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Hao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
- The Key Laboratory for Chemical Biology of Fujian Province (Xiamen University), Xiamen, People's Republic of China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
| | - Xihuang Lin
- Analysis and Test Center, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, People's Republic of China.
| | - Xueping Ling
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China.
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China.
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4
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Chon NL, Tran S, Miller CS, Lin H, Knight JD. A conserved electrostatic membrane-binding surface in synaptotagmin-like proteins revealed using molecular phylogenetic analysis and homology modeling. Protein Sci 2024; 33:e4850. [PMID: 38038838 PMCID: PMC10731544 DOI: 10.1002/pro.4850] [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: 07/12/2023] [Revised: 10/29/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Protein structure prediction has emerged as a core technology for understanding biomolecules and their interactions. Here, we combine homology-based structure prediction with molecular phylogenetic analysis to study the evolution of electrostatic membrane binding among the vertebrate synaptotagmin-like protein (Slp) family. Slp family proteins play key roles in the membrane trafficking of large dense-core secretory vesicles. Our previous experimental and computational study found that the C2A domain of Slp-4 (also called granuphilin) binds with high affinity to anionic phospholipids in the cytoplasmic leaflet of the plasma membrane through a large positively charged protein surface centered on a cluster of phosphoinositide-binding lysine residues. Because this surface contributes greatly to Slp-4 C2A domain membrane binding, we hypothesized that the net charge on the surface might be evolutionarily conserved. To test this hypothesis, the known C2A sequences of Slp-4 among vertebrates were organized by class (from mammalia to pisces) using molecular phylogenetic analysis. Consensus sequences for each class were then identified and used to generate homology structures, from which Poisson-Boltzmann electrostatic potentials were calculated. For comparison, homology structures and electrostatic potentials were also calculated for the five human Slp protein family members. The results demonstrate that the charge on the membrane-binding surface is highly conserved throughout the evolution of Slp-4, and more highly conserved than many individual residues among the human Slp family paralogs. Such molecular phylogenetic-driven computational analysis can help to describe the evolution of electrostatic interactions between proteins and membranes which are crucial for their function.
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Affiliation(s)
- Nara L. Chon
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Sherleen Tran
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | | | - Hai Lin
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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5
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Kato M, Watari M, Tsuge T, Zhong S, Gu H, Qu LJ, Fujiwara T, Aoyama T. Redundant function of the Arabidopsis phosphatidylinositol 4-phosphate 5-kinase genes PIP5K4-6 is essential for pollen germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:212-225. [PMID: 37828913 DOI: 10.1111/tpj.16490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/02/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) is a key enzyme producing the signaling lipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2 ] in eukaryotes. Although PIP5K genes are reported to be involved in pollen tube germination and growth, the essential roles of PIP5K in these processes remain unclear. Here, we performed a comprehensive genetic analysis of the Arabidopsis thaliana PIP5K4, PIP5K5, and PIP5K6 genes and revealed that their redundant function is essential for pollen germination. Pollen with the pip5k4pip5k5pip5k6 triple mutation was sterile, while pollen germination efficiency and pollen tube growth were reduced in the pip5k6 single mutant and further reduced in the pip5k4pip5k6 and pip5k5pip5k6 double mutants. YFP-fusion proteins, PIP5K4-YFP, PIP5K5-YFP, and PIP5K6-YFP, which could rescue the sterility of the triple mutant pollen, preferentially localized to the tricolpate aperture area and the future germination site on the plasma membrane prior to germination. Triple mutant pollen grains under the germination condition, in which spatiotemporal localization of the PtdIns(4,5)P2 fluorescent marker protein 2xmCHERRY-2xPHPLC as seen in the wild type was abolished, exhibited swelling and rupture of the pollen wall, but neither the conspicuous protruding site nor site-specific deposition of cell wall materials for germination. These data indicate that PIP5K4-6 and their product PtdIns(4,5)P2 are essential for pollen germination, possibly through the establishment of the germination polarity in a pollen grain.
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Affiliation(s)
- Mariko Kato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Machiko Watari
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Sheng Zhong
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Hongya Gu
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Li-Jia Qu
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Takashi Fujiwara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
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6
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Liu DA, Tao K, Wu B, Yu Z, Szczepaniak M, Rames M, Yang C, Svitkina T, Zhu Y, Xu F, Nan X, Guo W. A phosphoinositide switch mediates exocyst recruitment to multivesicular endosomes for exosome secretion. Nat Commun 2023; 14:6883. [PMID: 37898620 PMCID: PMC10613218 DOI: 10.1038/s41467-023-42661-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
Exosomes are secreted to the extracellular milieu when multivesicular endosomes (MVEs) dock and fuse with the plasma membrane. However, MVEs are also known to fuse with lysosomes for degradation. How MVEs are directed to the plasma membrane for exosome secretion rather than to lysosomes is unclear. Here we report that a conversion of phosphatidylinositol-3-phosphate (PI(3)P) to phosphatidylinositol-4-phosphate (PI(4)P) catalyzed sequentially by Myotubularin 1 (MTM1) and phosphatidylinositol 4-kinase type IIα (PI4KIIα) on the surface of MVEs mediates the recruitment of the exocyst complex. The exocyst then targets the MVEs to the plasma membrane for exosome secretion. We further demonstrate that disrupting PI(4)P generation or exocyst function blocked exosomal secretion of Programmed death-ligand 1 (PD-L1), a key immune checkpoint protein in tumor cells, and led to its accumulation in lysosomes. Together, our study suggests that the PI(3)P to PI(4)P conversion on MVEs and the recruitment of the exocyst direct the exocytic trafficking of MVEs for exosome secretion.
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Affiliation(s)
- Di-Ao Liu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Tao
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
| | - Bin Wu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ziyan Yu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Malwina Szczepaniak
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
| | - Matthew Rames
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Changsong Yang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tatyana Svitkina
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yueyao Zhu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, 19104, USA
| | - Fengyuan Xu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaolin Nan
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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7
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Nikolatou K, Sandilands E, Román‐Fernández A, Cumming EM, Freckmann E, Lilla S, Buetow L, McGarry L, Neilson M, Shaw R, Strachan D, Miller C, Huang DT, McNeish IA, Norman JC, Zanivan S, Bryant DM. PTEN deficiency exposes a requirement for an ARF GTPase module for integrin-dependent invasion in ovarian cancer. EMBO J 2023; 42:e113987. [PMID: 37577760 PMCID: PMC10505920 DOI: 10.15252/embj.2023113987] [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: 03/09/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Dysregulation of the PI3K/AKT pathway is a common occurrence in high-grade serous ovarian carcinoma (HGSOC), with the loss of the tumour suppressor PTEN in HGSOC being associated with poor prognosis. The cellular mechanisms of how PTEN loss contributes to HGSOC are largely unknown. We here utilise time-lapse imaging of HGSOC spheroids coupled to a machine learning approach to classify the phenotype of PTEN loss. PTEN deficiency induces PI(3,4,5)P3 -rich and -dependent membrane protrusions into the extracellular matrix (ECM), resulting in a collective invasion phenotype. We identify the small GTPase ARF6 as a crucial vulnerability of HGSOC cells upon PTEN loss. Through a functional proteomic CRISPR screen of ARF6 interactors, we identify the ARF GTPase-activating protein (GAP) AGAP1 and the ECM receptor β1-integrin (ITGB1) as key ARF6 interactors in HGSOC regulating PTEN loss-associated invasion. ARF6 functions to promote invasion by controlling the recycling of internalised, active β1-integrin to maintain invasive activity into the ECM. The expression of the CYTH2-ARF6-AGAP1 complex in HGSOC patients is inversely associated with outcome, allowing the identification of patient groups with improved versus poor outcome. ARF6 may represent a therapeutic vulnerability in PTEN-depleted HGSOC.
