1
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Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Ogunmowo TH, Ho A, Mackay JP, Ha T, Watanabe S, Robinson PJ. Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. EMBO J 2024; 43:3327-3357. [PMID: 38907032 PMCID: PMC11329700 DOI: 10.1038/s44318-024-00145-x] [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: 03/08/2024] [Revised: 04/26/2024] [Accepted: 05/24/2024] [Indexed: 06/23/2024] Open
Abstract
Dynamin 1 mediates fission of endocytic synaptic vesicles in the brain and has two major splice variants, Dyn1xA and Dyn1xB, which are nearly identical apart from the extended C-terminal region of Dyn1xA. Despite a similar set of binding partners, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that Dyn1xA achieves this localization by preferentially binding to Endophilin A1 through a newly defined binding site within its long C-terminal tail extension. Endophilin A1 binds this site at higher affinity than the previously reported site, and the affinity is determined by amino acids within the Dyn1xA tail but outside the binding site. This interaction is regulated by the phosphorylation state of two serine residues specific to the Dyn1xA variant. Dyn1xA and Endophilin A1 colocalize in patches near the active zone, and mutations disrupting Endophilin A binding to the long tail cause Dyn1xA mislocalization and stalled endocytic pits on the plasma membrane during ultrafast endocytosis. Together, these data suggest that the specificity for ultrafast endocytosis is defined by the phosphorylation-regulated interaction of Endophilin A1 with the C-terminal extension of Dyn1xA.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Xue
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia
| | - Lin Luo
- Institute for Molecular Bioscience, Institute for Molecular Bioscience Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - George E Craft
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences and Sydney Nano Institute, University of Sydney, Camperdown, NSW, Australia
| | - Tyler H Ogunmowo
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Annie Ho
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville, 2145, NSW, Australia.
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2
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Jiang A, Kudo K, Gormal RS, Ellis S, Guo S, Wallis TP, Longfield SF, Robinson PJ, Johnson ME, Joensuu M, Meunier FA. Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nat Commun 2024; 15:4060. [PMID: 38744819 PMCID: PMC11094030 DOI: 10.1038/s41467-024-47677-8] [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: 03/11/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed across the plasma membrane remains poorly understood. Two dynamin-1 major splice variants differ by the length of their C-terminal proline-rich region (short-tail and long-tail). Using sptPALM in PC12 cells, neurons and MEF cells, we demonstrate that short-tail dynamin-1 isoforms ab and bb display an activity-dependent recruitment to the membrane, promptly followed by their concentration into nanoclusters. These nanoclusters are sensitive to both Calcineurin and dynamin GTPase inhibitors, and are larger, denser, and more numerous than that of long-tail isoform aa. Spatiotemporal modelling confirms that dynamin-1 isoforms perform distinct search patterns and undergo dimensional reduction to generate endocytic nanoclusters, with short-tail isoforms more robustly exploiting lateral trapping in the generation of nanoclusters compared to the long-tail isoform.
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Affiliation(s)
- Anmin Jiang
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kye Kudo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sevannah Ellis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sikao Guo
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shanley F Longfield
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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3
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Gnyliukh N, Johnson A, Nagel MK, Monzer A, Babić D, Hlavata A, Alotaibi SS, Isono E, Loose M, Friml J. Role of the dynamin-related protein 2 family and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. J Cell Sci 2024; 137:jcs261720. [PMID: 38506228 PMCID: PMC11112126 DOI: 10.1242/jcs.261720] [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: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development through controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of the plant dynamin-related protein 2 (DRP2) family (hereafter DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to recruiters of dynamins, such as endophilin and amphiphysin, in CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggest that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that, despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME.
