1
|
Hashimoto M, Miki T, Niwa T, Mihara H. Proximity labeling and identification of endogenous client proteins recruited to Y15-based artificial granules tethering a bait protein. J Pept Sci 2024; 30:e3536. [PMID: 37580979 DOI: 10.1002/psc.3536] [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: 04/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Protein clustering is a ubiquitous event in diverse cellular processes. Self-association of proteins triggers recruitment of downstream proteins to regulate cellular signaling. To investigate the interactions in detail, chemical biology tools to identify proteins recruited to defined assemblies are required. Here, we exploit an identification of proteins recruited in artificial granules (IPRAG) platform that combines intracellular Y15-based supramolecule construction with a proximity labeling method. We validated the IPRAG tool using Nck1 as a target bait protein. We constructed Nck1-tethering granules, labeled the recruited proteins with biotin, and analyzed them by LC-MS/MS. As a result, we successfully identified proteins that directly or indirectly interact with Nck1.
Collapse
Affiliation(s)
- Masahiro Hashimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Tokyo, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
2
|
Spona D, Hanisch PT, Hegemann JH, Mölleken K. A single chlamydial protein reshapes the plasma membrane and serves as recruiting platform for central endocytic effector proteins. Commun Biol 2023; 6:520. [PMID: 37179401 PMCID: PMC10182996 DOI: 10.1038/s42003-023-04913-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Uptake of obligate intracellular bacterial pathogens into mammalian epithelial cells is critically dependent on modulation of the host's endocytic machinery. It is an open question how the invading pathogens generate a membrane-bound vesicle appropriate to their size. This requires extensive deformation of the host plasma membrane itself by pathogen-derived membrane-binding proteins, accompanied by substantial F-actin-based forces to further expand and finally pinch off the vesicle. Here we show that upon adhesion to the host cell, the human pathogenic bacterium Chlamydia pneumoniae secretes the scaffolding effector protein CPn0677, which binds to the inner leaflet of the invaginating host's PM, induces inwardly directed, negative membrane curvature, and forms a recruiting platform for the membrane-deforming BAR-domain containing proteins Pacsin and SNX9. In addition, while bound to the membrane, CPn0677 recruits monomeric G-actin, and its C-terminal region binds and activates N-WASP, which initiates branching actin polymerization via the Arp2/3 complex. Together, these membrane-bound processes enable the developing endocytic vesicle to engulf the infectious elementary body, while the associated actin network generates the forces required to reshape and detach the nascent vesicle from the PM. Thus, Cpn0677 (now renamed SemD) acts as recruiting platform for central components of the endocytic machinery during uptake of chlamydia.
Collapse
Affiliation(s)
- Dominik Spona
- Institute for Functional Microbial Genomics, Heinrich-Heine-University, Düsseldorf, Germany
| | - Philipp T Hanisch
- Institute for Functional Microbial Genomics, Heinrich-Heine-University, Düsseldorf, Germany
| | - Johannes H Hegemann
- Institute for Functional Microbial Genomics, Heinrich-Heine-University, Düsseldorf, Germany
| | - Katja Mölleken
- Institute for Functional Microbial Genomics, Heinrich-Heine-University, Düsseldorf, Germany.
