1
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Aranda RG, Fatima S, Rafid MI, McGill I, Hadwiger JA. Regulatory differences between atypical and typical MAP kinases in Dictyostelium discoideum. Cell Signal 2025; 130:111701. [PMID: 40020888 PMCID: PMC11908898 DOI: 10.1016/j.cellsig.2025.111701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 02/14/2025] [Accepted: 02/23/2025] [Indexed: 03/03/2025]
Abstract
Within the large family of mitogen activated protein kinases (MAPKs), one outlier group referred to as atypical MAPKs is not regulated by conventional upstream MAPK kinases (MAP2Ks). This includes the Dictyostelium discoideum atypical MAPK Erk2, a protein kinase essential for chemotactic movement and development. The regulation and functional specificity of Erk2 was investigated through phenotypic analysis of chimeric and mutant MAPKs. Chimeric MAPKs containing regions of Erk2 were created using complementary regions of the more typical MAPK Erk1, that provides very different functions in this amoeba. The chimeric MAPKs were not phosphorylated at levels observed for wild-type MAPKs and none rescued wild-type MAPK function to erk1- or erk2- cells. Endogenous Erk1 and Erk2 MAPKs were destabilized in cells expressing chimeric MAPKs containing the same carboxyl terminus. A carboxyl terminal motif conserved among atypical MAPKs was important but not essential for Erk2 regulation and function and the motif did not confer atypical MAPK regulation when present in Erk1. A kinase-dead version of Erk2 was phosphorylated in response to folate or cAMP chemotactic stimulation, suggesting Erk2 is activated in vivo by an upstream protein kinase, contrary to previous predictions of autophosphorylation. This regulation implies a protein kinase distinct from the single conventional MAP2K in Dictyostelium regulates atypical MAPK signaling. A non-activatable form of Erk2 was not capable of rescuing Erk2 function in erk2- cells. These findings suggest that the regulation of atypical and typical MAPKs is substantially different and carried out by distinct upstream protein kinases.
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Affiliation(s)
- Ramee G Aranda
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Saher Fatima
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Md Ikram Rafid
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Imani McGill
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Jeffrey A Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America.
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2
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Brimson CA, Baines R, Sams-Dodd E, Stefanescu I, Evans B, Kuwana S, Hashimura H, Sawai S, Thompson CRL. Collective oscillatory signaling in Dictyostelium discoideum acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal. Dev Cell 2025; 60:918-933.e4. [PMID: 39672161 DOI: 10.1016/j.devcel.2024.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 07/18/2024] [Accepted: 11/17/2024] [Indexed: 12/15/2024]
Abstract
Oscillatory phenomena play widespread roles in the control of biological systems. In D. discoideum, oscillatory cyclic adenosine monophosphate (cAMP) signaling drives collective behavior and induces a temporal developmental gene expression program. How collective cAMP oscillations emerge or how they encode temporal transcriptional information is still poorly understood. To address this, we identified a transcription factor required for the initiation of collective behavior. Hbx5 activity is cAMP dependent and provides a sensitive single-cell readout for cAMP signaling. Extensive stochastic pulsatile cAMP signaling is found to precede collective oscillations. Stochastic signaling induces Hbx5-dependent transcriptional feedback, which enhances signal sensitivity and cell-cell coupling. This results in the emergence of synchronized collective oscillations, which subsequently activates the GtaC transcription factor and triggers shifts in developmental gene expression. Our results suggest this temporal coordination is encoded by changes in the amplitude of cAMP oscillations and differential sensitivity of these transcription factors to the cAMP-regulated kinase ErkB.
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Affiliation(s)
- Christopher A Brimson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Robert Baines
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Elisabeth Sams-Dodd
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Ioanina Stefanescu
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Bethany Evans
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Satoshi Kuwana
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Hidenori Hashimura
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Satoshi Sawai
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
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3
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Kakizuka T, Nakaoka H, Hara Y, Ichiraku A, Arai Y, Itoga H, Onami S, Ichimura T, Nagai T, Horikawa K. Mesoscale heterogeneity is a critical determinant for spiral pattern formation in developing social amoeba. Sci Rep 2025; 15:1422. [PMID: 39789232 PMCID: PMC11717926 DOI: 10.1038/s41598-025-85759-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 01/06/2025] [Indexed: 01/12/2025] Open
Abstract
Heterogeneity is a critical determinant for multicellular pattern formation. Although the importance of microscale and macroscale heterogeneity at the single-cell and whole-system levels, respectively, has been well accepted, the presence and functions of mesoscale heterogeneity, such as cell clusters with distinct properties, have been poorly recognized. We investigated the biological importance of mesoscale heterogeneity in signal-relaying abilities (excitability) in the self-organization of spiral waves of intercellular communications by studying the self-organized pattern formation in a population of Dictyostelium discoideum cells, a classical signal-relaying system model. By utilizing pulse-count analysis to evaluate cellular excitability, we successfully visualized the development of mesoscale heterogeneity in excitability, whose spatial scale was comparably large to that of the traveling waves of intercellular communication. Together with perturbation experiments, our detailed analysis of the structural change in mesoscale heterogeneity and associated wave dynamics demonstrated the functional importance of mesoscale heterogeneity in generating the spiral wave pattern, whose experimental observations were first realized. We propose that mesoscale heterogeneity, in addition to microscale and macroscale heterogeneities, is a critical determinant of diverse multicellular pattern formations.
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Affiliation(s)
- Taishi Kakizuka
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, 567-0047, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, 565-0871, Osaka, Japan
| | - Hidenori Nakaoka
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima City, 770-8503, Tokushima, Japan
| | - Yusuke Hara
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima City, 770-8503, Tokushima, Japan
| | - Aya Ichiraku
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima City, 770-8503, Tokushima, Japan
| | - Yoshiyuki Arai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, 567-0047, Osaka, Japan
| | - Hiroya Itoga
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Kobe, 650-0047, Japan
| | - Shuichi Onami
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, 565-0871, Osaka, Japan
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Kobe, 650-0047, Japan
| | - Taro Ichimura
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, 565-0871, Osaka, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, 567-0047, Osaka, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, 565-0871, Osaka, Japan.
| | - Kazuki Horikawa
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, 565-0871, Osaka, Japan.
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima City, 770-8503, Tokushima, Japan.
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4
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Yamashita K, Shimane K, Muramoto T. Optogenetic control of cAMP oscillations reveals frequency-selective transcription factor dynamics in Dictyostelium. Development 2025; 152:dev204403. [PMID: 39775856 PMCID: PMC11829771 DOI: 10.1242/dev.204403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025]
Abstract
Oscillatory dynamics and their modulation are crucial for cellular decision-making; however, analysing these dynamics remains challenging. Here, we present a tool that combines the light-activated adenylate cyclase mPAC with the cAMP biosensor Pink Flamindo, enabling precise manipulation and real-time monitoring of cAMP oscillation frequencies in Dictyostelium. High-frequency modulation of cAMP oscillations induced cell aggregation and multicellular formation, even at low cell densities, such as a few dozen cells. At the population level, chemotactic aggregation is driven by modulated frequency signals. Additionally, modulation of cAMP frequency significantly reduced the amplitude of the shuttling behaviour of the transcription factor GtaC, demonstrating low-pass filter characteristics capable of converting subtle oscillation changes, such as from 6 min to 4 min, into gene expression. These findings enhance our understanding of frequency-selective cellular decoding and its role in cellular signalling and development.
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Affiliation(s)
- Kensuke Yamashita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Kazuya Shimane
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Tetsuya Muramoto
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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5
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Deng Y, Banerjee T, Pal DS, Banerjee P, Zhan H, Borleis J, Igleias PA, Devreotes PN. PIP5K-Ras bistability initiates plasma membrane symmetry breaking to regulate cell polarity and migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.15.613115. [PMID: 39314378 PMCID: PMC11419139 DOI: 10.1101/2024.09.15.613115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Symmetry breaking, polarity establishment, and spontaneous cell protrusion formation are fundamental but poorly explained cell behaviors. Here, we demonstrate that a biochemical network, where the mutually inhibitory localization of PIP5K and Ras activities plays a central role, governs these processes. First, in resting cells devoid of cytoskeletal activity, PIP5K is uniformly elevated on the plasma membrane, while Ras activity remains minimal. Symmetry is broken by spontaneous local displacements of PIP5K, coupled with simultaneous activations of Ras and downstream signaling events, including PI3K activation. Second, knockout of PIP5K dramatically increases both the incidence and size of Ras-PI3K activation patches, accompanied by branched F-actin assembly. This leads to enhanced cortical wave formation, increased protrusive activity, and a shift in migration mode. Third, high inducible overexpression of PIP5K virtually eliminates Ras-PI3K signaling, cytoskeletal activity, and cell migration, while acute recruitment of cytosolic PIP5K to the membrane induces contraction and blebs in cancer cells. These arrested phenotypes are reversed by reducing myosin II activity, indicating myosin's involvement in the PIP5K-Ras-centered regulatory network. Remarkably, low inducible overexpression of PIP5K unexpectedly facilitates polarity establishment, highlighting PIP5K as a highly sensitive master regulator of these processes. Simulations of a computational model combining an excitable system, cytoskeletal loops, and dynamic partitioning of PIP5K recreates the experimental observations. Taken together, our results reveal that a bistable, mutually exclusive localization of PIP5K and active Ras on the plasma membrane triggers the initial symmetry breaking. Coupled actomyosin reduction and increased actin polymerization lead to intermittently extended protrusions and, with feedback from the cytoskeleton, self-organizing, complementary gradients of PIP5K versus Ras steepen, raising the threshold of the networks at the rear and lowering it at the front to generate polarity for cell migration.