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Affiliation(s)
- Nataliia Gnyliukh
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Alexander Johnson
- Division of Anatomy, Centre for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Aline Monzer
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - David Babić
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Annamaria Hlavata
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia
| | - Erika Isono
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Martin Loose
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
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Sim PF, Chek MF, Nguyen NTH, Nishimura T, Inaba T, Hakoshima T, Suetsugu S. The SH3 binding site in front of the WH1 domain contributes to the membrane binding of the BAR domain protein endophilin A2. J Biochem 2023; 175:57-67. [PMID: 37812440 DOI: 10.1093/jb/mvad065] [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: 06/07/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
The Bin-Amphiphysin-Rvs (BAR) domain of endophilin binds to the cell membrane and shapes it into a tubular shape for endocytosis. Endophilin has a Src-homology 3 (SH3) domain at their C-terminal. The SH3 domain interacts with the proline-rich motif (PRM) that is found in proteins such as neural Wiskott-Aldrich syndrome protein (N-WASP). Here, we re-examined the binding sites of the SH3 domain of endophilin in N-WASP by machine learning-based prediction and identified the previously unrecognized binding site. In addition to the well-recognized PRM at the central proline-rich region, we found a PRM in front of the N-terminal WASP homology 1 (WH1) domain of N-WASP (NtPRM) as a binding site of the endophilin SH3 domain. Furthermore, the diameter of the membrane tubules in the presence of NtPRM mutant was narrower and wider than that in the presence of N-WASP and in its absence, respectively. Importantly, the NtPRM of N-WASP was involved in the membrane localization of endophilin A2 in cells. Therefore, the NtPRM contributes to the binding of endophilin to N-WASP in membrane remodeling.
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Affiliation(s)
- Pei Fang Sim
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Min Fey Chek
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Nhung Thi Hong Nguyen
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tamako Nishimura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Takehiko Inaba
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Toshio Hakoshima
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shiro Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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5
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Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Mackay JP, Ha T, Watanabe S, Robinson PJ. Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558797. [PMID: 37790502 PMCID: PMC10542163 DOI: 10.1101/2023.09.21.558797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Dynamin 1 (Dyn1) has two major splice variants, xA and xB, with unique C-terminal extensions of 20 and 7 amino acids, respectively. Of these, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that the long tail variant, Dyn1xA, achieves this localization by preferentially binding to Endophilin A through a newly defined Class II binding site overlapping with its extension, at a site spanning the splice boundary. Endophilin binds this site at higher affinity than the previously reported site, and this affinity is determined by amino acids outside the binding sites acting as long distance elements within the xA tail. Their interaction is regulated by the phosphorylation state of two serine residues specific to the xA variant. Dyn1xA and Endophilin colocalize in patches near the active zone of synapses. Mutations selectively disrupting Endophilin binding to the long extension cause Dyn1xA mislocalization along axons. In these mutants, endocytic pits are stalled on the plasma membrane during ultrafast endocytosis. These data suggest that the specificity for ultrafast endocytosis is defined by the phospho-regulated interaction of Endophilin A through a newly identified site of Dyn1xA's long tail.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Jing Xue
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
| | - Lin Luo
- Institute for Molecular Bioscience, Institute for Molecular Bioscience Centre for Inflammation and Disease Research, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - George E. Craft
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences and Sydney Nano Institute, University of Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore MD, USA
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore MD, USA
| | - Phillip J. Robinson
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Locked Bag 23, Wentworthville 2145, NSW, Australia
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6
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Mai X, Shang J, Chen Q, Gu S, Hong Y, Zhou J, Zhang M. Endophilin A2 protects against renal fibrosis by targeting TGF-β/Smad signaling. FASEB J 2022; 36:e22603. [PMID: 36259445 DOI: 10.1096/fj.202101769r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Renal fibrosis underlies all forms of end-stage kidney disease. Endophilin A2 (EndoA2) plays a role in nephrotic syndrome; however, its effect on renal fibrosis remains unknown. Here, we demonstrate that EndoA2 protects against kidney interstitial fibrosis via the transforming growth factor-β (TGF-β)/Smad signaling pathway. Mouse kidneys with fibrosis or kidney biopsy specimens from patients with fibrotic nephropathy had lower levels of EndoA2 protein expression than that in kidneys without fibrosis. In vivo overexpression of EndoA2 with the endophilin A2 transgene (EndoA2Tg ) notably prevented renal fibrosis, decreased the protein expression of profibrotic molecules, suppressed tubular injury, and reduced apoptotic tubular cells in the obstructed kidney cortex of mice with unilateral ureteral obstruction (UUO). In vivo and in vitro overexpression of EndoA2 markedly inhibited UUO- or TGF-β1-induced phosphorylation of Smad2/3 and tubular epithelial cells dedifferentiation. Furthermore, EndoA2 was co-immunoprecipitated with the type II TGF-β receptor (TβRII), thus inhibiting the binding of the type I TGF-β receptor (TβRI) to TβRII. These findings indicate that EndoA2 mitigates renal fibrosis, at least partially, via modulating the TGF-β/Smad signaling. Targeting EndoA2 may be a new potential therapeutic strategy for treatment of renal fibrosis.