| |
Collapse
|
3
|
Diab AM, Wigerius M, Quinn DP, Qi J, Shahin I, Paffile J, Krueger K, Karten B, Krueger SR, Fawcett JP. NCK1 Modulates Neuronal Actin Dynamics and Promotes Dendritic Spine, Synapse, and Memory Formation. J Neurosci 2023; 43:885-901. [PMID: 36535770 PMCID: PMC9908320 DOI: 10.1523/jneurosci.0495-21.2022] [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: 03/08/2021] [Revised: 12/05/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Memory formation and maintenance is a dynamic process involving the modulation of the actin cytoskeleton at synapses. Understanding the signaling pathways that contribute to actin modulation is important for our understanding of synapse formation and function, as well as learning and memory. Here, we focused on the importance of the actin regulator, noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1), in hippocampal dependent behaviors and development. We report that male mice lacking NCK1 have impairments in both short-term and working memory, as well as spatial learning. Additionally, we report sex differences in memory impairment showing that female mice deficient in NCK1 fail at reversal learning in a spatial learning task. We find that NCK1 is expressed in postmitotic neurons but is dispensable for neuronal proliferation and migration in the developing hippocampus. Morphologically, NCK1 is not necessary for overall neuronal dendrite development. However, neurons lacking NCK1 have lower dendritic spine and synapse densities in vitro and in vivo EM analysis reveal increased postsynaptic density (PSD) thickness in the hippocampal CA1 region of NCK1-deficient mice. Mechanistically, we find the turnover of actin-filaments in dendritic spines is accelerated in neurons that lack NCK1. Together, these findings suggest that NCK1 contributes to hippocampal-dependent memory by stabilizing actin dynamics and dendritic spine formation.SIGNIFICANCE STATEMENT Understanding the molecular signaling pathways that contribute to memory formation, maintenance, and elimination will lead to a better understanding of the genetic influences on cognition and cognitive disorders and will direct future therapeutics. Here, we report that the noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1) adaptor protein modulates actin-filament turnover in hippocampal dendritic spines. Mice lacking NCK1 show sex-dependent deficits in hippocampal memory formation tasks, have altered postsynaptic densities, and reduced synaptic density. Together, our work implicates NCK1 in the regulation of actin cytoskeleton dynamics and normal synapse development which is essential for memory formation.
Collapse
Affiliation(s)
- Antonios M Diab
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Michael Wigerius
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Dylan P Quinn
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jiansong Qi
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Ibrahim Shahin
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Julia Paffile
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kavita Krueger
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Barbara Karten
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Stefan R Krueger
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - James P Fawcett
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Surgery, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
4
|
Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
Collapse
Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
5
|
Abstract
The non-catalytic region of tyrosine kinase (Nck) family of adaptors, consisting of Nck1 and Nck2, contributes to selectivity and specificity in the flow of cellular information by recruiting components of signaling networks. Known to play key roles in cytoskeletal remodeling, Nck adaptors modulate host cell-pathogen interactions, immune cell receptor activation, cell adhesion and motility, and intercellular junctions in kidney podocytes. Genetic inactivation of both members of the Nck family results in embryonic lethality; however, viability of mice lacking either one of these adaptors suggests partial functional redundancy. In this Cell Science at a Glance and the accompanying poster, we highlight the molecular organization and functions of the Nck family, focusing on key interactions and pathways, regulation of cellular processes, development, homeostasis and pathogenesis, as well as emerging and non-redundant functions of Nck1 compared to those of Nck2. This article thus aims to provide a timely perspective on the biology of Nck adaptors and their potential as therapeutic targets.
Collapse
Affiliation(s)
- Briana C. Bywaters
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
| | - Gonzalo M. Rivera
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
| |
Collapse
|
6
|
Miki T, Nakai T, Hashimoto M, Kajiwara K, Tsutsumi H, Mihara H. Intracellular artificial supramolecules based on de novo designed Y15 peptides. Nat Commun 2021; 12:3412. [PMID: 34099696 DOI: 10.1038/s41467-021-23794-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/17/2021] [Indexed: 12/11/2022] Open
Abstract
De novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.
Collapse
Affiliation(s)
- Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
| | - Taichi Nakai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Masahiro Hashimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Keigo Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Hiroshi Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| |
Collapse
|
7
|
The multiple roles of actin-binding proteins at invadopodia. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021. [PMID: 33962752 DOI: 10.1016/bs.ircmb.2021.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Invadopodia are actin-rich membrane protrusions that facilitate cancer cell dissemination by focusing on proteolytic activity and clearing paths for migration through physical barriers, such as basement membranes, dense extracellular matrices, and endothelial cell junctions. Invadopodium formation and activity require spatially and temporally regulated changes in actin filament organization and dynamics. About three decades of research have led to a remarkable understanding of how these changes are orchestrated by sequential recruitment and coordinated activity of different sets of actin-binding proteins. In this chapter, we provide an update on the roles of the actin cytoskeleton during the main stages of invadopodium development with a particular focus on actin polymerization machineries and production of pushing forces driving extracellular matrix remodeling.
