1
|
Bayer K, Taeb M, Koch B, Yoshimura SH, Wombacher R. Dual SLIPT-A Lipid Mimic to Enable Spatiotemporally Defined, Sequential Protein Dimerization. ACS Chem Biol 2025; 20:1038-1047. [PMID: 40234022 PMCID: PMC12090181 DOI: 10.1021/acschembio.4c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/17/2025]
Abstract
Spatiotemporal control of proteins is crucial for cellular phenomena such as signal integration, propagation, as well as managing crosstalk. In membrane-associated signaling, this regulation is often enabled by lipids, wherein highly dynamic, sequential recruitment of interacting proteins is key to successful signaling. Here, we present dual SLIPT (self-localizing ligand-induced protein translocation), a lipid-analog tool, capable of emulating this lipid-mediated sequential recruitment of any two proteins of interest. Dual SLIPT self-localizes to the inner leaflet of the plasma membrane (PM). There, dual SLIPT presents trimethoprim (TMP) and HaloTag ligand (HTL) to cytosolic proteins of interest (POIs), whereupon POIs fused to the protein tags iK6eDHFR, or to HOB are recruited. A systematic extension of the linkers connecting the two mutually orthogonal headgroups was implemented to overcome the steric clash between the recruited POIs. Using Förster resonance energy transfer (FRET), we verify that the resulting probe is capable of simultaneous binding of both proteins of interest, as well as their dimerization. Dual SLIPT was found to be particularly suitable for use in physiologically relevant concentrations, such as recruitment via tightly regulated, transient lipid species. We further expanded dual SLIPT to the photocontrollable dual SLIPTNVOC, by introducing a photocaging group onto the TMP moiety. Dual SLIPTNVOC enables sequential and spatiotemporally defined dimerization upon blue light irradiation. Thus, dual SLIPTNVOC serves as a close mimic of physiology, enabling interrogation of dynamic cytosol-to-plasma membrane recruitment events and their impact on signaling.
Collapse
Affiliation(s)
- Kristina
V. Bayer
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Heidelberg
Biosciences International Graduate School (HBIGS), Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Maedeh Taeb
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Birgit Koch
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Shige H. Yoshimura
- Graduate
School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Center
for Living Systems Information Science (CeLiSIS), Kyoto University, Kyoto 606-8501, Japan
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Richard Wombacher
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| |
Collapse
|
2
|
Boob AG, Tan SI, Zaidi A, Singh N, Xue X, Zhou S, Martin TA, Chen LQ, Zhao H. Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder. Nat Commun 2025; 16:4151. [PMID: 40320395 PMCID: PMC12050285 DOI: 10.1038/s41467-025-59499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 04/16/2025] [Indexed: 05/08/2025] Open
Abstract
Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.
Collapse
Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Airah Zaidi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nilmani Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueyi Xue
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shuaizhen Zhou
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Li-Qing Chen
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
3
|
Khaliq SA, Park SY, Maham S, Cho Y, Lee M, Nam S, Seong JK, Chen J, Choi CS, Yoon MS. ARHGEF3 coordinates adipocyte hypertrophy and differentiation through dual YAP-RhoA and PPARγ activation. J Adv Res 2025:S2090-1232(25)00229-2. [PMID: 40216078 DOI: 10.1016/j.jare.2025.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 03/19/2025] [Accepted: 04/08/2025] [Indexed: 04/15/2025] Open
Abstract
INTRODUCTION Obesity presents a significant global health burden, necessitating insights into the molecular drivers of adipogenesis and adipose tissue regulation. OBJECTIVES This study investigates the role of Rho guanine nucleotide exchange factor 3 (ARHGEF3) in adipocyte differentiation and hypertrophy, focusing on its influence on adipogenesis and body weight regulation under high-fat diet conditions. METHODS ARHGEF3-/- mice and littermate controls were subjected to a high-fat diet (HFD) and underwent comprehensive metabolic phenotyping. In vitro studies in C3H10T1/2 cells were conducted to assess ARHGEF3's role in adipogenesis, utilizing quantitative PCR, western blotting, chromatin immunoprecipitation (ChIP), immunoprecipitation (IP), immunostaining, and luciferase reporter assays. RESULTS ARHGEF3 expression increased in white adipose tissue (WAT) of HFD-fed mice and during adipogenic differentiation in C3H10T1/2 cells. ARHGEF3-deficient mice exhibited reduced weight gain and adipocyte size, correlating with decreased RhoA expression and altered cytoskeletal dynamics. Additionally, ARHGEF3 facilitated yes-associated protein (YAP) nuclear translocation and its direct binding to the RhoA promoter, an effect reliant on ARHGEF3. ARHGEF3 also enhanced the transcriptional activity of peroxisome proliferator-activated receptor gamma (PPARγ), establishing a reciprocal activation loop to drive adipocyte differentiation and hypertrophy. CONCLUSION ARHGEF3 emerges as a pivotal regulator of adipocyte dynamics by coordinating YAP-RhoA signaling and enhancing PPARγ activity. These findings offer novel therapeutic insights for addressing obesity and related metabolic disorders.
Collapse
Affiliation(s)
- Sana Abdul Khaliq
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, Gachon University College of Medicine, Incheon 21999, Republic of Korea
| | - Shi-Young Park
- Gachon Biomedical Convergence Institute, Gachon University Gil Medical Center, Incheon 21565, Republic of Korea; Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
| | - Syeda Maham
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
| | - Yoonil Cho
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea; Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
| | - Miseon Lee
- Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea; Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Model Animal Priority Center (KMPC), Seoul National University, Seoul 08826, Republic of Korea
| | - Jie Chen
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Cheol Soo Choi
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon 21999, Republic of Korea; Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea; Department of Internal Medicine, Gil Medical Center, Gachon University, Incheon 21565, Republic of Korea.
| | - Mee-Sup Yoon
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, Gachon University College of Medicine, Incheon 21999, Republic of Korea; Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea.
| |
Collapse
|
4
|
Lee J, Lai S, Yang S, Zhao S, Blanco FA, Lyons AC, Merino-Urteaga R, Ahrens JF, Nguyen NA, Liu H, Liu Z, Lambert GG, Shaner NC, Chen L, Tolias KF, Zhang J, Ha T, St-Pierre F. Bright and photostable yellow fluorescent proteins for extended imaging. Nat Commun 2025; 16:3241. [PMID: 40185748 PMCID: PMC11971446 DOI: 10.1038/s41467-025-58223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 03/14/2025] [Indexed: 04/07/2025] Open
Abstract
Fluorescent proteins are indispensable molecular tools for visualizing biological structures and processes, but their limited photostability restricts the duration of dynamic imaging experiments. Yellow fluorescent proteins (YFPs), in particular, photobleach rapidly. Here, we introduce mGold2s and mGold2t, YFPs with up to 25-fold greater photostability than mVenus and mCitrine, two commonly used YFPs, while maintaining comparable brightness. These variants were identified using a high-throughput pooled single-cell platform, simultaneously screening for high brightness and photostability. Compared with our previous benchmark, mGold, the mGold2 variants display a ~4-fold increase in photostability without sacrificing brightness. mGold2s and mGold2t extend imaging durations across diverse modalities, including widefield, total internal reflection fluorescence (TIRF), super-resolution, single-molecule, and laser-scanning confocal microscopy. When incorporated into fluorescence resonance energy transfer (FRET)-based biosensors, the proposed YFPs enable more reliable, prolonged imaging of dynamic cellular processes. Overall, the enhanced photostability of mGold2s and mGold2t enables high-sensitivity imaging of subcellular structures and cellular activity over extended periods, broadening the scope and precision of biological imaging.