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Affiliation(s)
- Konstantina Nikolatou
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Emma Sandilands
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Alvaro Román‐Fernández
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Erin M Cumming
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Eva Freckmann
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | | | | | | | | | | | | | | | - Danny T Huang
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Iain A McNeish
- Department of Surgery and Cancer, Ovarian Cancer Action Research CentreImperial College LondonLondonUK
| | - James C Norman
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - Sara Zanivan
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
| | - David M Bryant
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- The CRUK Beatson InstituteGlasgowUK
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8
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Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:ijms24098096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [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: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: Phafin1 and Phafin2. This protein family is unique because both the PH and FYVE domains bind to phosphatidylinositol 3-phosphate [PtdIns(3)P], a phosphoinositide primarily found in endosomal and lysosomal membranes. Phafin proteins act as PtdIns(3)P effectors in apoptosis, endocytic cargo trafficking, and autophagy. Additionally, Phafin2 is recruited to macropinocytic compartments through coincidence detection of PtdIns(3)P and PtdIns(4)P. Membrane-associated Phafins serve as adaptor proteins that recruit other binding partners. In addition to the phosphoinositide-binding domains, Phafin proteins present a poly aspartic acid motif that regulates membrane binding specificity. In this review, we summarize the involvement of Phafins in several cellular pathways and their potential physiological functions while highlighting the similarities and differences between Phafin1 and Phafin2. Besides, we discuss research perspectives for Phafins.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahmudul Hasan
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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9
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Carpenter AP, Khuu P, Weidner T, Johnson CP, Roeters SJ, Baio JE. Orientation of the Dysferlin C2A Domain is Responsive to the Composition of Lipid Membranes. J Phys Chem B 2023; 127:577-589. [PMID: 36608331 DOI: 10.1021/acs.jpcb.2c06716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Dysferlin is a 230 kD protein that plays a critical function in the active resealing of micron-sized injuries to the muscle sarcolemma by recruiting vesicles to patch the injured site via vesicle fusion. Muscular dystrophy is observed in humans when mutations disrupt this repair process or dysferlin is absent. While lipid binding by dysferlin's C2A domain (dysC2A) is considered fundamental to the membrane resealing process, the molecular mechanism of this interaction is not fully understood. By applying nonlinear surface-specific vibrational spectroscopy, we have successfully demonstrated that dysferlin's N-terminal C2A domain (dysC2A) alters its binding orientation in response to a membrane's lipid composition. These experiments reveal that dysC2A utilizes a generic electrostatic binding interaction to bind to most anionic lipid surfaces, inserting its calcium binding loops into the lipid surface while orienting its β-sheets 30-40° from surface normal. However, at lipid surfaces, where PI(4,5)P2 is present, dysC2A tilts its β-sheets more than 60° from surface normal to expose a polybasic face, while it binds to the PI(4,5)P2 surface. Both lipid binding mechanisms are shown to occur alongside dysC2A-induced lipid clustering. These different binding mechanisms suggest that dysC2A could provide a molecular cue to the larger dysferlin protein as to signal whether it is bound to the sarcolemma or another lipid surface.
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Affiliation(s)
- Andrew P Carpenter
- The School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon97331, United States
| | - Patricia Khuu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon97331, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | - Colin P Johnson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon97331, United States
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | - Joe E Baio
- The School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon97331, United States
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10
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11
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Jeschke A. An In Vitro System to Analyze Generation and Degradation of Phagosomal Phosphatidylinositol Phosphates. Methods Mol Biol 2023; 2692:261-274. [PMID: 37365474 DOI: 10.1007/978-1-0716-3338-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Phagosomes are formed when phagocytic cells take up large particles, and they develop into phagolysosomes where the particles are degraded. The transformation of nascent phagosomes into phagolysosomes is a complex multi-step process, and the precise timing of these steps depends at least in part on phosphatidylinositol phosphates (PIPs). Some such-called "intracellular pathogens" are not delivered to microbicidal phagolysosomes and manipulate the PIP composition of the phagosomes they reside in. Studying the dynamic changes of the PIP composition of inert-particle phagosomes will help to understand why the pathogens' manipulations reprogram phagosome maturation.We here describe a method to detect and to follow generation and degradation of PIPs on purified phagosomes. To this end, phagosomes formed around inert latex beads are purified from J774E macrophages and incubated in vitro with PIP-binding protein domains or PIP-binding antibodies. Binding of such PIP sensors to phagosomes indicates presence of the cognate PIP and is quantified by immunofluorescence microscopy. When phagosomes are incubated with PIP sensors and ATP at a physiological temperature, the generation and degradation of PIPs can be followed, and PIP-metabolizing enzymes can be identified using specific inhibitory agents.
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Affiliation(s)
- Andreas Jeschke
- Institute for Cell Biology, University of Bonn, Bonn, Germany.
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12
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The Role of Primary Cilia-Associated Phosphoinositide Signaling in Development. J Dev Biol 2022; 10:jdb10040051. [PMID: 36547473 PMCID: PMC9785882 DOI: 10.3390/jdb10040051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/07/2022] Open
Abstract
Primary cilia are microtube-based organelles that extend from the cell surface and function as biochemical and mechanical extracellular signal sensors. Primary cilia coordinate a series of signaling pathways during development. Cilia dysfunction leads to a pleiotropic group of developmental disorders, termed ciliopathy. Phosphoinositides (PIs), a group of signaling phospholipids, play a crucial role in development and tissue homeostasis by regulating membrane trafficking, cytoskeleton reorganization, and organelle identity. Accumulating evidence implicates the involvement of PI species in ciliary defects and ciliopathies. The abundance and localization of PIs in the cell are tightly regulated by the opposing actions of kinases and phosphatases, some of which are recently discovered in the context of primary cilia. Here, we review several cilium-associated PI kinases and phosphatases, including their localization along cilia, function in regulating the ciliary biology under normal conditions, as well as the connection of their disease-associated mutations with ciliopathies.
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13
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Jani RA, Di Cicco A, Keren-Kaplan T, Vale-Costa S, Hamaoui D, Hurbain I, Tsai FC, Di Marco M, Macé AS, Zhu Y, Amorim MJ, Bassereau P, Bonifacino JS, Subtil A, Marks MS, Lévy D, Raposo G, Delevoye C. PI4P and BLOC-1 remodel endosomal membranes into tubules. J Biophys Biochem Cytol 2022; 221:213508. [PMID: 36169638 PMCID: PMC9524204 DOI: 10.1083/jcb.202110132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 12/11/2022] Open
Abstract
Intracellular trafficking is mediated by transport carriers that originate by membrane remodeling from donor organelles. Tubular carriers contribute to the flux of membrane lipids and proteins to acceptor organelles, but how lipids and proteins impose a tubular geometry on the carriers is incompletely understood. Using imaging approaches on cells and in vitro membrane systems, we show that phosphatidylinositol-4-phosphate (PI4P) and biogenesis of lysosome-related organelles complex 1 (BLOC-1) govern the formation, stability, and functions of recycling endosomal tubules. In vitro, BLOC-1 binds and tubulates negatively charged membranes, including those containing PI4P. In cells, endosomal PI4P production by type II PI4-kinases is needed to form and stabilize BLOC-1-dependent recycling endosomal tubules. Decreased PI4KIIs expression impairs the recycling of endosomal cargoes and the life cycles of intracellular pathogens such as Chlamydia bacteria and influenza virus that exploit the membrane dynamics of recycling endosomes. This study demonstrates how a phospholipid and a protein complex coordinate the remodeling of cellular membranes into functional tubules.
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Affiliation(s)
- Riddhi Atul Jani
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Silvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Daniel Hamaoui
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Ilse Hurbain
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Feng-Ching Tsai
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Mathilde Di Marco
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Anne-Sophie Macé
- Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Yueyao Zhu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research Centre, Palma de Cima, Lisboa, Portugal
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Agathe Subtil
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Graça Raposo
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Cédric Delevoye
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
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14
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Kunduri G, Le SH, Baena V, Vijaykrishna N, Harned A, Nagashima K, Blankenberg D, Yoshihiro I, Narayan K, Bamba T, Acharya U, Acharya JK. Delivery of ceramide phosphoethanolamine lipids to the cleavage furrow through the endocytic pathway is essential for male meiotic cytokinesis. PLoS Biol 2022; 20:e3001599. [PMID: 36170207 PMCID: PMC9550178 DOI: 10.1371/journal.pbio.3001599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 10/10/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Cell division, wherein 1 cell divides into 2 daughter cells, is fundamental to all living organisms. Cytokinesis, the final step in cell division, begins with the formation of an actomyosin contractile ring, positioned midway between the segregated chromosomes. Constriction of the ring with concomitant membrane deposition in a specified spatiotemporal manner generates a cleavage furrow that physically separates the cytoplasm. Unique lipids with specific biophysical properties have been shown to localize to intercellular bridges (also called midbody) connecting the 2 dividing cells; however, their biological roles and delivery mechanisms remain largely unknown. In this study, we show that ceramide phosphoethanolamine (CPE), the structural analog of sphingomyelin, has unique acyl chain anchors in Drosophila spermatocytes and is essential for meiotic cytokinesis. The head group of CPE is also important for spermatogenesis. We find that aberrant central spindle and contractile ring behavior but not mislocalization of phosphatidylinositol phosphates (PIPs) at the plasma membrane is responsible for the male meiotic cytokinesis defect in CPE-deficient animals. Further, we demonstrate the enrichment of CPE in multivesicular bodies marked by Rab7, which in turn localize to cleavage furrow. Volume electron microscopy analysis using correlative light and focused ion beam scanning electron microscopy shows that CPE-enriched Rab7 positive endosomes are juxtaposed on contractile ring material. Correlative light and transmission electron microscopy reveal Rab7 positive endosomes as a multivesicular body-like organelle that releases its intraluminal vesicles in the vicinity of ingressing furrows. Genetic ablation of Rab7 or Rab35 or expression of dominant negative Rab11 results in significant meiotic cytokinesis defects. Further, we show that Rab11 function is required for localization of CPE positive endosomes to the cleavage furrow. Our results imply that endosomal delivery of CPE to ingressing membranes is crucial for meiotic cytokinesis.