Collapse
|
8
|
Xie J, Lai L. Protein topology and allostery. Curr Opin Struct Biol 2020; 62:158-165. [DOI: 10.1016/j.sbi.2020.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 01/07/2023]
|
9
|
Chan KMC, Son S, Schmid EM, Fletcher DA. A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion. eLife 2020; 9:51358. [PMID: 32441254 PMCID: PMC7244324 DOI: 10.7554/elife.51358] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 05/08/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-cell fusion, which is essential for tissue development and used by some viruses to form pathological syncytia, is typically driven by fusogenic membrane proteins with tall (>10 nm) ectodomains that undergo conformational changes to bring apposing membranes in close contact prior to fusion. Here we report that a viral fusogen with a short (<2 nm) ectodomain, the reptilian orthoreovirus p14, accomplishes the same task by hijacking the actin cytoskeleton. We show that phosphorylation of the cytoplasmic domain of p14 triggers N-WASP-mediated assembly of a branched actin network. Using p14 mutants, we demonstrate that fusion is abrogated when binding of an adaptor protein is prevented and that direct coupling of the fusogenic ectodomain to branched actin assembly is sufficient to drive cell-cell fusion. This work reveals how the actin cytoskeleton can be harnessed to overcome energetic barriers to cell-cell fusion.
Collapse
Affiliation(s)
- Ka Man Carmen Chan
- UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, United States.,Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Sungmin Son
- Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Eva M Schmid
- Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Daniel A Fletcher
- UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, United States.,Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| |
Collapse
|
10
|
Nck1 promotes the progression of ovarian carcinoma by enhancing the PI3K/AKT/p70S6K signaling. Hum Cell 2020; 33:768-779. [PMID: 32166565 DOI: 10.1007/s13577-020-00344-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/02/2020] [Indexed: 02/05/2023]
Abstract
Non-catalytic region of tyrosine kinase adaptor protein 1 (Nck1) is crucial for the progression of cancers. However, little is known on the role of Nck1 in the progression of ovarian carcinoma (OC). Here, we show that Nck1 expression is up-regulated in 176 OC tissues, compared with non-carcinoma ovarian tissues, and the up-regulated Nck1 expression is associated with the aggressiveness of OC and shorter overall and disease-free survival in this population. Higher Nck1 expression was an independent risk factor for poor prognosis of OC. Furthermore, Nck1 silencing by short hairpin RNA (shRNA) technology significantly inhibited the proliferation, migration and invasion of OC cells in vitro and the growth and metastasis of implanted OC tumors in vivo. Human kinase phosphorylation array indicated that Nck1 silencing significantly reduced the relative levels of 11 kinase expression and phosphorylation in OC cells, particularly for decreased levels of p70S6 kinase (p70S6K) and protein kinase B (AKT) expression in SKOV3 cells. Actually, Nck1 silencing significantly decreased PI3K and AKT expression, and reduced AKT and p70S6K phosphorylation while Nck1 over-expression had opposite effects in OC cells. Therefore, our data indicate that Nck1 promotes the progression of OC by enhancing the PI3k/AKT/p70S6K signaling in OC. Our findings suggest that Nck1 expression may be valuable for evaluating the prognosis of OC and as a target for design of new therapies for OC.
Collapse
|
11
|
Martin CE, New LA, Phippen NJ, Keyvani Chahi A, Mitro AE, Takano T, Pawson T, Blasutig IM, Jones N. Multivalent nephrin-Nck interactions define a threshold for clustering and tyrosine-dependent nephrin endocytosis. J Cell Sci 2020; 133:jcs236877. [PMID: 31974115 DOI: 10.1242/jcs.236877] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022] Open
Abstract
Assembly of signaling molecules into micrometer-sized clusters is driven by multivalent protein-protein interactions, such as those found within the nephrin-Nck (Nck1 or Nck2) complex. Phosphorylation on multiple tyrosine residues within the tail of the nephrin transmembrane receptor induces recruitment of the cytoplasmic adaptor protein Nck, which binds via its triple SH3 domains to various effectors, leading to actin assembly. The physiological consequences of nephrin clustering are not well understood. Here, we demonstrate that nephrin phosphorylation regulates the formation of membrane clusters in podocytes. We also reveal a connection between clustering and endocytosis, which appears to be driven by threshold levels of nephrin tyrosine phosphorylation and Nck SH3 domain signaling. Finally, we expose an in vivo correlation between transient changes in nephrin tyrosine phosphorylation, nephrin localization and integrity of the glomerular filtration barrier during podocyte injury. Altogether, our results suggest that nephrin phosphorylation determines the composition of effector proteins within clusters to dynamically regulate nephrin turnover and podocyte health.