Collapse
Affiliation(s)
- Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Shiqun Zhao
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China
| | - Francisco A Blanco
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Anne C Lyons
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Raquel Merino-Urteaga
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - John F Ahrens
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Nathan A Nguyen
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Haixin Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Zhuohe Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerard G Lambert
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Nathan C Shaner
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Kimberley F Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Jin Zhang
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Moore's Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Taekjip Ha
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
| |
Collapse
|
5
|
Chen X, Cardenas AE, Hudson RB, Elber R, Senning EN, Baiz CR. Cooperativity of PIP2 and PS lipids modulates PH domain binding. Biophys J 2025; 124:1146-1157. [PMID: 40012203 PMCID: PMC11993920 DOI: 10.1016/j.bpj.2025.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 01/20/2025] [Accepted: 02/24/2025] [Indexed: 02/28/2025] Open
Abstract
Phosphatidylinositides constitute only 1%-3% of plasma membranes but play vital roles in cellular signaling. In particular, phosphatidylinositol 4,5-bisphosphate (PIP2) is involved in processes such as cytoskeleton organization and ion-channel regulation. Pleckstrin homology (PH) domains are modular domains found in many proteins and are known for their strong affinity for PIP2 headgroups. The role of lipid composition in PH domain binding to PIP2, particularly the inclusion of phosphatidylserine (PS), is not well understood. This study explores the mechanisms of PH domain binding to PIP2 using fluorescence spectroscopy, Fourier transform infrared spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations. We find that anionic PIP2 and PS alter the interfacial environment compared to phosphatidylcholines. Additionally, the PH domain promotes the localization of anionic lipid domains upon binding. Our results highlight the role of PS in lipid domain formation within membranes and its potential influence on protein binding affinities and lipid geometries. Specifically, we discovered a strong interaction between PIP2 and PS whereby hydrogen bonding within these anionic lipids drives localization in the membrane. This interaction also regulates protein binding at the membrane interface. Our findings suggest that cooperativity between PIP2 and PS is key to the formation of localized lipid domains and the recruitment of proteins such as the PH domain of phospholipase C-δ1.
Collapse
Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| | | | - Rose B Hudson
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry, The University of Texas at Austin, Austin, Texas; The Oden Institute, The University of Texas at Austin, Austin, Texas
| | - Eric N Senning
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas.
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas.
| |
Collapse
|
6
|
Qi Y, Yu CH. PI(3,4,5)P3-mediated Cdc42 activation regulates macrophage podosome assembly. Cell Mol Life Sci 2025; 82:127. [PMID: 40126693 PMCID: PMC11933580 DOI: 10.1007/s00018-025-05664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 02/23/2025] [Accepted: 03/16/2025] [Indexed: 03/26/2025]
Abstract
Podosomes are adhesion structures with densely-polymerized F-actin. While PI(3,4,5)P3 and Cdc42-GTP are known factors to trigger WASP-mediated actin polymerization at the macrophage podosome, their causal mechanism to activate WASP remains unclear. Here, we demonstrate that spatially elevated Cdc42-GTP is a downstream effector of local PI(3,4,5)P3 production at the podosome. We further examine the expression and distribution of 19 Cdc42 guanine exchange factors (GEFs) and identify VAV1 as the key PI(3,4,5)P3-dependent Cdc42 GEF. VAV1 is spatially enriched at the macrophage podosome, and the association of VAV1 with the membrane plays a critical role in upregulating its GEF activity. Reintroduction of wildtype VAV1, rather than the PI(3,4,5)P3-binding deficient or catalytically dead mutants restores the matrix degradation and chemotactic migration of VAV1-knockdown macrophage. Thus, the biogenesis of PI(3,4,5)P3 acts as an upstream signal to locally recruit VAV1 and in turn triggers the guanine nucleotide exchange of Cdc42. Elevated levels of Cdc42-GTP then promote WASP-mediated podosome assembly and macrophage chemotaxis.
Collapse
Affiliation(s)
- Yaoyue Qi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Cheng-Han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| |
Collapse
|
7
|
Chytła A, Rattay S, Akgül B, Sztacho M. Plasma membrane and nuclear phosphatidylinositol 4,5-bisphosphate signalling in cancer. Lipids Health Dis 2025; 24:39. [PMID: 39915829 PMCID: PMC11800418 DOI: 10.1186/s12944-025-02452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 01/27/2025] [Indexed: 02/11/2025] Open
Abstract
The development of metastasis is a leading cause of cancer-related death that involves specific changes in the plasma membrane (PM) and nucleus of cancer cells. Elevated levels of membrane lipids, including sphingomyelin, cholesterol, and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), in the PM, contribute to changes in membrane rigidity, lipid raft formation, and actin polymerisation dynamics, processes that drive cell invasion. This review discusses the relationship between well-studied cytoplasmic phosphoinositides and their lesser-known nuclear counterparts, highlighting their functional role in metastatic progression. Nuclear phosphoinositides, particularly PI(4,5)P2, are essential for regulating transcription factors and chromatin organisation, thereby shaping gene expression patterns. We also explore the role of PI(4,5)P2 and its metabolism in cancer cell invasiveness and metastasis, proposing a model in which the dysregulation of cytosolic and/or nuclear PI(4,5)P2 pool triggers malignant transformation. Understanding the PI(4,5)P2-related mechanisms underlying metastasis may provide insights into potential therapeutic targets, paving the way for more effective therapies and improved patient outcomes.
Collapse
Affiliation(s)
- Agnieszka Chytła
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, 128 00, Czech Republic
| | - Stephanie Rattay
- Institute of Virology, Medical Faculty, University of Cologne, University Hospital Cologne, 50935, Cologne, Germany
| | - Baki Akgül
- Institute of Virology, Medical Faculty, University of Cologne, University Hospital Cologne, 50935, Cologne, Germany
- National Reference Center for Papilloma- and Polyomaviruses, Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935, Cologne, Germany
| | - Martin Sztacho
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, 128 00, Czech Republic.
| |
Collapse
|
8
|
Kostyanovskaya E, Lasser MC, Wang B, Schmidt J, Bader E, Buteo C, Arbelaez J, Sindledecker AR, McCluskey KE, Castillo O, Wang S, Dea J, Helde KA, Graglia JM, Brimble E, Kastner DB, Ehrlich AT, State MW, Willsey AJ, Willsey HR. Convergence of autism proteins at the cilium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.05.626924. [PMID: 39677731 PMCID: PMC11643032 DOI: 10.1101/2024.12.05.626924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Hundreds of high-confidence autism genes have been identified, yet the relevant etiological mechanisms remain unclear. Gene ontology analyses have repeatedly identified enrichment of proteins with annotated functions in gene expression regulation and neuronal communication. However, proteins are often pleiotropic and these annotations are inherently incomplete. Our recent autism functional genetics work has suggested that these genes may share a common mechanism at the cilium, a membrane-bound organelle critical for neurogenesis, brain patterning, and neuronal activity-all processes strongly implicated in autism. Moreover, autism commonly co-occurs with conditions that are known to involve ciliary-related pathologies, including congenital heart disease, hydrocephalus, and blindness. However, the role of autism genes at the cilium has not been systematically investigated. Here we demonstrate that autism proteins spanning disparate functional annotations converge in expression, localization, and function at cilia, and that patients with pathogenic variants in these genes have cilia-related co-occurring conditions and biomarkers of disrupted ciliary function. This degree of convergence among genes spanning diverse functional annotations strongly suggests that cilia are relevant to autism, as well as to commonly co-occurring conditions, and that this organelle should be explored further for therapeutic potential.