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Affiliation(s)
- Yu Deng
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tatsat Banerjee
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
- These authors contributed equally to this work
| | - Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- These authors contributed equally to this work
| | - Parijat Banerjee
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD, USA
| | - Huiwang Zhan
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jane Borleis
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pablo A. Igleias
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N. Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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6
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Chao X, Yang Y, Gong W, Zou S, Tu H, Li D, Feng W, Cai H. Leep2A and Leep2B function as a RasGAP complex to regulate macropinosome formation. J Cell Biol 2024; 223:e202401110. [PMID: 38888895 PMCID: PMC11187982 DOI: 10.1083/jcb.202401110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/12/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Macropinocytosis mediates the non-selective bulk uptake of extracellular fluid, enabling cells to survey the environment and obtain nutrients. A conserved set of signaling proteins orchestrates the actin dynamics that lead to membrane ruffling and macropinosome formation across various eukaryotic organisms. At the center of this signaling network are Ras GTPases, whose activation potently stimulates macropinocytosis. However, how Ras signaling is initiated and spatiotemporally regulated during macropinocytosis is not well understood. By using the model system Dictyostelium and a proteomics-based approach to identify regulators of macropinocytosis, we uncovered Leep2, consisting of Leep2A and Leep2B, as a RasGAP complex. The Leep2 complex specifically localizes to emerging macropinocytic cups and nascent macropinosomes, where it modulates macropinosome formation by regulating the activities of three Ras family small GTPases. Deletion or overexpression of the complex, as well as disruption or sustained activation of the target Ras GTPases, impairs macropinocytic activity. Our data reveal the critical role of fine-tuning Ras activity in directing macropinosome formation.
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Affiliation(s)
- Xiaoting Chao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yihong Yang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weibin Gong
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Songlin Zou
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui Tu
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Peking University, Beijing, China
| | - Dong Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Feng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huaqing Cai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Hao Y, Yang Y, Tu H, Guo Z, Chen P, Chao X, Yuan Y, Wang Z, Miao X, Zou S, Li D, Yang Y, Wu C, Li B, Li L, Cai H. A transcription factor complex in Dictyostelium enables adaptive changes in macropinocytosis during the growth-to-development transition. Dev Cell 2024; 59:645-660.e8. [PMID: 38325371 DOI: 10.1016/j.devcel.2024.01.012] [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: 06/14/2023] [Revised: 11/14/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Macropinocytosis, an evolutionarily conserved endocytic pathway, mediates nonselective bulk uptake of extracellular fluid. It is the primary route for axenic Dictyostelium cells to obtain nutrients and has also emerged as a nutrient-scavenging pathway for mammalian cells. How cells adjust macropinocytic activity in various physiological or developmental contexts remains to be elucidated. We discovered that, in Dictyostelium cells, the transcription factors Hbx5 and MybG form a functional complex in the nucleus to maintain macropinocytic activity during the growth stage. In contrast, during starvation-induced multicellular development, the transcription factor complex undergoes nucleocytoplasmic shuttling in response to oscillatory cyclic adenosine 3',5'-monophosphate (cAMP) signals, which leads to increased cytoplasmic retention of the complex and progressive downregulation of macropinocytosis. Therefore, by coupling macropinocytosis-related gene expression to the cAMP oscillation system, which facilitates long-range cell-cell communication, the dynamic translocation of the Hbx5-MybG complex orchestrates a population-level adjustment of macropinocytic activity to adapt to changing environmental conditions.
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Affiliation(s)
- Yazhou Hao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihong Yang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Tu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Pengcheng Chen
- Department of Engineering Mechanics, Applied Mechanics Laboratory, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing 100084, China
| | - Xiaoting Chao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Yuan
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhimeng Wang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xilin Miao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Zou
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanzhi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Congying Wu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Bo Li
- Department of Engineering Mechanics, Applied Mechanics Laboratory, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing 100084, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
| | - Huaqing Cai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Shi Y, Ma L, Zhou M, He Z, Zhao Y, Hong J, Zou X, Zhang L, Shu L. Copper stress shapes the dynamic behavior of amoebae and their associated bacteria. THE ISME JOURNAL 2024; 18:wrae100. [PMID: 38848278 PMCID: PMC11197307 DOI: 10.1093/ismejo/wrae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/15/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024]
Abstract
Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.
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Affiliation(s)
- Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Zhou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanchen Zhao
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Junyue Hong
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinyue Zou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
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9
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Westbrook ER, Lenn T, Chubb JR, Antolović V. Collective signalling drives rapid jumping between cell states. Development 2023; 150:dev201946. [PMID: 37921687 PMCID: PMC10730084 DOI: 10.1242/dev.201946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Development can proceed in 'fits and starts', with rapid transitions between cell states involving concerted transcriptome-wide changes in gene expression. However, it is not clear how these transitions are regulated in complex cell populations, in which cells receive multiple inputs. We address this issue using Dictyostelium cells undergoing development in their physiological niche. A continuous single cell transcriptomics time series identifies a sharp 'jump' in global gene expression marking functionally different cell states. By simultaneously imaging the physiological dynamics of transcription and signalling, we show the jump coincides with the onset of collective oscillations of cAMP. Optogenetic control of cAMP pulses shows that different jump genes respond to distinct dynamic features of signalling. Late jump gene expression changes are almost completely dependent on cAMP, whereas transcript changes at the onset of the jump require additional input. The coupling of collective signalling with gene expression is a potentially powerful strategy to drive robust cell state transitions in heterogeneous signalling environments. Based on the context of the jump, we also conclude that sharp gene expression transitions may not be sufficient for commitment.
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Affiliation(s)
- Elizabeth R. Westbrook
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Tchern Lenn
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jonathan R. Chubb
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Vlatka Antolović
- UCL Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
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10
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Hadwiger JA, Aranda RG, Fatima S. Atypical MAP kinases - new insights and directions from amoeba. J Cell Sci 2023; 136:jcs261447. [PMID: 37850857 PMCID: PMC10617611 DOI: 10.1242/jcs.261447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) have been the focus of many studies over the past several decades, but the understanding of one subgroup of MAPKs, orthologs of MAPK15, known as atypical MAPKs, has lagged behind others. In most organisms, specific activating signals or downstream responses of atypical MAPK signaling pathways have not yet been identified even though these MAPKs are associated with many eukaryotic processes, including cancer and embryonic development. In this Review, we discuss recent studies that are shedding new light on both the regulation and function of atypical MAPKs in different organisms. In particular, the analysis of the atypical MAPK in the amoeba Dictyostelium discoideum has revealed important roles in chemotactic responses and gene regulation. The rapid and transient phosphorylation of the atypical MAPK in these responses suggest a highly regulated activation mechanism in vivo despite the ability of atypical MAPKs to autophosphorylate in vitro. Atypical MAPK function can also impact the activation of other MAPKs in amoeba. These advances are providing new perspectives on possible MAPK roles in animals that have not been previously considered, and this might lead to the identification of potential targets for regulating cell movement in the treatment of diseases.
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Affiliation(s)
- Jeffrey A. Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
| | - Ramee G. Aranda
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
| | - Saher Fatima
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
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11
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Yamamoto T, Tsuge T, Araki M, Maeda M. Cyclic AMP (cAMP)-dependent proteolysis of GATA6 by proteasome: Zinc-finger domain of GATA6 has signals for nuclear export and proteolysis, both of which are responsive to cAMP. Drug Discov Ther 2023; 17:1-9. [PMID: 36740253 DOI: 10.5582/ddt.2022.01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcription factor GATA6 stably expressed in Chinese hamster ovary (CHO)-K1 cells is exported from the nucleus to the cytoplasm and degraded there by proteasome upon treatment with dibutylyl-cyclic AMP (dbcAMP), which is a membrane-permeable cyclic AMP (cAMP) analogue. The cAMP-dependent proteolysis of GATA6 was characterized by dissection of the GATA6 protein into a zinc-finger domain (Zf) and the surrounding region (ΔZf). These segments were separately expressed in CHO-K1 cells stably, and followed by treatment with dbcAMP. The nuclear localized Zf was degraded by proteasome similarly to the full-length GATA6. Site-directed mutants of nuclear localizing signal (NLS) (345RKRKPK350 → AAAAPK and AAAAPA) and closely related GATA4 showed the same behavior. Although nuclear-localized ΔZf was degraded by proteasome, the cytoplasmic-located ΔZf was resistant to proteolysis in contrast to the NLS mutants. We also searched for a potential NLS and nuclear export signal (NES) with computational prediction programs and compared the results with ours. All these results suggest that the amino acid sequence(s) of the Zf of GATA6 is responsive to cAMP-dependent nuclear export and proteolysis.