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Affiliation(s)
- Govind Kunduri
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
| | - Si-Hung Le
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Valentina Baena
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nagampalli Vijaykrishna
- Genomic Medicine Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kunio Nagashima
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Daniel Blankenberg
- Genomic Medicine Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Izumi Yoshihiro
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Usha Acharya
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
| | - Jairaj K. Acharya
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
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15
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Zhou C, Dong X, Wang M, Qian X, Hu M, Liang K, Liang Y, Zhang R, Huang Y, Lyu H, Xiao S, Tang Y, Ali DW, Michalak M, Chen XZ, Tang J. Phosphorylated STYK1 restrains the inhibitory role of EGFR in autophagy initiation and EGFR-TKIs sensitivity. CELL INSIGHT 2022; 1:100045. [PMID: 37192859 PMCID: PMC10120315 DOI: 10.1016/j.cellin.2022.100045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 05/18/2023]
Abstract
Epidermal growth factor receptor (EGFR) plays critical roles in cell proliferation and tumorigenesis. Autophagy has emerged as a potential mechanism involved in the acquired resistance to anti-EGFR treatments, however, the molecular mechanisms has not been fully addressed. In this study, we identified EGFR interacts with STYK1, a positive autophagy regulator, in EGFR kinase activity dependent manner. We found that EGFR phosphorylates STYK1 at Y356 site and STYK1 inhibits activated EGFR mediated Beclin1 tyrosine phosphorylation and interaction between Bcl2 and Beclin1, thus enhances PtdIns3K-C1 complex assembly and autophagy initiation. We also demonstrated that STYK1 depletion increased the sensitivity of NSCLC cells to EGFR-TKIs in vitro and in vivo. Moreover, EGFR-TKIs induced activation of AMPK phosphorylates STYK1 at S304 site. STYK1 S304 collaborated with Y356 phosphorylation to enhance the EGFR-STYK1 interaction and reverse the inhibitory effects of EGFR to autophagy flux. Collectively, these data revealed new roles and cross-talk between STYK1 and EGFR in autophagy regulation and EGFR-TKIs sensitivity in NSCLC.
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Affiliation(s)
- Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Xueying Dong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xuehong Qian
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Miao Hu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Kai Liang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Yanyan Liang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Yuan Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Yongfei Tang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
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16
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Nguyen Trung M, Furkert D, Fiedler D. Versatile signaling mechanisms of inositol pyrophosphates. Curr Opin Chem Biol 2022; 70:102177. [PMID: 35780751 DOI: 10.1016/j.cbpa.2022.102177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 01/03/2023]
Abstract
Inositol pyrophosphates (PP-InsPs) constitute a group of highly charged messengers, which regulate central biological processes in health and disease, such as cellular phosphate and general energy homeostasis. Deciphering the molecular mechanisms underlying PP-InsP-mediated signaling remains a challenge due to the unique properties of these molecules, the different modes of action they can access, and a somewhat limited chemical and analytical toolset. Herein, we summarize the most recent mechanistic insights into PP-InsP signaling, which illustrate our progress in connecting mechanism and function of PP-InsPs.
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Affiliation(s)
- Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany.
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17
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Lahree A, Baptista SDJS, Marques S, Perschin V, Zuzarte-Luís V, Goel M, Choudhary HH, Mishra S, Stigloher C, Zerial M, Sundaramurthy V, Mota MM. Active APPL1 sequestration by Plasmodium favors liver-stage development. Cell Rep 2022; 39:110886. [PMID: 35649358 DOI: 10.1016/j.celrep.2022.110886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/10/2022] [Accepted: 05/06/2022] [Indexed: 11/03/2022] Open
Abstract
Intracellular pathogens manipulate host cells to survive and thrive. Cellular sensing and signaling pathways are among the key host machineries deregulated to favor infection. In this study, we show that liver-stage Plasmodium parasites compete with the host to sequester a host endosomal-adaptor protein (APPL1) known to regulate signaling in response to endocytosis. The enrichment of APPL1 at the parasitophorous vacuole membrane (PVM) involves an atypical Plasmodium Rab5 isoform (Rab5b). Depletion of host APPL1 alters neither the infection nor parasite development; however, upon overexpression of a GTPase-deficient host Rab5 mutant (hRab5_Q79L), the parasites are smaller and their PVM is stripped of APPL1. Infection with the GTPase-deficient Plasmodium berghei Rab5b mutant (PbRab5b_Q91L) in this case rescues the PVM APPL1 signal and parasite size. In summary, we observe a robust correlation between the level of APPL1 retention at the PVM and parasite size during exoerythrocytic development.
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Affiliation(s)
- Aparajita Lahree
- Instituto de Medicina Molecular- João Lobo Antunes (iMM-JLA), Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; Departamento de Bioengenharia, Instituto Superior Técnico, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Sara de Jesus Santos Baptista
- Instituto de Medicina Molecular- João Lobo Antunes (iMM-JLA), Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sofia Marques
- Instituto de Medicina Molecular- João Lobo Antunes (iMM-JLA), Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Veronika Perschin
- Imaging Core Facility, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Vanessa Zuzarte-Luís
- Instituto de Medicina Molecular- João Lobo Antunes (iMM-JLA), Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Manisha Goel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS), Bellary Road, Bangalore 560065, Karnataka, India
| | - Hadi Hasan Choudhary
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Satish Mishra
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Christian Stigloher
- Imaging Core Facility, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Varadharajan Sundaramurthy
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS), Bellary Road, Bangalore 560065, Karnataka, India
| | - Maria M Mota
- Instituto de Medicina Molecular- João Lobo Antunes (iMM-JLA), Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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18
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A Phosphoinositide-Binding Protein Acts in the Trafficking Pathway of Hemoglobin in the Malaria Parasite Plasmodium falciparum. mBio 2022; 13:e0323921. [PMID: 35038916 PMCID: PMC8764524 DOI: 10.1128/mbio.03239-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phosphoinositide lipids play key roles in a variety of processes in eukaryotic cells, but our understanding of their functions in the malaria parasite Plasmodium falciparum is still very much limited. To gain a deeper comprehension of the roles of phosphoinositides in this important pathogen, we attempted gene inactivation for 24 putative effectors of phosphoinositide metabolism. Our results reveal that 79% of the candidates are refractory to genetic deletion and are therefore potentially essential for parasite growth. Inactivation of the gene coding for a Plasmodium-specific putative phosphoinositide-binding protein, which we named PfPX1, results in a severe growth defect. We show that PfPX1 likely binds phosphatidylinositol-3-phosphate and that it localizes to the membrane of the digestive vacuole of the parasite and to vesicles filled with host cell cytosol and labeled with endocytic markers. Critically, we provide evidence that it is important in the trafficking pathway of hemoglobin from the host erythrocyte to the digestive vacuole. Finally, inactivation of PfPX1 renders parasites resistant to artemisinin, the frontline antimalarial drug. Globally, the minimal redundancy in the putative phosphoinositide proteins uncovered in our work supports that targeting this pathway has potential for antimalarial drug development. Moreover, our identification of a phosphoinositide-binding protein critical for the trafficking of hemoglobin provides key insight into this essential process. IMPORTANCE Malaria represents an enormous burden for a significant proportion of humanity, and the lack of vaccines and problems with drug resistance to all antimalarials demonstrate the need to develop new therapeutics. Inhibitors of phosphoinositide metabolism are currently being developed as antimalarials but our understanding of this biological pathway is incomplete. The malaria parasite lives inside human red blood cells where it imports hemoglobin to cover some of its nutritional needs. In this work, we have identified a phosphoinositide-binding protein that is important for the transport of hemoglobin in the parasite. Inactivation of this protein decreases the ability of the parasite to proliferate. Our results have therefore identified a potential new target for antimalarial development.
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19
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Doumane M, Caillaud MC, Jaillais Y. Experimental manipulation of phosphoinositide lipids: from cells to organisms. Trends Cell Biol 2022; 32:445-461. [DOI: 10.1016/j.tcb.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/14/2022]
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20
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Quilici G, Berardi A, Fabris C, Ghitti M, Punta M, Gourlay LJ, Bolognesi M, Musco G. Solution Structure of the BPSL1445 Protein of Burkholderia pseudomallei Reveals the SYLF Domain Three-Dimensional Fold. ACS Chem Biol 2022; 17:230-239. [PMID: 34968022 DOI: 10.1021/acschembio.1c00886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The SYLF domain is an evolutionary conserved protein domain with phosphatidylinositol binding ability, whose three-dimensional structure is unknown. Here, we present the solution structure and the dynamics characterization of the SYLF domain of the bacterial BPSL1445 protein. BPSL1445 is a seroreactive antigen and a diagnostic marker of Burkholderia pseudomallei, the etiological agent of melioidosis, a severe infectious disease in the tropics. The BPSL1445 SYLF domain (BPSL1445-SYLF) consists of a β-barrel core, with two flexible loops protruding out of the barrel and three helices packing on its surface. Our structure allows for a more precise definition of the boundaries of the SYLF domain compared to the previously reported one and suggests common ancestry with bacterial EipA domains. We also demonstrate by phosphatidyl-inositol phosphate arrays and nuclear magnetic resonance titrations that BPSL1445-SYLF weakly interacts with phosphoinositides, thus supporting lipid binding abilities of this domain also in prokaryotes.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Chantal Fabris
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology and Center for Omics Sciences, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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21
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Fratini E, Salvemini M, Lombardo F, Muzzi M, Molfini M, Gisondi S, Roma E, D'Ezio V, Persichini T, Gasperi T, Mariottini P, Di Giulio A, Bologna MA, Cervelli M, Mancini E. Unraveling the role of male reproductive tract and haemolymph in cantharidin-exuding Lydus trimaculatus and Mylabris variabilis (Coleoptera: Meloidae): a comparative transcriptomics approach. BMC Genomics 2021; 22:808. [PMID: 34749651 PMCID: PMC8576976 DOI: 10.1186/s12864-021-08118-8] [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: 11/13/2020] [Accepted: 10/23/2021] [Indexed: 12/13/2022] Open
Abstract
Background Meloidae (blister beetles) are known to synthetize cantharidin (CA), a toxic and defensive terpene mainly stored in male accessory glands (MAG) and emitted outward through reflex-bleeding. Recent progresses in understanding CA biosynthesis and production organ(s) in Meloidae have been made, but the way in which self-protection is achieved from the hazardous accumulation and release of CA in blister beetles has been experimentally neglected. To provide hints on this pending question, a comparative de novo assembly transcriptomic approach was performed by targeting two tissues where CA is largely accumulated and regularly circulates in Meloidae: the male reproductive tract (MRT) and the haemolymph. Differential gene expression profiles in these tissues were examined in two blister beetle species, Lydus trimaculatus (Fabricius, 1775) (tribe Lyttini) and Mylabris variabilis (Pallas, 1781) (tribe Mylabrini). Upregulated transcripts were compared between the two species to identify conserved genes possibly involved in CA detoxification and transport. Results Based on our results, we hypothesize that, to avoid auto-intoxication, ABC, MFS or other solute transporters might sequester purported glycosylated CA precursors into MAG, and lipocalins could bind CA and mitigate its reactivity when released into the haemolymph during the autohaemorrhaging response. We also found an over-representation in haemolymph of protein-domains related to coagulation and integument repairing mechanisms that likely reflects the need to limit fluid loss during reflex-bleeding. Conclusions The de novo assembled transcriptomes of L. trimaculatus and M. variabilis here provided represent valuable genetic resources to further explore the mechanisms employed to cope with toxicity of CA in blister beetle tissues. These, if revealed, might help conceiving safe and effective drug-delivery approaches to enhance the use of CA in medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08118-8.