Collapse
Affiliation(s)
- Elina Kostyanovskaya
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Micaela C. Lasser
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - James Schmidt
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Ethel Bader
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Chad Buteo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Juan Arbelaez
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Aria Rani Sindledecker
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Kate E. McCluskey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Octavio Castillo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | | | | | | | - David B. Kastner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Aliza T. Ehrlich
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Matthew W. State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - A. Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
| |
Collapse
|
9
|
Chaturvedi S, Sonawane A. Recapitulating the potential contribution of protein S-palmitoylation in cancer. Cancer Metastasis Rev 2024; 44:20. [PMID: 39725785 DOI: 10.1007/s10555-024-10217-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 11/14/2024] [Indexed: 12/28/2024]
Abstract
Protein S-palmitoylation is a reversible form of protein lipidation in which the formation of a thioester bond occurs between a cysteine (Cys) residue of a protein and a 16-carbon fatty acid chain. This modification is catalyzed by a family of palmitoyl acyl transferases, the DHHC enzymes, so called because of their Asp-His-His-Cys (DHHC) catalytic motif. Deregulation of DHHC enzymes has been linked to various diseases, including cancer and infections. Cancer, a major cause of global mortality, is characterized by features like uncontrolled cell growth, resistance to cell death, angiogenesis, invasion, and metastasis. Several of these processes are controlled by DHHC-mediated S-palmitoylation of oncogenes or tumor suppressors, including growth factor receptors (e.g., EGFR), kinases (e.g., AKT), and transcription factors (e.g., β-catenin). Dynamic regulation of S-palmitoylation is also governed by protein depalmitoylases. These enzymes balance the cycling of palmitoylation and regulate cellular signaling, cell growth, and its organization. Given the significance of S-palmitoylation in cancer, the DHHCs and protein depalmitoylases are promising targets for cancer therapy. Here we summarize the catalytic mechanisms of DHHC enzymes and depalmitoylases, their role in cancer progression and prevention, as well as the crosstalk of palmitoylation with other post-translational modifications. Additionally, we discuss the methods to detect S-palmitoylation, the limitations of available DHHC-targeting inhibitors, and ongoing research efforts to address these obstacles.
Collapse
Affiliation(s)
- Suchi Chaturvedi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, 453552, Simrol, Madhya Pradesh, India
| | - Avinash Sonawane
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, 453552, Simrol, Madhya Pradesh, India.
| |
Collapse
|
10
|
Garcia P, Celador R, Edreira T, Sanchez Y. Rho1 and Rgf1 establish a new actin-dependent signal to determine growth poles in yeast independently of microtubules and the Tea1-Tea4 complex. PLoS Biol 2024; 22:e3002491. [PMID: 39509469 PMCID: PMC11602027 DOI: 10.1371/journal.pbio.3002491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 11/27/2024] [Accepted: 10/13/2024] [Indexed: 11/15/2024] Open
Abstract
Cellular asymmetry begins with the selection of a discrete point on the cell surface that triggers Rho-GTPases activation and localized assembly of the cytoskeleton to establish new growth zones. The cylindrical shape of fission yeast is organized by microtubules (MT) that deliver the landmark Tea1-Tea4 complex at the cell tips to define the growth poles. However, only a few tea1Δ cells mistaken the direction of growth, indicating that they manage to detect their growth sites. Here, we show that Rgf1 (Rho1-GEF) and Tea4 are components of the same complex and that Rgf1 activity toward Rho1 is required for strengthen Tea4 at the cell tips. Moreover, in cells lacking Tea1, selection of the correct growth site depends on Rgf1 and on a correctly polarized actin cytoskeleton, both necessary for Rho1 activation at the pole. We propose an actin-dependent mechanism driven by Rgf1-Rho1 that marks the poles independently of MTs and the Tea1-Tea4 complex.
Collapse
Affiliation(s)
- Patricia Garcia
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca. C/ Zacarías González, Salamanca, Spain
| | - Ruben Celador
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca. C/ Zacarías González, Salamanca, Spain
| | - Tomas Edreira
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca. C/ Zacarías González, Salamanca, Spain
| | - Yolanda Sanchez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca. C/ Zacarías González, Salamanca, Spain
| |
Collapse
|
11
|
de Souza Cardoso R, Ono A. The Effects of Viral Structural Proteins on Acidic Phospholipids in Host Membranes. Viruses 2024; 16:1714. [PMID: 39599829 PMCID: PMC11599007 DOI: 10.3390/v16111714] [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: 09/13/2024] [Revised: 10/23/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024] Open
Abstract
Enveloped viruses rely on host membranes for trafficking and assembly. A substantial body of literature published over the years supports the involvement of cellular membrane lipids in the enveloped virus assembly processes. In particular, the knowledge regarding the relationship between viral structural proteins and acidic phospholipids has been steadily increasing in recent years. In this review, we will briefly review the cellular functions of plasma membrane-associated acidic phospholipids and the mechanisms that regulate their local distribution within this membrane. We will then explore the interplay between viruses and the plasma membrane acidic phospholipids in the context of the assembly process for two enveloped viruses, the influenza A virus (IAV) and the human immunodeficiency virus type 1 (HIV-1). Among the proteins encoded by these viruses, three viral structural proteins, IAV hemagglutinin (HA), IAV matrix protein-1 (M1), and HIV-1 Gag protein, are known to interact with acidic phospholipids, phosphatidylserine and/or phosphatidylinositol (4,5)-bisphosphate. These interactions regulate the localization of the viral proteins to and/or within the plasma membrane and likely facilitate the clustering of the proteins. On the other hand, these viral proteins, via their ability to multimerize, can also alter the distribution of the lipids and may induce acidic-lipid-enriched membrane domains. We will discuss the potential significance of these interactions in the virus assembly process and the property of the progeny virions. Finally, we will outline key outstanding questions that need to be answered for a better understanding of the relationships between enveloped virus assembly and acidic phospholipids.
Collapse
Affiliation(s)
| | - Akira Ono
- Department of Microbiology and Immunology, The University of Michigan, Ann Arbor, MI 48109, USA;
| |
Collapse
|
12
|
Hutchins CM, Gorfe AA. From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor. Curr Opin Struct Biol 2024; 87:102869. [PMID: 38943706 PMCID: PMC11283958 DOI: 10.1016/j.sbi.2024.102869] [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: 04/15/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024]
Abstract
The intrinsically disordered, lipid-modified membrane anchor of small GTPases is emerging as a critical modulator of function through its ability to sort lipids in a conformation-dependent manner. We reviewed recent computational and experimental studies that have begun to shed light on the sequence-ensemble-function relationship in this unique class of lipidated intrinsically disordered regions (LIDRs).