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Affiliation(s)
- Tomohisa Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Takeshi Tsuge
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | | | - Masatomo Maeda
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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12
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Ford HZ, Manhart A, Chubb JR. Controlling periodic long-range signalling to drive a morphogenetic transition. eLife 2023; 12:83796. [PMID: 36856269 PMCID: PMC10027319 DOI: 10.7554/elife.83796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/28/2023] [Indexed: 03/02/2023] Open
Abstract
Cells use signal relay to transmit information across tissue scales. However, the production of information carried by signal relay remains poorly characterised. To determine how the coding features of signal relay are generated, we used the classic system for long-range signalling: the periodic cAMP waves that drive Dictyostelium collective migration. Combining imaging and optogenetic perturbation of cell signalling states, we find that migration is triggered by an increase in wave frequency generated at the signalling centre. Wave frequency is regulated by cAMP wave circulation, which organises the long-range signal. To determine the mechanisms modulating wave circulation, we combined mathematical modelling, the general theory of excitable media, and mechanical perturbations to test competing models. Models in which cell density and spatial patterning modulate the wave frequency cannot explain the temporal evolution of signalling waves. Instead, our evidence leads to a model where wave circulation increases the ability for cells to relay the signal, causing further increase in the circulation rate. This positive feedback between cell state and signalling pattern regulates the long-range signal coding that drives morphogenesis.
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Affiliation(s)
- Hugh Z Ford
- Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Angelika Manhart
- Department of Mathematics, University College London, London, United Kingdom
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Jonathan R Chubb
- Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, United Kingdom
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13
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Levesque MV, Hla T. Signal Transduction and Gene Regulation in the Endothelium. Cold Spring Harb Perspect Med 2023; 13:a041153. [PMID: 35667710 PMCID: PMC9722983 DOI: 10.1101/cshperspect.a041153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Extracellular signals act on G-protein-coupled receptors (GPCRs) to regulate homeostasis and adapt to stress. This involves rapid intracellular post-translational responses and long-lasting gene-expression changes that ultimately determine cellular phenotype and fate changes. The lipid mediator sphingosine 1-phosphate (S1P) and its receptors (S1PRs) are examples of well-studied GPCR signaling axis essential for vascular development, homeostasis, and diseases. The biochemical cascades involved in rapid S1P signaling are well understood. However, gene-expression regulation by S1PRs are less understood. In this review, we focus our attention to how S1PRs regulate nuclear chromatin changes and gene transcription to modulate vascular and lymphatic endothelial phenotypic changes during embryonic development and adult homeostasis. Because S1PR-targeted drugs approved for use in the treatment of autoimmune diseases cause substantial vascular-related adverse events, these findings are critical not only for general understanding of stimulus-evoked gene regulation in the vascular endothelium, but also for therapeutic development of drugs for autoimmune and perhaps vascular diseases.
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Affiliation(s)
- Michel V Levesque
- Vascular Biology Program, Boston Children's Hospital and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Timothy Hla
- Vascular Biology Program, Boston Children's Hospital and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Hadwiger JA, Cai H, Aranda RG, Fatima S. An atypical MAPK regulates translocation of a GATA transcription factor in response to chemoattractant stimulation. J Cell Sci 2022; 135:jcs260148. [PMID: 35916164 PMCID: PMC9481928 DOI: 10.1242/jcs.260148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
The Dictyostelium atypical mitogen-activated protein kinase (MAPK) Erk2 is required for chemotactic responses to cAMP as amoeba undergo multicellular development. In this study, Erk2 was found to be essential for the cAMP-stimulated translocation of the GATA transcription factor GtaC as indicated by the distribution of a GFP-GtaC reporter. Erk2 was also found to be essential for the translocation of GtaC in response to external folate, a foraging signal that directs the chemotaxis of amoeba to bacteria. Erk1, the only other Dictyostelium MAPK, was not required for the GtaC translocation to either chemoattractant, indicating that GFP-GtaC is a kinase translocation reporter specific for atypical MAPKs. The translocation of GFP-GtaC in response to folate was absent in mutants lacking the folate receptor Far1 or the coupled G-protein subunit Gα4. Loss of GtaC function resulted in enhanced chemotactic movement to folate, suggesting that GtaC suppresses responses to folate. The alteration of four Erk2-preferred phosphorylation sites in GtaC impacted the translocation of GFP-GtaC in response to folate and the GFP-GtaC-mediated rescue of aggregation and development of gtaC- cells. The ability of different chemoattractants to stimulate Erk2-regulated GtaC translocation suggests that atypical MAPK-mediated regulation of transcription factors can contribute to different cell fates.
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Affiliation(s)
- Jeffrey A. Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Ramee G. Aranda
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
| | - Saher Fatima
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, USA
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15
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Ogasawara T, Watanabe J, Adachi R, Ono Y, Kamimura Y, Muramoto T. CRISPR/Cas9-based genome-wide screening of Dictyostelium. Sci Rep 2022; 12:11215. [PMID: 35780186 PMCID: PMC9250498 DOI: 10.1038/s41598-022-15500-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
Genome-wide screening is powerful method used to identify genes and pathways associated with a phenotype of interest. The simple eukaryote Dictyostelium discoideum has a unique life cycle and is often used as a crucial research model for a wide range of biological processes and rare metabolites. To address the inadequacies of conventional genetic screening approaches, we developed a highly efficient CRISPR/Cas9-based genome-wide screening system for Dictyostelium. A genome-wide library of 27,405 gRNAs and a kinase library of 4,582 gRNAs were compiled and mutant pools were generated. The resulting mutants were screened for defects in cell growth and more than 10 candidate genes were identified. Six of these were validated and five recreated mutants presented with growth abnormalities. Finally, the genes implicated in developmental defects were screened to identify the unknown genes associated with a phenotype of interest. These findings demonstrate the potential of the CRISPR/Cas9 system as an efficient genome-wide screening method.
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Affiliation(s)
- Takanori Ogasawara
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Jun Watanabe
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Remi Adachi
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yusuke Ono
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yoichiro Kamimura
- Laboratory for Cell Signaling Dynamics, RIKEN, Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan
| | - Tetsuya Muramoto
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
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16
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Zhang Y, Lu Y, El Sayyed H, Bian J, Lin J, Li X. Transcription factor dynamics in plants: Insights and technologies for in vivo imaging. PLANT PHYSIOLOGY 2022; 189:23-36. [PMID: 35134239 PMCID: PMC9070795 DOI: 10.1093/plphys/kiac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Biochemical and genetic approaches have been extensively used to study transcription factor (TF) functions, but their dynamic behaviors and the complex ways in which they regulate transcription in plant cells remain unexplored, particularly behaviors such as translocation and binding to DNA. Recent developments in labeling and imaging techniques provide the necessary sensitivity and resolution to study these behaviors in living cells. In this review, we present an up-to-date portrait of the dynamics and regulation of TFs under physiologically relevant conditions and then summarize recent advances in fluorescent labeling strategies and imaging techniques. We then discuss future prospects and challenges associated with the application of these techniques to examine TFs' intricate dance in living plants.
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Affiliation(s)
- Yuan Zhang
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yuqing Lu
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Jiahui Bian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
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17
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Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression. Cell Syst 2022; 13:353-364.e6. [PMID: 35298924 DOI: 10.1016/j.cels.2022.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/18/2021] [Accepted: 02/17/2022] [Indexed: 12/27/2022]
Abstract
Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling edge pulse detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.
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18
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Li D, Sun F, Yang Y, Tu H, Cai H. Gradients of PI(4,5)P2 and PI(3,5)P2 Jointly Participate in Shaping the Back State of Dictyostelium Cells. Front Cell Dev Biol 2022; 10:835185. [PMID: 35186938 PMCID: PMC8855053 DOI: 10.3389/fcell.2022.835185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Polarity, which refers to the molecular or structural asymmetry in cells, is essential for diverse cellular functions. Dictyostelium has proven to be a valuable system for dissecting the molecular mechanisms of cell polarity. Previous studies in Dictyostelium have revealed a range of signaling and cytoskeletal proteins that function at the leading edge to promote pseudopod extension and migration. In contrast, how proteins are localized to the trailing edge is not well understood. By screening for asymmetrically localized proteins, we identified a novel trailing-edge protein we named Teep1. We show that a charged surface formed by two pleckstrin homology (PH) domains in Teep1 is necessary and sufficient for targeting it to the rear of cells. Combining biochemical and imaging analyses, we demonstrate that Teep1 interacts preferentially with PI(4,5)P2 and PI(3,5)P2in vitro and simultaneous elimination of these lipid species in cells blocks the membrane association of Teep1. Furthermore, a leading-edge localized myotubularin phosphatase likely mediates the removal of PI(3,5)P2 from the front, as well as the formation of a back-to-front gradient of PI(3,5)P2. Together our data indicate that PI(4,5)P2 and PI(3,5)P2 on the plasma membrane jointly participate in shaping the back state of Dictyostelium cells.
