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Fooladi H, Moradi P, Sharifi-Zarchi A, Hosein Khalaj B. Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization. Bioinformatics 2019; 35:4081-4088. [PMID: 30903147 DOI: 10.1093/bioinformatics/btz201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 02/09/2019] [Accepted: 03/20/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon. RESULTS Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape with cell-cell communication, in order to enable pattern and tissue formation. We have shown the sufficiency of a simple mechanism by using a minimal number of parameters in the model, in order to address a variety of experimental observations such as the formation of three germ layers and trophectoderm, responses to altered culture conditions and micropattern diameters and unexpected spotted forms of the germ layers under certain conditions. Moreover, we have tested different boundary conditions as well as various shapes, observing that the pattern is initiated from the boundary and gradually spreads towards the center. This model provides a basis for in-silico modeling of self-organization. AVAILABILITY AND IMPLEMENTATION https://github.com/HFooladi/Self_Organization. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hosein Fooladi
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
| | - Parsa Moradi
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Babak Hosein Khalaj
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
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Xu J, Wang AH, Oses-Prieto J, Makhijani K, Katsuno Y, Pei M, Yan L, Zheng YG, Burlingame A, Brückner K, Derynck R. Arginine Methylation Initiates BMP-Induced Smad Signaling. Mol Cell 2013; 51:5-19. [PMID: 23747011 PMCID: PMC3951972 DOI: 10.1016/j.molcel.2013.05.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 10/12/2012] [Accepted: 05/02/2013] [Indexed: 11/15/2022]
Abstract
Kinase activation and substrate phosphorylation commonly form the backbone of signaling cascades. Bone morphogenetic proteins (BMPs), a subclass of TGF-β family ligands, induce activation of their signaling effectors, the Smads, through C-terminal phosphorylation by transmembrane receptor kinases. However, the slow kinetics of Smad activation in response to BMP suggests a preceding step in the initiation of BMP signaling. We now show that arginine methylation, which is known to regulate gene expression, yet also modifies some signaling mediators, initiates BMP-induced Smad signaling. BMP-induced receptor complex formation promotes interaction of the methyltransferase PRMT1 with the inhibitory Smad6, resulting in Smad6 methylation and relocalization at the receptor, leading to activation of effector Smads through phosphorylation. PRMT1 is required for BMP-induced biological responses across species, as evidenced by the role of its ortholog Dart1 in BMP signaling during Drosophila wing development. Activation of signaling by arginine methylation may also apply to other signaling pathways.
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Affiliation(s)
- Jian Xu
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - A. Hongjun Wang
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Kalpana Makhijani
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Yoko Katsuno
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Ming Pei
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Leilei Yan
- Department of Chemistry, Georgia State University, Atlanta, GA30302-4098
| | - Y. George Zheng
- Department of Chemistry, Georgia State University, Atlanta, GA30302-4098
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Katja Brückner
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
| | - Rik Derynck
- Departments of Cell and Tissue Biology, and Anatomy, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143-0512. USA
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BMP2 and GDF5 induce neuronal differentiation through a Smad dependant pathway in a model of human midbrain dopaminergic neurons. Mol Cell Neurosci 2013; 56:263-71. [PMID: 23831389 DOI: 10.1016/j.mcn.2013.06.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/12/2023] Open
Abstract
Parkinson's disease is the second most common neurodegenerative disease, and is characterised by the progressive degeneration of the nigrostriatal dopaminergic (DA) system. Current treatments are symptomatic, and do not protect against the DA neuronal loss. One of the most promising treatment approaches is the application of neurotrophic factors to rescue the remaining population of nigrostriatal DA neurons. Therefore, the identification of new neurotrophic factors for midbrain DA neurons, and the subsequent elucidation of the molecular bases of their effects, are important. Two related members of the bone morphogenetic protein (BMP) family, BMP2 and growth differentiation factor 5 (GDF5), have been shown to have neurotrophic effects on midbrain DA neurons both in vitro and in vivo. However, the molecular (signalling pathway(s)) and cellular (direct neuronal or indirect via glial cells) mechanisms of their effects remain to be elucidated. Using the SH-SH5Y human neuronal cell line, as a model of human midbrain DA neurons, we have shown that GDF5 and BMP2 induce neurite outgrowth via a direct mechanism. Furthermore, we demonstrate that these effects are dependent on BMP type I receptor activation of canonical Smad 1/5/8 signalling.
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Arabidopsis nanodomain-delimited ABA signaling pathway regulates the anion channel SLAH3. Proc Natl Acad Sci U S A 2013; 110:8296-301. [PMID: 23630285 DOI: 10.1073/pnas.1211667110] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phytohormone abscisic acid (ABA) plays a key role in the plant response to drought stress. Hence, ABA-dependent gene transcription and ion transport is regulated by a variety of protein kinases and phosphatases. However, the nature of the membrane-delimited ABA signal transduction steps remains largely unknown. To gain insight into plasma membrane-bound ABA signaling, we identified sterol-dependent proteins associated with detergent resistant membranes from Arabidopsis thaliana mesophyll cells. Among those, we detected the central ABA signaling phosphatase ABI1 (abscisic-acid insensitive 1) and the calcium-dependent protein kinase 21 (CPK21). Using fluorescence microscopy, we found these proteins to localize in membrane nanodomains, as observed by colocalization with the nanodomain marker remorin Arabidopsis thaliana remorin 1.3 (AtRem 1.3). After transient coexpression, CPK21 interacted with SLAH3 [slow anion channel 1 (SLAC1) homolog 3] and activated this anion channel. Upon CPK21 stimulation, SLAH3 exhibited the hallmark properties of S-type anion channels. Coexpression of SLAH3/CPK21 with ABI1, however, prevented proper nanodomain localization of the SLAH3/CPK21 protein complex, and as a result anion channel activation failed. FRET studies revealed enhanced interaction of SLAH3 and CPK21 within the plasma membrane in response to ABA and thus confirmed our initial observations. Interestingly, the ABA-induced SLAH3/CPK21 interaction was modulated by ABI1 and the ABA receptor RCAR1/PYL9 [regulatory components of ABA receptor 1/PYR1 (pyrabactin resistance 1)-like protein 9]. We therefore propose that ABA signaling via inhibition of ABI1 modulates the apparent association of a signaling and transport complex within membrane domains that is necessary for phosphorylation and activation of the S-type anion channel SLAH3 by CPK21.