Collapse
Affiliation(s)
- Chase M Hutchins
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA. https://twitter.com/chasedsims
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA.
| |
Collapse
|
13
|
Simsek Papur O, Glatz JFC, Luiken JJFP. Protein kinase-D1 and downstream signaling mechanisms involved in GLUT4 translocation in cardiac muscle. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119748. [PMID: 38723678 DOI: 10.1016/j.bbamcr.2024.119748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 02/21/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024]
Abstract
The Ser/Thr kinase protein kinase-D1 (PKD1) is involved in induction of various cell physiological processes in the heart such as myocellular hypertrophy and inflammation, which may turn maladaptive during long-term stimulation. Of special interest is a key role of PKD1 in the regulation of cardiac substrate metabolism. Glucose and fatty acids are the most important substrates for cardiac energy provision, and the ratio at which they are utilized determines the health status of the heart. Cardiac glucose uptake is mainly regulated by translocation of the glucose transporter GLUT4 from intracellular stores (endosomes) to the sarcolemma, and fatty acid uptake via a parallel translocation of fatty acid transporter CD36 from endosomes to the sarcolemma. PKD1 is involved in the regulation of GLUT4 translocation, but not CD36 translocation, giving it the ability to modulate glucose uptake without affecting fatty acid uptake, thereby altering the cardiac substrate balance. PKD1 would therefore serve as an attractive target to combat cardiac metabolic diseases with a tilted substrate balance, such as diabetic cardiomyopathy. However, PKD1 activation also elicits cardiac hypertrophy and inflammation. Therefore, identification of the events upstream and downstream of PKD1 may provide superior therapeutic targets to alter the cardiac substrate balance. Recent studies have identified the lipid kinase phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ) as signaling hub downstream of PKD1 to selectively stimulate GLUT4-mediated myocardial glucose uptake without inducing hypertrophy. Taken together, the PKD1 signaling pathway serves a pivotal role in cardiac glucose metabolism and is a promising target to selectively modulate glucose uptake in cardiac disease.
Collapse
Affiliation(s)
- Ozlenen Simsek Papur
- Department of Molecular Medicine, Institute of Health Science, Dokuz Eylül University, Izmir, Turkey
| | - Jan F C Glatz
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center(+), Maastricht, the Netherlands
| | - Joost J F P Luiken
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center(+), Maastricht, the Netherlands.
| |
Collapse
|
14
|
Amokrane L, Pokotylo I, Acket S, Ducloy A, Troncoso-Ponce A, Cacas JL, Ruelland E. Phospholipid Signaling in Crop Plants: A Field to Explore. PLANTS (BASEL, SWITZERLAND) 2024; 13:1532. [PMID: 38891340 PMCID: PMC11174929 DOI: 10.3390/plants13111532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
In plant models such as Arabidopsis thaliana, phosphatidic acid (PA), a key molecule of lipid signaling, was shown not only to be involved in stress responses, but also in plant development and nutrition. In this article, we highlight lipid signaling existing in crop species. Based on open access databases, we update the list of sequences encoding phospholipases D, phosphoinositide-dependent phospholipases C, and diacylglycerol-kinases, enzymes that lead to the production of PA. We show that structural features of these enzymes from model plants are conserved in equivalent proteins from selected crop species. We then present an in-depth discussion of the structural characteristics of these proteins before focusing on PA binding proteins. For the purpose of this article, we consider RESPIRATORY BURST OXIDASE HOMOLOGUEs (RBOHs), the most documented PA target proteins. Finally, we present pioneering experiments that show, by different approaches such as monitoring of gene expression, use of pharmacological agents, ectopic over-expression of genes, and the creation of silenced mutants, that lipid signaling plays major roles in crop species. Finally, we present major open questions that require attention since we have only a perception of the peak of the iceberg when it comes to the exciting field of phospholipid signaling in plants.
Collapse
Affiliation(s)
- Lucas Amokrane
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Igor Pokotylo
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Sébastien Acket
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Amélie Ducloy
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Adrian Troncoso-Ponce
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Jean-Luc Cacas
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Eric Ruelland
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| |
Collapse
|
15
|
Narayan KB, Baeyens L, James HP, Swain A, Baumgart T. Fluorescence imaging of lamellipodin-mediated biomolecular condensates on solid supported lipid bilayer membranes. Methods Enzymol 2024; 700:33-48. [PMID: 38971606 PMCID: PMC12026695 DOI: 10.1016/bs.mie.2024.04.007] [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] [Indexed: 07/08/2024]
Abstract
Biomolecular condensates play a major role in numerous cellular processes, including several that occur on the surface of lipid bilayer membranes. There is increasing evidence that cellular membrane trafficking phenomena, including the internalization of the plasma membrane through endocytosis, are mediated by multivalent protein-protein interactions that can lead to phase separation. We have recently found that proteins involved in the clathrin-independent endocytic pathway named Fast Endophilin Mediated Endocytosis can undergo liquid-liquid phase separation (LLPS) in solution and on lipid bilayer membranes. Here, the protein solution concentrations required for phase separation to be observed are significantly smaller compared to those required for phase separation in solution. LLPS is challenging to systematically characterize in cellular systems in general, and on biological membranes in particular. Model membrane approaches are more suitable for this purpose as they allow for precise control over the nature and amount of the components present in a mixture. Here we describe a method that enables the imaging of LLPS domain formation on solid supported lipid bilayers. These allow for facile imaging, provide long-term stability, and avoid clustering of vesicles and vesicle-attached features (such as buds and tethers) in the presence of multi-valent membrane interacting proteins.
Collapse
Affiliation(s)
- Karthik B Narayan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Laura Baeyens
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Honey Priya James
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Aparna Swain
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA.
| |
Collapse
|
16
|
Houngue R, Sangaré LO, Alayi TD, Dieng A, Bitard-Feildel T, Boulogne C, Slomianny C, Atindehou CM, Fanou LA, Hathout Y, Callebaut I, Tomavo S. Toxoplasma membrane inositol phospholipid binding protein TgREMIND is essential for secretory organelle function and host infection. Cell Rep 2024; 43:113601. [PMID: 38157297 DOI: 10.1016/j.celrep.2023.113601] [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: 03/20/2023] [Revised: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Apicomplexan parasites possess specialized secretory organelles called rhoptries, micronemes, and dense granules that play a vital role in host infection. In this study, we demonstrate that TgREMIND, a protein found in Toxoplasma gondii, is necessary for the biogenesis of rhoptries and dense granules. TgREMIND contains a Fes-CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain, which binds to membrane phospholipids, as well as a novel uncharacterized domain that we have named REMIND (regulator of membrane-interacting domain). Both the F-BAR domain and the REMIND are crucial for TgREMIND functions. When TgREMIND is depleted, there is a significant decrease in the abundance of dense granules and abnormal transparency of rhoptries, leading to a reduction in protein secretion from these organelles. The absence of TgREMIND inhibits host invasion and parasite dissemination, demonstrating that TgREMIND is essential for the proper function of critical secretory organelles required for successful infection by Toxoplasma.