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Affiliation(s)
- Xiaoyi Mai
- Intensive Care Research Team of Traditional Chinese Medicine & AMI Key Lab of Chinese Medicine in Guangzhou, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinyan Shang
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Qiuyuan Chen
- Department of Organ Transplantation, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shijie Gu
- Department of Organ Transplantation, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yu Hong
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jiaguo Zhou
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Minzhou Zhang
- Intensive Care Research Team of Traditional Chinese Medicine & AMI Key Lab of Chinese Medicine in Guangzhou, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Critical Care Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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7
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Boll E, Cantrelle FX, Landrieu I, Hirel M, Sinnaeve D, Levy G. 1H, 13C, and 15N chemical shift assignment of human PACSIN1/syndapin I SH3 domain in solution. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:175-178. [PMID: 32236802 DOI: 10.1007/s12104-020-09940-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Human neuron-specific PACSIN1 plays a key role in synaptic vesicle recycling and endocytosis, as well as reorganization of the microtubule dynamics to maintain axonal plasticity. PACSIN1 contains a highly conserved C-terminal SH3 domain and an F-bar domain at its N-terminus. Due to its remarkable interaction network, PACSIN1 plays a central role in key neuronal functions. Here, we present a robust backbone and side-chain assignment of PACSIN1 SH3 domain based on 2D [1H,15N] HSQC or HMQC, and 3D BEST-HNCO, -HNCACB, -HN(CO)CACB, -HN(CA)CO, and standard (H)CC(CO)NH, HN(CA)NNH, HN(COCA)NH, HBHANNH, HNHA, HBHA(CO)NH, H(CC)(CO)NH, HCCH-TOCSY, that covers 96% for all 13CO, 13Cα and 13Cβ, 28% of 13Cγδε, and 95% of 1HN and 15N chemical shifts. Modelling based on sequence homology with a known related structure, and chemical shift-based secondary structure predictions, identified the presence of five β-strands linked by flexible loops. Taken together, these results open up new avenues to investigate and develop new therapeutic strategies.
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Affiliation(s)
- Emmanuelle Boll
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Francois-Xavier Cantrelle
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Isabelle Landrieu
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Matthieu Hirel
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Davy Sinnaeve
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France
- CNRS ERL Integrative Structural Biology, 59000, Lille, France
| | - Géraldine Levy
- Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Univ. Lille, Inserm, CHU Lille, 59000, Lille, France.
- CNRS ERL Integrative Structural Biology, 59000, Lille, France.
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8
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A Novel Glycine Receptor Variant with Startle Disease Affects Syndapin I and Glycinergic Inhibition. J Neurosci 2020; 40:4954-4969. [PMID: 32354853 DOI: 10.1523/jneurosci.2490-19.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
Glycine receptors (GlyRs) are the major mediators of fast synaptic inhibition in the adult human spinal cord and brainstem. Hereditary mutations to GlyRs can lead to the rare, but potentially fatal, neuromotor disorder hyperekplexia. Most mutations located in the large intracellular domain (TM3-4 loop) of the GlyRα1 impair surface expression levels of the receptors. The novel GLRA1 mutation P366L, located in the TM3-4 loop, showed normal surface expression but reduced chloride currents, and accelerated whole-cell desensitization observed in whole-cell recordings. At the single-channel level, we observed reduced unitary conductance accompanied by spontaneous opening events in the absence of extracellular glycine. Using peptide microarrays and tandem MS-based analysis methods, we show that the proline-rich stretch surrounding P366 mediates binding to syndapin I, an F-BAR domain protein involved in membrane remodeling. The disruption of the noncanonical Src homology 3 recognition motif by P366L reduces syndapin I binding. These data suggest that the GlyRα1 subunit interacts with intracellular binding partners and may therefore play a role in receptor trafficking or synaptic anchoring, a function thus far only ascribed to the GlyRβ subunit. Hence, the P366L GlyRα1 variant exhibits a unique set of properties that cumulatively affect GlyR functionality and thus might explain the neuropathological mechanism underlying hyperekplexia in the mutant carriers. P366L is the first dominant GLRA1 mutation identified within the GlyRα1 TM3-4 loop that affects GlyR physiology without altering protein expression at the whole-cell and surface levels.SIGNIFICANCE STATEMENT We show that the intracellular domain of the inhibitory glycine receptor α1 subunit contributes to trafficking and synaptic anchoring. A proline-rich stretch in this receptor domain forms a noncanonical recognition motif important for the interaction with syndapin I (PACSIN1). The disruption of this motif, as present in a human patient with hyperekplexia led to impaired syndapin I binding. Functional analysis revealed that the altered proline-rich stretch determines several functional physiological parameters of the ion channel (e.g., faster whole-cell desensitization) reduced unitary conductance and spontaneous opening events. Thus, the proline-rich stretch from the glycine receptor α1 subunit represents a multifunctional intracellular protein motif.