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Affiliation(s)
- Dong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Feifei Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yihong Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hui Tu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Huaqing Cai,
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19
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Adhikari N, McGill IN, Hadwiger JA. MAPK docking motif in the Dictyostelium Gα2 subunit is required for aggregation and transcription factor translocation. Cell Signal 2021; 87:110117. [PMID: 34418534 DOI: 10.1016/j.cellsig.2021.110117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/05/2023]
Abstract
Some G protein alpha subunits contain a mitogen-activated protein kinase (MAPK) docking motif (D-motif) near the amino terminus that can impact cellular responses to external signals. The Dictyostelium Gα2 G protein subunit is required for chemotaxis to cAMP during the onset of multicellular development and this subunit contains a putative D-motif near the amino terminus. The Gα2 subunit D-motif was altered to examine its potential role in chemotaxis and multicellular development. In gα2- cells the expression of the D-motif mutant (Gα2D-) or wild-type subunit from high copy number vectors rescued cell aggregation but blocked the transition of mounds into slugs. This phenotype was also observed in parental strains with a wild-type gα2 locus indicating that the heterologous Gα2 subunit expression interferes with multicellular morphogenesis. Expression of the Gα2D- subunit from a low copy number vectors in gα2- cells did not rescue aggregation whereas the wild-type Gα2 subunit rescued aggregation efficiently and allowed wild-type morphological development. The Gα2D- and Gα2 subunit were both capable of restoring comparable levels of cAMP stimulated motility and the ability to co-aggregate with wild-type cells implying that the aggregation defect of Gα2D- expressing cells is due to insufficient intercellular signaling. Expression of the Gα2 subunit but not the Gα2D- subunit fully restored the ability of cAMP to stimulate the translocation of the GtaC transcription factor suggesting the D-motif is important for transcription factor regulation. These results suggest that the D-motif of Gα2 plays a role in aggregation and other developmental responses involved with cAMP signaling.
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Affiliation(s)
- Nirakar Adhikari
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Imani N McGill
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Jeffrey A Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America.
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20
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Katoh-Kurasawa M, Hrovatin K, Hirose S, Webb A, Ho HI, Zupan B, Shaulsky G. Transcriptional milestones in Dictyostelium development. Genome Res 2021; 31:1498-1511. [PMID: 34183452 PMCID: PMC8327917 DOI: 10.1101/gr.275496.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/23/2021] [Indexed: 02/02/2023]
Abstract
Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly coregulated with cell division genes, so they are expressed in mid-development although chromosomal DNA is not replicated. Our data set includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We show its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The data set is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Karin Hrovatin
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Shigenori Hirose
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Webb
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hsing-I Ho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Blaž Zupan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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21
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Yang Y, Li D, Chao X, Singh SP, Thomason P, Yan Y, Dong M, Li L, Insall RH, Cai H. Leep1 interacts with PIP3 and the Scar/WAVE complex to regulate cell migration and macropinocytosis. J Cell Biol 2021; 220:212090. [PMID: 33978708 PMCID: PMC8127007 DOI: 10.1083/jcb.202010096] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/23/2021] [Accepted: 04/21/2021] [Indexed: 12/20/2022] Open
Abstract
Polarity is essential for diverse functions in many cell types. Establishing polarity requires targeting a network of specific signaling and cytoskeleton molecules to different subregions of the cell, yet the full complement of polarity regulators and how their activities are integrated over space and time to form morphologically and functionally distinct domains remain to be uncovered. Here, by using the model system Dictyostelium and exploiting the characteristic chemoattractant-stimulated translocation of polarly distributed molecules, we developed a proteomic screening approach, through which we identified a leucine-rich repeat domain–containing protein we named Leep1 as a novel polarity regulator. We combined imaging, biochemical, and phenotypic analyses to demonstrate that Leep1 localizes selectively at the leading edge of cells by binding to PIP3, where it modulates pseudopod and macropinocytic cup dynamics by negatively regulating the Scar/WAVE complex. The spatiotemporal coordination of PIP3 signaling, Leep1, and the Scar/WAVE complex provides a cellular mechanism for organizing protrusive structures at the leading edge.
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Affiliation(s)
- Yihong Yang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dong Li
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoting Chao
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shashi P Singh
- Cancer Research UK Beatson Institute, Glasgow, UK.,University of Glasgow Institute of Cancer Sciences, Glasgow, UK
| | - Peter Thomason
- Cancer Research UK Beatson Institute, Glasgow, UK.,University of Glasgow Institute of Cancer Sciences, Glasgow, UK
| | - Yonghong Yan
- National Institute of Biological Sciences, Beijing, China
| | - Mengqiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Robert H Insall
- Cancer Research UK Beatson Institute, Glasgow, UK.,University of Glasgow Institute of Cancer Sciences, Glasgow, UK
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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22
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A tunable population timer in multicellular consortia. iScience 2021; 24:102347. [PMID: 33898944 PMCID: PMC8059065 DOI: 10.1016/j.isci.2021.102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Accepted: 03/17/2021] [Indexed: 11/26/2022] Open
Abstract
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits. However, such systems are difficult to implement in single cells due to saturation in molecular components and stochasticity in the limited intracellular space. In contrast, multicellular implementations outsource some of the components of information-processing circuits to the extracellular space, potentially escaping these constraints. Here, we develop a theoretical framework, based on trilinear coordinate representation, to study the collective behavior of populations composed of three cell types under stationary conditions. This framework reveals that distributing different processes (in our case the production, detection and degradation of a time-encoding signal) across distinct strains enables the implementation of a multicellular timer. Our analysis also shows that the circuit can be easily tunable by varying the cellular composition of the consortium. We propose a chemical wire architecture for distributed biological computation Our model predicts how input signals can be restored or modulated in the output Chemical wires can store temporal information and the system can act as a timer Digital periodic input signals can be filtered by altering the strain ratios
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23
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Kundert P, Sarrion-Perdigones A, Gonzalez Y, Katoh-Kurasawa M, Hirose S, Lehmann P, Venken KJT, Shaulsky G. A GoldenBraid cloning system for synthetic biology in social amoebae. Nucleic Acids Res 2020; 48:4139-4146. [PMID: 32232356 PMCID: PMC7192589 DOI: 10.1093/nar/gkaa185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
GoldenBraid is a rapid, modular, and robust cloning system used to assemble and combine genetic elements. Dictyostelium amoebae represent an intriguing synthetic biological chassis with tractable applications in development, chemotaxis, bacteria–host interactions, and allorecognition. We present GoldenBraid as a synthetic biological framework for Dictyostelium, including a library of 250 DNA parts and assemblies and a proof-of-concept strain that illustrates cAMP-chemotaxis with four fluorescent reporters coded by one plasmid.
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Affiliation(s)
- Peter Kundert
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shigenori Hirose
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Peter Lehmann
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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24
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Nichols JME, Antolović V, Reich JD, Brameyer S, Paschke P, Chubb JR. Cell and molecular transitions during efficient dedifferentiation. eLife 2020; 9:e55435. [PMID: 32255425 PMCID: PMC7190356 DOI: 10.7554/elife.55435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023] Open
Abstract
Dedifferentiation is a critical response to tissue damage, yet is not well understood, even at a basic phenomenological level. Developing Dictyostelium cells undergo highly efficient dedifferentiation, completed by most cells within 24 hr. We use this rapid response to investigate the control features of dedifferentiation, combining single cell imaging with high temporal resolution transcriptomics. Gene expression during dedifferentiation was predominantly a simple reversal of developmental changes, with expression changes not following this pattern primarily associated with ribosome biogenesis. Mutation of genes induced early in dedifferentiation did not strongly perturb the reversal of development. This apparent robustness may arise from adaptability of cells: the relative temporal ordering of cell and molecular events was not absolute, suggesting cell programmes reach the same end using different mechanisms. In addition, although cells start from different fates, they rapidly converged on a single expression trajectory. These regulatory features may contribute to dedifferentiation responses during regeneration.
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Affiliation(s)
- John ME Nichols
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Vlatka Antolović
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jacob D Reich
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | | | - Peggy Paschke
- CRUK Beatson Institute, Garscube Estate, Switchback Road, BearsdenGlasgowUnited Kingdom
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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25
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Ferreira F, Luxardi G, Reid B, Ma L, Raghunathan V, Zhao M. Real-time physiological measurements of oxygen using a non-invasive self-referencing optical fiber microsensor. Nat Protoc 2020; 15:207-235. [PMID: 31925402 PMCID: PMC7980673 DOI: 10.1038/s41596-019-0231-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 07/31/2019] [Indexed: 12/21/2022]
Abstract
Reactive molecular oxygen (O2) plays important roles in bioenergetics and metabolism and is implicated in biochemical pathways underlying angiogenesis, fertilization, wound healing and regeneration. Here we describe how to use the scanning micro-optrode technique (SMOT) to measure extracellular fluxes of dissolved O2. The self-referencing O2-specific micro-optrode (also termed micro-optode and optical fiber microsensor) is a tapered optical fiber with an O2-sensitive fluorophore coated onto the tip. The O2 concentration is quantified by fluorescence quenching of the fluorophore emission upon excitation with blue-green light. The micro-optrode presents high spatial and temporal resolutions with improved signal-to-noise ratio (in the picomole range). In this protocol, we provide step-by-step instructions for micro-optrode calibration, validation, example applications and data analysis. We describe how to use the technique for cells (Xenopus oocyte), tissues (Xenopus epithelium and rat cornea), organs (Xenopus gills and mouse skin) and appendages (Xenopus tail), and provide recommendations on how to adapt the approach to different model systems. The basic, user-friendly system presented here can be readily installed to reliably and accurately measure physiological O2 fluxes in a wide spectrum of biological models and physiological responses. The full protocol can be performed in ~4 h.