Collapse
Affiliation(s)
- Rodrigue Houngue
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France
| | - Lamba Omar Sangaré
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Tchilabalo Dilezitoko Alayi
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Johnson City, NY 13790, USA
| | - Aissatou Dieng
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Claire Boulogne
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France; Plateforme Imagerie-Gif, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif sur Yvette, France
| | - Christian Slomianny
- University of Lille, Laboratory of Cell Physiology, INSERM U 1003, 59655 Villeneuve d'Ascq, France
| | - Cynthia Menonve Atindehou
- Université d'Abomey Calavi, Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences et Technologies, Cotonou, Bénin
| | - Lucie Ayi Fanou
- Université d'Abomey Calavi, Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences et Technologies, Cotonou, Bénin
| | - Yetrib Hathout
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Johnson City, NY 13790, USA
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Stanislas Tomavo
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France.
| |
Collapse
|
17
|
Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
Collapse
Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
18
|
Llorente A, Loughran RM, Emerling BM. Targeting phosphoinositide signaling in cancer: relevant techniques to study lipids and novel avenues for therapeutic intervention. Front Cell Dev Biol 2023; 11:1297355. [PMID: 37954209 PMCID: PMC10634348 DOI: 10.3389/fcell.2023.1297355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Phosphoinositides serve as essential players in numerous biological activities and are critical for overall cellular function. Due to their complex chemical structures, localization, and low abundance, current challenges in the phosphoinositide field include the accurate measurement and identification of specific variants, particularly those with acyl chains. Researchers are intensively developing innovative techniques and approaches to address these challenges and advance our understanding of the impact of phosphoinositide signaling on cellular biology. This article provides an overview of recent advances in the study of phosphoinositides, including mass spectrometry, lipid biosensors, and real-time activity assays using fluorometric sensors. These methodologies have proven instrumental for a comprehensive exploration of the cellular distribution and dynamics of phosphoinositides and have shed light on the growing significance of these lipids in human health and various pathological processes, including cancer. To illustrate the importance of phosphoinositide signaling in disease, this perspective also highlights the role of a family of lipid kinases named phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks), which have recently emerged as exciting therapeutic targets for cancer treatment. The ongoing exploration of phosphoinositide signaling not only deepens our understanding of cellular biology but also holds promise for novel interventions in cancer therapy.
Collapse
Affiliation(s)
| | | | - Brooke M. Emerling
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys, La Jolla, CA, United States
| |
Collapse
|
19
|
Madsen RR, Toker A. PI3K signaling through a biochemical systems lens. J Biol Chem 2023; 299:105224. [PMID: 37673340 PMCID: PMC10570132 DOI: 10.1016/j.jbc.2023.105224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Following 3 decades of extensive research into PI3K signaling, it is now evidently clear that the underlying network does not equate to a simple ON/OFF switch. This is best illustrated by the multifaceted nature of the many diseases associated with aberrant PI3K signaling, including common cancers, metabolic disease, and rare developmental disorders. However, we are still far from a complete understanding of the fundamental control principles that govern the numerous phenotypic outputs that are elicited by activation of this well-characterized biochemical signaling network, downstream of an equally diverse set of extrinsic inputs. At its core, this is a question on the role of PI3K signaling in cellular information processing and decision making. Here, we review the determinants of accurate encoding and decoding of growth factor signals and discuss outstanding questions in the PI3K signal relay network. We emphasize the importance of quantitative biochemistry, in close integration with advances in single-cell time-resolved signaling measurements and mathematical modeling.
Collapse
Affiliation(s)
- Ralitsa R Madsen
- MRC-Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
20
|
Ngubo M, Moradi F, Ito CY, Stanford WL. Tissue-Specific Tumour Suppressor and Oncogenic Activities of the Polycomb-like Protein MTF2. Genes (Basel) 2023; 14:1879. [PMID: 37895228 PMCID: PMC10606531 DOI: 10.3390/genes14101879] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a conserved chromatin-remodelling complex that catalyses the trimethylation of histone H3 lysine 27 (H3K27me3), a mark associated with gene silencing. PRC2 regulates chromatin structure and gene expression during organismal and tissue development and tissue homeostasis in the adult. PRC2 core subunits are associated with various accessory proteins that modulate its function and recruitment to target genes. The multimeric composition of accessory proteins results in two distinct variant complexes of PRC2, PRC2.1 and PRC2.2. Metal response element-binding transcription factor 2 (MTF2) is one of the Polycomb-like proteins (PCLs) that forms the PRC2.1 complex. MTF2 is highly conserved, and as an accessory subunit of PRC2, it has important roles in embryonic stem cell self-renewal and differentiation, development, and cancer progression. Here, we review the impact of MTF2 in PRC2 complex assembly, catalytic activity, and spatiotemporal function. The emerging paradoxical evidence suggesting that MTF2 has divergent roles as either a tumour suppressor or an oncogene in different tissues merits further investigations. Altogether, our review illuminates the context-dependent roles of MTF2 in Polycomb group (PcG) protein-mediated epigenetic regulation. Its impact on disease paves the way for a deeper understanding of epigenetic regulation and novel therapeutic strategies.
Collapse
Affiliation(s)
- Mzwanele Ngubo
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Fereshteh Moradi
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caryn Y. Ito
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| |
Collapse
|
21
|
Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [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: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
Collapse
Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| |
Collapse
|
22
|
Oh BC. Phosphoinositides and intracellular calcium signaling: novel insights into phosphoinositides and calcium coupling as negative regulators of cellular signaling. Exp Mol Med 2023; 55:1702-1712. [PMID: 37524877 PMCID: PMC10474053 DOI: 10.1038/s12276-023-01067-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 08/02/2023] Open
Abstract
Intracellular calcium (Ca2+) and phosphoinositides (PIPs) are crucial for regulating cellular activities such as metabolism and cell survival. Cells maintain precise intracellular Ca2+ and PIP levels via the actions of a complex system of Ca2+ channels, transporters, Ca2+ ATPases, and signaling effectors, including specific lipid kinases, phosphatases, and phospholipases. Recent research has shed light on the complex interplay between Ca2+ and PIP signaling, suggesting that elevated intracellular Ca2+ levels negatively regulate PIP signaling by inhibiting the membrane localization of PIP-binding proteins carrying specific domains, such as the pleckstrin homology (PH) and Ca2+-independent C2 domains. This dysregulation is often associated with cancer and metabolic diseases. PIPs recruit various proteins with PH domains to the plasma membrane in response to growth hormones, which activate signaling pathways regulating metabolism, cell survival, and growth. However, abnormal PIP signaling in cancer cells triggers consistent membrane localization and activation of PIP-binding proteins. In the context of obesity, an excessive intracellular Ca2+ level prevents the membrane localization of the PIP-binding proteins AKT, IRS1, and PLCδ via Ca2+-PIPs, contributing to insulin resistance and other metabolic diseases. Furthermore, an excessive intracellular Ca2+ level can cause functional defects in subcellular organelles such as the endoplasmic reticulum (ER), lysosomes, and mitochondria, causing metabolic diseases. This review explores how intracellular Ca2+ overload negatively regulates the membrane localization of PIP-binding proteins.