Collapse
Affiliation(s)
- Claire E Martin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Laura A New
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Noah J Phippen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ava Keyvani Chahi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Alexander E Mitro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tomoko Takano
- Department of Medicine, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ivan M Blasutig
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
12
|
Yin J, Wu K, Ma Q, Dong H, Zhu Y, Hu L, Kong X. Revisiting Non-BRCA1/2 Familial Whole Exome Sequencing Datasets Implicates NCK1 as a Cancer Gene. Front Genet 2019; 10:527. [PMID: 31214250 PMCID: PMC6557995 DOI: 10.3389/fgene.2019.00527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC patients, to search for novel BC predisposition genes. Based on the infinite mutation model, we supposed that rare non-silent variants that cooccurred between familial and TCGA-germline datasets, might play a predisposition contributing role. In our analysis, we not only identified novel potential pathogenic variants from known cancer predisposition genes, such as MRE11, CTR9 but also identified novel candidate predisposition genes, such as NCK1. According to the TCGA mRNA expression dataset of BC, NCK1 was significantly upregulated in basal-like subtypes and downregulated in luminal subtypes. In vitro, NCK1 mutants (D73H and R42Q) transfected MCF7 cell lines, which attributed to the luminal subtype, were much more viable and invasive than the wild type. On the other side, our results also showed that overall survival and disease-free survival of patients with NCK1 variations might be dependent on the genomic context. In conclusion, genetic heterogeneity exists among non-BRCA1/2 BC pedigrees and NCK1 could be a novel BC predisposition gene.
Collapse
Affiliation(s)
- Jie Yin
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qingyang Ma
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hang Dong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
13
|
Petrov P, Sarapulov AV, Eöry L, Scielzo C, Scarfò L, Smith J, Burt DW, Mattila PK. Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control. Sci Rep 2019; 9:4155. [PMID: 30858428 PMCID: PMC6411742 DOI: 10.1038/s41598-019-40697-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
Missing in Metastasis (MIM), or Metastasis Suppressor 1 (MTSS1), is a highly conserved protein, which links the plasma membrane to the actin cytoskeleton. MIM has been implicated in various cancers, however, its modes of action remain largely enigmatic. Here, we performed an extensive in silico characterisation of MIM to gain better understanding of its function. We detected previously unappreciated functional motifs including adaptor protein (AP) complex interaction site and a C-helix, pointing to a role in endocytosis and regulation of actin dynamics, respectively. We also identified new functional regions, characterised with phosphorylation sites or distinct hydrophilic properties. Strong negative selection during evolution, yielding high conservation of MIM, has been combined with positive selection at key sites. Interestingly, our analysis of intra-molecular co-evolution revealed potential regulatory hotspots that coincided with reduced potentially pathogenic polymorphisms. We explored databases for the mutations and expression levels of MIM in cancer. Experimentally, we focused on chronic lymphocytic leukaemia (CLL), where MIM showed high overall expression, however, downregulation on poor prognosis samples. Finally, we propose strong conservation of MTSS1 also on the transcriptional level and predict novel transcriptional regulators. Our data highlight important targets for future studies on the role of MIM in different tissues and cancers.