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Affiliation(s)
- Fernando Ferreira
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Davis, CA, USA.
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia, Universidade do Minho, Braga, Portugal.
| | - Guillaume Luxardi
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Davis, CA, USA
| | - Brian Reid
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Davis, CA, USA
| | - Li Ma
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Davis, CA, USA
- Skin and Cosmetic Research Department, Shanghai Skin Disease Hospital, Shanghai, China
| | - VijayKrishna Raghunathan
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
- The Ocular Surface Institute, College of Optometry, University of Houston, Houston, TX, USA
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Min Zhao
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Davis, CA, USA.
- Department of Ophthalmology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA, USA.
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26
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mTORC1/AMPK responses define a core gene set for developmental cell fate switching. BMC Biol 2019; 17:58. [PMID: 31319820 PMCID: PMC6637605 DOI: 10.1186/s12915-019-0673-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background Kinases mTORC1 and AMPK act as energy sensors, controlling nutrient responses and cellular growth. Changes in nutrient levels affect diverse transcriptional networks, making it challenging to identify downstream paths that regulate cellular growth or a switch to development via nutrient variation. The life cycle of Dictyostelium presents an excellent model to study the mTORC1 signaling function for growth and development. Dictyostelium grow as single cells in nutrient-rich media, but, upon nutrient withdrawal, growth ceases and cells enter a program for multi-cell development. While nearly half the genome shows gene expression changes upon nutrient removal, we hypothesized that not all of these genes are required for the switch to program development. Through manipulation of mTORC1 activity alone, without nutrient removal, we focused on a core network of genes that are required for switching between growth and development for regulation of cell fate decisions. Results To identify developmentally essential genes, we sought ways to promote development in the absence of nutrient loss. We first examined the activities of mTORC1 and AMPK in Dictyostelium during phases of rapid growth and starvation-induced development and showed they exhibited reciprocal patterns of regulation under various conditions. Using these as initial readouts, we identified rich media conditions that promoted rapid cell growth but, upon mTORC1 inactivation by rapamycin, led to a growth/development switch. Examination of gene expression during cell fate switching showed that changes in expression of most starvation-regulated genes were not required for developmental induction. Approximately 1000 genes which become downregulated upon rapamycin treatment comprise a cellular growth network involving ribosome biogenesis, protein synthesis, and cell cycle processes. Conversely, the upregulation of ~ 500 genes by rapamycin treatment defines essential signaling pathways for developmental induction, and ~ 135 of their protein products intersect through the well-defined cAMP/PKA network. Many of the rapamycin-induced genes we found are currently unclassified, and mutation analyses of 5 such genes suggest a novel gene class essential for developmental regulation. Conclusions We show that manipulating activities of mTORC1/AMPK in the absence of nutrient withdrawal is sufficient for a growth-to-developmental fate switch in Dictyostelium, providing a means to identify transcriptional networks and signaling pathways essential for early development. Electronic supplementary material The online version of this article (10.1186/s12915-019-0673-1) contains supplementary material, which is available to authorized users.
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27
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Yang Y, Wu M. Rhythmicity and waves in the cortex of single cells. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0116. [PMID: 29632268 PMCID: PMC5904302 DOI: 10.1098/rstb.2017.0116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2017] [Indexed: 12/15/2022] Open
Abstract
Emergence of dynamic patterns in the form of oscillations and waves on the cortex of single cells is a fascinating and enigmatic phenomenon. Here we outline various theoretical frameworks used to model pattern formation with the goal of reducing complex, heterogeneous patterns into key parameters that are biologically tractable. We also review progress made in recent years on the quantitative and molecular definitions of these terms, which we believe have begun to transform single-cell dynamic patterns from a purely observational and descriptive subject to more mechanistic studies. Specifically, we focus on the nature of local excitable and oscillation events, their spatial couplings leading to propagating waves and the role of active membrane. Instead of arguing for their functional importance, we prefer to consider such patterns as basic properties of dynamic systems. We discuss how knowledge of these patterns could be used to dissect the structure of cellular organization and how the network-centric view could help define cellular functions as transitions between different dynamical states. Last, we speculate on how these patterns could encode temporal and spatial information. This article is part of the theme issue ‘Self-organization in cell biology’.
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Affiliation(s)
- Yang Yang
- Department of Biological Sciences, Centre for Bioimaging Sciences, Mechanobiology Institute, National University of Singapore, Singapore
| | - Min Wu
- Department of Biological Sciences, Centre for Bioimaging Sciences, Mechanobiology Institute, National University of Singapore, Singapore
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28
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Kin K, Forbes G, Cassidy A, Schaap P. Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells. BMC Genomics 2018; 19:764. [PMID: 30348074 PMCID: PMC6198379 DOI: 10.1186/s12864-018-5146-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here aim to retrace the nature and ancestry of the novel "cup" cells by comparing their transcriptome to that of other cell types. RESULTS RNA-Seq was performed on purified mature spore, stalk and cup cells and on vegetative amoebas. Clustering and phylogenetic analyses showed that cup cells were most similar to stalk cells, suggesting that they share a common ancestor. The affinity between cup and stalk cells was also evident from promoter-reporter studies of newly identified cell-type genes, which revealed late expression in cups of many stalk genes. However, GO enrichment analysis reveal the unexpected prominence of GTPase mediated signalling in cup cells, in contrast to enrichment of autophagy and cell wall synthesis related transcripts in stalk cells. Combining the cell type RNA-Seq data with developmental expression profiles revealed complex expression dynamics in each cell type as well as genes exclusively expressed during terminal differentiation. Most notable were nine related hssA-like genes that were highly and exclusively expressed in cup cells. CONCLUSIONS This study reveals the unique transcriptomes of the mature cup, stalk and spore cells of D. discoideum and provides insight into the ancestry of cup cells and roles in signalling that were not previously realized. The data presented in this study will serve as an important resource for future studies into the regulation and evolution of cell type specialization.
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Affiliation(s)
- Koryu Kin
- School of Life Sciences, University of Dundee, Angus, Dundee, DD15EH UK
| | - Gillian Forbes
- School of Life Sciences, University of Dundee, Angus, Dundee, DD15EH UK
| | - Andrew Cassidy
- Tayside Centre for Genomic Analysis, University of Dundee, Angus, Dundee, DD19SY UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Angus, Dundee, DD15EH UK
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29
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Ferreira F, Raghunathan V, Luxardi G, Zhu K, Zhao M. Early redox activities modulate Xenopus tail regeneration. Nat Commun 2018; 9:4296. [PMID: 30327466 PMCID: PMC6191437 DOI: 10.1038/s41467-018-06614-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/10/2018] [Indexed: 12/15/2022] Open
Abstract
Redox state sustained by reactive oxygen species (ROS) is crucial for regeneration; however, the interplay between oxygen (O2), ROS and hypoxia-inducible factors (HIF) remains elusive. Here we observe, using an optic-based probe (optrode), an elevated and steady O2 influx immediately upon amputation. The spatiotemporal O2 influx profile correlates with the regeneration of Xenopus laevis tadpole tails. Inhibition of ROS production but not ROS scavenging decreases O2 influx. Inhibition of HIF-1α impairs regeneration and stabilization of HIF-1α induces regeneration in the refractory period. In the regeneration bud, hypoxia correlates with O2 influx, ROS production, and HIF-1α stabilization that modulate regeneration. Further analyses reveal that heat shock protein 90 is a putative downstream target of HIF-1α while electric current reversal is a de facto downstream target of HIF-1α. Collectively, the results show a mechanism for regeneration via the orchestration of O2 influx, ROS production, and HIF-1α stabilization.
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Affiliation(s)
- Fernando Ferreira
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, 95616, CA, USA.
- Departamento de Biologia, Centro de Biologia Molecular e Ambiental (CBMA), Universidade do Minho, Braga, 4704, Portugal.
| | - VijayKrishna Raghunathan
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, 77204, TX, USA
- The Ocular Surface Institute, College of Optometry, University of Houston, Houston, 77204, TX, USA
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, 77204, TX, USA
| | - Guillaume Luxardi
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, 95616, CA, USA
| | - Kan Zhu
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, 95616, CA, USA
| | - Min Zhao
- Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, 95616, CA, USA.