Collapse
Affiliation(s)
- Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon College of Medicine, Incheon, 21999, Republic of Korea.
| |
Collapse
|
23
|
Petsana M, Roumia AF, Bagos PG, Boleti H, Braliou GG. In Silico Identification and Analysis of Proteins Containing the Phox Homology Phosphoinositide-Binding Domain in Kinetoplastea Protists: Evolutionary Conservation and Uniqueness of Phox-Homology-Domain-Containing Protein Architectures. Int J Mol Sci 2023; 24:11521. [PMID: 37511280 PMCID: PMC10380299 DOI: 10.3390/ijms241411521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like PIs are key regulators of vital functions in all eukaryotes including signal transduction, protein transport and sorting, membrane trafficking, and cytoskeleton and membrane remodeling. A large repertoire of PI-metabolizing enzymes and PI-binding proteins/effectors carrying distinct PI-binding modules like the PX (phox homology) module could play significant roles in the life and virulence of pathogenic Kinetoplastea. The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module (PX-proteins), predict their structures, and identify in them evolutionary conserved and unique traits. Using a large array of bioinformatics tools, protein IDs from two searches (based on PFam's pHMM for PX domain (PF00787)) were combined, aligned, and utilized for the construction of a new Kinetoplastea_PX pHMM. This three-step search retrieved 170 PX-protein sequences. Structural domain configuration analysis identified PX, Pkinase, Lipocalin_5, and Vps5/BAR3-WASP domains and clustered them into five distinct subfamilies. Phylogenetic tree and domain architecture analysis showed that some domain architectures exist in proteomes of all Kinetoplastea spp., while others are genus-specific. Finally, amino acid conservation logos of the Kinetoplastea spp. and Homo sapiens PX domains revealed high evolutionary conservation in residues forming the critical structural motifs for PtdIns3P recognition. This study highlights the PX-Pkinase domain architecture as unique within Trypanosoma spp. and forms the basis for a targeted functional analysis of Kinetoplastea PX-proteins as putative targets for a rational design of anti-parasitic drugs.
Collapse
Affiliation(s)
- Marina Petsana
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Ahmed F Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
- Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
| | - Haralabia Boleti
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Georgia G Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
| |
Collapse
|
24
|
Ru B, Hao X, Li W, Peng Q, Miao J, Liu X. A Novel FYVE Domain-Containing Protein Kinase, PsZFPK1, Plays a Critical Role in Vegetative Growth, Sporangium Formation, Oospore Production, and Virulence in Phytophthora sojae. J Fungi (Basel) 2023; 9:709. [PMID: 37504698 PMCID: PMC10381902 DOI: 10.3390/jof9070709] [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: 06/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Proteins containing both FYVE and serine/threonine kinase catalytic (STKc) domains are exclusive to protists. However, the biological function of these proteins in oomycetes has rarely been reported. In the Phytophthora sojae genome database, we identified five proteins containing FYVE and STKc domains, which we named PsZFPK1, PsZFPK2, PsZFPK3, PsZFPK4, and PsZFPK5. In this study, we characterized the biological function of PsZFPK1 using a CRISPR/Cas9-mediated gene replacement system. Compared with the wild-type strain, P6497, the PsZFPK1-knockout mutants exhibited significantly reduced growth on a nutrient-rich V8 medium, while a more pronounced defect was observed on a nutrient-poor Plich medium. The PsZFPK1-knockout mutants also showed a significant increase in sporangium production. Furthermore, PsZFPK1 was found to be essential for oospore production and complete virulence but dispensable for the stress response in P. sojae. The N-terminal region, FYVE and STKc domains, and T602 phosphorylation site were found to be vital for the function of PsZFPK1. Conversely, these domains were not required for the localization of PsZFPK1 protein in the cytoplasm. Our results demonstrate that PsZFPK1 plays a critical role in vegetative growth, sporangium formation, oospore production, and virulence in P. sojae.
Collapse
Affiliation(s)
- Binglu Ru
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Xinchang Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Wenhao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Qin Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China
| |
Collapse
|
25
|
Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
Collapse
Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| |
Collapse
|
26
|
Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:8096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [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: 03/22/2023] [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.
Collapse
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
| |
Collapse
|
27
|
Mackrill JJ. Non-inositol 1,4,5-trisphosphate (IP3) receptor IP3-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2023; 1870:119470. [PMID: 37011730 DOI: 10.1016/j.bbamcr.2023.119470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Conventionally, myo-D-inositol 1, 4,5-trisphosphate (IP3) is thought to exert its second messenger effects through the gating of IP3R Ca2+ release channels, located in Ca2+-storage organelles like the endoplasmic reticulum. However, there is considerable indirect evidence to support the concept that IP3 might interact with other, non-IP3R proteins within cells. To explore this possibility further, the Protein Data Bank was searched using the term "IP3". This resulted in the retrieval of 203 protein structures, the majority of which were members of the IP3R/ryanodine receptor superfamily of channels. Only 49 of these structures were complexed with IP3. These were inspected for their ability to interact with the carbon-1 phosphate of IP3, since this is the least accessible phosphate group of its precursor, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This reduced the number of structures retrieved to 35, of which 9 were IP3Rs. The remaining 26 structures represent a diverse range of proteins, including inositol-lipid metabolizing enzymes, signal transducers, PH domain containing proteins, cytoskeletal anchor proteins, the TRPV4 ion channel, a retroviral Gag protein and fibroblast growth factor 2. Such proteins may impact on IP3 signalling and its effects on cell-biology. This represents an area open for exploration in the field of IP3 signalling.
Collapse
Affiliation(s)
- John James Mackrill
- Department of Physiology, University College Cork, Western Gateway Building, Western Road, Cork T12 XF62, Ireland.
| |
Collapse
|
28
|
He R, Liu F, Wang H, Huang S, Xu K, Zhang C, Liu Y, Yu H. ORP9 and ORP10 form a heterocomplex to transfer phosphatidylinositol 4-phosphate at ER-TGN contact sites. Cell Mol Life Sci 2023; 80:77. [PMID: 36853333 PMCID: PMC11072704 DOI: 10.1007/s00018-023-04728-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
Oxysterol-binding protein (OSBP) and its related proteins (ORPs) are a family of lipid transfer proteins (LTPs) that mediate non-vesicular lipid transport. ORP9 and ORP10, members of the OSBP/ORPs family, are located at the endoplasmic reticulum (ER)-trans-Golgi network (TGN) membrane contact sites (MCSs). It remained unclear how they mediate lipid transport. In this work, we discovered that ORP9 and ORP10 form a binary complex through intermolecular coiled-coil (CC) domain-CC domain interaction. The PH domains of ORP9 and ORP10 specially interact with phosphatidylinositol 4-phosphate (PI4P), mediating the TGN targeting. The ORP9-ORP10 complex plays a critical role in regulating PI4P levels at the TGN. Using in vitro reconstitution assays, we observed that while full-length ORP9 efficiently transferred PI4P between two apposed membranes, the lipid transfer kinetics was further accelerated by ORP10. Interestingly, our data showed that the PH domains of ORP9 and ORP10 participate in membrane tethering simultaneously, whereas ORDs of both ORP9 and ORP10 are required for lipid transport. Furthermore, our data showed that the depletion of ORP9 and ORP10 led to increased vesicle transport to the plasma membrane (PM). These findings demonstrate that ORP9 and ORP10 form a binary complex through the CC domains, maintaining PI4P homeostasis at ER-TGN MCSs and regulating vesicle trafficking.
