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Guo Q, Yang YX, Li DX, Ji XJ, Wu N, Wang YT, Ye C, Shi TQ. Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory. Biotechnol Adv 2024; 77:108453. [PMID: 39278372 DOI: 10.1016/j.biotechadv.2024.108453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Na Wu
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
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2
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Laursen L, Inturi R, Østergaard S, Jemth P. Determinants of affinity, specificity, and phase separation in a supramodule from Post-synaptic density protein 95. iScience 2022; 25:105069. [PMID: 36157580 PMCID: PMC9490041 DOI: 10.1016/j.isci.2022.105069] [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: 05/19/2022] [Revised: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The post-synaptic density (PSD) is a phase-separated membraneless compartment of proteins including PSD-95 that undergoes morphological alteration in response to synaptic activity. Here, we investigated the interactome of a three-domain supramodule, PDZ3-SH3-GK (PSG) from PSD-95 using bioinformatics to identify potential binding partners, and biophysical methods to characterize the interaction with peptides from these proteins. PSG and the single PDZ3 domain bound similar peptides, but with different specificity. Furthermore, we found that the protein ADGRB1 formed liquid droplets with the PSG supramodule, extending the model for PSD formation. Moreover, certain mutations, introduced outside of the binding pocket in PDZ3, increased the affinity and specificity of the interaction and the size of liquid droplets. Other mutations within the ligand binding pocket lead to a new binding motif specificity. Our results show how the context in terms of supertertiary structure modulates affinity, specificity, and phase separation, and how these properties can evolve by point mutation. Identification of potential binding partners for PSD-95 in the post-synaptic density ADGRB1 and PSD-95 undergo liquid-liquid phase separation (LLPS) Single domain PDZ3 cannot induce LLPS and binds weakly to ADGRB1 and SynGap Supertertiary structure alters the affinity, specificity, and phase separation
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Affiliation(s)
- Louise Laursen
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Søren Østergaard
- Global Research Technology, Novo Nordisk A/S, Novo Nordisk Research Park, 2760 Maalov, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
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3
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Caillet-Saguy C, Brûlé S, Wolff N, Raynal B. PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations. Methods Mol Biol 2021; 2256:89-124. [PMID: 34014518 DOI: 10.1007/978-1-0716-1166-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.
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Affiliation(s)
| | - Sébastien Brûlé
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS UMR 3571, Paris, France.
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
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Guillen-Chable F, Rodríguez Corona U, Pereira-Santana A, Bayona A, Rodríguez-Zapata LC, Aquino C, Šebestová L, Vitale N, Hozak P, Castano E. Fibrillarin Ribonuclease Activity is Dependent on the GAR Domain and Modulated by Phospholipids. Cells 2020; 9:cells9051143. [PMID: 32384686 PMCID: PMC7290794 DOI: 10.3390/cells9051143] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.
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Affiliation(s)
- Francisco Guillen-Chable
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Ulises Rodríguez Corona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Alejandro Pereira-Santana
- Industrial Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Camino Arenero 1227, el Bajio, Zapopan C.P. 45019, Jalisco, Mexico;
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Alcaldia Benito Juarez C.P. 03940, Ciudad de Mexico, Mexico
| | - Andrea Bayona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Luis Carlos Rodríguez-Zapata
- Biotechnology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatan, Mexico;
| | - Cecilia Aquino
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Lenka Šebestová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Nicolas Vitale
- Institute of Celullar and Integrative Neuroscience (INCI), UPR-3212 The French National Centre for Scientific Research & University of Strasbourg, 67000 Strasbourg, France;
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
| | - Enrique Castano
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
- Correspondence:
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5
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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6
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Sette P, O'Connor SK, Yerramilli VS, Dussupt V, Nagashima K, Chutiraka K, Lingappa J, Scarlata S, Bouamr F. HIV-1 Nucleocapsid Mimics the Membrane Adaptor Syntenin PDZ to Gain Access to ESCRTs and Promote Virus Budding. Cell Host Microbe 2016; 19:336-48. [PMID: 26962944 DOI: 10.1016/j.chom.2016.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/07/2016] [Accepted: 02/11/2016] [Indexed: 01/09/2023]
Abstract
HIV-1 recruits cellular endosomal sorting complexes required for transport (ESCRTs) to bud virions from the membrane. Disruption of the viral nucleocapsid (NC) domain integrity affects HIV-1 budding. However, the molecular mechanisms of NC's involvement in HIV budding remain unclear. We find that NC mimics the PDZ domains of syntenin, a membrane-binding adaptor involved in cell-to-cell contact/communication, to capture the Bro1 domain of ALIX, which is an ESCRTs recruiting cellular adaptor. NC binds membranes via basic residues in either the distal or proximal zinc fingers, and NC-membrane binding is essential for Bro1 capture and HIV-1 budding. Removal of RNA enhances NC membrane binding, suggesting a dynamic competition between membrane lipids and RNA for the same binding sites in NC. Remarkably, syntenin PDZ can substitute for NC function in HIV-1 budding. Thus, NC mimics syntenin PDZs to function as a membrane-binding adaptor critical for HIV-1 budding at specific microdomains of the membrane.