- Department of Ophthalmology, Institute for Regenerative Cures, University of California, Davis, 95817, CA, USA.
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30
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Molenaar C, Weeks KL. Nucleocytoplasmic shuttling: The ins and outs of quantitative imaging. Clin Exp Pharmacol Physiol 2018; 45:1087-1094. [DOI: 10.1111/1440-1681.12969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 04/15/2018] [Accepted: 05/03/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Kate L Weeks
- Baker Heart and Diabetes Institute; Melbourne Victoria Australia
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31
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Shi X, Reimers JR. Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling. Sci Rep 2018; 8:2147. [PMID: 29391550 PMCID: PMC5795017 DOI: 10.1038/s41598-018-20466-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Analytical equations are derived depicting four possible scenarios resulting from pulsed signaling of a system subject to Hill-type dynamics. Pulsed Hill-type dynamics involves the binding of multiple signal molecules to a receptor and occurs e.g., when transcription factor p53 orchestrates cancer prevention, during calcium signaling, and during circadian rhythms. The scenarios involve: (i) enhancement of high-affinity binders compared to low-affinity ones, (ii) slowing reactions involving high-affinity binders, (iii) transfer of the clocking of low-affinity binders from the signal molecule to the products, and (iv) a unique clocking process that produces incremental increases in the activity of high-affinity binders with each signal pulse. In principle, these mostly non-linear effects could control cellular outcomes. An applications to p53 signaling is developed, with binding to most gene promoters identified as category (iii) responses. However, currently unexplained enhancement of high-affinity promoters such as CDKN1a (p21) by pulsed signaling could be an example of (i). In general, provision for all possible scenarios is required in the design of mathematical models incorporating pulsed Hill-type signaling as some aspect.
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Affiliation(s)
- Xiaomin Shi
- International Centre for Quantum and Molecular Structures and Mathematics Department, Shanghai University, Shanghai, 200444, China.
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and Physics Department, Shanghai University, Shanghai, 200444, China.
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, 2006, Australia.
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32
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Lacal Romero J, Shen Z, Baumgardner K, Wei J, Briggs SP, Firtel RA. The Dictyostelium GSK3 kinase GlkA coordinates signal relay and chemotaxis in response to growth conditions. Dev Biol 2018; 435:56-72. [PMID: 29355521 DOI: 10.1016/j.ydbio.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 12/21/2022]
Abstract
GSK3 plays a central role in orchestrating key biological signaling pathways, including cell migration. Here, we identify GlkA as a GSK3 family kinase with functions that overlap with and are distinct from those of GskA. We show that GlkA, as previously shown for GskA, regulates the cell's cytoskeleton through MyoII assembly and control of Ras and Rap1 function, leading to aberrant cell migration. However, there are both qualitative and quantitative differences in the regulation of Ras and Rap1 and their downstream effectors, including PKB, PKBR1, and PI3K, with glkA- cells exhibiting a more severe chemotaxis phenotype than gskA- cells. Unexpectedly, the severe glkA- phenotypes, but not those of gskA-, are only exhibited when cells are grown attached to a substratum but not in suspension, suggesting that GlkA functions as a key kinase of cell attachment signaling. Using proteomic iTRAQ analysis we show that there are quantitative differences in the pattern of protein expression depending on the growth conditions in wild-type cells. We find that GlkA expression affects the cell's proteome during vegetative growth and development, with many of these changes depending on whether the cells are grown attached to a substratum or in suspension. These changes include key cytoskeletal and signaling proteins known to be essential for proper chemotaxis and signal relay during the aggregation stage of Dictyostelium development.
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Affiliation(s)
- Jesus Lacal Romero
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Kimberly Baumgardner
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Jing Wei
- JadeBio, Inc., 505 Coast Boulevard South Suite 206, La Jolla, CA 92037, USA
| | - Steven P Briggs
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
| | - Richard A Firtel
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA.
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33
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Pittayakanchit W, Lu Z, Chew J, Rust MJ, Murugan A. Biophysical clocks face a trade-off between internal and external noise resistance. eLife 2018; 7:37624. [PMID: 29988019 PMCID: PMC6059770 DOI: 10.7554/elife.37624] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/23/2018] [Indexed: 01/27/2023] Open
Abstract
Many organisms use free running circadian clocks to anticipate the day night cycle. However, others organisms use simple stimulus-response strategies ('hourglass clocks') and it is not clear when such strategies are sufficient or even preferable to free running clocks. Here, we find that free running clocks, such as those found in the cyanobacterium Synechococcus elongatus and humans, can efficiently project out light intensity fluctuations due to weather patterns ('external noise') by exploiting their limit cycle attractor. However, such limit cycles are necessarily vulnerable to 'internal noise'. Hence, at sufficiently high internal noise, point attractor-based 'hourglass' clocks, such as those found in a smaller cyanobacterium with low protein copy number, Prochlorococcus marinus, can outperform free running clocks. By interpolating between these two regimes in a diverse range of oscillators drawn from across biology, we demonstrate biochemical clock architectures that are best suited to different relative strengths of external and internal noise.
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Affiliation(s)
- Weerapat Pittayakanchit
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
| | - Zhiyue Lu
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
| | - Justin Chew
- Medical Scientist Training Program, Pritzker School of MedicineUniversity of ChicagoChicagoUnited States
| | - Michael J Rust
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States,Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoUnited States
| | - Arvind Murugan
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
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34
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Pergolizzi B, Bozzaro S, Bracco E. G-Protein Dependent Signal Transduction and Ubiquitination in Dictyostelium. Int J Mol Sci 2017; 18:ijms18102180. [PMID: 29048338 PMCID: PMC5666861 DOI: 10.3390/ijms18102180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/20/2022] Open
Abstract
Signal transduction through G-protein-coupled receptors (GPCRs) is central for the regulation of virtually all cellular functions, and it has been widely implicated in human diseases. These receptors activate a common molecular switch that is represented by the heterotrimeric G-protein generating a number of second messengers (cAMP, cGMP, DAG, IP3, Ca2+ etc.), leading to a plethora of diverse cellular responses. Spatiotemporal regulation of signals generated by a given GPCR is crucial for proper signalling and is accomplished by a series of biochemical modifications. Over the past few years, it has become evident that many signalling proteins also undergo ubiquitination, a posttranslational modification that typically leads to protein degradation, but also mediates processes such as protein-protein interaction and protein subcellular localization. The social amoeba Dictyostelium discoideum has proven to be an excellent model to investigate signal transduction triggered by GPCR activation, as cAMP signalling via GPCR is a major regulator of chemotaxis, cell differentiation, and multicellular morphogenesis. Ubiquitin ligases have been recently involved in these processes. In the present review, we will summarize the most significant pathways activated upon GPCRs stimulation and discuss the role played by ubiquitination in Dictyostelium cells.
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Affiliation(s)
- Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Turin, AOUS. Luigi, 10043 Orbassano TO, Italy.
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Turin, AOUS. Luigi, 10043 Orbassano TO, Italy.
| | - Enrico Bracco
- Department of Oncology, University of Turin, AOU S. Luigi, 10043 Orbassano TO, Italy.
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35
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Chubb JR. Symmetry breaking in development and stochastic gene expression. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [DOI: 10.1002/wdev.284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/11/2017] [Accepted: 06/05/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Jonathan R. Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology; University College London; London UK
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36
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Antolović V, Miermont A, Corrigan AM, Chubb JR. Generation of Single-Cell Transcript Variability by Repression. Curr Biol 2017; 27:1811-1817.e3. [PMID: 28602650 PMCID: PMC5483230 DOI: 10.1016/j.cub.2017.05.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 12/02/2022]
Abstract
Gene expression levels vary greatly within similar cells, even within clonal cell populations [1]. These spontaneous expression differences underlie cell fate diversity in both differentiation and disease [2]. The mechanisms responsible for generating expression variability are poorly understood. Using single-cell transcriptomics, we show that transcript variability emerging during Dictyostelium differentiation is driven predominantly by repression rather than activation. The increased variability of repressed genes was observed over a broad range of expression levels, indicating that variability is actively imposed and not a passive statistical effect of the reduced numbers of molecules accompanying repression. These findings can be explained by a simple model of transcript production, with expression controlled by the frequency, rather than the magnitude, of transcriptional firing events. Our study reveals that the generation of differences between cells can be a direct consequence of the basic mechanisms of transcriptional regulation. Transcript variability during development is generated predominantly by repression Repression-derived variability can arise from frequency modulation of transcription Sub-populations of undifferentiated cells are primed to express developmental genes
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Affiliation(s)
- Vlatka Antolović
- Laboratory for Molecular Cell Biology and Division of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Agnes Miermont
- Laboratory for Molecular Cell Biology and Division of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Adam M Corrigan
- Laboratory for Molecular Cell Biology and Division of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jonathan R Chubb
- Laboratory for Molecular Cell Biology and Division of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development. G3-GENES GENOMES GENETICS 2017; 7:387-398. [PMID: 27932387 PMCID: PMC5295588 DOI: 10.1534/g3.116.037150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.