Collapse
Affiliation(s)
- Ruyue He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Furong Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Hui Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shuai Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Conggang Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Haijia Yu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| |
Collapse
|
29
|
Balaban C, Sztacho M, Antiga L, Miladinović A, Harata M, Hozák P. PIP2-Effector Protein MPRIP Regulates RNA Polymerase II Condensation and Transcription. Biomolecules 2023; 13:biom13030426. [PMID: 36979361 PMCID: PMC10046169 DOI: 10.3390/biom13030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
The specific post-translational modifications of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (RNAPII) correlate with different stages of transcription. The phosphorylation of the Ser5 residues of this domain associates with the initiation condensates, which are formed through liquid-liquid phase separation (LLPS). The subsequent Tyr1 phosphorylation of the CTD peaks at the promoter-proximal region and is involved in the pause-release of RNAPII. By implementing super-resolution microscopy techniques, we previously reported that the nuclear Phosphatidylinositol 4,5-bisphosphate (PIP2) associates with the Ser5-phosphorylated-RNAPII complex and facilitates the RNAPII transcription. In this study, we identified Myosin Phosphatase Rho-Interacting Protein (MPRIP) as a novel regulator of the RNAPII transcription that recruits Tyr1-phosphorylated CTD (Tyr1P-CTD) to nuclear PIP2-containing structures. The depletion of MPRIP increases the number of the initiation condensates, indicating a defect in the transcription. We hypothesize that MPRIP regulates the condensation and transcription through affecting the association of the RNAPII complex with nuclear PIP2-rich structures. The identification of Tyr1P-CTD as an interactor of PIP2 and MPRIP further points to a regulatory role in RNAPII pause-release, where the susceptibility of the transcriptional complex to leave the initiation condensate depends on its association with nuclear PIP2-rich structures. Moreover, the N-terminal domain of MPRIP, which is responsible for the interaction with the Tyr1P-CTD, contains an F-actin binding region that offers an explanation of how nuclear F-actin formations can affect the RNAPII transcription and condensation. Overall, our findings shed light on the role of PIP2 in RNAPII transcription through identifying the F-actin binding protein MPRIP as a transcription regulator and a determinant of the condensation of RNAPII.
Collapse
Affiliation(s)
- Can Balaban
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
- Correspondence: (M.S.); (P.H.)
| | - Ludovica Antiga
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Ana Miladinović
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Masahiko Harata
- Laboratory of Molecular Biochemistry, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
- Correspondence: (M.S.); (P.H.)
| |
Collapse
|
30
|
Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3. Int J Mol Sci 2023; 24:ijms24021125. [PMID: 36674645 PMCID: PMC9865853 DOI: 10.3390/ijms24021125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Arap3, a dual GTPase-activating protein (GAP) for the small GTPases Arf6 and RhoA, plays key roles in regulating a wide range of biological processes, including cancer cell invasion and metastasis. It is known that Arap3 is a PI3K effector that can bind directly to PI(3,4,5)P3, and the PI(3,4,5)P3-mediated plasma membrane recruitment is crucial for its function. However, the molecular mechanism of how the protein recognizes PI(3,4,5)P3 remains unclear. Here, using liposome pull-down and surface plasmon resonance (SPR) analysis, we found that the N-terminal first pleckstrin homology (PH) domain (Arap3-PH1) can interact with PI(3,4,5)P3 and, with lower affinity, with PI(4,5)P2. To understand how Arap3-PH1 and phosphoinositide (PIP) lipids interact, we solved the crystal structure of the Arap3-PH1 in the apo form and complex with diC4-PI(3,4,5)P3. We also characterized the interactions of Arap3-PH1 with diC4-PI(3,4,5)P3 and diC4-PI(4,5)P2 in solution by nuclear magnetic resonance (NMR) spectroscopy. Furthermore, we found overexpression of Arap3 could inhibit breast cancer cell invasion in vitro, and the PIPs-binding ability of the PH1 domain is essential for this function.
Collapse
|
31
|
Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability. Int J Mol Sci 2022; 23:ijms232213888. [PMID: 36430366 PMCID: PMC9697909 DOI: 10.3390/ijms232213888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
Collapse
|
32
|
PRMT4-mediated arginine methylation promotes tyrosine phosphorylation of VEGFR-2 and regulates filopodia protrusions. iScience 2022; 25:104736. [PMID: 35942094 PMCID: PMC9356023 DOI: 10.1016/j.isci.2022.104736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/09/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Through tightly controlled multilayer mechanisms, vascular endothelial growth factor receptor-2 (VEGFR-2) activation and its downstream signal transduction govern vasculogenesis and pathological angiogenesis, such as tumor angiogenesis. Therefore, it is critical to understand the molecular mechanisms governing VEGFR-2 signal transduction. We report that protein arginine methyltransferase 4 (PRMT4) via its highly conserved EVH1 and PH domain-like N-terminal domain binds to VEGFR-2 and mediates methylation of the juxtamembrane arginine 817 (R817) on VEGFR-2. Methylation of R817 selectively increases phosphorylation of tyrosine 820 (Y820). Phosphorylation of Y820 facilitates the c-Src binding with VEGFR-2 via Src homology domain 2 (SH2). Interfering with the methylation of R817 or phosphorylation of Y820 inhibits VEGFR-2-induced filopodia protrusions, a process that is critical for the core angiogenic responses of VEGFR-2. Methylation of R817 is an important previously unrecognized mechanism of the angiogenic signaling of VEGFR-2, with implications for the development of novel-targeted VEGFR-2 inhibitors. Arginine 817 methylation regulates phosphorylation of Y820 on VEGFR-2 Phosphorylation of Y820 recruits c-Src kinase to VEGFR-2, leading to its activation VEGFR-2/c-Src axis mediates filopodia protrusions in endothelial cells
Collapse
|
33
|
Le Huray KIP, Wang H, Sobott F, Kalli AC. Systematic simulation of the interactions of pleckstrin homology domains with membranes. SCIENCE ADVANCES 2022; 8:eabn6992. [PMID: 35857458 PMCID: PMC9258823 DOI: 10.1126/sciadv.abn6992] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Pleckstrin homology (PH) domains can recruit proteins to membranes by recognition of phosphatidylinositol phosphate (PIP) lipids. Several family members are linked to diseases including cancer. We report the systematic simulation of the interactions of 100 mammalian PH domains with PIP-containing membranes. The observed PIP interaction hotspots recapitulate crystallographic binding sites and reveal a number of insights: (i) The β1 and β2 strands and their connecting loop constitute the primary PIP interaction site but are typically supplemented by interactions at the β3-β4 and β5-β6 loops; (ii) we reveal exceptional cases such as the Exoc8 PH domain; (iii) PH domains adopt different membrane-bound orientations and induce clustering of anionic lipids; and (iv) beyond family-level insights, our dataset sheds new light on individual PH domains, e.g., by providing molecular detail of secondary PIP binding sites. This work provides a global view of PH domain/membrane association involving multivalent association with anionic lipids.