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Affiliation(s)
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Maurizio Muzzi
- Department of Sciences, University of Roma Tre, Rome, Italy
| | - Marco Molfini
- Department of Sciences, University of Roma Tre, Rome, Italy
| | - Silvia Gisondi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy.,Natural History Museum of Denmark, Copenhagen, Denmark
| | - Elia Roma
- Department of Sciences, University of Roma Tre, Rome, Italy
| | | | | | - Tecla Gasperi
- Department of Sciences, University of Roma Tre, Rome, Italy
| | | | | | | | | | - Emiliano Mancini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy.
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22
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Piras C, Pibiri M, Leoni VP, Balsamo A, Tronci L, Arisci N, Mariotti S, Atzori L. Analysis of metabolomics profile in hypothyroid patients before and after thyroid hormone replacement. J Endocrinol Invest 2021; 44:1309-1319. [PMID: 33025552 DOI: 10.1007/s40618-020-01434-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE The serum metabolic changes occurring during the transition from hypothyroidism to euthyroidism are not known. This study aimed to determine the metabolomic profile in hypothyroid patients before (HypoT0) and after (HypoT1) euthyroidism achieved through levothyroxine (L-T4) treatment. METHODS Eighteen patients with overt primary hypothyroidism were recruited for the study. All patients were treated with L-T4 to achieve euthyroidism. Thyrotropin (TSH), free thyroxine (FT4), free triiodothyronine (FT3) and metabolomics profiles were measured before and after 3 months of treatment. The euthyroid control group consisted of 28 healthy volunteers. Metabolomics analysis was performed using Nuclear Magnetic Resonance (NMR) spectroscopy. RESULTS 1H NMR-based metabolomics profiling of patients with newly diagnosed hypothyroidism (HypoT0) showed significantly higher levels of citrate, creatinine, glycerol, myo-inositol and serine, and lower levels of proline and taurine compared to controls. Interestingly, some metabolic changes were persistent three months after pharmacological treatments, despite normal serum TSH and thyroid hormone concentrations (HypoT1). When an Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) model was built to evaluate possible differences in the metabolic profile between HypoT0 and HypoT1, the data obtained were not significantly different. CONCLUSION These results suggest that metabolic changes in the patients with hypothyroidism may persist after normalization of serum levels of FT3, FT4, and TSH, which currently represent the gold standard in laboratory testing for diagnosis and evaluation of thyroid pathology. So, the metabolomics approach may contribute to integrate classical hormone assays and to determine the euthyroid status achievement with greater efficacy.
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Affiliation(s)
- C Piras
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - M Pibiri
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - V P Leoni
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - A Balsamo
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - L Tronci
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - N Arisci
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy
| | - S Mariotti
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy.
| | - L Atzori
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
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23
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Larsen AH, Sansom MSP. Binding of Ca 2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021; 29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
Abstract
C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins. Binding of Ca2+-independent C2 domains to membranes was explored by MD simulation C2 domains from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2 were compared C2 domains formed longer-lived interactions with lipid bilayers containing PIP2 For PTEN and SHIP2, simulations of their phosphatase plus C2 domains were performed
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Affiliation(s)
- Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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24
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Dubois GA, Jaillais Y. Anionic phospholipid gradients: an uncharacterized frontier of the plant endomembrane network. PLANT PHYSIOLOGY 2021; 185:577-592. [PMID: 33793905 PMCID: PMC8133617 DOI: 10.1093/plphys/kiaa056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/16/2020] [Indexed: 05/19/2023]
Abstract
Anionic phospholipids include phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylinositol (PI), and its phosphorylated derivatives the phosphoinositides (e.g. phosphatidylinositol-4-phosphate [PI4P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]). Although anionic phospholipids are low-abundant lipids, they are particularly important for membrane functions. In particular, anionic lipids act as biochemical and biophysical landmarks that contribute to the establishment of membrane identity, signaling activities, and compartment morphodynamics. Each anionic lipid accumulates in different endomembranes according to a unique subcellular pattern, where they locally provide docking platforms for proteins. As such, they are mostly believed to act in the compartments in which they accumulate. However, mounting evidence throughout eukaryotes suggests that anionic lipids are not as compartment-specific as initially thought and that they are instead organized as concentration gradients across different organelles. In this update, we review the evidence for the existence of anionic lipid gradients in plants. We then discuss the possible implication of these gradients in lipid dynamics and homeostasis, and also in coordinating subcellular activities. Finally, we introduce the notion that anionic lipid gradients at the cellular scale may translate into gradients at the tissue level, which could have implications for plant development.
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Affiliation(s)
- Gwennogan A Dubois
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
- Author for communication:
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25
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Ernest James Phillips T, Maguire E. Phosphoinositides: Roles in the Development of Microglial-Mediated Neuroinflammation and Neurodegeneration. Front Cell Neurosci 2021; 15:652593. [PMID: 33841102 PMCID: PMC8032904 DOI: 10.3389/fncel.2021.652593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
Microglia are increasingly recognized as vital players in the pathology of a variety of neurodegenerative conditions including Alzheimer’s (AD) and Parkinson’s (PD) disease. While microglia have a protective role in the brain, their dysfunction can lead to neuroinflammation and contributes to disease progression. Also, a growing body of literature highlights the seven phosphoinositides, or PIPs, as key players in the regulation of microglial-mediated neuroinflammation. These small signaling lipids are phosphorylated derivates of phosphatidylinositol, are enriched in the brain, and have well-established roles in both homeostasis and disease.Disrupted PIP levels and signaling has been detected in a variety of dementias. Moreover, many known AD disease modifiers identified via genetic studies are expressed in microglia and are involved in phospholipid metabolism. One of these, the enzyme PLCγ2 that hydrolyzes the PIP species PI(4,5)P2, displays altered expression in AD and PD and is currently being investigated as a potential therapeutic target.Perhaps unsurprisingly, neurodegenerative conditions exhibiting PIP dyshomeostasis also tend to show alterations in aspects of microglial function regulated by these lipids. In particular, phosphoinositides regulate the activities of proteins and enzymes required for endocytosis, toll-like receptor signaling, purinergic signaling, chemotaxis, and migration, all of which are affected in a variety of neurodegenerative conditions. These functions are crucial to allow microglia to adequately survey the brain and respond appropriately to invading pathogens and other abnormalities, including misfolded proteins. AD and PD therapies are being developed to target many of the above pathways, and although not yet investigated, simultaneous PIP manipulation might enhance the beneficial effects observed. Currently, only limited therapeutics are available for dementia, and although these show some benefits for symptom severity and progression, they are far from curative. Given the importance of microglia and PIPs in dementia development, this review summarizes current research and asks whether we can exploit this information to design more targeted, or perhaps combined, dementia therapeutics. More work is needed to fully characterize the pathways discussed in this review, but given the strength of the current literature, insights in this area could be invaluable for the future of neurodegenerative disease research.
