1
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Casagrande S, Loveland JL, Oefele M, Boner W, Lupi S, Stier A, Hau M. Dietary nucleotides can prevent glucocorticoid-induced telomere attrition in a fast-growing wild vertebrate. Mol Ecol 2023; 32:5429-5447. [PMID: 37658759 DOI: 10.1111/mec.17114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023]
Abstract
Telomeres are chromosome protectors that shorten during eukaryotic cell replication and in stressful conditions. Developing individuals are susceptible to telomere erosion when their growth is fast and resources are limited. This is critical because the rate of telomere attrition in early life is linked to health and life span of adults. The metabolic telomere attrition hypothesis (MeTA) suggests that telomere dynamics can respond to biochemical signals conveying information about the organism's energetic state. Among these signals are glucocorticoids, hormones that promote catabolic processes, potentially impairing costly telomere maintenance, and nucleotides, which activate anabolic pathways through the cellular enzyme target of rapamycin (TOR), thus preventing telomere attrition. During the energetically demanding growth phase, the regulation of telomeres in response to two contrasting signals - one promoting telomere maintenance and the other attrition - provides an ideal experimental setting to test the MeTA. We studied nestlings of a rapidly developing free-living passerine, the great tit (Parus major), that either received glucocorticoids (Cort-chicks), nucleotides (Nuc-chicks) or a combination of both (NucCort-chicks), comparing these with controls (Cnt-chicks). As expected, Cort-chicks showed telomere attrition, while NucCort- and Nuc-chicks did not. NucCort-chicks was the only group showing increased expression of a proxy for TOR activation (the gene TELO2), of mitochondrial enzymes linked to ATP production (cytochrome oxidase and ATP-synthase) and a higher efficiency in aerobically producing ATP. NucCort-chicks had also a higher expression of telomere maintenance genes (shelterin protein TERF2 and telomerase TERT) and of enzymatic antioxidant genes (glutathione peroxidase and superoxide dismutase). The findings show that nucleotide availability is crucial for preventing telomere erosion during fast growth in stressful environments.
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Affiliation(s)
- Stefania Casagrande
- Max Planck Institute for Biological Intelligence, Evolutionary Physiology Group, Seewiesen, Germany
| | - Jasmine L Loveland
- Department of Cognitive and Behavioral Biology, University of Vienna, Vienna, Austria
| | - Marlene Oefele
- Max Planck Institute for Biological Intelligence, Evolutionary Physiology Group, Seewiesen, Germany
| | - Winnie Boner
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sara Lupi
- Konrad Lorenz Institute of Ethology, Vienna, Austria
| | - Antoine Stier
- Université de Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR7178, Strasbourg, France
- Department of Biology, University of Turku, Turku, Finland
| | - Michaela Hau
- Max Planck Institute for Biological Intelligence, Evolutionary Physiology Group, Seewiesen, Germany
- Department of Biology, University of Konstanz, Constance, Germany
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2
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Baskaran P, Mihaylov SR, Vinsland E, Shah K, Granat L, Ultanir SK, Tee AR, Murn J, Bateman JM. Phosphorylation of the novel mTOR substrate Unkempt regulates cellular morphogenesis. J Biol Chem 2023; 299:102788. [PMID: 36509146 PMCID: PMC9852543 DOI: 10.1016/j.jbc.2022.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) is a protein kinase that integrates multiple inputs to regulate anabolic cellular processes. For example, mTOR complex 1 (mTORC1) has key functions in growth control, autophagy, and metabolism. However, much less is known about the signaling components that act downstream of mTORC1 to regulate cellular morphogenesis. Here, we show that the RNA-binding protein Unkempt, a key regulator of cellular morphogenesis, is a novel substrate of mTORC1. We show that Unkempt phosphorylation is regulated by nutrient levels and growth factors via mTORC1. To analyze Unkempt phosphorylation, we immunoprecipitated Unkempt from cells in the presence or the absence of the mTORC1 inhibitor rapamycin and used mass spectrometry to identify mTORC1-dependent phosphorylated residues. This analysis showed that mTORC1-dependent phosphorylation is concentrated in a serine-rich intrinsically disordered region in the C-terminal half of Unkempt. We also found that Unkempt physically interacts with and is directly phosphorylated by mTORC1 through binding to the regulatory-associated protein of mTOR, Raptor. Furthermore, analysis in the developing brain of mice lacking TSC1 expression showed that phosphorylation of Unkempt is mTORC1 dependent in vivo. Finally, mutation analysis of key serine/threonine residues in the serine-rich region indicates that phosphorylation inhibits the ability of Unkempt to induce a bipolar morphology. Phosphorylation within this serine-rich region thus profoundly affects the ability of Unkempt to regulate cellular morphogenesis. Taken together, our findings reveal a novel molecular link between mTORC1 signaling and cellular morphogenesis.
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Affiliation(s)
- Pranetha Baskaran
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Simeon R Mihaylov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Elin Vinsland
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Kriti Shah
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Lucy Granat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Andrew R Tee
- Cancer and Genetics Building, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park Way, Cardiff, UK
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, California, USA.
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
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3
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Ogienko AA, Omelina ES, Bylino OV, Batin MA, Georgiev PG, Pindyurin AV. Drosophila as a Model Organism to Study Basic Mechanisms of Longevity. Int J Mol Sci 2022; 23:11244. [PMID: 36232546 PMCID: PMC9569508 DOI: 10.3390/ijms231911244] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The spatio-temporal regulation of gene expression determines the fate and function of various cells and tissues and, as a consequence, the correct development and functioning of complex organisms. Certain mechanisms of gene activity regulation provide adequate cell responses to changes in environmental factors. Aside from gene expression disorders that lead to various pathologies, alterations of expression of particular genes were shown to significantly decrease or increase the lifespan in a wide range of organisms from yeast to human. Drosophila fruit fly is an ideal model system to explore mechanisms of longevity and aging due to low cost, easy handling and maintenance, large number of progeny per adult, short life cycle and lifespan, relatively low number of paralogous genes, high evolutionary conservation of epigenetic mechanisms and signalling pathways, and availability of a wide range of tools to modulate gene expression in vivo. Here, we focus on the organization of the evolutionarily conserved signaling pathways whose components significantly influence the aging process and on the interconnections of these pathways with gene expression regulation.
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Affiliation(s)
- Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Laboratory of Biotechnology, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Alexey V. Pindyurin
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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4
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Zinc in Cognitive Impairment and Aging. Biomolecules 2022; 12:biom12071000. [PMID: 35883555 PMCID: PMC9312494 DOI: 10.3390/biom12071000] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
Zinc, an essential micronutrient for life, was first discovered in 1869 and later found to be indispensable for the normal development of plants and for the normal growth of rats and birds. Zinc plays an important role in many physiological and pathological processes in normal mammalian brain development, especially in the development of the central nervous system. Zinc deficiency can lead to neurodegenerative diseases, mental abnormalities, sleep disorders, tumors, vascular diseases, and other pathological conditions, which can cause cognitive impairment and premature aging. This study aimed to review the important effects of zinc and zinc-associated proteins in cognitive impairment and aging, to reveal its molecular mechanism, and to highlight potential interventions for zinc-associated aging and cognitive impairments.