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Affiliation(s)
- Paola Sette
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - Sarah K O'Connor
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - V Siddartha Yerramilli
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Vincent Dussupt
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA
| | - Kunio Nagashima
- Electron Microscope Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Kasana Chutiraka
- Department of Global Health, University of Washington, Seattle, WA 98102, USA
| | - Jaisri Lingappa
- Department of Global Health, University of Washington, Seattle, WA 98102, USA
| | - Suzanne Scarlata
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Fadila Bouamr
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20894, USA.
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7
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Compartmentalization of the Cell Membrane. J Mol Biol 2016; 428:4739-4748. [DOI: 10.1016/j.jmb.2016.09.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 11/20/2022]
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8
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Egea-Jimenez AL, Gallardo R, Garcia-Pino A, Ivarsson Y, Wawrzyniak AM, Kashyap R, Loris R, Schymkowitz J, Rousseau F, Zimmermann P. Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling. Nat Commun 2016; 7:12101. [PMID: 27386966 PMCID: PMC5515355 DOI: 10.1038/ncomms12101] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/27/2016] [Indexed: 01/01/2023] Open
Abstract
PDZ domain-containing proteins work as intracellular scaffolds to control spatio-temporal aspects of cell signalling. This function is supported by the ability of their PDZ domains to bind other proteins such as receptors, but also phosphoinositide lipids important for membrane trafficking. Here we report a crystal structure of the syntenin PDZ tandem in complex with the carboxy-terminal fragment of Frizzled 7 and phosphatidylinositol 4,5-bisphosphate (PIP2). The crystal structure reveals a tripartite interaction formed via the second PDZ domain of syntenin. Biophysical and biochemical experiments establish co-operative binding of the tripartite complex and identify residues crucial for membrane PIP2-specific recognition. Experiments with cells support the importance of the syntenin-PIP2 interaction for plasma membrane targeting of Frizzled 7 and c-jun phosphorylation. This study contributes to our understanding of the biology of PDZ proteins as key players in membrane compartmentalization and dynamics.
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Affiliation(s)
- Antonio Luis Egea-Jimenez
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Rodrigo Gallardo
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
- VIB Switch Laboratory, Department of Molecular Cellular and Molecular Medicine, VIB-KU Leuven, B-3000 Leuven, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Deptartment of Biotechnology (DBIT), Vrije Universiteit Brussel and Molecular Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Ylva Ivarsson
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Anna Maria Wawrzyniak
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Rudra Kashyap
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Remy Loris
- Structural Biology Brussels, Deptartment of Biotechnology (DBIT), Vrije Universiteit Brussel and Molecular Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Joost Schymkowitz
- VIB Switch Laboratory, Department of Molecular Cellular and Molecular Medicine, VIB-KU Leuven, B-3000 Leuven, Belgium
| | - Frederic Rousseau
- VIB Switch Laboratory, Department of Molecular Cellular and Molecular Medicine, VIB-KU Leuven, B-3000 Leuven, Belgium
| | - Pascale Zimmermann
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
- Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
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Parvani JG, Davuluri G, Wendt MK, Espinosa C, Tian M, Danielpour D, Sossey-Alaoui K, Schiemann WP. Deptor enhances triple-negative breast cancer metastasis and chemoresistance through coupling to survivin expression. Neoplasia 2015; 17:317-28. [PMID: 25810016 PMCID: PMC4372649 DOI: 10.1016/j.neo.2015.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 12/12/2022] Open
Abstract
Transforming growth factor-β (TGF-β) functions to suppress tumorigenesis in normal mammary tissues and early-stage breast cancers and, paradoxically, acts to promote the metastasis and chemoresistance in late-stage breast cancers, particularly triple-negative breast cancers (TNBCs). Precisely how TGF-β acquires oncogenic characteristics in late-stage breast cancers remains unknown, as does the role of the endogenous mammalian target of rapamycin (mTOR) inhibitor, Dep domain-containing mTOR-interacting protein (Deptor), in coupling TGF-β to TNBC development and metastatic progression. Here we demonstrate that Deptor expression was downregulated in basal-like/TNBCs relative to their luminal counterparts. Additionally, Deptor expression was 1) inversely correlated with the metastatic ability of human (MCF10A) and mouse (4T1) TNBC progression series and 2) robustly repressed by several inducers of epithelial-mesenchymal transition programs. Functional disruption of Deptor expression in 4T07 cells significantly inhibited their proliferation and organoid growth in vitro, as well as prevented their colonization and tumor formation in the lungs of mice. In stark contrast, elevated Deptor expression was significantly associated with poorer overall survival of patients harboring estrogen receptor α-negative breast cancers. Accordingly, enforced Deptor expression in MDA-MB-231 cells dramatically enhanced their 1) organoid growth in vitro, 2) pulmonary outgrowth in mice, and 3) resistance to chemotherapies, an event dependent on the coupling of Deptor to survivin expression. Collectively, our findings highlight the dichotomous functions of Deptor in modulating the proliferation and survival of TNBCs during metastasis; they also implicate Deptor and its stimulation of survivin as essential components of TNBC resistance to chemotherapies and apoptotic stimuli.