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Affiliation(s)
| | - Emily Maguire
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
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26
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Characterization of Protein-Phospholipid/Membrane Interactions Using a "Membrane-on-a-Chip" Microfluidic System. Methods Mol Biol 2021. [PMID: 33481237 DOI: 10.1007/978-1-0716-1142-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
It is now clear that organelles of a mammalian cell can be distinguished by phospholipid profiles, both as ratios of common phospholipids and by the absence or presence of certain phospholipids. Organelle-specific phospholipids can be used to provide a specific shape and fluidity to the membrane and/or used to recruit and/or traffic proteins to the appropriate subcellular location and to restrict protein function to this location. Studying the interactions of proteins with specific phospholipids using soluble derivatives in isolation does not always provide useful information because the context in which the headgroups are presented almost always matters. Our laboratory has shown this circumstance to be the case for a viral protein binding to phosphoinositides in solution and in membranes. The system we have developed to study protein-phospholipid interactions in the context of a membrane benefits from the creation of tailored membranes in a channel of a microfluidic device, with a fluorescent lipid in the membrane serving as an indirect reporter of protein binding. This system is amenable to the study of myriad interactions occurring at a membrane surface as long as a net change in surface charge occurs in response to the binding event of interest.
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27
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Hanley SE, Cooper KF. Sorting Nexins in Protein Homeostasis. Cells 2020; 10:cells10010017. [PMID: 33374212 PMCID: PMC7823608 DOI: 10.3390/cells10010017] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis is maintained by removing misfolded, damaged, or excess proteins and damaged organelles from the cell by three major pathways; the ubiquitin-proteasome system, the autophagy-lysosomal pathway, and the endo-lysosomal pathway. The requirement for ubiquitin provides a link between all three pathways. Sorting nexins are a highly conserved and diverse family of membrane-associated proteins that not only traffic proteins throughout the cells but also provide a second common thread between protein homeostasis pathways. In this review, we will discuss the connections between sorting nexins, ubiquitin, and the interconnected roles they play in maintaining protein quality control mechanisms. Underlying their importance, genetic defects in sorting nexins are linked with a variety of human diseases including neurodegenerative, cardiovascular diseases, viral infections, and cancer. This serves to emphasize the critical roles sorting nexins play in many aspects of cellular function.
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28
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Pace C, Tumino D, Russo M, Le Moli R, Naselli A, Borzì G, Malandrino P, Frasca F. Role of selenium and myo-inositol supplementation on autoimmune thyroiditis progression. Endocr J 2020; 67:1093-1098. [PMID: 32669509 DOI: 10.1507/endocrj.ej20-0062] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Previous reports indicate that selenium supplementation may be useful to reduce cell oxidative stress. In particular, selenium may decrease the level of thyroid autoantibodies in patients with Hashimoto's thyroiditis (HT). Recent studies also indicate that myo-inositol may have beneficial effects on thyroid function in patients with HT. Hence, the aim of the present study is to evaluate whether myo-inositol may enhance the protective effect of selenium on HT progression to hypothyroidism. The study was designed as observational and retrospective. Thyroid hormones were evaluated in patients with HT who were either euthyroid or subclinically hypothyroid. These patients were subdivided into three groups: untreated, treated with selenomethionine alone (Se-meth: 83 μg/day) and treated with Se-meth plus myo-inositol (Se-meth + Myo-I: 83 μg/day + 600 mg/day). Outcome evaluation was performed at baseline and after 6 and 12 months of treatment. High-resolution ultrasound of the thyroid gland was performed to evaluate changes in thyroid echoic pattern during the study. Compared to baseline, levels of thyroid-stimulating hormone (TSH) increased significantly in untreated patients but decreased by 31% and 38%, respectively, in those treated with Se-meth and Se-meth + Myo-I. Moreover, in the latter group the TSH reduction was observed earlier than in the Se-meth-treated group. Densitometric analysis of thyroid ultrasonography showed an echoic pattern improvement in both treated groups compared to untreated patients, although this difference was not statistically significant. Thus, Se-meth treatment is effective in patients with HT and its effect may be improved in combination with Myo-I through earlier achievement of TSH levels closer to physiological concentrations.
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Affiliation(s)
- Cinzia Pace
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Dario Tumino
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Marco Russo
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Rosario Le Moli
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Adriano Naselli
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Graziella Borzì
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Pasqualino Malandrino
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
| | - Francesco Frasca
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Medical Center, Via Palermo 636, 95122 Catania, Italy
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29
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Reeh K, Summers PA, Gould IR, Woscholski R, Vilar R. Design, synthesis and evaluation of a tripodal receptor for phosphatidylinositol phosphates. Sci Rep 2020; 10:18450. [PMID: 33116198 PMCID: PMC7595110 DOI: 10.1038/s41598-020-75484-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/15/2020] [Indexed: 11/30/2022] Open
Abstract
Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular processes. Their function is dictated by the number and positions of the phosphate groups in the inositol ring (with seven different PIPs being active in the cell). Therefore, there is significant interest in developing small-molecule receptors that can bind selectively to these species and in doing so affect their cellular function or be the basis for molecular probes. However, to date there are very few examples of such molecular receptors. Towards this aim, herein we report a novel tripodal molecule that acts as receptor for mono- and bis-phosphorylated PIPs in a cell free environment. To assess their affinity to PIPs we have developed a new cell free assay based on the ability of the receptor to prevent alkaline phosphatase from hydrolysing these substrates. The new receptor displays selectivity towards two out of the seven PIPs, namely PI(3)P and PI(3,4)P2. To rationalise these results, a DFT computational study was performed which corroborated the experimental results and provided insight into the host-guest binding mode.
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Affiliation(s)
- Katharina Reeh
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Peter A Summers
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Ian R Gould
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Rudiger Woscholski
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK.
- Institute of Chemical Biology, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK.
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30
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Lee MF, Trotman LC. PTEN: Bridging Endocytosis and Signaling. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036103. [PMID: 31818848 DOI: 10.1101/cshperspect.a036103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The transduction of signals in the PTEN/PI3-kinase (PI3K) pathway is built around a phosphoinositide (PIP) lipid messenger, phosphatidylinositol trisphosphate, PI(3,4,5)P3 or PIP3 Another, more ancient role of this family of messengers is the control of endocytosis, where a handful of separate PIPs act like postal codes. Prominent among them is PI(3)P, which helps to ensure that endocytic vesicles, their cargo, and membranes themselves reach their correct destinations. Traditionally, the cancer and the endocytic functions of the PI3K signaling pathway have been studied by cancer and membrane biologists, respectively, with some notable but overall minimal overlap. Modern microscopy has enabled monitoring of the PTEN/PI3K pathway in action. Here, we explore the flurry of groundbreaking concepts emerging from those efforts. The discovery that PTEN contains an autonomous PI(3)P reader domain, fused to the catalytic PIP3 eraser domain has prompted us to explore the relationship between PI3K signaling and endocytosis. This revealed how PTEN can achieve signal termination in a precisely controlled fashion, because endocytosis can package the PIP3 signal into discrete units that PTEN will erase. We explore how PTEN can bridge the worlds of endocytosis and PI3K signaling and discuss progress on how PI3K/AKT signaling can be acting from internal membranes. We discuss how the PTEN/PI3K system for growth control may have emerged from principles of endocytosis, and how this development could have affected the evolution of multicellular organisms.
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Affiliation(s)
- Matthew F Lee
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Lloyd C Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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31
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Katan M, Cockcroft S. Phosphatidylinositol(4,5)bisphosphate: diverse functions at the plasma membrane. Essays Biochem 2020; 64:513-531. [PMID: 32844214 PMCID: PMC7517351 DOI: 10.1042/ebc20200041] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/25/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Phosphatidylinositol(4,5) bisphosphate (PI(4,5)P2) has become a major focus in biochemistry, cell biology and physiology owing to its diverse functions at the plasma membrane. As a result, the functions of PI(4,5)P2 can be explored in two separate and distinct roles - as a substrate for phospholipase C (PLC) and phosphoinositide 3-kinase (PI3K) and as a primary messenger, each having unique properties. Thus PI(4,5)P2 makes contributions in both signal transduction and cellular processes including actin cytoskeleton dynamics, membrane dynamics and ion channel regulation. Signalling through plasma membrane G-protein coupled receptors (GPCRs), receptor tyrosine kinases (RTKs) and immune receptors all use PI(4,5)P2 as a substrate to make second messengers. Activation of PI3K generates PI(3,4,5)P3 (phosphatidylinositol(3,4,5)trisphosphate), a lipid that recruits a plethora of proteins with pleckstrin homology (PH) domains to the plasma membrane to regulate multiple aspects of cellular function. In contrast, PLC activation results in the hydrolysis of PI(4,5)P2 to generate the second messengers, diacylglycerol (DAG), an activator of protein kinase C and inositol(1,4,5)trisphosphate (IP3/I(1,4,5)P3) which facilitates an increase in intracellular Ca2+. Decreases in PI(4,5)P2 by PLC also impact on functions that are dependent on the intact lipid and therefore endocytosis, actin dynamics and ion channel regulation are subject to control. Spatial organisation of PI(4,5)P2 in nanodomains at the membrane allows for these multiple processes to occur concurrently.