Collapse
Affiliation(s)
- Kyle I. P. Le Huray
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - He Wang
- School of Computing, University of Leeds, Leeds, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C. Kalli
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| |
Collapse
|
34
|
The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. MEMBRANES 2022; 12:membranes12070696. [PMID: 35877899 PMCID: PMC9324892 DOI: 10.3390/membranes12070696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023]
Abstract
Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key roles in membrane binding, whereas the C-terminal poly aspartic acid (polyD) motif specifically autoinhibits the PH domain binding to the membrane phosphatidylinositol 3-phosphate (PtdIns3P). Since the Phafin2 FYVE domain also binds PtdIns3P, the role of the polyD motif remains unclear. In this study, bioinformatics tools and resources were employed to determine the concurrence of the PH-FYVE module with the polyD motif among Phafin2 and PH-, FYVE-, or polyD-containing proteins from bacteria to humans. FYVE was found to be an ancient domain of Phafin2 and is related to proteins that are present in both prokaryotes and eukaryotes. Interestingly, the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals. PolyD motifs are absent in PH domain-free FYVE-containing proteins, which usually display cellular trafficking or autophagic functions. Moreover, the prediction of the Phafin2-interacting network indicates that Phafin2 primarily cross-talks with proteins involved in autophagy, protein trafficking, and neuronal function. Taken together, the concurrence of the polyD motif with the PH domain may be associated with complex cellular functions that evolved specifically in animals.
Collapse
|
35
|
Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
Collapse
Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
| |
Collapse
|
36
|
Khaliq SA, Umair Z, Yoon MS. Role of ARHGEF3 as a GEF and mTORC2 Regulator. Front Cell Dev Biol 2022; 9:806258. [PMID: 35174167 PMCID: PMC8841341 DOI: 10.3389/fcell.2021.806258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
Guanine nucleotide exchange factors (GEFs) activate GTPases by stimulating the release of guanosine diphosphate to permit the binding of guanosine triphosphate. ARHGEF3 or XPLN (exchange factor found in platelets, leukemic, and neuronal tissues) is a selective guanine nucleotide exchange factor for Rho GTPases (RhoGEFs) that activates RhoA and RhoB but not RhoC, RhoG, Rac1, or Cdc42. ARHGEF3 contains the diffuse B-cell lymphoma homology and pleckstrin homology domains but lacks similarity with other known functional domains. ARHGEF3 also binds the mammalian target of rapamycin complex 2 (mTORC2) and subsequently inhibits mTORC2 and Akt. In vivo investigation has also indicated the communication between ARHGEF3 and autophagy-related muscle pathologies. Moreover, studies on genetic variation in ARHGEF3 and genome-wide association studies have predicted exciting novel roles of ARHGEF3 in controlling bone mineral density, platelet formation and differentiation, and Hirschsprung disease. In conclusion, we hypothesized that additional biochemical and functional studies are required to elucidate the detailed mechanism of ARHGEF3-related pathologies and therapeutics.
Collapse
Affiliation(s)
- Sana Abdul Khaliq
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
| | - Zobia Umair
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
| | - Mee-Sup Yoon
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
| |
Collapse
|
37
|
He J, Zeng Z, Wang Y, Deng J, Tang X, Liu F, Huang J, Chen H, Liang R, Zan X, Liu Z, Tong A, Guo G, Xu J, Zhu X, Zhou L, Peng Y. Characterization of novel CTNNB1 mutation in Craniopharyngioma by whole-genome sequencing. Mol Cancer 2021; 20:168. [PMID: 34922552 PMCID: PMC8684236 DOI: 10.1186/s12943-021-01468-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Craniopharyngioma (CP) is rare histologically benign but clinically challenging tumor because of its intimate relationship with the critical structure in the central brain. CP can be divided into two major histologic subtypes: adamantinomatous-type CP (ACP) and papillary-type CP (PCP). Although some genetic aberrations for both categories have been revealed in previous studies, the complete spectrum of genetic changes of this tumor remains unknown. Methods In this study, we conducted whole genome sequencing (WGS) on twenty-six CPs including 16 ACPs and 10 PCPs together with their matched blood samples. Somatic variants (SNVs, InDels, SVs and CNVs) were identified and mutational signatures were characterized for each patient. We investigated the impact of a novel CTNNB1 mutant on its protein stability, ubiquitination and Wnt pathway activity. Cell proliferation ability of the CTNNB1 mutant in ACP primary cells was additionally analyzed by CCK8 and colony formation assays. Results We found that CPs had showed less complexity with fewer somatic mutations compared with malignant tumors. Moreover, mutations in CTNNB1 (68.75% of ACP) and BRAF V600E (70.00% of PCP) are mutually exclusive in ACP and PCP, consolidating that the driving roles of these two genes in ACP and PCP, respectively. A novel mutation in the exon 3 of CTNNB1 which compromised both a transversion and in-frame deletion was identified in ACP. This mutation was experimentally validated to confer β-catenin increased stability by inhibiting its ubiquitination, thus activating Wnt-signaling pathway and promoting cell proliferation. Conclusions Whole genome landscape for CP was revealed by WGS analysis, and a novel mutation in the exon 3 of CTNNB1 was identified. This novel mutation activates Wnt-signaling pathway through increasing the stability of β-catenin. Our findings provided us with more comprehensive insight into the spectrum of genetic alterations in CP. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01468-7.
Collapse
Affiliation(s)
- Juan He
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhen Zeng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yuelong Wang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 20040, China
| | - Xin Tang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fujun Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianhan Huang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongxu Chen
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruichao Liang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Zan
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Aiping Tong
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gang Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianguo Xu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaofeng Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Liangxue Zhou
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
38
|
Ryan A, Hammond GRV, Deiters A. Optical Control of Phosphoinositide Binding: Rapid Activation of Subcellular Protein Translocation and Cell Signaling. ACS Synth Biol 2021; 10:2886-2895. [PMID: 34748306 DOI: 10.1021/acssynbio.1c00328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells utilize protein translocation to specific compartments for spatial and temporal regulation of protein activity, in particular in the context of signaling processes. Protein recognition and binding to various subcellular membranes is mediated by a network of phosphatidylinositol phosphate (PIP) species bearing one or multiple phosphate moieties on the polar inositol head. Here, we report a new, highly efficient method for optical control of protein localization through the site-specific incorporation of a photocaged amino acid for steric and electrostatic disruption of inositol phosphate recognition and binding. We demonstrate general applicability of the approach by photocaging two unrelated proteins, sorting nexin 3 (SNX3) and the pleckstrin homology (PH) domain of phospholipase C delta 1 (PLCδ1), with two distinct PIP binding domains and distinct subcellular localizations. We have established the applicability of this methodology through its application to Son of Sevenless 2 (SOS2), a signaling protein involved in the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) cascade. Upon fusing the photocaged plasma membrane-targeted construct PH-enhanced green fluorescent protein (EGFP), to the catalytic domain of SOS2, we demonstrated light-induced membrane localization of the construct resulting in fast and extensive activation of the ERK signaling pathway in NIH 3T3 cells. This approach can be readily extended to other proteins, with minimal protein engineering, and provides a method for acute optical control of protein translocation with rapid and complete activation.
Collapse
Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|