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5
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Terakawa A, Hu Y, Kokaji T, Yugi K, Morita K, Ohno S, Pan Y, Bai Y, Parkhitko AA, Ni X, Asara JM, Bulyk ML, Perrimon N, Kuroda S. Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes. iScience 2022; 25:104231. [PMID: 35494245 PMCID: PMC9044165 DOI: 10.1016/j.isci.2022.104231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/09/2022] [Accepted: 04/06/2022] [Indexed: 12/16/2022] Open
Abstract
Insulin signaling promotes anabolic metabolism to regulate cell growth through multi-omic interactions. To obtain a comprehensive view of the cellular responses to insulin, we constructed a trans-omic network of insulin action in Drosophila cells that involves the integration of multi-omic data sets. In this network, 14 transcription factors, including Myc, coordinately upregulate the gene expression of anabolic processes such as nucleotide synthesis, transcription, and translation, consistent with decreases in metabolites such as nucleotide triphosphates and proteinogenic amino acids required for transcription and translation. Next, as cell growth is required for cell proliferation and insulin can stimulate proliferation in a context-dependent manner, we integrated the trans-omic network with results from a CRISPR functional screen for cell proliferation. This analysis validates the role of a Myc-mediated subnetwork that coordinates the activation of genes involved in anabolic processes required for cell growth. A trans-omic network of insulin action in Drosophila cells was constructed Insulin co-regulates various anabolic processes in a time-dependent manner The trans-omic network and a CRISPR screen for cell proliferation were integrated A Myc-mediated subnetwork promoting anabolic processes is required for cell growth
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Affiliation(s)
- Akira Terakawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Toshiya Kokaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan
| | - Keigo Morita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Ohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Yifei Pan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yunfan Bai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Andrey A. Parkhitko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Aging Institute of UPMC and the University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaochun Ni
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02175, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Corresponding author
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Corresponding author
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6
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Känel P, Noll GA, Schroedter K, Naffin E, Kronenberg J, Busswinkel F, Twyman RM, Klämbt C, Prüfer D. The tobacco phosphatidylethanolamine-binding protein NtFT4 increases the lifespan of Drosophila melanogaster by interacting with the proteostasis network. Aging (Albany NY) 2022; 14:2989-3029. [PMID: 35396341 PMCID: PMC9037272 DOI: 10.18632/aging.204005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
Proteostasis reflects the well-balanced synthesis, trafficking and degradation of cellular proteins. This is a fundamental aspect of the dynamic cellular proteome, which integrates multiple signaling pathways, but it becomes increasingly error-prone during aging. Phosphatidylethanolamine-binding proteins (PEBPs) are highly conserved regulators of signaling networks and could therefore affect aging-related processes. To test this hypothesis, we expressed PEPBs in a heterologous context to determine their ectopic activity. We found that heterologous expression of the tobacco (Nicotiana tabacum) PEBP NtFT4 in Drosophila melanogaster significantly increased the lifespan of adult flies and reduced age-related locomotor decline. Similarly, overexpression of the Drosophila ortholog CG7054 increased longevity, whereas its suppression by RNA interference had the opposite effect. In tobacco, NtFT4 acts as a floral regulator by integrating environmental and intrinsic stimuli to promote the transition to reproductive growth. In Drosophila, NtFT4 engaged distinct targets related to proteostasis, such as HSP26. In older flies, it also prolonged Hsp26 gene expression, which promotes longevity by maintaining protein integrity. In NtFT4-transgenic flies, we identified deregulated genes encoding proteases that may contribute to proteome stability at equilibrium. Our results demonstrate that the expression of NtFT4 influences multiple aspects of the proteome maintenance system via both physical interactions and transcriptional regulation, potentially explaining the aging-related phenotypes we observed.
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Affiliation(s)
- Philip Känel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Katrin Schroedter
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Elke Naffin
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Julia Kronenberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Franziska Busswinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | | | - Christian Klämbt
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
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7
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Vinsland E, Baskaran P, Mihaylov SR, Hobbs C, Wood H, Bouybayoune I, Shah K, Houart C, Tee AR, Murn J, Fernandes C, Bateman JM. The zinc finger/RING domain protein Unkempt regulates cognitive flexibility. Sci Rep 2021; 11:16299. [PMID: 34381067 PMCID: PMC8357790 DOI: 10.1038/s41598-021-95286-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Correct orchestration of nervous system development is a profound challenge that involves coordination of complex molecular and cellular processes. Mechanistic target of rapamycin (mTOR) signaling is a key regulator of nervous system development and synaptic function. The mTOR kinase is a hub for sensing inputs including growth factor signaling, nutrients and energy levels. Activation of mTOR signaling causes diseases with severe neurological manifestations, such as tuberous sclerosis complex and focal cortical dysplasia. However, the molecular mechanisms by which mTOR signaling regulates nervous system development and function are poorly understood. Unkempt is a conserved zinc finger/RING domain protein that regulates neurogenesis downstream of mTOR signaling in Drosophila. Unkempt also directly interacts with the mTOR complex I component Raptor. Here we describe the generation and characterisation of mice with a conditional knockout of Unkempt (UnkcKO) in the nervous system. Loss of Unkempt reduces Raptor protein levels in the embryonic nervous system but does not affect downstream mTORC1 targets. We also show that nervous system development occurs normally in UnkcKO mice. However, we find that Unkempt is expressed in the adult cerebellum and hippocampus and behavioural analyses show that UnkcKO mice have improved memory formation and cognitive flexibility to re-learn. Further understanding of the role of Unkempt in the nervous system will provide novel mechanistic insight into the role of mTOR signaling in learning and memory.
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Affiliation(s)
- Elin Vinsland
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Pranetha Baskaran
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Simeon R Mihaylov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Carl Hobbs
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Hannah Wood
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London, PO82SE5 8AF, UK
| | - Ihssane Bouybayoune
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall 1415A - MURN, Riverside, CA, 92521, USA
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Andrew R Tee
- Cancer and Genetics Building, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park Way, Cardiff, CF14 4XN, UK
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall 1415A - MURN, Riverside, CA, 92521, USA
| | - Cathy Fernandes
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London, PO82SE5 8AF, UK
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 4th Floor, New Hunt's House, London, SE1 1UL, UK
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK.
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8
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Kerbler SM, Natale R, Fernie AR, Zhang Y. From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants. Int J Mol Sci 2021; 22:ijms22137101. [PMID: 34281155 PMCID: PMC8267905 DOI: 10.3390/ijms22137101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems.
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Affiliation(s)
- Sandra M. Kerbler
- Theodor-Echtermeyer-Weg 1, Leibniz-Institut für Gemüse- und Zierpflanzenbau, 14979 Groβbeeren, Germany;
| | - Roberto Natale
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence:
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9
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Pacheco JM, Canal MV, Pereyra CM, Welchen E, Martínez-Noël GMA, Estevez JM. The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4085-4101. [PMID: 33462577 DOI: 10.1093/jxb/eraa603] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.
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Affiliation(s)
| | - María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Cintia M Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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10
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Maierbrugger KT, Sousa-Nunes R, Bateman JM. The mTOR pathway component Unkempt regulates neural stem cell and neural progenitor cell cycle in the Drosophila central nervous system. Dev Biol 2020; 461:55-65. [PMID: 31978396 DOI: 10.1016/j.ydbio.2020.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/21/2022]
Abstract
The formation of a complex nervous system requires the coordinated action of progenitor cell proliferation, differentiation and maturation. The Drosophila postembryonic central nervous system provides a powerful model for dissecting the cellular and molecular mechanisms underpinning neurogenesis. We previously identified the conserved zinc finger/RING protein Unkempt (Unk) as a key temporal regulator of neuronal differentiation in the Drosophila developing eye and showed that Unk acts downstream of the mechanistic target of rapamycin (mTOR) pathway together with its binding partner Headcase (Hdc). Here we investigate the role of Unk in Drosophila postembryonic thoracic neurogenesis. The Drosophila central nervous system contains neural stem cells, called neuroblasts, and neural progenitors, known as ganglion mother cells (GMCs). Unk is highly expressed in the central brain and ventral nerve cord but is not required to maintain neuroblast numbers or for the regulation of temporal series factor expression in neuroblasts. However, loss of Unk increases the number of neuroblasts and GMCs in S-phase of the cell cycle, resulting in the overproduction of neurons. We also show that Unk interacts with Hdc through its zinc finger domain. The zinc finger domain is required for the synergistic activity of Unk with Hdc during eye development but is not necessary for the activity of Unk in thoracic neurogenesis. Overall, this study shows that Unk and Hdc are novel negative regulators of neurogenesis in Drosophila and indicates a conserved role of mTOR signalling in nervous system development.
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Affiliation(s)
- Katja T Maierbrugger
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour lane, London, SE5 9NU, UK
| | - Rita Sousa-Nunes
- Centre for Developmental Neurobiology, King's College London, New Hunts House, Newcomen Street, London, SE1 1UL, UK
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour lane, London, SE5 9NU, UK.
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11
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Li N, Liu Q, Xiong Y, Yu J. Headcase and Unkempt Regulate Tissue Growth and Cell Cycle Progression in Response to Nutrient Restriction. Cell Rep 2020; 26:733-747.e3. [PMID: 30650363 PMCID: PMC6350942 DOI: 10.1016/j.celrep.2018.12.086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/24/2018] [Accepted: 12/19/2018] [Indexed: 11/26/2022] Open
Abstract
Nutrient restriction (NR) decreases the incidence and growth of many types of tumors, yet the underlying mechanisms are not fully understood. In this study, we identified Headcase (Hdc) and Unkempt (Unk) as two NR-specific tumor suppressor proteins that form a complex to restrict cell cycle progression and tissue growth in response to NR in Drosophila. Loss of Hdc or Unk does not confer apparent growth advantage under normal nutrient conditions but leads to accelerated cell cycle progression and tissue overgrowth under NR. Hdc and Unk bind to the TORC1 component Raptor and preferentially regulate S6 phosphorylation in a TORC1-dependent manner. We further show that HECA and UNK, the human counterparts of Drosophila Hdc and Unk, respectively, have a conserved function in regulating S6 phosphorylation and tissue growth. The identification of Hdc and Unk as two NR-specific tumor suppressors provides insight into molecular mechanisms underlying the anti-tumorigenic effects of NR. The molecular mechanisms underlying nutrient restriction resistance remain unclear. Li et al. find that Hdc and Unk function in the mTOR signaling pathway to restrict tissue growth and cell cycle progression in response to nutrient restriction.