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Affiliation(s)
- Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Shamshad Cockcroft
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, 21 University Street, London WC1E 6JJ, U.K
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Anand PK. Lipids, inflammasomes, metabolism, and disease. Immunol Rev 2020; 297:108-122. [PMID: 32562313 DOI: 10.1111/imr.12891] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022]
Abstract
Inflammasomes are multi-protein complexes that regulate the cleavage of cysteine protease caspase-1, secretion of inflammatory cytokines, and induction of inflammatory cell death, pyroptosis. Several members of the nod-like receptor family assemble inflammasome in response to specific ligands. An exception to this is the NLRP3 inflammasome which is activated by structurally diverse entities. Recent studies have suggested that NLRP3 might be a sensor of cellular homeostasis, and any perturbation in distinct metabolic pathways results in the activation of this inflammasome. Lipid metabolism is exceedingly important in maintaining cellular homeostasis, and it is recognized that cells and tissues undergo extensive lipid remodeling during activation and disease. Some lipids are involved in instigating chronic inflammatory diseases, and new studies have highlighted critical upstream roles for lipids, particularly cholesterol, in regulating inflammasome activation implying key functions for inflammasomes in diseases with defective lipid metabolism. The focus of this review is to highlight how lipids regulate inflammasome activation and how this leads to the progression of inflammatory diseases. The key roles of cholesterol metabolism in the activation of inflammasomes have been comprehensively discussed. Besides, the roles of oxysterols, fatty acids, phospholipids, and lipid second messengers are also summarized in the context of inflammasomes. The overriding theme is that lipid metabolism has numerous but complex functions in inflammasome activation. A detailed understanding of this area will help us develop therapeutic interventions for diseases where dysregulated lipid metabolism is the underlying cause.
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Affiliation(s)
- Paras K Anand
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
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33
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Fatunmbi O, Bradley RP, Kandy SK, Bucki R, Janmey PA, Radhakrishnan R. A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface. SOFT MATTER 2020; 16:4941-4954. [PMID: 32436537 PMCID: PMC7373224 DOI: 10.1039/d0sm00267d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The dynamics and organization of the actin cytoskeleton are crucial to many cellular events such as motility, polarization, cell shaping, and cell division. The intracellular and extracellular signaling associated with this cytoskeletal network is communicated through cell membranes. Hence the organization of membrane macromolecules and actin filament assembly are highly interdependent. Although the actin-membrane linkage is known to happen through many routes, the major class of interactions is through the direct interaction of actin-binding proteins with the lipid class containing poly-phosphatidylinositols (PPIs). Among the PPIs, phosphatidylinositol bisphosphate (PI(4,5)P2) acts as a significant factor controlling actin polymerization in the proximity of the membrane by binding to actin-associated proteins. The molecular interactions between these actin-binding proteins and the membrane lipids remain elusive. Here, using molecular modeling, analytical theory, and experimental methods, we investigate the binding of three different actin-binding proteins, mDia2, NWASP, and gelsolin, to membranes containing PI(4,5)P2 lipids. We perform molecular dynamics simulations on the protein-bilayer system and analyze the membrane binding in the form of hydrogen bonds and salt bridges at various PI(4,5)P2 and cholesterol concentrations. Our experimental study with PI(4,5)P2-containing large unilamellar vesicles mimics the computational experiments. Using the multivalencies of the proteins obtained in molecular simulations and the cooperative binding mechanisms of the proteins, we also propose a multivalent binding model that predicts the actin filament distributions at various PI(4,5)P2 and protein concentrations.
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Affiliation(s)
- Ololade Fatunmbi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.
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Kluck GEG, Durham KK, Yoo JA, Trigatti BL. High Density Lipoprotein and Its Precursor Protein Apolipoprotein A1 as Potential Therapeutics to Prevent Anthracycline Associated Cardiotoxicity. Front Cardiovasc Med 2020; 7:65. [PMID: 32411725 PMCID: PMC7198830 DOI: 10.3389/fcvm.2020.00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/06/2020] [Indexed: 01/01/2023] Open
Abstract
Cardiovascular disease and cancer are the leading causes of death in developed societies. Despite their effectiveness, many cancer therapies exhibit deleterious cardiovascular side effects such as cardiotoxicity and heart failure. The cardiotoxic effects of anthracyclines such as doxorubicin are the most well-characterized of cardiotoxic anti-cancer therapies. While other anti-neoplastic drugs also induce cardiotoxicity, often leading to heart failure, they are beyond the scope of this review. This review first summarizes the mechanisms of doxorubicin-induced cardiotoxicity. It then reviews emerging preclinical evidence that high density lipoprotein and its precursor protein apolipoprotein A1, which are known for their protective effects against ischemic cardiovascular disease, may also protect against doxorubicin-induced cardiotoxicity both directly and indirectly, when used therapeutically.
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Affiliation(s)
- George E. G. Kluck
- Department of Biochemistry and Biomedical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada
| | - Kristina K. Durham
- Faculty of Health Sciences, Institute of Applied Health Sciences, School of Rehabilitation Sciences, McMaster University, Hamilton, ON, Canada
| | - Jeong-Ah Yoo
- Department of Biochemistry and Biomedical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada
| | - Bernardo L. Trigatti
- Department of Biochemistry and Biomedical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada
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Pant S, Tajkhorshid E. Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. J Comput Chem 2020; 41:489-499. [PMID: 31762060 PMCID: PMC7000246 DOI: 10.1002/jcc.26109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023]
Abstract
The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1-PHD) binds specifically to phosphatidylinositol (3,4,5)-triphosphate (PIP3 ), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1-PHD in the presence of membranes containing PC, PS, and PIP3 lipids in varying compositions. While GRP1-PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane-bound configurations. We report the first observation of two distinct PIP3 binding modes on GRP1-PHD, involving PIP3 interactions at a "canonical" and at an "alternate" site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1-PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1-PHD to the membrane, we demonstrate that along with the bound PIP3 , surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1-PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1-PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Shashank Pant
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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The C-terminal acidic motif of Phafin2 inhibits PH domain binding to phosphatidylinositol 3-phosphate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183230. [PMID: 32126233 DOI: 10.1016/j.bbamem.2020.183230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Changes in membrane curvature are required to control the function of subcellular compartments; malfunctions of such processes are associated with a wide range of human diseases. Membrane remodeling often depends upon the presence of phosphoinositides, which recruit protein effectors for a variety of cellular functions. Phafin2 is a phosphatidylinositol 3-phosphate (PtdIns3P)-binding effector involved in endosomal and lysosomal membrane-associated signaling. Both the Phafin2 PH and the FYVE domains bind PtdIns3P, although their redundant function in the protein is unclear. Through a combination of lipid-binding assays, we found that, unlike the FYVE domain, recognition of the PH domain to PtdIns3P requires a lipid bilayer. Using site-directed mutagenesis and truncation constructs, we discovered that the Phafin2 FYVE domain is constitutive for PtdIns3P binding, whereas PH domain binding to PtdIns3P is autoinhibited by a conserved C-terminal acidic motif. These findings suggest that binding of the Phafin2 PH domain to PtdIns3P in membrane compartments occurs through a highly regulated mechanism. Potential mechanisms are discussed throughout this report.
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Corey RA, Stansfeld PJ, Sansom MS. The energetics of protein-lipid interactions as viewed by molecular simulations. Biochem Soc Trans 2020; 48:25-37. [PMID: 31872229 PMCID: PMC7054751 DOI: 10.1042/bst20190149] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Abstract
Membranes are formed from a bilayer containing diverse lipid species with which membrane proteins interact. Integral, membrane proteins are embedded in this bilayer, where they interact with lipids from their surroundings, whilst peripheral membrane proteins bind to lipids at the surface of membranes. Lipid interactions can influence the function of membrane proteins, either directly or allosterically. Both experimental (structural) and computational approaches can reveal lipid binding sites on membrane proteins. It is, therefore, important to understand the free energies of these interactions. This affords a more complete view of the engagement of a particular protein with the biological membrane surrounding it. Here, we describe many computational approaches currently in use for this purpose, including recent advances using both free energy and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide-containing membranes. We summarise the current state of the field and provide an outlook on likely future directions of investigation.
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Affiliation(s)
- Robin A. Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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Cernikova L, Faso C, Hehl AB. Phosphoinositide-binding proteins mark, shape and functionally modulate highly-diverged endocytic compartments in the parasitic protist Giardia lamblia. PLoS Pathog 2020; 16:e1008317. [PMID: 32092130 PMCID: PMC7058353 DOI: 10.1371/journal.ppat.1008317] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/05/2020] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
Phosphorylated derivatives of phosphatidylinositol (PIPs) are key membrane lipid residues involved in clathrin-mediated endocytosis (CME). CME relies on PIP species PI(4,5)P2 to mark endocytic sites at the plasma membrane (PM) associated to clathrin-coated vesicle (CCV) formation. The highly diverged parasitic protist Giardia lamblia presents disordered and static clathrin assemblies at PM invaginations, contacting specialized endocytic organelles called peripheral vacuoles (PVs). The role for clathrin assemblies in fluid phase uptake and their link to internal membranes via PIP-binding adaptors is unknown. Here we provide evidence for a robust link between clathrin assemblies and fluid-phase uptake in G. lamblia mediated by proteins carrying predicted PX, FYVE and NECAP1 PIP-binding modules. We show that chemical and genetic perturbation of PIP-residue binding and turnover elicits novel uptake and organelle-morphology phenotypes. A combination of co-immunoprecipitation and in silico analysis techniques expands the initial PIP-binding network with addition of new members. Our data indicate that, despite the partial conservation of lipid markers and protein cohorts known to play important roles in dynamic endocytic events in well-characterized model systems, the Giardia lineage presents a strikingly divergent clathrin-centered network. This includes several PIP-binding modules, often associated to domains of currently unknown function that shape and modulate fluid-phase uptake at PVs. In well-characterized model eukaryotes, clathrin-mediated endocytosis is a key process for uptake of extracellular material and is regulated by more than 50 known proteins. A large number of these carry phosphoinositide (PIP)-binding domains and play a central role in the regulation of endocytosis. Here, we report on the detailed functional characterization of PIP-binding proteins in the intestinal parasitic protist Giardia lamblia. We show evidence that proteins carrying specific PIP-binding domains are directly involved in fluid-phase uptake. Furthermore, using co-immunoprecipitation assays, we confirm these proteins’ association to G. lamblia’s clathrin assemblies. In addition, using state-of-the-art imaging strategies, we demonstrate a previously unappreciated level of complexity involving PIPs and their partner proteins in marking and shaping G. lamblia’s unique endocytic compartments. Our data contribute substantially to an updated working model for G. lamblia’s host-parasite interface, demonstrating how uptake in this parasite is directly regulated by a variety of PIP residues and PIP-binding modules, which have been re-routed from conserved pathways, likely as a result of host-parasite co-evolution.