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Mi HW, Lee MC, Chiang YC, Chow LP, Lin CP. Single-Molecule Imaging of Bmp4 Dimerization on Human Periodontal Ligament Cells. J Dent Res 2011; 90:1318-24. [DOI: 10.1177/0022034511418340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We expressed bone morphogenetic protein 4 (BMP4) fused with enhanced green fluorescent protein (BMP4-EGFP) in the secretory pathways of producer cells. Fluorescent EGFP was acquired only after we interrupted the transport of BMP4-EGFP by culturing cells at a lower temperature (20°C), and the dynamics of BMP4-EGFP could be monitored by single-molecule microscopy. Western blotting analysis confirmed that exposure to low temperature helped the integrated formation of BMP4-EGFP fusion proteins. In this study, for the first time, we could image the fluorescently labeled BMP4 molecules localized on the plasma membrane of living hPDL cells. The one-step photobleaching with EGFP and the “blinking” behavior of quantum dots suggest that the fluorescent spots represent the events of single BMP4 molecules. Single-molecule tracking showed that the BMP receptors (BMPR) dimerize after BMP4 stimulation, or that a complex of one BMP4 molecule and a pre-formed BMPR dimer develops first, followed by the binding of the second BMP4 molecule. Furthermore, BMP4-EGFP enhanced the osteogenic differentiation of hPDL cells via signal transduction involving BMP receptors. This single-molecule imaging technique might be a valuable tool for the future development of BMP4 gene therapy and regenerative medicine mediated by hPDLs. Abbreviations: BMP4, bone morphogenetic protein 4; BMPR, BMP receptor; EGFP, enhanced green fluorescent protein; hPDL cells, human periodontal ligament cells; QDs, quantum dots; TIRFM, total internal reflection fluorescence microscopy; 293 cells, human embryonic kidney cells; oDM, osteogenic differentiation medium; HcoI, type I collagen; ALP, alkaline phosphatase; BSP, bone sialoprotein; GAPDH, glyceraldehyde-3-phosphate dehydrogenase.
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Affiliation(s)
- H.-W. Mi
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
| | - M.-C. Lee
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Y.-C. Chiang
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
| | - L.-P. Chow
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - C.-P. Lin
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
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Rotational diffusion of the α(2a) adrenergic receptor revealed by FlAsH labeling in living cells. Biophys J 2011; 100:1139-48. [PMID: 21320460 DOI: 10.1016/j.bpj.2010.08.080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/03/2010] [Accepted: 08/13/2010] [Indexed: 11/24/2022] Open
Abstract
The fluorescein arsenical hairpin binder (FlAsH) shows much promise to determine the relative orientations of protein regions and structures even in living cells and in the plasma membrane. In this study, we characterized FlAsH's photophysical properties by steady-state anisotropy and time-resolved single photon counting for further applications with G-protein coupled receptors. We find that FlAsH has a relatively high initial anisotropy of 0.31 ± 0.01 and a three-component fluorescence lifetime with an average of 4.1 ± 0.1 ns. We characterized the FlAsH fluorophore orientation in the α(2A) adrenergic receptor revealing rigid orientations of FlAsH in the membrane plane for rotational correlation times of ∼50 ns in living cells. To elucidate the fluorophore-membrane orientation and rotational correlation time, an anisotropy treatment similar to that of another researcher (Axelrod, D. 1979. Biophys. J. 26:557-573) was developed. The rotational correlation times were observed to increase by up to 16 ns after agonist addition. The rotational correlation time also allowed for a comparison to the theoretical relationship between translational and rotational diffusion (originally proposed by Saffman, P. G., and M. Delbrück. 1975. Proc. Natl. Acad. Sci. USA. 72:3111-3113) and revealed a discrepancy of a factor between 10 and 100.
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Wagner T, Kraeussling M, Fedorov L, Reiss C, Kneitz B, Schartl M. STAT3 and SMAD1 Signaling in Medaka Embryonic Stem-Like Cells and Blastula Embryos. Stem Cells Dev 2009; 18:151-60. [DOI: 10.1089/scd.2007.0262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T.U. Wagner
- University of Wurzburg, Physiological Chemistry I, Wurzburg, Germany
| | - M. Kraeussling
- University of Wurzburg, Physiological Chemistry I, Wurzburg, Germany
| | - L.M. Fedorov
- University of Wurzburg, Physiological Chemistry I, Wurzburg, Germany
| | - C. Reiss
- University of Wurzburg, Physiological Chemistry I, Wurzburg, Germany
| | - B. Kneitz
- Department of Urology and Paediatric Urology, Bavarian Julius Maximilians University Medical School, Wurzburg, Germany
| | - M. Schartl
- University of Wurzburg, Physiological Chemistry I, Wurzburg, Germany
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