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Affiliation(s)
- Naren Li
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
| | - Qinfang Liu
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
| | - Yulan Xiong
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA.
| | - Jianzhong Yu
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA.
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12
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Maruzs T, Simon-Vecsei Z, Kiss V, Csizmadia T, Juhász G. On the Fly: Recent Progress on Autophagy and Aging in Drosophila. Front Cell Dev Biol 2019; 7:140. [PMID: 31396511 PMCID: PMC6667644 DOI: 10.3389/fcell.2019.00140] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/09/2019] [Indexed: 01/03/2023] Open
Abstract
Autophagy ensures the lysosome-mediated breakdown and recycling of self-material, as it not only degrades obsolete or damaged intracellular constituents but also provides building blocks for biosynthetic and energy producing reactions. Studies in animal models including Drosophila revealed that autophagy defects lead to the rapid decline of neuromuscular function, neurodegeneration, sensitivity to stress (such as starvation or oxidative damage), and stem cell loss. Of note, recently identified human Atg gene mutations cause similar symptoms including ataxia and mental retardation. Physiologically, autophagic degradation (flux) is known to decrease during aging, and this defect likely contributes to the development of such age-associated diseases. Many manipulations that extend lifespan (including dietary restriction, reduced TOR kinase signaling, exercise or treatment with various anti-aging substances) require autophagy for their beneficial effect on longevity, pointing to the key role of this housekeeping process. Importantly, genetic (e.g., Atg8a overexpression in either neurons or muscle) or pharmacological (e.g., feeding rapamycin or spermidine to animals) promotion of autophagy has been successfully used to extend lifespan in Drosophila, suggesting that this intracellular degradation pathway can rejuvenate cells and organisms. In this review, we highlight key discoveries and recent progress in understanding the relationship of autophagy and aging in Drosophila.
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Affiliation(s)
- Tamás Maruzs
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsófia Simon-Vecsei
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Viktória Kiss
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Tamás Csizmadia
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
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13
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Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. NATURE PLANTS 2019; 5:316-327. [PMID: 30833711 DOI: 10.1038/s41477-019-0378-z] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/28/2019] [Indexed: 05/18/2023]
Abstract
The target of rapamycin (TOR) kinase is a conserved regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Despite the increased appreciation of the essential role of the TOR complex in plants, no large-scale phosphoproteomics or interactomics studies have been performed to map TOR signalling events in plants. To fill this gap, we combined a systematic phosphoproteomics screen with a targeted protein complex analysis in the model plant Arabidopsis thaliana. Integration of the phosphoproteome and protein complex data on the one hand shows that both methods reveal complementary subspaces of the plant TOR signalling network, enabling proteome-wide discovery of both upstream and downstream network components. On the other hand, the overlap between both data sets reveals a set of candidate direct TOR substrates. The integrated network embeds both evolutionarily-conserved and plant-specific TOR signalling components, uncovering an intriguing complex interplay with protein synthesis. Overall, the network provides a rich data set to start addressing fundamental questions about how TOR controls key processes in plants, such as autophagy, auxin signalling, chloroplast development, lipid metabolism, nucleotide biosynthesis, protein translation or senescence.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte Van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francis Impens
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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14
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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15
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Zheng H, Zhang Y, Chen Y, Guo P, Wang X, Yuan X, Ge W, Yang R, Yan Q, Yang X, Xi Y. Prominin-like, a homolog of mammalian CD133, suppresses di lp6 and TOR signaling to maintain body size and weight in Drosophila. FASEB J 2018; 33:2646-2658. [PMID: 30307770 DOI: 10.1096/fj.201800123r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
CD133 (AC133/prominin-1) has been identified as a stem cell marker and a putative cancer stem cell marker in many solid tumors. Its biologic function and molecular mechanisms remain largely elusive. Here, we show that a fly mutant for prominin-like, a homolog of mammalian CD133, shows a larger body size and excess weight accompanied with higher fat deposits as compared with the wild type. The expression levels of prominin-like are mediated by ecdysone signaling where its protein levels increase dramatically in the fat body during metamorphosis. Prominin-like mutants exhibit higher Drosophila insulin-like peptide 6 (di lp6) levels during nonfeeding stages and increased Akt/ Drosophila target of rapamycin (dTOR) signaling. On an amino acid-restricted diet, prominin-like mutants exhibit a significantly larger body size than the wild type does, similar to that which occurs upon the activation of the dTOR pathway in the fat body. Our data suggest that prominin-like functions by suppressing TOR and dilp6 signaling to control body size and weight. The identification of the physiologic function of prominin-like in Drosophila may provide valuable insight into the understanding of the metabolic function of CD133 in mammals.-Zheng, H., Zhang, Y., Chen, Y., Guo, P., Wang, X., Yuan, X., Ge, W., Yang, R., Yan, Q., Yang, X., Xi, Y. Prominin-like, a homolog of mammalian CD133, suppresses di lp6 and TOR signaling to maintain body size and weight in Drosophila.
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Affiliation(s)
- Huimei Zheng
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China.,College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yafei Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China.,Beijing Genomics Institute, Shanghai, China
| | - Yuchen Chen
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengfei Guo
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China.,College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuexiang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xin Yuan
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Ru Yang
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China; and
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University-University of Toronto Joint Institute of Genetics and Genomic Medicine, Zhejiang University, Hangzhou, China
| | - Yongmei Xi
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University, Hangzhou, China.,Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
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16
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Bontinck M, Van Leene J, Gadeyne A, De Rybel B, Eeckhout D, Nelissen H, De Jaeger G. Recent Trends in Plant Protein Complex Analysis in a Developmental Context. FRONTIERS IN PLANT SCIENCE 2018; 9:640. [PMID: 29868093 PMCID: PMC5962756 DOI: 10.3389/fpls.2018.00640] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/26/2018] [Indexed: 05/30/2023]
Abstract
Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.
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Affiliation(s)
- Michiel Bontinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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17
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Zur Lage P, Stefanopoulou P, Styczynska-Soczka K, Quinn N, Mali G, von Kriegsheim A, Mill P, Jarman AP. Ciliary dynein motor preassembly is regulated by Wdr92 in association with HSP90 co-chaperone, R2TP. J Cell Biol 2018; 217:2583-2598. [PMID: 29743191 PMCID: PMC6028525 DOI: 10.1083/jcb.201709026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 02/21/2018] [Accepted: 04/06/2018] [Indexed: 01/12/2023] Open
Abstract
Wdr92 is associated with the multifunctional cochaperone, R2TP, but its function is unknown. In this study, the authors show that Drosophila Wdr92 is exclusively required for preassembly of ciliary dynein motor complexes, which are confined to sensory neuron ciliary dendrites and sperm flagella. Wdr92 is proposed to direct R2TP/HSP90 to dynein chain clients to chaperone cytoplasmic preassembly. The massive dynein motor complexes that drive ciliary and flagellar motility require cytoplasmic preassembly, a process requiring dedicated dynein assembly factors (DNAAFs). How DNAAFs interact with molecular chaperones to control dynein assembly is not clear. By analogy with the well-known multifunctional HSP90-associated cochaperone, R2TP, several DNAAFs have been suggested to perform novel R2TP-like functions. However, the involvement of R2TP itself (canonical R2TP) in dynein assembly remains unclear. Here we show that in Drosophila melanogaster, the R2TP-associated factor, Wdr92, is required exclusively for axonemal dynein assembly, likely in association with canonical R2TP. Proteomic analyses suggest that in addition to being a regulator of R2TP chaperoning activity, Wdr92 works with the DNAAF Spag1 at a distinct stage in dynein preassembly. Wdr92/R2TP function is likely distinct from that of the DNAAFs proposed to form dynein-specific R2TP-like complexes. Our findings thus establish a connection between dynein assembly and a core multifunctional cochaperone.
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Affiliation(s)
- Petra Zur Lage
- Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, Scotland, UK
| | - Panagiota Stefanopoulou
- Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, Scotland, UK
| | - Katarzyna Styczynska-Soczka
- Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, Scotland, UK
| | - Niall Quinn
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Girish Mali
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Pleasantine Mill
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Andrew P Jarman
- Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, Scotland, UK
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18
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Drosophila melanogaster as a Model for Diabetes Type 2 Progression. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1417528. [PMID: 29854726 PMCID: PMC5941822 DOI: 10.1155/2018/1417528] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/03/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022]
Abstract
Drosophila melanogaster has been used as a very versatile and potent model in the past few years for studies in metabolism and metabolic disorders, including diabetes types 1 and 2. Drosophila insulin signaling, despite having seven insulin-like peptides with partially redundant functions, is very similar to the human insulin pathway and has served to study many different aspects of diabetes and the diabetic state. Yet, very few studies have addressed the chronic nature of diabetes, key for understanding the full-blown disease, which most studies normally explore. One of the advantages of having Drosophila mutant viable combinations at different levels of the insulin pathway, with significantly reduced insulin pathway signaling, is that the abnormal metabolic state can be studied from the onset of the life cycle and followed throughout. In this review, we look at the chronic nature of impaired insulin signaling. We also compare these results to the results gleaned from vertebrate model studies.