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9
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Wang X, Garvanska DH, Nasa I, Ueki Y, Zhang G, Kettenbach AN, Peti W, Nilsson J, Page R. A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment. eLife 2020; 9:55966. [PMID: 32195664 PMCID: PMC7108865 DOI: 10.7554/elife.55966] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/14/2020] [Indexed: 12/16/2022] Open
Abstract
The recruitment of substrates by the ser/thr protein phosphatase 2A (PP2A) is poorly understood, limiting our understanding of PP2A-regulated signaling. Recently, the first PP2A:B56 consensus binding motif, LxxIxE, was identified. However, most validated LxxIxE motifs bind PP2A:B56 with micromolar affinities, suggesting that additional motifs exist to enhance PP2A:B56 binding. Here, we report the requirement of a positively charged motif in a subset of PP2A:B56 interactors, including KIF4A, to facilitate B56 binding via dynamic, electrostatic interactions. Using molecular and cellular experiments, we show that a conserved, negatively charged groove on B56 mediates dynamic binding. We also discovered that this positively charged motif, in addition to facilitating KIF4A dephosphorylation, is essential for condensin I binding, a function distinct and exclusive from PP2A-B56 binding. Together, these results reveal how dynamic, charge-charge interactions fine-tune the interactions mediated by specific motifs, providing a new framework for understanding how PP2A regulation drives cellular signaling.
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Affiliation(s)
- Xinru Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, United States
| | - Dimitriya H Garvanska
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Yumi Ueki
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gang Zhang
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Medical Center Drive, Lebanon, United States
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, United States
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, United States
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10
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TLR Crosstalk Activates LRP1 to Recruit Rab8a and PI3Kγ for Suppression of Inflammatory Responses. Cell Rep 2019; 24:3033-3044. [PMID: 30208326 DOI: 10.1016/j.celrep.2018.08.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/28/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
The multi-ligand endocytic receptor, low-density lipoprotein-receptor-related protein 1 (LRP1), has anti-inflammatory roles in disease. Here, we reveal that pathogen-activated Toll-like receptors (TLRs) activate LRP1 in human and mouse primary macrophages, resulting in phosphorylation of LRP1 at Y4507. In turn, this allows LRP1 to activate and recruit the guanosine triphosphatase (GTPase), Rab8a, with p110γ/p101 as its phosphatidylinositol 3-kinase (PI3K) effector complex. PI3Kγ is a known regulator of TLR signaling and macrophage reprogramming. LRP1 coincides with Rab8a at signaling sites on macropinosomal membranes. In LRP1-deficient cells, TLR-induced Rab8 activation is abolished. CRISPR-mediated knockout of LRP1 in macrophages alters Akt/mTOR signaling and produces a pro-inflammatory bias in cytokine outputs, mimicking the Rab8a knockout and PI3Kγ-null phenotype. Thus, TLR-LRP1 crosstalk activates the Rab8a/PI3Kγ complex for reprogramming macrophages, revealing this as a key mechanism through which LRP1 helps to suppress inflammation.