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38
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Pergolizzi B, Bracco E, Bozzaro S. A new HECT ubiquitin ligase regulating chemotaxis and development in Dictyostelium discoideum. J Cell Sci 2017; 130:551-562. [PMID: 28049717 DOI: 10.1242/jcs.194225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/04/2016] [Indexed: 01/10/2023] Open
Abstract
Cyclic AMP (cAMP) binding to G-protein-coupled receptors (GPCRs) orchestrates chemotaxis and development in Dictyostelium. By activating the RasC-TORC2-PKB (PKB is also known as AKT in mammals) module, cAMP regulates cell polarization during chemotaxis. TORC2 also mediates GPCR-dependent stimulation of adenylyl cyclase A (ACA), enhancing cAMP relay and developmental gene expression. Thus, mutants defective in the TORC2 Pia subunit (also known as Rictor in mammals) are impaired in chemotaxis and development. Near-saturation mutagenesis of a Pia mutant by random gene disruption led to selection of two suppressor mutants in which spontaneous chemotaxis and development were restored. PKB phosphorylation and chemotactic cell polarization were rescued, whereas Pia-dependent ACA stimulation was not restored but bypassed, leading to cAMP-dependent developmental gene expression. Knocking out the gene encoding the adenylylcyclase B (ACB) in the parental strain showed ACB to be essential for this process. The gene tagged in the suppressor mutants encodes a newly unidentified HECT ubiquitin ligase that is homologous to mammalian HERC1, but harbours a pleckstrin homology domain. Expression of the isolated wild-type HECT domain, but not a mutant HECT C5185S form, from this protein was sufficient to reconstitute the parental phenotype. The new ubiquitin ligase appears to regulate cell sensitivity to cAMP signalling and TORC2-dependent PKB phosphorylation.
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Affiliation(s)
- Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, Orbassano (TO) 10043, Italy
| | - Enrico Bracco
- Department of Oncology, University of Torino, AOU S. Luigi, Orbassano (TO) 10043, Italy
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, Orbassano (TO) 10043, Italy
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39
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Zhang C, Tsoi R, Wu F, You L. Processing Oscillatory Signals by Incoherent Feedforward Loops. PLoS Comput Biol 2016; 12:e1005101. [PMID: 27623175 PMCID: PMC5021367 DOI: 10.1371/journal.pcbi.1005101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/04/2016] [Indexed: 11/19/2022] Open
Abstract
From the timing of amoeba development to the maintenance of stem cell pluripotency, many biological signaling pathways exhibit the ability to differentiate between pulsatile and sustained signals in the regulation of downstream gene expression. While the networks underlying this signal decoding are diverse, many are built around a common motif, the incoherent feedforward loop (IFFL), where an input simultaneously activates an output and an inhibitor of the output. With appropriate parameters, this motif can exhibit temporal adaptation, where the system is desensitized to a sustained input. This property serves as the foundation for distinguishing input signals with varying temporal profiles. Here, we use quantitative modeling to examine another property of IFFLs—the ability to process oscillatory signals. Our results indicate that the system’s ability to translate pulsatile dynamics is limited by two constraints. The kinetics of the IFFL components dictate the input range for which the network is able to decode pulsatile dynamics. In addition, a match between the network parameters and input signal characteristics is required for optimal “counting”. We elucidate one potential mechanism by which information processing occurs in natural networks, and our work has implications in the design of synthetic gene circuits for this purpose. From circadian clocks to ultradian rhythms, oscillatory signals are found ubiquitously in nature. These oscillations are crucial in the regulation of cellular processes. While the fundamental design principles underlying the generation of these oscillations are extensively studied, the mechanisms for decoding these signals are underappreciated. With implications in both the basic understanding of how cells process temporal signals and the design of synthetic systems, we use quantitative modeling to probe one mechanism, the counting of pulses. We demonstrate the capability of an Incoherent Feedforward Loop motif for the differentiation between sustained and oscillatory input signals.
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Affiliation(s)
- Carolyn Zhang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail:
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40
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Schaap P. Evolution of developmental signalling in Dictyostelid social amoebas. Curr Opin Genet Dev 2016; 39:29-34. [PMID: 27318097 PMCID: PMC5113120 DOI: 10.1016/j.gde.2016.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/16/2016] [Accepted: 05/26/2016] [Indexed: 11/17/2022]
Abstract
Dictyostelia represent a tractable system to resolve the evolution of cell-type specialization, with some taxa differentiating into spores only, and other taxa with additionally one or up to four somatic cell types. One of the latter forms, Dictyostelium discoideum, is a popular model system for cell biology and developmental biology with key signalling pathways controlling cell-specialization being resolved recently. For the most dominant pathways, evolutionary origins were retraced to a stress response in the unicellular ancestor, while modifications in the ancestral pathway were associated with acquisition of multicellular complexity. This review summarizes our current understanding of developmental signalling in D. discoideum and its evolution.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, DD15EH Dundee, UK.
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41
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Fukujin F, Nakajima A, Shimada N, Sawai S. Self-organization of chemoattractant waves in Dictyostelium depends on F-actin and cell-substrate adhesion. J R Soc Interface 2016; 13:20160233. [PMID: 27358278 PMCID: PMC4938087 DOI: 10.1098/rsif.2016.0233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/01/2016] [Indexed: 12/25/2022] Open
Abstract
In the social amoeba Dictyostelium discoideum, travelling waves of extracellular cyclic adenosine monophosphate (cAMP) self-organize in cell populations and direct aggregation of individual cells to form multicellular fruiting bodies. In contrast to the large body of studies that addressed how movement of cells is determined by spatial and temporal cues encoded in the dynamic cAMP gradients, how cell mechanics affect the formation of a self-generated chemoattractant field has received less attention. Here, we show, by live cell imaging analysis, that the periodicity of the synchronized cAMP waves increases in cells treated with the actin inhibitor latrunculin. Detail analysis of the extracellular cAMP-induced transients of cytosolic cAMP (cAMP relay response) in well-isolated cells demonstrated that their amplitude and duration were markedly reduced in latrunculin-treated cells. Similarly, in cells strongly adhered to a poly-l-lysine-coated surface, the response was suppressed, and the periodicity of the population-level oscillations was markedly lengthened. Our results suggest that cortical F-actin is dispensable for the basic low amplitude relay response but essential for its full amplification and that this enhanced response is necessary to establish high-frequency signalling centres. The observed F-actin dependence may prevent aggregation centres from establishing in microenvironments that are incompatible with cell migration.
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Affiliation(s)
- Fumihito Fukujin
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Akihiko Nakajima
- Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Nao Shimada
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Sawai
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan PRESTO, Japan Science and Technology Agency, Kawaguchi-shi, Saitama 332-0012, Japan
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42
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Katoh-Kurasawa M, Santhanam B, Shaulsky G. The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium. J Cell Sci 2016; 129:1722-1733. [PMID: 26962009 DOI: 10.1242/jcs.181545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The GATA transcription factor GtaG is conserved in Dictyostelids and essential for terminal differentiation in Dictyostelium discoideum, but its function is not well understood. Here we show that gtaG is expressed in prestalk cells at the anterior region of fingers and in the extending stalk during culmination. The gtaG- phenotype is cell-autonomous in prestalk cells and non-cell-autonomous in prespore cells. Transcriptome analyses reveal that GtaG regulates prestalk gene expression during cell differentiation before culmination and is required for progression into culmination. GtaG-dependent genes include genetic suppressors of the Dd-STATa-defective phenotype as well as Dd-STATa target-genes, including extra cellular matrix genes. We show that GtaG may be involved in the production of two culmination-signaling molecules, cyclic di-GMP and the spore differentiation factor SDF-1 and that addition of c-di-GMP rescues the gtaG- culmination and spore formation deficiencies. We propose that GtaG is a regulator of terminal differentiation that functions in concert with Dd-STATa and controls culmination through regulating c-di-GMP and SDF-1 production in prestalk cells.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Balaji Santhanam
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
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43
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Nichols JME, Veltman D, Kay RR. Chemotaxis of a model organism: progress with Dictyostelium. Curr Opin Cell Biol 2015; 36:7-12. [DOI: 10.1016/j.ceb.2015.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/22/2015] [Accepted: 06/27/2015] [Indexed: 11/25/2022]
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44
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Du Q, Kawabe Y, Schilde C, Chen ZH, Schaap P. The Evolution of Aggregative Multicellularity and Cell-Cell Communication in the Dictyostelia. J Mol Biol 2015; 427:3722-33. [PMID: 26284972 PMCID: PMC5055082 DOI: 10.1016/j.jmb.2015.08.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/30/2015] [Accepted: 08/03/2015] [Indexed: 10/30/2022]
Abstract
Aggregative multicellularity, resulting in formation of a spore-bearing fruiting body, evolved at least six times independently amongst both eukaryotes and prokaryotes. Amongst eukaryotes, this form of multicellularity is mainly studied in the social amoeba Dictyostelium discoideum. In this review, we summarise trends in the evolution of cell-type specialisation and behavioural complexity in the four major groups of Dictyostelia. We describe the cell-cell communication systems that control the developmental programme of D. discoideum, highlighting the central role of cAMP in the regulation of cell movement and cell differentiation. Comparative genomic studies showed that the proteins involved in cAMP signalling are deeply conserved across Dictyostelia and their unicellular amoebozoan ancestors. Comparative functional analysis revealed that cAMP signalling in D. discoideum originated from a second messenger role in amoebozoan encystation. We highlight some molecular changes in cAMP signalling genes that were responsible for the novel roles of cAMP in multicellular development.