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19
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Ren S, Huang Z, Jiang Y, Wang T. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol 2017; 217:517-526. [PMID: 29187524 PMCID: PMC5800808 DOI: 10.1083/jcb.201706027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 12/31/2022] Open
Abstract
The insulin signaling pathway plays key roles in systemic growth. TBC1D7 has recently been identified as the third subunit of the tuberous sclerosis complex (TSC), a negative regulator of cell growth. Here, we used Drosophila as a model system to dissect the physiological function of TBC1D7 in vivo. In mutants lacking TBC1D7, cell and organ growth were promoted, and TBC1D7 limited cell growth in a cell-nonautonomous and TSC-independent manner. TBC1D7 is specifically expressed in insulin-producing cells in the fly brain and regulated biosynthesis and release of insulin-like peptide 2, leading to systemic growth. Furthermore, animals carrying the dTBC1D7 mutation were hypoglycemic, short-lived, and sensitive to oxidative stress. Our findings provide new insights into the physiological function of TBC1D7 in the systemic control of growth, as well as insights into human disorders caused by TBC1D7 mutation.
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Affiliation(s)
- Suxia Ren
- College of Biological Sciences, China Agricultural University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Zengyi Huang
- National Institute of Biological Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- National Institute of Biological Sciences, Beijing, China
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20
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Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Rep 2017; 18:3219-3226. [PMID: 28355572 PMCID: PMC5382234 DOI: 10.1016/j.celrep.2017.03.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/02/2022] Open
Abstract
Spatiotemporal organization of protein interactions in cell signaling is a fundamental process that drives cellular functions. Given differential protein expression across tissues and developmental stages, the architecture and dynamics of signaling interaction proteomes is, likely, highly context dependent. However, current interaction information has been almost exclusively obtained from transformed cells. In this study, we applied an advanced and robust workflow combining mouse genetics and affinity purification (AP)-SWATH mass spectrometry to profile the dynamics of 53 high-confidence protein interactions in primary T cells, using the scaffold protein GRB2 as a model. The workflow also provided a sufficient level of robustness to pinpoint differential interaction dynamics between two similar, but functionally distinct, primary T cell populations. Altogether, we demonstrated that precise and reproducible quantitative measurements of protein interaction dynamics can be achieved in primary cells isolated from mammalian tissues, allowing resolution of the tissue-specific context of cell-signaling events.
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Affiliation(s)
- Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Takeshi Hase
- The Systems Biology Institute, Tokyo 108-0071, Japan
| | - Witold E Wolski
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Meena Choi
- College of Science, College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA
| | - Marisa G Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Stephane Durand
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Antonio García-Blesa
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Ivo Fierro-Monti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Marie Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Samik Ghosh
- The Systems Biology Institute, Tokyo 108-0071, Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Tokyo 108-0071, Japan; Okinawa Institute of Science and Technology Garuda School, 904-0495 Okinawa, Japan
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France.
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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21
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Chen D, Tao X, Zhou L, Sun F, Sun M, Fang X. Spaghetti, a homolog of human RPAP3 (RNA polymerase II-associated protein 3), determines the fate of germline stem cells in Drosophila ovary. Cell Biol Int 2017; 42:769-780. [PMID: 29110400 DOI: 10.1002/cbin.10900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/22/2017] [Indexed: 11/11/2022]
Abstract
The Drosophila ovary provides an attractive model for studying the extrinsic or intrinsic factors that regulate the fate of germline stem cells (GSCs). Using this model, we identified a new role for Drosophila spaghetti (spag), encoding a homolog of human RNA polymerase II-associated protein 3 (RPAP3), in regulating the fate of ovarian GSCs. Results from spag knockdown and genetic mosaic studies suggest that spag functions as an intrinsic factor for GSCs maintenance. Loss of Spag by, either spag RNAi or null mutation failed to trigger apoptosis in ovarian GSCs. Overexpression of spag led to negligible increases in the number of GSC/Cystoblast (CB) cells, suggesting that an excess of Spag is not sufficient to accelerate the proliferation of GSCs or delay CBs' differentiation. Our study provides evidence supporting that spag is involved in adult stem cells maintenance. In addition, the RNAi screen results showed that knockdown of Hsp90, one of known Spag interacting partners, led to loss of ovarian GSCs in Drosophila. Heterozygous mutations in hsp90 (hsp90/+) dramatically accelerated the GSC loss in spag RNAi ovaries, suggesting that the Spag-contained complex possibly plays an essential role in controlling the GSCs fate.
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Affiliation(s)
- Dongsheng Chen
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China.,The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Xiaoqian Tao
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China
| | - Lijuan Zhou
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China
| | - Fuling Sun
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China
| | - Mingzhong Sun
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China
| | - Xin Fang
- Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, 241000, P.R. China
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22
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An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling. Cell Rep 2017; 16:3062-3074. [PMID: 27626673 DOI: 10.1016/j.celrep.2016.08.029] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/21/2016] [Accepted: 08/09/2016] [Indexed: 11/20/2022] Open
Abstract
Insulin regulates an essential conserved signaling pathway affecting growth, proliferation, and metabolism. To expand our understanding of the insulin pathway, we combine biochemical, genetic, and computational approaches to build a comprehensive Drosophila InR/PI3K/Akt network. First, we map the dynamic protein-protein interaction network surrounding the insulin core pathway using bait-prey interactions connecting 566 proteins. Combining RNAi screening and phospho-specific antibodies, we find that 47% of interacting proteins affect pathway activity, and, using quantitative phosphoproteomics, we demonstrate that ∼10% of interacting proteins are regulated by insulin stimulation at the level of phosphorylation. Next, we integrate these orthogonal datasets to characterize the structure and dynamics of the insulin network at the level of protein complexes and validate our method by identifying regulatory roles for the Protein Phosphatase 2A (PP2A) and Reptin-Pontin chromatin-remodeling complexes as negative and positive regulators of ribosome biogenesis, respectively. Altogether, our study represents a comprehensive resource for the study of the evolutionary conserved insulin network.
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23
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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24
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David-Morrison G, Xu Z, Rui YN, Charng WL, Jaiswal M, Yamamoto S, Xiong B, Zhang K, Sandoval H, Duraine L, Zuo Z, Zhang S, Bellen HJ. WAC Regulates mTOR Activity by Acting as an Adaptor for the TTT and Pontin/Reptin Complexes. Dev Cell 2016; 36:139-51. [PMID: 26812014 DOI: 10.1016/j.devcel.2015.12.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/16/2015] [Accepted: 12/18/2015] [Indexed: 01/09/2023]
Abstract
The ability to sense energy status is crucial in the regulation of metabolism via the mechanistic Target of Rapamycin Complex 1 (mTORC1). The assembly of the TTT-Pontin/Reptin complex is responsive to changes in energy status. Under energy-sufficient conditions, the TTT-Pontin/Reptin complex promotes mTORC1 dimerization and mTORC1-Rag interaction, which are critical for mTORC1 activation. We show that WAC is a regulator of energy-mediated mTORC1 activity. In a Drosophila screen designed to isolate mutations that cause neuronal dysfunction, we identified wacky, the homolog of WAC. Loss of Wacky leads to neurodegeneration, defective mTOR activity, and increased autophagy. Wacky and WAC have conserved physical interactions with mTOR and its regulators, including Pontin and Reptin, which bind to the TTT complex to regulate energy-dependent activation of mTORC1. WAC promotes the interaction between TTT and Pontin/Reptin in an energy-dependent manner, thereby promoting mTORC1 activity by facilitating mTORC1 dimerization and mTORC1-Rag interaction.
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Affiliation(s)
| | - Zhen Xu
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Yan-Ning Rui
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lita Duraine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sheng Zhang
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA; Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX 77030, USA; Programs in Human and Molecular Genetics and Neuroscience, The Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
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25
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Sanchez CG, Teixeira FK, Czech B, Preall JB, Zamparini AL, Seifert JRK, Malone CD, Hannon GJ, Lehmann R. Regulation of Ribosome Biogenesis and Protein Synthesis Controls Germline Stem Cell Differentiation. Cell Stem Cell 2016; 18:276-90. [PMID: 26669894 PMCID: PMC4744108 DOI: 10.1016/j.stem.2015.11.004] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/01/2015] [Accepted: 11/06/2015] [Indexed: 12/18/2022]
Abstract
Complex regulatory networks regulate stem cell behavior and contributions to tissue growth, repair, and homeostasis. A full understanding of the networks controlling stem cell self-renewal and differentiation, however, has not yet been realized. To systematically dissect these networks and identify their components, we performed an unbiased, transcriptome-wide in vivo RNAi screen in female Drosophila germline stem cells (GSCs). Based on characterized cellular defects, we classified 646 identified genes into phenotypic and functional groups and unveiled a comprehensive set of networks regulating GSC maintenance, survival, and differentiation. This analysis revealed an unexpected role for ribosomal assembly factors in controlling stem cell cytokinesis. Moreover, our data show that the transition from self-renewal to differentiation relies on enhanced ribosome biogenesis accompanied by increased protein synthesis. Collectively, these results detail the extensive genetic networks that control stem cell homeostasis and highlight the intricate regulation of protein synthesis during differentiation.