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11
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Functional recruitment of dynamin requires multimeric interactions for efficient endocytosis. Nat Commun 2019; 10:4462. [PMID: 31575863 PMCID: PMC6773865 DOI: 10.1038/s41467-019-12434-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/10/2019] [Indexed: 02/06/2023] Open
Abstract
During clathrin mediated endocytosis (CME), the concerted action of dynamin and its interacting partners drives membrane scission. Essential interactions occur between the proline/arginine-rich domain of dynamin (dynPRD) and the Src-homology domain 3 (SH3) of various proteins including amphiphysins. Here we show that multiple SH3 domains must bind simultaneously to dynPRD through three adjacent motifs for dynamin’s efficient recruitment and function. First, we show that mutant dynamins modified in a single motif, including the central amphiphysin SH3 (amphSH3) binding motif, partially rescue CME in dynamin triple knock-out cells. However, mutating two motifs largely prevents that ability. Furthermore, we designed divalent dynPRD-derived peptides. These ligands bind multimers of amphSH3 with >100-fold higher affinity than monovalent ones in vitro. Accordingly, dialyzing living cells with these divalent peptides through a patch-clamp pipette blocks CME much more effectively than with monovalent ones. We conclude that dynamin drives vesicle scission via multivalent interactions in cells. During clathrin mediated endocytosis (CME), membrane scission is achieved by the concerted action of dynamin and its interacting partners such as amphiphysins. Here authors show that efficient recruitment and function of dynamin requires simultaneous binding of multiple amphiphysin SH3 domains.
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12
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Meirson T, Bomze D, Kahlon L, Gil-Henn H, Samson AO. A helical lock and key model of polyproline II conformation with SH3. Bioinformatics 2019; 36:154-159. [DOI: 10.1093/bioinformatics/btz527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
Motivation
More than half of the human proteome contains the proline-rich motif, PxxP. This motif has a high propensity for adopting a left-handed polyproline II (PPII) helix and can potentially bind SH3 domains. SH3 domains are generally grouped into two classes, based on whether the PPII binds in a positive (N-to-C terminal) or negative (C-to-N terminal) orientation. Since the discovery of this structural motif, over six decades ago, a systematic understanding of its binding remains poor and the consensus amino acid sequence that binds SH3 domains is still ill defined.
Results
Here, we show that the PPII interaction with SH3 domains is governed by the helix backbone and its prolines, and their rotation angle around the PPII helical axis. Based on a geometric analysis of 131 experimentally solved SH3 domains in complex with PPIIs, we observed a rotary translation along the helical screw axis, and separated them by 120° into three categories we name α (0–120°), β (120–240°) and γ (240–360°). Furthermore, we found that PPII helices are distinguished by a shifting PxxP motif preceded by positively charged residues which act as a structural reading frame and dictates the organization of SH3 domains; however, there is no one single consensus motif for all classified PPIIs. Our results demonstrate a remarkable apparatus of a lock with a rotating and translating key with no known equivalent machinery in molecular biology. We anticipate our model to be a starting point for deciphering the PPII code, which can unlock an exponential growth in our understanding of the relationship between protein structure and function.
Availability and implementation
We have implemented the proposed methods in the R software environment and in an R package freely available at https://github.com/Grantlab/bio3d.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tomer Meirson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Safed 1589, Israel
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1589, Israel
| | - David Bomze
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 39040, Israel
| | - Liron Kahlon
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1589, Israel
| | - Hava Gil-Henn
- Laboratory of Cell Migration and Invasion, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1589, Israel
| | - Abraham O Samson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Safed 1589, Israel
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13
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Bertran MT, Mouilleron S, Zhou Y, Bajaj R, Uliana F, Kumar GS, van Drogen A, Lee R, Banerjee JJ, Hauri S, O'Reilly N, Gstaiger M, Page R, Peti W, Tapon N. ASPP proteins discriminate between PP1 catalytic subunits through their SH3 domain and the PP1 C-tail. Nat Commun 2019; 10:771. [PMID: 30770806 PMCID: PMC6377682 DOI: 10.1038/s41467-019-08686-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/25/2019] [Indexed: 11/26/2022] Open
Abstract
Serine/threonine phosphatases such as PP1 lack substrate specificity and associate with a large array of targeting subunits to achieve the requisite selectivity. The tumour suppressor ASPP (apoptosis-stimulating protein of p53) proteins associate with PP1 catalytic subunits and are implicated in multiple functions from transcriptional regulation to cell junction remodelling. Here we show that Drosophila ASPP is part of a multiprotein PP1 complex and that PP1 association is necessary for several in vivo functions of Drosophila ASPP. We solve the crystal structure of the human ASPP2/PP1 complex and show that ASPP2 recruits PP1 using both its canonical RVxF motif, which binds the PP1 catalytic domain, and its SH3 domain, which engages the PP1 C-terminal tail. The ASPP2 SH3 domain can discriminate between PP1 isoforms using an acidic specificity pocket in the n-Src domain, providing an exquisite mechanism where multiple motifs are used combinatorially to tune binding affinity to PP1.