Collapse
Affiliation(s)
- Petar Petrov
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Tykistökatu 6A, 20520, Turku, Finland.
| | - Alexey V Sarapulov
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Tykistökatu 6A, 20520, Turku, Finland
| | - Lel Eöry
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Easter Bush campus, Midlothian, EH25 9RG, United Kingdom
| | - Cristina Scielzo
- Unit of B Cell Neoplasia, Division of Molecular Oncology, IRCCS, San Raffaele Scientific Institute, Milano, Italy.,Università Vita-Salute San Raffaele, Milan, Italy
| | - Lydia Scarfò
- Unit of B Cell Neoplasia, Division of Molecular Oncology, IRCCS, San Raffaele Scientific Institute, Milano, Italy.,Università Vita-Salute San Raffaele, Milan, Italy.,Strategic Research Program on CLL, Division of Experimental Oncology, IRCCS, San Raffaele Scientific Institute, Milano, Italy
| | - Jacqueline Smith
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Easter Bush campus, Midlothian, EH25 9RG, United Kingdom
| | - David W Burt
- University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Pieta K Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Tykistökatu 6A, 20520, Turku, Finland.
| |
Collapse
|
14
|
Hu X, Mullins RD. LC3 and STRAP regulate actin filament assembly by JMY during autophagosome formation. J Cell Biol 2019; 218:251-266. [PMID: 30420355 PMCID: PMC6314544 DOI: 10.1083/jcb.201802157] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 01/22/2023] Open
Abstract
During autophagy, actin filament networks move and remodel cellular membranes to form autophagosomes that enclose and metabolize cytoplasmic contents. Two actin regulators, WHAMM and JMY, participate in autophagosome formation, but the signals linking autophagy to actin assembly are poorly understood. We show that, in nonstarved cells, cytoplasmic JMY colocalizes with STRAP, a regulator of JMY's nuclear functions, on nonmotile vesicles with no associated actin networks. Upon starvation, JMY shifts to motile, LC3-containing membranes that move on actin comet tails. LC3 enhances JMY's de novo actin nucleation activity via a cryptic actin-binding sequence near JMY's N terminus, and STRAP inhibits JMY's ability to nucleate actin and activate the Arp2/3 complex. Cytoplasmic STRAP negatively regulates autophagy. Finally, we use purified proteins to reconstitute LC3- and JMY-dependent actin network formation on membranes and inhibition of network formation by STRAP. We conclude that LC3 and STRAP regulate JMY's actin assembly activities in trans during autophagy.
Collapse
Affiliation(s)
- Xiaohua Hu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, School of Medicine, San Francisco, CA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, School of Medicine, San Francisco, CA
- Howard Hughes Medical Institute, Chevy Chase, MD
| |
Collapse
|
15
|
Velle KB, Campellone KG. Enteropathogenic E. coli relies on collaboration between the formin mDia1 and the Arp2/3 complex for actin pedestal biogenesis and maintenance. PLoS Pathog 2018; 14:e1007485. [PMID: 30550556 PMCID: PMC6310289 DOI: 10.1371/journal.ppat.1007485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/28/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
Enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC) are closely related extracellular pathogens that reorganize host cell actin into “pedestals” beneath the tightly adherent bacteria. This pedestal-forming activity is both a critical step in pathogenesis, and it makes EPEC and EHEC useful models for studying the actin rearrangements that underlie membrane protrusions. To generate pedestals, EPEC relies on the tyrosine phosphorylated bacterial effector protein Tir to bind host adaptor proteins that recruit N-WASP, a nucleation-promoting factor that activates the Arp2/3 complex to drive actin polymerization. In contrast, EHEC depends on the effector EspFU to multimerize N-WASP and promote Arp2/3 activation. Although these core pathways of pedestal assembly are well-characterized, the contributions of additional actin nucleation factors are unknown. We investigated potential cooperation between the Arp2/3 complex and other classes of nucleators using chemical inhibitors, siRNAs, and knockout cell lines. We found that inhibition of formins impairs actin pedestal assembly, motility, and cellular colonization for bacteria using the EPEC, but not the EHEC, pathway of actin polymerization. We also identified mDia1 as the formin contributing to EPEC pedestal assembly, as its expression level positively correlates with the efficiency of pedestal formation, and it localizes to the base of pedestals both during their initiation and once they have reached steady state. Collectively, our data suggest that mDia1 enhances EPEC pedestal