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Affiliation(s)
- Carlos G Sanchez
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Felipe Karam Teixeira
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
| | - Benjamin Czech
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jonathan B Preall
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Andrea L Zamparini
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Jessica R K Seifert
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA; Department of Biology, Farmingdale State College, State University of New York, Farmingdale, NY 11735, USA
| | - Colin D Malone
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ruth Lehmann
- Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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26
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Bateman JM. Mechanistic insights into the role of mTOR signaling in neuronal differentiation. NEUROGENESIS 2015; 2:e1058684. [PMID: 27604337 PMCID: PMC4973600 DOI: 10.1080/23262133.2015.1058684] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/16/2015] [Accepted: 04/19/2015] [Indexed: 01/01/2023]
Abstract
Temporal control of neuronal differentiation is critical to produce a complete and fully functional nervous system. Loss of the precise temporal control of neuronal cell fate can lead to defects in cognitive development and to disorders such as epilepsy and autism. Mechanistic target of rapamycin (mTOR) is a large serine/threonine kinase that acts as a crucial sensor of cellular homeostasis. mTOR signaling has recently emerged as a key regulator of neurogenesis. However, the mechanism by which mTOR regulates neurogenesis is poorly understood. In constrast to other functions of the pathway, ‘neurogenic mTOR pathway factors’ have not previously been identified. We have very recently used Drosophila as a model system to identify the gene unkempt as the first component of the mTOR pathway regulating neuronal differentiation. Our study demonstrates that specific adaptor proteins exist that channel mTOR signaling toward the regulation of neuronal cell fate. In this Commentary we discuss the role of mTOR signaling in neurogenesis and the significance of these findings in advancing our understanding of the mechanism by which mTOR signaling controls neuronal differentiation.
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Affiliation(s)
- Joseph M Bateman
- Wolfson Center for Age-Related Diseases, King's College London ; London, UK
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27
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Dibble CC, Cantley LC. Regulation of mTORC1 by PI3K signaling. Trends Cell Biol 2015; 25:545-55. [PMID: 26159692 DOI: 10.1016/j.tcb.2015.06.002] [Citation(s) in RCA: 571] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022]
Abstract
The class I phosphoinositide 3-kinase (PI3K)-mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) signaling network directs cellular metabolism and growth. Activation of mTORC1 [composed of mTOR, regulatory-associated protein of mTOR (Raptor), mammalian lethal with SEC13 protein 8(mLST8), 40-kDa proline-rich Akt substrate (PRAS40), and DEP domain-containing mTOR-interacting protein (DEPTOR)] depends on the Ras-related GTPases (Rags) and Ras homolog enriched in brain (Rheb) GTPase and requires signals from amino acids, glucose, oxygen, energy (ATP), and growth factors (including cytokines and hormones such as insulin). Here we discuss the signal transduction mechanisms through which growth factor-responsive PI3K signaling activates mTORC1. We focus on how PI3K-dependent activation of Akt and spatial regulation of the tuberous sclerosis complex (TSC) complex (TSC complex) [composed of TSC1, TSC2, and Tre2-Bub2-Cdc16-1 domain family member 7 (TBC1D7)] switches on Rheb at the lysosome, where mTORC1 is activated. Integration of PI3K- and amino acid-dependent signals upstream of mTORC1 at the lysosome is detailed in a working model. A coherent understanding of the PI3K-mTORC1 network is imperative as its dysregulation has been implicated in diverse pathologies including cancer, diabetes, autism, and aging.
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Affiliation(s)
- Christian C Dibble
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
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28
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Jevtov I, Zacharogianni M, van Oorschot MM, van Zadelhoff G, Aguilera-Gomez A, Vuillez I, Braakman I, Hafen E, Stocker H, Rabouille C. TORC2 mediates the heat stress response in Drosophila by promoting the formation of stress granules. J Cell Sci 2015; 128:2497-508. [PMID: 26054799 PMCID: PMC4510851 DOI: 10.1242/jcs.168724] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/03/2015] [Indexed: 12/29/2022] Open
Abstract
The kinase TOR is found in two complexes, TORC1, which is involved in growth control, and TORC2, whose roles are less well defined. Here, we asked whether TORC2 has a role in sustaining cellular stress. We show that TORC2 inhibition in Drosophila melanogaster leads to a reduced tolerance to heat stress, whereas sensitivity to other stresses is not affected. Accordingly, we show that upon heat stress, both in the animal and Drosophila cultured S2 cells, TORC2 is activated and is required for maintaining the level of its known target, Akt1 (also known as PKB). We show that the phosphorylation of the stress-activated protein kinases is not modulated by TORC2 nor is the heat-induced upregulation of heat-shock proteins. Instead, we show, both in vivo and in cultured cells, that TORC2 is required for the assembly of heat-induced cytoprotective ribonucleoprotein particles, the pro-survival stress granules. These granules are formed in response to protein translation inhibition imposed by heat stress that appears to be less efficient in the absence of TORC2 function. We propose that TORC2 mediates heat resistance in Drosophila by promoting the cell autonomous formation of stress granules.
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Affiliation(s)
- Irena Jevtov
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | | | - Marinke M van Oorschot
- Hubrecht Institute of the KNAW and UMC Utrecht, Uppsalalaan 8, Utrecht 3584 CT, Netherlands
| | - Guus van Zadelhoff
- Cellular Protein Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | | | - Igor Vuillez
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Ineke Braakman
- Cellular Protein Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Ernst Hafen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Hugo Stocker
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW and UMC Utrecht, Uppsalalaan 8, Utrecht 3584 CT, Netherlands Department of Cell Biology, UMC Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
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29
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Sopko R, Lin YB, Makhijani K, Alexander B, Perrimon N, Brückner K. A systems-level interrogation identifies regulators of Drosophila blood cell number and survival. PLoS Genet 2015; 11:e1005056. [PMID: 25749252 PMCID: PMC4352040 DOI: 10.1371/journal.pgen.1005056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 02/05/2015] [Indexed: 12/12/2022] Open
Abstract
In multicellular organisms, cell number is typically determined by a balance of intracellular signals that positively and negatively regulate cell survival and proliferation. Dissecting these signaling networks facilitates the understanding of normal development and tumorigenesis. Here, we study signaling by the Drosophila PDGF/VEGF Receptor (Pvr) in embryonic blood cells (hemocytes) and in the related cell line Kc as a model for the requirement of PDGF/VEGF receptors in vertebrate cell survival and proliferation. The system allows the investigation of downstream and parallel signaling networks, based on the ability of Pvr to activate Ras/Erk, Akt/TOR, and yet-uncharacterized signaling pathway/s, which redundantly mediate cell survival and contribute to proliferation. Using Kc cells, we performed a genome wide RNAi screen for regulators of cell number in a sensitized, Pvr deficient background. We identified the receptor tyrosine kinase (RTK) Insulin-like receptor (InR) as a major Pvr Enhancer, and the nuclear hormone receptors Ecdysone receptor (EcR) and ultraspiracle (usp), corresponding to mammalian Retinoid X Receptor (RXR), as Pvr Suppressors. In vivo analysis in the Drosophila embryo revealed a previously unrecognized role for EcR to promote apoptotic death of embryonic blood cells, which is balanced with pro-survival signaling by Pvr and InR. Phosphoproteomic analysis demonstrates distinct modes of cell number regulation by EcR and RTK signaling. We define common phosphorylation targets of Pvr and InR that include regulators of cell survival, and unique targets responsible for specialized receptor functions. Interestingly, our analysis reveals that the selection of phosphorylation targets by signaling receptors shows qualitative changes depending on the signaling status of the cell, which may have wide-reaching implications for other cell regulatory systems.