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Affiliation(s)
- M Teresa Bertran
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stéphane Mouilleron
- Structural Biology - Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Yanxiang Zhou
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rakhi Bajaj
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Ganesan Senthil Kumar
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Rebecca Lee
- Structural Biology - Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jennifer J Banerjee
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simon Hauri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Nicola O'Reilly
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Rebecca Page
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Wolfgang Peti
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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14
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Goretzki B, Glogowski NA, Diehl E, Duchardt-Ferner E, Hacker C, Gaudet R, Hellmich UA. Structural Basis of TRPV4 N Terminus Interaction with Syndapin/PACSIN1-3 and PIP 2. Structure 2018; 26:1583-1593.e5. [PMID: 30244966 DOI: 10.1016/j.str.2018.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
Transient receptor potential (TRP) channels are polymodally regulated ion channels. TRPV4 (vanilloid 4) is sensitized by PIP2 and desensitized by Syndapin3/PACSIN3, which bind to the structurally uncharacterized TRPV4 N terminus. We determined the nuclear magnetic resonance structure of the Syndapin3/PACSIN3 SH3 domain in complex with the TRPV4 N-terminal proline-rich region (PRR), which binds as a class I polyproline II (PPII) helix. This PPII conformation is broken by a conserved proline in a cis conformation. Beyond the PPII, we find that the proximal TRPV4 N terminus is unstructured, a feature conserved across species thus explaining the difficulties in resolving it in previous structural studies. Syndapin/PACSIN SH3 domain binding leads to rigidification of both the PRR and the adjacent PIP2 binding site. We determined the affinities of the TRPV4 N terminus for PACSIN1, 2, and 3 SH3 domains and PIP2 and deduce a hierarchical interaction network where Syndapin/PACSIN binding influences the PIP2 binding site but not vice versa.
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Affiliation(s)
- Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Nina A Glogowski
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Erika Diehl
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany; Institute for Molecular Biosciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Carolin Hacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany; Institute for Molecular Biosciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany.
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15
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Makaraci P, Kim K. trans-Golgi network-bound cargo traffic. Eur J Cell Biol 2018; 97:137-149. [PMID: 29398202 DOI: 10.1016/j.ejcb.2018.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
Cargo following the retrograde trafficking are sorted at endosomes to be targeted the trans-Golgi network (TGN), a central receiving organelle. Though molecular requirements and their interaction networks have been somewhat established, the complete understanding of the intricate nature of their action mechanisms in every step of the retrograde traffic pathway remains unachieved. This review focuses on elucidating known functions of key regulators, including scission factors at the endosome and tethering/fusion mediators at the receiving dock, TGN, as well as a diverse range of cargo.
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Affiliation(s)
- Pelin Makaraci
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA.
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16
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Eich ML, Dembla E, Wahl S, Dembla M, Schwarz K, Schmitz F. The Calcineurin-Binding, Activity-Dependent Splice Variant Dynamin1xb Is Highly Enriched in Synapses in Various Regions of the Central Nervous System. Front Mol Neurosci 2017; 10:230. [PMID: 28790889 PMCID: PMC5524891 DOI: 10.3389/fnmol.2017.00230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022] Open
Abstract
In the present study, we generated and characterized a splice site-specific monoclonal antibody that selectively detects the calcineurin-binding dynamin1 splice variant dynamin1xb. Calcineurin is a Ca2+-regulated phosphatase that enhances dynamin1 activity and is an important Ca2+-sensing mediator of homeostatic synaptic plasticity in neurons. Using this dynamin1xb-specific antibody, we found dynamin1xb highly enriched in synapses of all analyzed brain regions. In photoreceptor ribbon synapses, dynamin1xb was enriched in close vicinity to the synaptic ribbon in a manner indicative of a peri-active zone immunolabeling. Interestingly, in dark-adapted mice we observed an enhanced and selective enrichment of dynamin1xb in both synaptic layers of the retina in comparison to light-adapted mice. This could be due to an illumination-dependent recruitment of dynamin1xb to retinal synapses and/or due to a darkness-induced increase of dynamin1xb biosynthesis. These latter findings indicate that dynamin1xb is part of a versatile and highly adjustable, activity-regulated endocytic synaptic machinery.