biogenesis and maintenance by generating seed filaments to be used by the N-WASP-Arp2/3-dependent actin nucleation machinery and by sustaining Src-mediated phosphorylation of Tir. Microbial pathogens that rearrange the host actin cytoskeleton have made valuable contributions to our understanding of cell signaling and movement. The assembly and organization of the actin cytoskeleton is driven by proteins called nucleators, which can be manipulated by bacteria including enteropathogenic Escherichia coli (EPEC), a frequent cause of pediatric diarrhea in developing countries. After ingestion, EPEC adhere tightly to cells of the intestine and hijack the underlying cytoskeleton to create protrusions called actin pedestals. While mechanisms of pedestal assembly involving a nucleator called the Arp2/3 complex have been defined for EPEC, the contribution of additional host nucleators has not been determined. We assessed the roles of several actin nucleators in EPEC pedestals and found that in addition to Arp2/3 complex-mediated nucleation, the formin mDia1 is a key contributor to actin assembly. These findings highlight the importance of nucleator collaboration in pathogenesis, and also advance our understanding of the molecular and cellular basis of EPEC infection, which is ultimately important for the discovery of new drug targets.
Collapse
Affiliation(s)
- Katrina B. Velle
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
| | - Kenneth G. Campellone
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
16
|
Yu SMW, Nissaisorakarn P, Husain I, Jim B. Proteinuric Kidney Diseases: A Podocyte's Slit Diaphragm and Cytoskeleton Approach. Front Med (Lausanne) 2018; 5:221. [PMID: 30255020 PMCID: PMC6141722 DOI: 10.3389/fmed.2018.00221] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 01/19/2023] Open
Abstract
Proteinuric kidney diseases are a group of disorders with diverse pathological mechanisms associated with significant losses of protein in the urine. The glomerular filtration barrier (GFB), comprised of the three important layers, the fenestrated glomerular endothelium, the glomerular basement membrane (GBM), and the podocyte, dictates that disruption of any one of these structures should lead to proteinuric disease. Podocytes, in particular, have long been considered as the final gatekeeper of the GFB. This specialized visceral epithelial cell contains a complex framework of cytoskeletons forming foot processes and mediate important cell signaling to maintain podocyte health. In this review, we will focus on slit diaphragm proteins such as nephrin, podocin, TRPC6/5, as well as cytoskeletal proteins Rho/small GTPases and synaptopodin and their respective roles in participating in the pathogenesis of proteinuric kidney diseases. Furthermore, we will summarize the potential therapeutic options targeting the podocyte to treat this group of kidney diseases.
Collapse
Affiliation(s)
- Samuel Mon-Wei Yu
- Department of Medicine, Jacobi Medical Center, Bronx, NY, United States
| | | | - Irma Husain
- Department of Medicine, James J. Peters VA Medical Center, Bronx, NY, United States
| | - Belinda Jim
- Department of Medicine, Jacobi Medical Center, Bronx, NY, United States.,Renal Division, Jacobi Medical Center, Bronx, NY, United States
| |
Collapse
|
17
|
Mittal A, Holehouse AS, Cohan MC, Pappu RV. Sequence-to-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins. J Mol Biol 2018; 430:2403-2421. [DOI: 10.1016/j.jmb.2018.05.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/16/2018] [Accepted: 05/07/2018] [Indexed: 12/20/2022]
|
18
|
Berlow RB, Dyson HJ, Wright PE. Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation. J Mol Biol 2018; 430:2309-2320. [PMID: 29634920 DOI: 10.1016/j.jmb.2018.04.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022]
Abstract
Allosteric regulatory processes are implicated at all levels of biological function. Recent advances in our understanding of the diverse and functionally significant class of intrinsically disordered proteins have identified a multitude of ways in which disordered proteins function within the confines of the allosteric paradigm. Allostery within or mediated by intrinsically disordered proteins ensures robust and efficient signal integration through mechanisms that would be extremely unfavorable or even impossible for globular protein interaction partners. Here, we highlight recent examples that indicate the breadth of biological outcomes that can be achieved through allosteric regulation by intrinsically disordered proteins. Ongoing and future work in this rapidly evolving area of research will expand our appreciation of the central role of intrinsically disordered proteins in ensuring the fidelity and efficiency of cellular regulation.