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Affiliation(s)
- Richelle Sopko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - You Bin Lin
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
| | - Kalpana Makhijani
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
| | - Brandy Alexander
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Katja Brückner
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
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30
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Li X, Wang W, Chen J. From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. Proteomics 2014; 15:188-202. [PMID: 25137225 DOI: 10.1002/pmic.201400147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/28/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
Abstract
Signal transductions are the basis of biological activities in all living organisms. Studying the signaling pathways, especially under physiological conditions, has become one of the most important facets of modern biological research. During the last decade, MS has been used extensively in biological research and is proven to be effective in addressing important biological questions. Here, we review the current progress in the understanding of signaling networks using MS approaches. We will focus on studies of protein-protein interactions that use affinity purification followed by MS approach. We discuss obstacles to affinity purification, data processing, functional validation, and identification of transient interactions and provide potential solutions for pathway-specific proteomics analysis, which we hope one day will lead to a comprehensive understanding of signaling networks in humans.
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Affiliation(s)
- Xu Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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31
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Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. J Proteomics 2014; 118:81-94. [PMID: 25281560 DOI: 10.1016/j.jprot.2014.09.011] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/04/2014] [Accepted: 09/07/2014] [Indexed: 12/19/2022]
Abstract
UNLABELLED Mapping protein-protein interactions for chromatin-associated proteins remains challenging. Here we explore the use of BioID, a proximity biotinylation approach in which a mutated biotin ligase (BirA*) is fused to a bait of interest, allowing for the local activation of biotin and subsequent biotinylation of proteins in the bait vicinity. BioID allowed for successful interactome mapping of core histones and members of the mediator complex. We explored the background signal produced by the BioID approach and found that using distinct types of controls increased the stringency of our statistical analysis with SAINTexpress. A direct comparison of BioID with our AP-MS protocol optimized for chromatin-associated protein complexes revealed that the approaches identified few shared interaction partners and enriched for distinct biological processes; yet, both approaches permitted the recovery of biologically meaningful interactions. While no clear bias could be observed for either technique toward protein complexes of particular functions, BioID allowed for the purification of proteins of lower cellular abundance. Finally, we were able to identify a strong association of MED4 with the centrosome by BioID and validated this finding by immunofluorescence. In summary, BioID complements AP-MS for the study of chromatin-associated protein complexes. BIOLOGICAL SIGNIFICANCE This manuscript describes the application of BioID, a proximity biotinylation approach, to chromatin-associated proteins, namely core histones and members of the mediator complex. We observed that BioID was successful at identifying known interaction partners for the baits tested, but also allowed novel putative interaction partners to be identified. By performing a detailed comparison of BioID versus a standard method for interactome mapping (affinity purification coupled to mass spectrometry, AP-MS), we show that the approaches were complementary, allowing for purification of different interaction partners. These interaction partners were different in the biological processes they are associated with, but also in their abundance. BioID represents a significant technical development in the field of chromatin research by expanding the search space for interactome mapping beyond what is possible with AP-MS. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Sopko R, Foos M, Vinayagam A, Zhai B, Binari R, Hu Y, Randklev S, Perkins LA, Gygi SP, Perrimon N. Combining genetic perturbations and proteomics to examine kinase-phosphatase networks in Drosophila embryos. Dev Cell 2014; 31:114-27. [PMID: 25284370 DOI: 10.1016/j.devcel.2014.07.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/24/2014] [Accepted: 07/28/2014] [Indexed: 02/07/2023]
Abstract
Connecting phosphorylation events to kinases and phosphatases is key to understanding the molecular organization and signaling dynamics of networks. We have generated a validated set of transgenic RNA-interference reagents for knockdown and characterization of all protein kinases and phosphatases present during early Drosophila melanogaster development. These genetic tools enable collection of sufficient quantities of embryos depleted of single gene products for proteomics. As a demonstration of an application of the collection, we have used multiplexed isobaric labeling for quantitative proteomics to derive global phosphorylation signatures associated with kinase-depleted embryos to systematically link phosphosites with relevant kinases. We demonstrate how this strategy uncovers kinase consensus motifs and prioritizes phosphoproteins for kinase target validation. We validate this approach by providing auxiliary evidence for Wee kinase-directed regulation of the chromatin regulator Stonewall. Further, we show how correlative phosphorylation at the site level can indicate function, as exemplified by Sterile20-like kinase-dependent regulation of Stat92E.
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Affiliation(s)
- Richelle Sopko
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Marianna Foos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | | | - Bo Zhai
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard Binari
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sakara Randklev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
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A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
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Avet-Rochex A, Carvajal N, Christoforou CP, Yeung K, Maierbrugger KT, Hobbs C, Lalli G, Cagin U, Plachot C, McNeill H, Bateman JM. Unkempt is negatively regulated by mTOR and uncouples neuronal differentiation from growth control. PLoS Genet 2014; 10:e1004624. [PMID: 25210733 PMCID: PMC4161320 DOI: 10.1371/journal.pgen.1004624] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/23/2014] [Indexed: 01/21/2023] Open
Abstract
Neuronal differentiation is exquisitely controlled both spatially and temporally during nervous system development. Defects in the spatiotemporal control of neurogenesis cause incorrect formation of neural networks and lead to neurological disorders such as epilepsy and autism. The mTOR kinase integrates signals from mitogens, nutrients and energy levels to regulate growth, autophagy and metabolism. We previously identified the insulin receptor (InR)/mTOR pathway as a critical regulator of the timing of neuronal differentiation in the Drosophila melanogaster eye. Subsequently, this pathway has been shown to play a conserved role in regulating neurogenesis in vertebrates. However, the factors that mediate the neurogenic role of this pathway are completely unknown. To identify downstream effectors of the InR/mTOR pathway we screened transcriptional targets of mTOR for neuronal differentiation phenotypes in photoreceptor neurons. We identified the conserved gene unkempt (unk), which encodes a zinc finger/RING domain containing protein, as a negative regulator of the timing of photoreceptor differentiation. Loss of unk phenocopies InR/mTOR pathway activation and unk acts downstream of this pathway to regulate neurogenesis. In contrast to InR/mTOR signalling, unk does not regulate growth. unk therefore uncouples the role of the InR/mTOR pathway in neurogenesis from its role in growth control. We also identified the gene headcase (hdc) as a second downstream regulator of the InR/mTOR pathway controlling the timing of neurogenesis. Unk forms a complex with Hdc, and Hdc expression is regulated by unk and InR/mTOR signalling. Co-overexpression of unk and hdc completely suppresses the precocious neuronal differentiation phenotype caused by loss of Tsc1. Thus, Unk and Hdc are the first neurogenic components of the InR/mTOR pathway to be identified. Finally, we show that Unkempt-like is expressed in the developing mouse retina and in neural stem/progenitor cells, suggesting that the role of Unk in neurogenesis may be conserved in mammals. The development of a functional nervous system requires that nerve cells are generated at exactly the right time and place to be correctly integrated. Defects in the timing at which nerve cells are generated, or ‘differentiate’, lead to neurological disorders such as epilepsy and autism. However, very little is known about the identity of the genes that control the timing of nerve cell differentiation. Using developing photoreceptor nerves in the eye of the fruit fly, Drosophila, as a model, we showed previously that a molecular pathway known as ‘mTOR signalling’ is a key regulator of the timing of differentiation. In this study we have identified two new genes, unkempt and headcase, which control the timing of photoreceptor differentiation in Drosophila. The activity of unkempt and headcase is controlled by mTOR signalling and it is through these genes that mTOR is able to control nerve cell differentiation. The proteins encoded by unkempt and headcase form a complex and act synergistically to control the development of Drosophila photoreceptors. mTOR signalling controls a number of important cellular processes, but unkempt and headcase are the first components of this pathway to be identified that control nerve cell differentiation.
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Affiliation(s)
- Amélie Avet-Rochex
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Nancy Carvajal
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | | | - Kelvin Yeung
- The Lunenfeld-Tanenbaum Research Centre, Toronto, Ontario, Canada
| | - Katja T. Maierbrugger
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Carl Hobbs
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Giovanna Lalli
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Umut Cagin
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Cedric Plachot
- The Lunenfeld-Tanenbaum Research Centre, Toronto, Ontario, Canada
| | - Helen McNeill
- The Lunenfeld-Tanenbaum Research Centre, Toronto, Ontario, Canada
| | - Joseph M. Bateman
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
- * E-mail:
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Handke B, Szabad J, Lidsky PV, Hafen E, Lehner CF. Towards long term cultivation of Drosophila wing imaginal discs in vitro. PLoS One 2014; 9:e107333. [PMID: 25203426 PMCID: PMC4159298 DOI: 10.1371/journal.pone.0107333] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/14/2014] [Indexed: 12/26/2022] Open
Abstract
The wing imaginal disc of Drosophila melanogaster is a prominent experimental system for research on control of cell growth, proliferation and death, as well as on pattern formation and morphogenesis during organogenesis. The precise genetic methodology applicable in this system has facilitated conceptual advances of fundamental importance for developmental biology. Experimental accessibility and versatility would gain further if long term development of wing imaginal discs could be studied also in vitro. For example, culture systems would allow live imaging with maximal temporal and spatial resolution. However, as clearly demonstrated here, standard culture methods result in a rapid cell proliferation arrest within hours of cultivation of dissected wing imaginal discs. Analysis with established markers for cells in S- and M phase, as well as with RGB cell cycle tracker, a novel reporter transgene, revealed that in vitro cultivation interferes with cell cycle progression throughout interphase and not just exclusively during G1. Moreover, quantification of EGFP expression from an inducible transgene revealed rapid adverse effects of disc culture on basic cellular functions beyond cell cycle progression. Disc transplantation experiments confirmed that these detrimental consequences do not reflect fatal damage of imaginal discs during isolation, arguing clearly for a medium insufficiency. Alternative culture media were evaluated, including hemolymph, which surrounds imaginal discs during growth in situ. But isolated larval hemolymph was found to be even less adequate than current culture media, presumably as a result of conversion processes during hemolymph isolation or disc culture. The significance of prominent growth-regulating pathways during disc culture was analyzed, as well as effects of insulin and disc co-culture with larval tissues as potential sources of endocrine factors. Based on our analyses, we developed a culture protocol that prolongs cell proliferation in cultured discs.