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Affiliation(s)
- Marie-Lisa Eich
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
| | - Ekta Dembla
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
| | - Silke Wahl
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
| | - Mayur Dembla
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
| | - Karin Schwarz
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
| | - Frank Schmitz
- Department of Neuroanatomy, Medical School Homburg/Saar, Institute for Anatomy and Cell Biology, Saarland UniversityHomburg/Saar, Germany
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17
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Bessonov K, Vassall KA, Harauz G. Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP)-Insights into a noncanonical and fuzzy interaction. Proteins 2017; 85:1336-1350. [PMID: 28380689 DOI: 10.1002/prot.25295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/03/2017] [Accepted: 03/27/2017] [Indexed: 01/06/2023]
Abstract
The molecular details of the association between the human Fyn-SH3 domain, and the fragment of 18.5-kDa myelin basic protein (MBP) spanning residues S38-S107 (denoted as xα2-peptide, murine sequence numbering), were studied in silico via docking and molecular dynamics over 50-ns trajectories. The results show that interaction between the two proteins is energetically favorable and heavily dependent on the MBP proline-rich region (P93-P98) in both aqueous and membrane environments. In aqueous conditions, the xα2-peptide/Fyn-SH3 complex adopts a "sandwich""-like structure. In the membrane context, the xα2-peptide interacts with the Fyn-SH3 domain via the proline-rich region and the β-sheets of Fyn-SH3, with the latter wrapping around the proline-rich region in a form of a clip. Moreover, the simulations corroborate prior experimental evidence of the importance of upstream segments beyond the canonical SH3-ligand. This study thus provides a more-detailed glimpse into the context-dependent interaction dynamics and importance of the β-sheets in Fyn-SH3 and proline-rich region of MBP. Proteins 2017; 85:1336-1350. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kyrylo Bessonov
- Systems and Modeling Unit, Montefiore Institute, Université de Liège, Quartier Polytech 1, Allée de la Découverte 10, Liège, 4000, Belgium
| | - Kenrick A Vassall
- Department of Molecular and Cellular Biology, Biophysics Interdepartmental Group, and Collaborative Program in Neuroscience, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - George Harauz
- Department of Molecular and Cellular Biology, Biophysics Interdepartmental Group, and Collaborative Program in Neuroscience, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
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18
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Wall AA, Luo L, Hung Y, Tong SJ, Condon ND, Blumenthal A, Sweet MJ, Stow JL. Small GTPase Rab8a-recruited Phosphatidylinositol 3-Kinase γ Regulates Signaling and Cytokine Outputs from Endosomal Toll-like Receptors. J Biol Chem 2017; 292:4411-4422. [PMID: 28130450 DOI: 10.1074/jbc.m116.766337] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/14/2017] [Indexed: 12/28/2022] Open
Abstract
LPS-mediated activation of Toll-like receptor 4 (TLR4) in macrophages results in the coordinated release of proinflammatory cytokines, followed by regulatory mediators, to ensure that this potentially destructive pathway is tightly regulated. We showed previously that Rab8a recruits PI3Kγ for Akt-dependent signaling during TLR4 activation to limit the production of the proinflammatory cytokines IL-6 and IL-12p40 while enhancing the release of the regulatory/anti-inflammatory cytokine IL-10. Here we broaden the array of immune receptors controlled by Rab8a-PI3Kγ and further define the Rab-mediated membrane domains required for signaling. With CRISPR/Cas9-mediated gene editing to stably knock out and recover Rab8a in macrophage cell lines, we match Akt signaling profiles with cytokine outputs, confirming that Rab8a is a novel regulator of the Akt/mammalian target of rapamycin (mTOR) pathway downstream of multiple TLRs. Upon developing a Rab8a activation assay, we show that TLR3 and 9 agonists also activate Rab8a. Live-cell imaging reveals that Rab8a is first recruited to the plasma membrane and dorsal ruffles, but it is retained during collapse of ruffles to form macropinosomes enriched for phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), suggesting that the macropinosome is the location where Rab8a is active. We pinpoint macropinosomes as the sites for Rab8-mediated biasing of inflammatory signaling responses via inducible production of anti-inflammatory cytokines. Thus, Rab8a and PI3Kγ are positioned in multiple TLR pathways, and this signaling axis may serve as a pharmacologically tractable target during infection and inflammation.