Collapse
Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
19
|
Vishwanath S, de Brevern AG, Srinivasan N. Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. PLoS Comput Biol 2018; 14:e1006008. [PMID: 29432415 PMCID: PMC5825166 DOI: 10.1371/journal.pcbi.1006008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/23/2018] [Accepted: 01/29/2018] [Indexed: 02/01/2023] Open
Abstract
The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties. High prevalence of multi-domain proteins in proteomes has been attributed to higher stability and functional and folding advantages of the multi-domain proteins. Influence of tethering of domains on the overall properties of proteins has been well studied but its influence on the properties of the constituent domains is largely unaddressed. Here, we investigate the influence of tethering of domains in multi-domain proteins on the structural, dynamics and energetics properties of the constituent domains and its implications on the functions of proteins. To this end, comparative analyses were carried out for identical protein domains crystallized in tethered and untethered forms. Also, comparative analyses of single-domain proteins and their homologous multi-domain proteins were performed. The analyses suggest that tethering influences the structural, dynamic and energetic properties of constituent protein domains. Our observations hint at regulation of protein domains by tethered domains in multi-domain systems, which may manifest at the differential function observed between single-domain and homologous multi-domain proteins.
Collapse
Grants
- IISc-DBT partnership programme
- DST, India (Mathematical Biology Initiative & J.C. Bose National Fellowship, FIST program)
- UGC, India – Centre for Advanced Studies
- Ministry of Human Resource Development
- Ministry of Research (France), University of Paris Diderot, Sorbonne Paris Cité
- National Institute for Blood Transfusion (INTS, France), Institute for Health and Medical Research (INSERM, France), Laboratory of Excellence GR-Ex
- The labex GR-Ex is funded by the program Investissements d’avenir of the French National Research Agency,
- Indo-French Centre for the Promotion of Advanced Research/CEFIPRA for a collaborative grant
Collapse
Affiliation(s)
- Sneha Vishwanath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G. de Brevern
- INSERM, U 1134, DSIMB, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR_S 1134, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- Laboratoire d' Excellence GR-Ex, Paris, France
| | | |
Collapse
|
20
|
Wu D, Chai Y, Zhu Z, Li W, Ou G, Li W. CED-10-WASP-Arp2/3 signaling axis regulates apoptotic cell corpse engulfment in C. elegans. Dev Biol 2017; 428:215-223. [DOI: 10.1016/j.ydbio.2017.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 01/08/2023]
|
21
|
Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck. Proc Natl Acad Sci U S A 2015; 112:E6426-35. [PMID: 26553976 DOI: 10.1073/pnas.1508778112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The organization of membranes, the cytosol, and the nucleus of eukaryotic cells can be controlled through phase separation of lipids, proteins, and nucleic acids. Collective interactions of multivalent molecules mediated by modular binding domains can induce gelation and phase separation in several cytosolic and membrane-associated systems. The adaptor protein Nck has three SRC-homology 3 (SH3) domains that bind multiple proline-rich segments in the actin regulatory protein neuronal Wiskott-Aldrich syndrome protein (N-WASP) and an SH2 domain that binds to multiple phosphotyrosine sites in the adhesion protein nephrin, leading to phase separation. Here, we show that the 50-residue linker between the first two SH3 domains of Nck enhances phase separation of Nck/N-WASP/nephrin assemblies. Two linear motifs within this element, as well as its overall positively charged character, are important for this effect. The linker increases the driving force for self-assembly of Nck, likely through weak interactions with the second SH3 domain, and this effect appears to promote phase separation. The linker sequence is highly conserved, suggesting that the sequence determinants of the driving forces for phase separation may be generally important to Nck functions. Our studies demonstrate that linker regions between modular domains can contribute to the driving forces for self-assembly and phase separation of multivalent proteins.
Collapse
|