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Affiliation(s)
- Björn Handke
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
| | - János Szabad
- Department of Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Peter V. Lidsky
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
| | - Ernst Hafen
- Department of Biology, Institute of Molecular Systems Biology (IMSB), ETH Zurich, Zurich, Switzerland
| | - Christian F. Lehner
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
- * E-mail:
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Fabre B, Lambour T, Bouyssié D, Menneteau T, Monsarrat B, Burlet-Schiltz O, Bousquet-Dubouch MP. Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.06.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Papatheodorou I, Petrovs R, Thornton JM. Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. ACTA ACUST UNITED AC 2014; 30:2999-3003. [PMID: 25064569 PMCID: PMC4201157 DOI: 10.1093/bioinformatics/btu493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION A large number of experimental studies on ageing focus on the effects of genetic perturbations of the insulin/insulin-like growth factor signalling pathway (IIS) on lifespan. Short-lived invertebrate laboratory model organisms are extensively used to quickly identify ageing-related genes and pathways. It is important to extrapolate this knowledge to longer lived mammalian organisms, such as mouse and eventually human, where such analyses are difficult or impossible to perform. Computational tools are needed to integrate and manipulate pathway knowledge in different species. RESULTS We performed a literature review and curation of the IIS and target of rapamycin signalling pathways in Mus Musculus. We compare this pathway model to the equivalent models in Drosophila melanogaster and Caenorhabtitis elegans. Although generally well-conserved, they exhibit important differences. In general, the worm and mouse pathways include a larger number of feedback loops and interactions than the fly. We identify 'functional orthologues' that share similar molecular interactions, but have moderate sequence similarity. Finally, we incorporate the mouse model into the web-service NetEffects and perform in silico gene perturbations of IIS components and analyses of experimental results. We identify sub-paths that, given a mutation in an IIS component, could potentially antagonize the primary effects on ageing via FOXO in mouse and via SKN-1 in worm. Finally, we explore the effects of FOXO knockouts in three different mouse tissues. AVAILABILITY AND IMPLEMENTATION http://www.ebi.ac.uk/thornton-srv/software/NetEffects.
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Affiliation(s)
- Irene Papatheodorou
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Institute of Healthy Ageing and Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, UK EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Institute of Healthy Ageing and Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Rudolfs Petrovs
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Institute of Healthy Ageing and Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Janet M Thornton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Institute of Healthy Ageing and Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, UK
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38
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Fabre B, Lambour T, Garrigues L, Ducoux-Petit M, Amalric F, Monsarrat B, Burlet-Schiltz O, Bousquet-Dubouch MP. Label-Free Quantitative Proteomics Reveals the Dynamics of Proteasome Complexes Composition and Stoichiometry in a Wide Range of Human Cell Lines. J Proteome Res 2014; 13:3027-37. [DOI: 10.1021/pr500193k] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bertrand Fabre
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Thomas Lambour
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Luc Garrigues
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Manuelle Ducoux-Petit
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - François Amalric
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Bernard Monsarrat
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Marie-Pierre Bousquet-Dubouch
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
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Benbahouche NEH, Iliopoulos I, Török I, Marhold J, Henri J, Kajava AV, Farkaš R, Kempf T, Schnölzer M, Meyer P, Kiss I, Bertrand E, Mechler BM, Pradet-Balade B. Drosophila Spag is the homolog of RNA polymerase II-associated protein 3 (RPAP3) and recruits the heat shock proteins 70 and 90 (Hsp70 and Hsp90) during the assembly of cellular machineries. J Biol Chem 2014; 289:6236-47. [PMID: 24394412 DOI: 10.1074/jbc.m113.499608] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R2TP is a recently identified Hsp90 co-chaperone, composed of four proteins as follows: Pih1D1, RPAP3, and the AAA(+)-ATPases RUVBL1 and RUVBL2. In mammals, the R2TP is involved in the biogenesis of cellular machineries such as RNA polymerases, small nucleolar ribonucleoparticles and phosphatidylinositol 3-kinase-related kinases. Here, we characterize the spaghetti (spag) gene of Drosophila, the homolog of human RPAP3. This gene plays an essential function during Drosophila development. We show that Spag protein binds Drosophila orthologs of R2TP components and Hsp90, like its yeast counterpart. Unexpectedly, Spag also interacts and stimulates the chaperone activity of Hsp70. Using null mutants and flies with inducible RNAi, we show that spaghetti is necessary for the stabilization of snoRNP core proteins and target of rapamycin activity and likely the assembly of RNA polymerase II. This work highlights the strong conservation of both the HSP90/R2TP system and its clients and further shows that Spag, unlike Saccharomyces cerevisiae Tah1, performs essential functions in metazoans. Interaction of Spag with both Hsp70 and Hsp90 suggests a model whereby R2TP would accompany clients from Hsp70 to Hsp90 to facilitate their assembly into macromolecular complexes.
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Affiliation(s)
- Nour El Houda Benbahouche
- From the Equipe Labellisée Ligue Contre le Cancer, Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, Gstaiger M. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol 2013; 9:713. [PMID: 24366813 PMCID: PMC4019981 DOI: 10.1002/msb.201304750] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/13/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022] Open
Abstract
Tissue homeostasis is controlled by signaling systems that coordinate cell proliferation, cell growth and cell shape upon changes in the cellular environment. Deregulation of these processes is associated with human cancer and can occur at multiple levels of the underlying signaling systems. To gain an integrated view on signaling modules controlling tissue growth, we analyzed the interaction proteome of the human Hippo pathway, an established growth regulatory signaling system. The resulting high-resolution network model of 480 protein-protein interactions among 270 network components suggests participation of Hippo pathway components in three distinct modules that all converge on the transcriptional co-activator YAP1. One of the modules corresponds to the canonical Hippo kinase cassette whereas the other two both contain Hippo components in complexes with cell polarity proteins. Quantitative proteomic data suggests that complex formation with cell polarity proteins is dynamic and depends on the integrity of cell-cell contacts. Collectively, our systematic analysis greatly enhances our insights into the biochemical landscape underlying human Hippo signaling and emphasizes multifaceted roles of cell polarity complexes in Hippo-mediated tissue growth control.
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Affiliation(s)
- Simon Hauri
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
| | | | | | - Markku Varjosalo
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Nic Tapon
- Cancer Research UKLondon Research InstituteLondonUK
| | - Ruedi Aebersold
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
- Faculty of ScienceUniversity of ZürichZürichSwitzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
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41
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Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods 2013; 10:1246-53. [PMID: 24162925 DOI: 10.1038/nmeth.2703] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 09/25/2013] [Indexed: 12/22/2022]
Abstract
Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies on the composition of protein complexes are carried out by affinity purification and mass spectrometry (AP-MS) and present a static view of the system. For a better understanding of inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential. Here we used affinity purification combined with sequential window acquisition of all theoretical spectra (AP-SWATH) mass spectrometry to study the dynamics of the 14-3-3β scaffold protein interactome after stimulation of the insulin-PI3K-AKT pathway. The consistent and reproducible quantification of 1,967 proteins across all stimulation time points provided insights into the 14-3-3β interactome and its dynamic changes following IGF1 stimulation. We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks.