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Affiliation(s)
- Adam A Wall
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Lin Luo
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Yu Hung
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Samuel J Tong
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Nicholas D Condon
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Antje Blumenthal
- the University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Matthew J Sweet
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Jennifer L Stow
- From the Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia and
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19
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Chalick M, Jacobi O, Pichinuk E, Garbar C, Bensussan A, Meeker A, Ziv R, Zehavi T, Smorodinsky NI, Hilkens J, Hanisch FG, Rubinstein DB, Wreschner DH. MUC1-ARF-A Novel MUC1 Protein That Resides in the Nucleus and Is Expressed by Alternate Reading Frame Translation of MUC1 mRNA. PLoS One 2016; 11:e0165031. [PMID: 27768738 PMCID: PMC5074479 DOI: 10.1371/journal.pone.0165031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 10/05/2016] [Indexed: 01/26/2023] Open
Abstract
Translation of mRNA in alternate reading frames (ARF) is a naturally occurring process heretofore underappreciated as a generator of protein diversity. The MUC1 gene encodes MUC1-TM, a signal-transducing trans-membrane protein highly expressed in human malignancies. Here we show that an AUG codon downstream to the MUC1-TM initiation codon initiates an alternate reading frame thereby generating a novel protein, MUC1-ARF. MUC1-ARF, like its MUC1-TM 'parent’ protein, contains a tandem repeat (VNTR) domain. However, the amino acid sequence of the MUC1-ARF tandem repeat as well as N- and C- sequences flanking it differ entirely from those of MUC1-TM. In vitro protein synthesis assays and extensive immunohistochemical as well as western blot analyses with MUC1-ARF specific monoclonal antibodies confirmed MUC1-ARF expression. Rather than being expressed at the cell membrane like MUC1-TM, immunostaining showed that MUC1-ARF protein localizes mainly in the nucleus: Immunohistochemical analyses of MUC1-expressing tissues demonstrated MUC1-ARF expression in the nuclei of secretory luminal epithelial cells. MUC1-ARF expression varies in different malignancies. While the malignant epithelial cells of pancreatic cancer show limited expression, in breast cancer tissue MUC1-ARF demonstrates strong nuclear expression. Proinflammatory cytokines upregulate expression of MUC1-ARF protein and co-immunoprecipitation analyses demonstrate association of MUC1-ARF with SH3 domain-containing proteins. Mass spectrometry performed on proteins coprecipitating with MUC1-ARF demonstrated Glucose-6-phosphate 1-dehydrogenase (G6PD) and Dynamin 2 (DNM2). These studies not only reveal that the MUC1 gene generates a previously unidentified MUC1-ARF protein, they also show that just like its ‘parent’ MUC1-TM protein, MUC1-ARF is apparently linked to signaling and malignancy, yet a definitive link to these processes and the roles it plays awaits a precise identification of its molecular functions. Comprising at least 524 amino acids, MUC1-ARF is, furthermore, the longest ARF protein heretofore described.
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Affiliation(s)
- Michael Chalick
- Department of Cell Research and Immunology, Tel Aviv University, Ramat Aviv, Israel
| | - Oded Jacobi
- Department of Cell Research and Immunology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward Pichinuk
- Department of Cell Research and Immunology, Tel Aviv University, Ramat Aviv, Israel
| | - Christian Garbar
- Department of Biopathology, Institut Jean-Godinot, Reims Cedex, France
| | | | - Alan Meeker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ravit Ziv
- Department of Cell Research and Immunology, Tel Aviv University, Ramat Aviv, Israel
| | - Tania Zehavi
- Department of Pathology, Meir Medical Center, Kfar Saba, Israel
| | | | - John Hilkens
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, University of Cologne, Köln, Germany
| | | | - Daniel H. Wreschner
- Department of Cell Research and Immunology, Tel Aviv University, Ramat Aviv, Israel
- * E-mail:
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