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Affiliation(s)
- Lenka Cernikova
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail: (CF); (AH)
| | - Adrian B. Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (CF); (AH)
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40
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Yamamoto E, Domański J, Naughton FB, Best RB, Kalli AC, Stansfeld PJ, Sansom MSP. Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes. SCIENCE ADVANCES 2020; 6:eaay5736. [PMID: 32128410 PMCID: PMC7030919 DOI: 10.1126/sciadv.aay5736] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/03/2019] [Indexed: 05/19/2023]
Abstract
Association of peripheral proteins with lipid bilayers regulates membrane signaling and dynamics. Pleckstrin homology (PH) domains bind to phosphatidylinositol phosphate (PIP) molecules in membranes. The effects of local PIP enrichment on the interaction of PH domains with membranes is unclear. Molecular dynamics simulations allow estimation of the binding energy of GRP1 PH domain to PIP3-containing membranes. The free energy of interaction of the PH domain with more than two PIP3 molecules is comparable to experimental values, suggesting that PH domain binding involves local clustering of PIP molecules within membranes. We describe a mechanism of PH binding proceeding via an encounter state to two bound states which differ in the orientation of the protein relative to the membrane, these orientations depending on the local PIP concentration. These results suggest that nanoscale clustering of PIP molecules can control the strength and orientation of PH domain interaction in a concentration-dependent manner.
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Affiliation(s)
- Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Jan Domański
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Fiona B. Naughton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Antreas C. Kalli
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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41
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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42
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Vanni S, Riccardi L, Palermo G, De Vivo M. Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids. Acc Chem Res 2019; 52:3087-3096. [PMID: 31364837 DOI: 10.1021/acs.accounts.9b00134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The regulatory chemical mechanisms of lipid trafficking and degradation are involved in many pathophysiological processes, being implicated in severe pain, inflammation, and cancer. In addition, the processing of lipids is also relevant for industrial and environmental applications. However, there is poor understanding of the chemical features that control lipid membrane trafficking and allow lipid-degrading enzymes to efficiently select and hydrolyze specific fatty acids from a complex cellular milieu of bioactive lipids. This is particularly true for lipid acyl chains, which have diverse structures that can critically affect the many complex reactions needed to elongate, desaturate, or transport fatty acids. Building upon our own contributions in this field, we will discuss how molecular simulations, integrated with experimental evidence, have revealed that the structure and dynamics of the lipid tail are actively involved in modulating membrane trafficking at cellular organelles, and enzymatic reactions at cell membranes. Further evidence comes from recent crystal structures of lipid receptors and remodeling enzymes. Taken together, these recent works have identified those structural features of the lipid acyl chain that are crucial for the regioselectivity and stereospecificity of essential desaturation reactions. In this context, we will first illustrate how atomistic and coarse-grained simulations have elucidated the structure-function relationships between the chemical composition of the lipid's acyl chains and the molecular properties of lipid bilayers. Particular emphasis will be given to the prominent chemical role of the number of double carbon-carbon bonds along the lipid acyl chain, that is, discriminating between saturated, monounsaturated, and polyunsaturated lipids. Different levels of saturation in fatty acid molecules dramatically influence the biophysical properties of lipid assemblies and their interaction with proteins. We will then discuss the processing of lipids by membrane-bound enzymes. Our focus will be on lipids such as anandamide and 2-arachidonoylglycerol. These are the main molecules that act as neurotransmitters in the endocannabinoid system. Specifically, recent findings indicate a crucial interplay between the level of saturation of the lipid tail, its energetically and sterically favored conformations, and the hydrophobic accessory cavities in lipid-degrading enzymes, which help form catalytically active conformations of the selected substrate. This Account will emphasize how the specific chemical structure of acyl chains affects the molecular mechanisms for modulating membrane trafficking and selective hydrolysis. The results examined here show that, by using molecular simulations to investigate lipid plasticity and substrate flexibility, researchers can enrich their interpretation of experimental results about the structure-function relationships of lipids. This could positively impact chemical and biological studies in the field and ultimately support protein engineering studies and structure-based drug discovery to target lipid-processing enzymes.
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Affiliation(s)
- Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Université Côte d’Azur, CNRS, IPMC, 06560 Valbonne, France
| | - Laura Riccardi
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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43
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Furlong RM, Lindsay A, Anderson KE, Hawkins PT, Sullivan AM, O'Neill C. The Parkinson's disease gene PINK1 activates Akt via PINK1 kinase-dependent regulation of the phospholipid PI(3,4,5)P 3. J Cell Sci 2019; 132:jcs.233221. [PMID: 31540955 DOI: 10.1242/jcs.233221] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
Akt signalling is central to cell survival, metabolism, protein and lipid homeostasis, and is impaired in Parkinson's disease (PD). Akt activation is reduced in the brain in PD, and by many PD-causing genes, including PINK1 This study investigated the mechanisms by which PINK1 regulates Akt signalling. Our results reveal for the first time that PINK1 constitutively activates Akt in a PINK1-kinase dependent manner in the absence of growth factors, and enhances Akt activation in normal growth medium. In PINK1-modified MEFs, agonist-induced Akt signalling failed in the absence of PINK1, due to PINK1 kinase-dependent increases in PI(3,4,5)P3 at both plasma membrane and Golgi being significantly impaired. In the absence of PINK1, PI(3,4,5)P3 levels did not increase in the Golgi, and there was significant Golgi fragmentation, a recognised characteristic of PD neuropathology. PINK1 kinase activity protected the Golgi from fragmentation in an Akt-dependent fashion. This study demonstrates a new role for PINK1 as a primary upstream activator of Akt via PINK1 kinase-dependent regulation of its primary activator PI(3,4,5)P3, providing novel mechanistic information on how loss of PINK1 impairs Akt signalling in PD.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Rachel M Furlong
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork City T12 YT20, Ireland.,Department of Anatomy and Neuroscience, Western Gateway Building, University College Cork, Cork City T12 XF62, Ireland.,Cork NeuroScience Centre, University College Cork, Cork City T12 YT20, Ireland
| | - Andrew Lindsay
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork City T12 YT20, Ireland
| | - Karen E Anderson
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Aideen M Sullivan
- Department of Anatomy and Neuroscience, Western Gateway Building, University College Cork, Cork City T12 XF62, Ireland.,Cork NeuroScience Centre, University College Cork, Cork City T12 YT20, Ireland
| | - Cora O'Neill
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork City T12 YT20, Ireland .,Cork NeuroScience Centre, University College Cork, Cork City T12 YT20, Ireland
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44
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Fraser J, Simpson J, Fontana R, Kishi‐Itakura C, Ktistakis NT, Gammoh N. Targeting of early endosomes by autophagy facilitates EGFR recycling and signalling. EMBO Rep 2019; 20:e47734. [PMID: 31448519 PMCID: PMC6776898 DOI: 10.15252/embr.201947734] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022] Open
Abstract
Despite recently uncovered connections between autophagy and the endocytic pathway, the role of autophagy in regulating endosomal function remains incompletely understood. Here, we find that the ablation of autophagy-essential players disrupts EGF-induced endocytic trafficking of EGFR. Cells lacking ATG7 or ATG16L1 exhibit increased levels of phosphatidylinositol-3-phosphate (PI(3)P), a key determinant of early endosome maturation. Increased PI(3)P levels are associated with an accumulation of EEA1-positive endosomes where EGFR trafficking is stalled. Aberrant early endosomes are recognised by the autophagy machinery in a TBK1- and Gal8-dependent manner and are delivered to LAMP2-positive lysosomes. Preventing this homeostatic regulation of early endosomes by autophagy reduces EGFR recycling to the plasma membrane and compromises downstream signalling and cell survival. Our findings uncover a novel role for the autophagy machinery in maintaining early endosome function and growth factor sensing.