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Affiliation(s)
- Jenny G Parvani
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Gangarao Davuluri
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Christine Espinosa
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Maozhen Tian
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - David Danielpour
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Khalid Sossey-Alaoui
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
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Membrane Binding and Modulation of the PDZ Domain of PICK1. MEMBRANES 2015; 5:597-615. [PMID: 26501328 PMCID: PMC4704001 DOI: 10.3390/membranes5040597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
Scaffolding proteins serve to assemble protein complexes in dynamic processes by means of specific protein-protein and protein-lipid binding domains. Many of these domains bind either proteins or lipids exclusively; however, it has become increasingly evident that certain domains are capable of binding both. Especially, many PDZ domains, which are highly abundant protein-protein binding domains, bind lipids and membranes. Here we provide an overview of recent large-scale studies trying to generalize and rationalize the binding patterns as well as specificity of PDZ domains towards membrane lipids. Moreover, we review how these PDZ-membrane interactions are regulated in the case of the synaptic scaffolding protein PICK1 and how this might affect cellular localization and function.
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Bacolod MD, Das SK, Sokhi UK, Bradley S, Fenstermacher DA, Pellecchia M, Emdad L, Sarkar D, Fisher PB. Examination of Epigenetic and other Molecular Factors Associated with mda-9/Syntenin Dysregulation in Cancer Through Integrated Analyses of Public Genomic Datasets. Adv Cancer Res 2015; 127:49-121. [PMID: 26093898 DOI: 10.1016/bs.acr.2015.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mda-9/Syntenin (melanoma differentiation-associated gene 9) is a PDZ domain containing, cancer invasion-related protein. In this study, we employed multiple integrated bioinformatic approaches to identify the probable epigenetic factors, molecular pathways, and functionalities associated with mda-9 dysregulation during cancer progression. Analyses of publicly available genomic data (e.g., expression, copy number, methylation) from TCGA, GEO, ENCODE, and Human Protein Atlas projects led to the following observations: (a) mda-9 expression correlates with both copy number and methylation level of an intronic CpG site (cg1719774) located downstream of the CpG island, (b) cg1719774 methylation is a likely prognostic marker in glioma, (c) among 22 cancer types, melanoma exhibits the highest mda-9 level, and lowest level of methylation at cg1719774, (d) cg1719774 hypomethylation is also associated with histone modifications (at the mda-9 locus) indicative of more active transcription, (e) using Gene Set Enrichment Analysis (GSEA), and the Virtual Gene Overexpression or Repression (VIGOR) analytical scheme, we were able to predict mda-9's association with extracellular matrix organization (e.g., MMPs, collagen, integrins), IGFBP2 and NF-κB signaling pathways, phospholipid metabolism, cytokines (e.g., interleukins), CTLA-4, and components of complement cascade pathways. Indeed, previous publications have shown that many of the aforementioned genes and pathways are associated with mda-9's functionality.
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Affiliation(s)
- Manny D Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Upneet K Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Steven Bradley
- VCU Bioinformatics Program, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - David A Fenstermacher
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA.
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Stahelin RV, Scott JL, Frick CT. Cellular and molecular interactions of phosphoinositides and peripheral proteins. Chem Phys Lipids 2014; 182:3-18. [PMID: 24556335 DOI: 10.1016/j.chemphyslip.2014.02.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 12/23/2022]
Abstract
Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection-specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.
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Affiliation(s)
- Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Cary T Frick
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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