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Ahrné E, Molzahn L, Glatter T, Schmidt A. Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013; 13:2567-78. [PMID: 23794183 DOI: 10.1002/pmic.201300135] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/27/2013] [Accepted: 06/17/2013] [Indexed: 11/06/2022]
Abstract
There is a great interest in reliable ways to obtain absolute protein abundances at a proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated abundance. Several variants of this quantification approach have been presented, based on either the number of spectral counts per protein or MS1 peak intensities. Equipped with several datasets representing real biological environments, containing a high number of accurately quantified reference proteins, we evaluate five popular low-cost and easily implemented quantification methods (Absolute Protein Expression, Exponentially Modified Protein Abundance Index, Intensity-Based Absolute Quantification Index, Top3, and MeanInt). Our results demonstrate considerably improved abundance estimates upon implementing accurately quantified reference proteins; that is, using spiked in stable isotope labeled standard peptides or a standard protein mix, to generate a properly calibrated quantification model. We show that only the Top3 method is directly proportional to protein abundance over the full quantification range and is the preferred method in the absence of reference protein measurements. Additionally, we demonstrate that spectral count based quantification methods are associated with higher errors than MS1 peak intensity based methods. Furthermore, we investigate the impact of miscleaved, modified, and shared peptides as well as protein size and the number of employed reference proteins on quantification accuracy.
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Affiliation(s)
- Erik Ahrné
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
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43
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Jünger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 3:83-112. [PMID: 24902836 DOI: 10.1002/wdev.121] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphorylation is the best-studied posttranslational modification and plays a role in virtually every biological process. Phosphoproteomics is the analysis of protein phosphorylation on a proteome-wide scale, and mainly uses the same instrumentation and analogous strategies as conventional mass spectrometry (MS)-based proteomics. Measurements can be performed either in a discovery-type, also known as shotgun mode, or in a targeted manner which monitors a set of a priori known phosphopeptides, such as members of a signal transduction pathway, across biological samples. Here, we delineate the different experimental levels at which measures can be taken to optimize the scope, reliability, and information content of phosphoproteomic analyses. Various chromatographic and chemical protocols exist to physically enrich phosphopeptides from proteolytic digests of biological samples. Subsequent mass spectrometric analysis revolves around peptide ion fragmentation to generate sequence information and identify the backbone sequence of phosphopeptides as well as the phosphate group attachment site(s), and different modes of fragmentation like collision-induced dissociation (CID), electron transfer dissociation (ETD), and higher energy collisional dissociation (HCD) have been established for phosphopeptide analysis. Computational tools are important for the identification and quantification of phosphopeptides and mapping of phosphorylation sites, the deposition of large-scale phosphoproteome datasets in public databases, and the extraction of biologically meaningful information by data mining, integration with other data types, and descriptive or predictive modeling. Finally, we discuss how orthogonal experimental approaches can be employed to validate newly identified phosphorylation sites on a biochemical, mechanistic, and physiological level.
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Affiliation(s)
- Martin A Jünger
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
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Almudi I, Poernbacher I, Hafen E, Stocker H. The Lnk/SH2B adaptor provides a fail-safe mechanism to establish the Insulin receptor-Chico interaction. Cell Commun Signal 2013; 11:26. [PMID: 23590848 PMCID: PMC3637499 DOI: 10.1186/1478-811x-11-26] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 04/06/2013] [Indexed: 12/14/2022] Open
Abstract
Background Insulin/insulin-like growth factor signalling (IIS) has been described as one of the major pathways involved in growth control and homeostasis in multicellular organisms. Whereas its core components are well established, less is known about the molecular functions of IIS regulators. The adaptor molecule Lnk/SH2B has been implicated in IIS but the mechanism by which it promotes IIS activity has remained enigmatic. Results In this study, we analyse genetic and physical interactions among InR, Chico and Lnk in Drosophila tissues. FRET analysis reveals in vivo binding between all three molecules. Genetically, Lnk acts upstream of Chico. We demonstrate that Chico’s plasma membrane localisation is ensured by both its PH domain and by the interaction with Lnk. Furthermore, Lnk is able to recruit an intracellular InR fragment to the membrane. Conclusions Thus, by acting as a scaffolding molecule that ensures InR and Chico enrichment at the membrane, Lnk provides a fail-safe mechanism for IIS activation.
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Affiliation(s)
- Isabel Almudi
- Institute of Molecular Systems Biology, ETH Zürich, Wolfgang-Pauli-Strasse 16, Zürich 8093, Switzerland.
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Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nat Methods 2013; 10:307-14. [DOI: 10.1038/nmeth.2400] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/29/2013] [Indexed: 12/19/2022]
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Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N. Protein complex-based analysis framework for high-throughput data sets. Sci Signal 2013; 6:rs5. [PMID: 23443684 DOI: 10.1126/scisignal.2003629] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Analysis of high-throughput data increasingly relies on pathway annotation and functional information derived from Gene Ontology. This approach has limitations, in particular for the analysis of network dynamics over time or under different experimental conditions, in which modules within a network rather than complete pathways might respond and change. We report an analysis framework based on protein complexes, which are at the core of network reorganization. We generated a protein complex resource for human, Drosophila, and yeast from the literature and databases of protein-protein interaction networks, with each species having thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat), a tool for data mining and visualization for complex-based analysis of high-throughput data sets, as well as analysis and integration of heterogeneous proteomics and gene expression data sets. With COMPLEAT, we identified dynamically regulated protein complexes among genome-wide RNA interference data sets that used the abundance of phosphorylated extracellular signal-regulated kinase in cells stimulated with either insulin or epidermal growth factor as the output. The analysis predicted that the Brahma complex participated in the insulin response.
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Affiliation(s)
- Arunachalam Vinayagam
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Miteva YV, Budayeva HG, Cristea IM. Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem 2013; 85:749-68. [PMID: 23157382 PMCID: PMC3666915 DOI: 10.1021/ac3033257] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ileana M. Cristea
- Corresponding author: Ileana M. Cristea 210 Lewis Thomas Laboratory Department of Molecular Biology Princeton University Princeton, NJ 08544 Tel: 6092589417 Fax: 6092584575
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Li S. Proteomics Defines Protein Interaction Network of Signaling Pathways. TRANSLATIONAL BIOINFORMATICS 2013. [PMCID: PMC7123116 DOI: 10.1007/978-94-007-5811-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Protein interactions play fundamental roles in signaling transduction. Analysis of protein–protein interaction (PPI) has contributed numerous insights to the understanding of the regulation of signal pathways. Different approaches have been used to discover PPI and characterize protein complexes. In addition to conventional PPI methods, such as yeast two-hybrid (YTH), affinity purification coupled with mass spectrometry (AP-MS) is emerging as an important and popular tool to unravel protein complex and elucidate protein function through the interaction partners. With the AP-MS method, protein complexes are prepared first by affinity purification directly from cell lysates, followed by characterization of their components by mass spectrometry. In contrast to most PPI methods, AP-MS reflects PPI under near physiological conditions in the relevant organism and cell type. AP-MS is also able to probe dynamic PPI dependent on protein posttranslational modifications, which is common for signal transduction. AP-MS mapping protein interaction network of various signal pathways has dramatically increased in recent years. Here, I’ll present the strategies toward obtaining an interactome map of signal pathway and the methodology, detailed protocols, and perspectives of AP-MS.
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Nesvizhskii AI. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 2012; 12:1639-55. [PMID: 22611043 DOI: 10.1002/pmic.201100537] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Analysis of protein interaction networks and protein complexes using affinity purification and mass spectrometry (AP/MS) is among most commonly used and successful applications of proteomics technologies. One of the foremost challenges of AP/MS data is a large number of false-positive protein interactions present in unfiltered data sets. Here we review computational and informatics strategies for detecting specific protein interaction partners in AP/MS experiments, with a focus on incomplete (as opposite to genome wide) interactome mapping studies. These strategies range from standard statistical approaches, to empirical scoring schemes optimized for a particular type of data, to advanced computational frameworks. The common denominator among these methods is the use of label-free quantitative information such as spectral counts or integrated peptide intensities that can be extracted from AP/MS data. We also discuss related issues such as combining multiple biological or technical replicates, and dealing with data generated using different tagging strategies. Computational approaches for benchmarking of scoring methods are discussed, and the need for generation of reference AP/MS data sets is highlighted. Finally, we discuss the possibility of more extended modeling of experimental AP/MS data, including integration with external information such as protein interaction predictions based on functional genomics data.
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50
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Abstract
Protein complex identification is an important goal of protein-protein interaction analysis. To date, development of computational methods for detecting protein complexes has been largely motivated by genome-scale interaction data sets from high-throughput assays such as yeast two-hybrid or tandem affinity purification coupled with mass spectrometry (TAP-MS). However, due to the popularity of small to intermediate-scale affinity purification-mass spectrometry (AP-MS) experiments, protein complex detection is increasingly discussed in local network analysis. In such data sets, protein complexes cannot be detected using binary interaction data alone because the data contain interactions with tagged proteins only and, as a result, interactions between all other proteins remain unobserved, limiting the scope of existing algorithms. In this article, we provide a pragmatic review of network graph-based computational algorithms for protein complex analysis in global interactome data, without requiring any computational background. We discuss the practical gap in applying these algorithms to recently surging small to intermediate-scale AP-MS data sets, and review alternative clustering algorithms using quantitative proteomics data and their limitations.
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Affiliation(s)
- Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
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