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Affiliation(s)
- Jane Fraser
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Joanne Simpson
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Rosa Fontana
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | | | | | - Noor Gammoh
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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45
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Volpatti JR, Al-Maawali A, Smith L, Al-Hashim A, Brill JA, Dowling JJ. The expanding spectrum of neurological disorders of phosphoinositide metabolism. Dis Model Mech 2019; 12:12/8/dmm038174. [PMID: 31413155 PMCID: PMC6737944 DOI: 10.1242/dmm.038174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phosphoinositides (PIPs) are a ubiquitous group of seven low-abundance phospholipids that play a crucial role in defining localized membrane properties and that regulate myriad cellular processes, including cytoskeletal remodeling, cell signaling cascades, ion channel activity and membrane traffic. PIP homeostasis is tightly regulated by numerous inositol kinases and phosphatases, which phosphorylate and dephosphorylate distinct PIP species. The importance of these phospholipids, and of the enzymes that regulate them, is increasingly being recognized, with the identification of human neurological disorders that are caused by mutations in PIP-modulating enzymes. Genetic disorders of PIP metabolism include forms of epilepsy, neurodegenerative disease, brain malformation syndromes, peripheral neuropathy and congenital myopathy. In this Review, we provide an overview of PIP function and regulation, delineate the disorders associated with mutations in genes that modulate or utilize PIPs, and discuss what is understood about gene function and disease pathogenesis as established through animal models of these diseases. Summary: This Review highlights the intersection between phosphoinositides and the enzymes that regulate their metabolism, which together are crucial regulators of myriad cellular processes and neurological disorders.
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Affiliation(s)
- Jonathan R Volpatti
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Almundher Al-Maawali
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Lindsay Smith
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aqeela Al-Hashim
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Neuroscience, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Julie A Brill
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James J Dowling
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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46
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Amos SBTA, Kalli AC, Shi J, Sansom MSP. Membrane Recognition and Binding by the Phosphatidylinositol Phosphate Kinase PIP5K1A: A Multiscale Simulation Study. Structure 2019; 27:1336-1346.e2. [PMID: 31204251 PMCID: PMC6688827 DOI: 10.1016/j.str.2019.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Phosphatidylinositol phosphates (PIPs) are lipid signaling molecules that play key roles in many cellular processes. PIP5K1A kinase catalyzes phosphorylation of PI4P to form PIP2, which in turn interacts with membrane and membrane-associated proteins. We explore the mechanism of membrane binding by the PIP5K1A kinase using a multiscale molecular dynamics approach. Coarse-grained simulations show binding of monomeric PIP5K1A to a model cell membrane containing PI4P. PIP5K1A did not bind to zwitterionic or anionic membranes lacking PIP molecules. Initial encounter of kinase and bilayer was followed by reorientation to enable productive binding to the PI4P-containing membrane. The simulations suggest that unstructured regions may be important for the preferred orientation for membrane binding. Atomistic simulations indicated that the dimeric kinase could not bind to the membrane via both active sites at the same time, suggesting a conformational change in the protein and/or bilayer distortion may be needed for dual-site binding to occur. PIP5K1A kinase interacts with PIP-containing membranes via its activation loop PIP5K1A does not bind to zwitterionic or anionic membranes lacking PIP molecules Initial encounter of protein and bilayer is followed by reorientation and binding Dimeric PIP5K1A binds with membrane contacts via only one catalytic site at a time
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Affiliation(s)
- Sarah-Beth T A Amos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Antreas C Kalli
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough SL1 3WE, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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47
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Polyphosphoinositides in the nucleus: Roadmap of their effectors and mechanisms of interaction. Adv Biol Regul 2019; 72:7-21. [PMID: 31003946 DOI: 10.1016/j.jbior.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Biomolecular interactions between proteins and polyphosphoinositides (PPIn) are essential in the regulation of the vast majority of cellular processes. Consequently, alteration of these interactions is implicated in the development of many diseases. PPIn are phosphorylated derivatives of phosphatidylinositol and consist of seven species with different phosphate combinations. PPIn signal by recruiting proteins via canonical domains or short polybasic motifs. Although their actions are predominantly documented on cytoplasmic membranes, six of the seven PPIn are present within the nucleus together with the PPIn kinases, phosphatases and phospholipases that regulate their turnover. Importantly, the contribution of nuclear PPIn in the regulation of nuclear processes has led to an increased recognition of their importance compared to their more accepted cytoplasmic roles. This review summarises our knowledge on the identification and functional characterisation of nuclear PPIn-effector proteins as well as their mode of interactions, which tend to favour polybasic motifs.
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48
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Iershov A, Nemazanyy I, Alkhoury C, Girard M, Barth E, Cagnard N, Montagner A, Chretien D, Rugarli EI, Guillou H, Pende M, Panasyuk G. The class 3 PI3K coordinates autophagy and mitochondrial lipid catabolism by controlling nuclear receptor PPARα. Nat Commun 2019; 10:1566. [PMID: 30952952 PMCID: PMC6451001 DOI: 10.1038/s41467-019-09598-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 03/20/2019] [Indexed: 12/19/2022] Open
Abstract
The class 3 phosphoinositide 3-kinase (PI3K) is required for lysosomal degradation by autophagy and vesicular trafficking, assuring nutrient availability. Mitochondrial lipid catabolism is another energy source. Autophagy and mitochondrial metabolism are transcriptionally controlled by nutrient sensing nuclear receptors. However, the class 3 PI3K contribution to this regulation is unknown. We show that liver-specific inactivation of Vps15, the essential regulatory subunit of the class 3 PI3K, elicits mitochondrial depletion and failure to oxidize fatty acids. Mechanistically, transcriptional activity of Peroxisome Proliferator Activated Receptor alpha (PPARα), a nuclear receptor orchestrating lipid catabolism, is blunted in Vps15-deficient livers. We find PPARα repressors Histone Deacetylase 3 (Hdac3) and Nuclear receptor co-repressor 1 (NCoR1) accumulated in Vps15-deficient livers due to defective autophagy. Activation of PPARα or inhibition of Hdac3 restored mitochondrial biogenesis and lipid oxidation in Vps15-deficient hepatocytes. These findings reveal roles for the class 3 PI3K and autophagy in transcriptional coordination of mitochondrial metabolism.
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Affiliation(s)
- Anton Iershov
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Ivan Nemazanyy
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, 75014, Paris, France
| | - Chantal Alkhoury
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Muriel Girard
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
- Pediatric Hepatology Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, 75015, France
| | - Esther Barth
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany
| | - Nicolas Cagnard
- Plateforme Bio-informatique, Université Paris Descartes, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, 75015, France
| | | | - Dominique Chretien
- INSERM UMR1141, Hôpital Robert Debré, Paris, 75019, France
- Université Paris 7, Faculté de Médecine Denis Diderot, Paris, 75019, France
| | - Elena I Rugarli
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany
| | - Herve Guillou
- Toxalim, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, 31027, France
| | - Mario Pende
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Ganna Panasyuk
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France.
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France.
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France.
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49
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Chandra M, Chin YKY, Mas C, Feathers JR, Paul B, Datta S, Chen KE, Jia X, Yang Z, Norwood SJ, Mohanty B, Bugarcic A, Teasdale RD, Henne WM, Mobli M, Collins BM. Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities. Nat Commun 2019; 10:1528. [PMID: 30948714 PMCID: PMC6449406 DOI: 10.1038/s41467-019-09355-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/21/2019] [Indexed: 01/05/2023] Open
Abstract
Phox homology (PX) domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays, biolayer interferometry and isothermal titration calorimetry. These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns3P, non-specifically to various di- and tri-phosphorylated phosphoinositides, bind both PtdIns3P and other phosphoinositides, or associate with none of the lipids tested. A comprehensive evaluation of PX domain structures reveals two distinct binding sites that explain these specificities, providing a basis for defining and predicting the functional membrane interactions of the entire PX domain protein family.
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Affiliation(s)
- Mintu Chandra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Caroline Mas
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Integrated Structural Biology Grenoble, Grenoble, France
| | - J Ryan Feathers
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Blessy Paul
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Sanchari Datta
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Xinying Jia
- Centre for Advanced Imaging and School of Chemistry and Molecular Biology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zhe Yang
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Suzanne J Norwood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, VIC, Australia
| | - Andrea Bugarcic
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Rohan D Teasdale
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mehdi Mobli
- Centre for Advanced Imaging and School of Chemistry and Molecular Biology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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50
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Marongiu L, Gornati L, Artuso I, Zanoni I, Granucci F. Below the surface: The inner lives of TLR4 and TLR9. J Leukoc Biol 2019; 106:147-160. [PMID: 30900780 PMCID: PMC6597292 DOI: 10.1002/jlb.3mir1218-483rr] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
TLRs are a class of pattern recognition receptors (PRRs) that detect invading microbes by recognizing pathogen-associated molecular patterns (PAMPs). Upon PAMP engagement, TLRs activate a signaling cascade that leads to the production of inflammatory mediators. The localization of TLRs, either on the plasma membrane or in the endolysosomal compartment, has been considered to be a fundamental aspect to determine to which ligands the receptors bind, and which transduction pathways are induced. However, new observations have challenged this view by identifying complex trafficking events that occur upon TLR-ligand binding. These findings have highlighted the central role that endocytosis and receptor trafficking play in the regulation of the innate immune response. Here, we review the TLR4 and TLR9 transduction pathways and the importance of their different subcellular localization during the inflammatory response. Finally, we discuss the implications of TLR9 subcellular localization in autoimmunity.
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Affiliation(s)
- Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Laura Gornati
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Irene Artuso
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Ivan Zanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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