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Affiliation(s)
- Qingyou Du
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Yoshinori Kawabe
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Christina Schilde
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Zhi-Hui Chen
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
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45
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Hansen AS, Hao N, O'Shea EK. High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nat Protoc 2015; 10:1181-97. [PMID: 26158443 PMCID: PMC4593625 DOI: 10.1038/nprot.2015.079] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microfluidics coupled to quantitative time-lapse fluorescence microscopy is transforming our ability to control, measure and understand signaling dynamics in single living cells. Here we describe a pipeline that incorporates multiplexed microfluidic cell culture, automated programmable fluid handling for cell perturbation, quantitative time-lapse microscopy and computational analysis of time-lapse movies. We illustrate how this setup can be used to control the nuclear localization of the budding yeast transcription factor Msn2. By using this protocol, we generate oscillations of Msn2 localization and measure the dynamic gene expression response of individual genes in single cells. The protocol allows a single researcher to perform up to 20 different experiments in a single day, while collecting data for thousands of single cells. Compared with other protocols, the present protocol is relatively easy to adopt and of higher throughput. The protocol can be widely used to control and monitor single-cell signaling dynamics in other signal transduction systems in microorganisms.
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Affiliation(s)
- Anders S Hansen
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA. [3] Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Erin K O'Shea
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA. [3] Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA. [4] Department of Molecular and Cellular Biology, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA
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46
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Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium. Nat Commun 2015; 6:7551. [PMID: 26144553 PMCID: PMC4506546 DOI: 10.1038/ncomms8551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC is essential for developmental progression, decoding extracellular cAMP pulses during early development and may play a role in mediating cell-type differentiation at later stages. We find that GtaC exhibits temporally distinctive DNA-binding patterns concordant with each developmental stage. We identify direct GtaC targets and observe cotemporaneous GtaC-binding and developmental expression regulation. Our results suggest that GtaC regulates multiple physiological processes as Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Development involves dynamic transcriptional changes. By serial ChIP- and RNA-sequencing, here, the authors show that GtaC, a GATA type transcription factor, exhibits temporally distinctive DNA binding and regulation of gene expression concordant with the development in the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Balaji Santhanam
- 1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huaqing Cai
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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47
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Loomis WF. Genetic control of morphogenesis in Dictyostelium. Dev Biol 2015; 402:146-61. [PMID: 25872182 PMCID: PMC4464777 DOI: 10.1016/j.ydbio.2015.03.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/12/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
Abstract
Cells grow, move, expand, shrink and die in the process of generating the characteristic shapes of organisms. Although the structures generated during development of the social amoeba Dictyostelium discoideum look nothing like the structures seen in metazoan embryogenesis, some of the morphogenetic processes used in their making are surprisingly similar. Recent advances in understanding the molecular basis for directed cell migration, cell type specific sorting, differential adhesion, secretion of matrix components, pattern formation, regulation and terminal differentiation are reviewed. Genes involved in Dictyostelium aggregation, slug formation, and culmination of fruiting bodies are discussed.
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Affiliation(s)
- William F Loomis
- Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, United States.
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48
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Micali G, Aquino G, Richards DM, Endres RG. Accurate encoding and decoding by single cells: amplitude versus frequency modulation. PLoS Comput Biol 2015; 11:e1004222. [PMID: 26030820 PMCID: PMC4452646 DOI: 10.1371/journal.pcbi.1004222] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022] Open
Abstract
Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule encodes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biological systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in signaling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on bursts may be more common in signaling networks than in gene regulation. We then extend our model to multiple receptors, where continuous and bursty signaling are equivalent to AM and FM respectively, finding that AM is always more accurate. This implies that the reason some cells use FM is related to factors other than accuracy, such as the ability to coordinate expression of multiple genes or to implement threshold crossing mechanisms. Signals, and hence information, can generally be transmitted either by amplitude (AM) or frequency (FM) modulation, as used, for example, in the transmission of radio waves since the 1930s. Both types of modulation are known to play a role in biology with AM conventionally associated with signaling and gene expression, and FM used to reliably transmit electrical signals over large distances between neurons. Surprisingly, FM was recently also observed in gene regulation, making their roles less distinct than previously thought. Although the engineering advantages and disadvantages of AM and FM are well understood, the equivalent question in biological systems is still largely unsolved. Here, we propose a simple model of signaling by receptors (or ion channels) with subsequent gene regulation, thus implementing both AM and FM in different types of biological pathways. We then compare the accuracy in the production of target proteins. We find that FM can be more accurate than AM only for a single receptor with fast signaling, whereas AM is more accurate in slow gene regulation and with signaling by multiple receptors. Finally, we propose possible reasons that cells use FM despite the potential decrease in accuracy.
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Affiliation(s)
- Gabriele Micali
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
- Dipartimento di Fisica, Università degli Studi di Milano, Milano, Italy
| | - Gerardo Aquino
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
| | - David M. Richards
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
| | - Robert G. Endres
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
- * E-mail:
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49
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Zhou W, Zhao L, Jiang JQ, Jiang WF, Yang YQ, Qiu XB. A novel TBX5 loss-of-function mutation associated with sporadic dilated cardiomyopathy. Int J Mol Med 2015; 36:282-8. [PMID: 25963046 DOI: 10.3892/ijmm.2015.2206] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/07/2015] [Indexed: 01/08/2023] Open
Abstract
Dilated cardiomyopathy (DCM) represents the most prevalent form of primary cardiomyopathy, and is the most common reason for heart transplantation and a major cause of congestive heart failure. Aggregating evidence demonstrates that genetic defects are associated with DCM, and a great number of mutations in >50 genes have been linked to DCM. However, DCM is a genetically heterogeneous disorder and the genetic components underpinning DCM in a significant proportion of patients remain unknown. In the present study, the coding exons and flanking exon‑intron boundaries of the T-Box 5 (TBX5) gene, which encodes a T‑box transcription factor required for normal cardiac development, were sequenced in 146 unrelated patients with sporadic DCM. The functional characteristics of the mutant TBX5 were assayed in contrast to its wild‑type counterpart by using a dual‑luciferase reporter assay system. As a result, a novel heterozygous TBX5 mutation, p.A143T, was identified in a patient with sporadic DCM. The missense mutation, which was absent in 400 control chromosomes, altered the amino acid that was completely conserved evolutionarily among species. Biological analyses revealed that the A143T mutation of TBX5 was associated with significantly decreased transcriptional activity on the promoter of the target gene atrial natriuretic factor (ANF), when compared to its wild‑type counterpart. Furthermore, the A143T mutation abolished the synergistic activation of the ANF promoter between TBX5 and GATA binding protein 4 (GATA4), another crucial transcriptional factor for heart development. To the best of our knowledge, this is the first report on the association of a TBX5 loss‑of‑function mutation with an enhanced susceptibility to sporadic DCM, providing novel insight into the molecular mechanisms of the pathogenesis of DCM and suggesting potential implications for the prenatal prophylaxis and personalized treatment of this commonest primary myocardial disease.
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Affiliation(s)
- Wei Zhou
- Department of Emergency Medicine, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, P.R. China
| | - Lan Zhao
- Department of Cardiology, Yantaishan Hospital, Yantai, Shandong 264001, P.R. China
| | - Jin-Qi Jiang
- Department of Emergency Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Wei-Feng Jiang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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Iglesias PA, Shi C. Comparison of adaptation motifs: temporal, stochastic and spatial responses. IET Syst Biol 2015; 8:268-81. [PMID: 25478701 DOI: 10.1049/iet-syb.2014.0026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The cells' ability to adapt to changes in the external environment is crucial for the survival of many organisms. There are two broad classes of signalling networks that achieve perfect adaptation. Both rely on complementary regulation of the response by an external signal and an inhibitory process. In one class of systems, inhibition comes about from the response itself, closing a negative feedback (NFB) loop. In the other, the inhibition comes directly from the external signal in what is referred to as an incoherent feedforward (IFF) loop. Although both systems show adaptive behaviour to constant changes in the level of the stimulus, their response to other forms of stimuli can differ. Here the authors consider the respective response to various such disturbances, including ramp increases, removal of the stimulus and pulses. The authors also consider the effect of stochastic fluctuations in signalling that come about from the interaction of the signalling elements. Finally, the authors consider the possible effect of spatially varying signals. The authors show that both the NFB and the IFF motifs can be used to sense static spatial gradients, under a local excitation, global inhibition assumption. The results may help experimentalists develop protocols that can discriminate between the two adaptation motifs.
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Affiliation(s)
- Pablo A Iglesias
- Departments of Cell Biology, Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Changji Shi
- Department of Electrical and Computer Engineering, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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