1
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Biological feedback control-Respect the loops. Cell Syst 2021; 12:477-487. [PMID: 34139160 DOI: 10.1016/j.cels.2021.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022]
Abstract
We, and all organisms, are an evolutionary masterpiece of multiscale feedback control. Feedback loops enable our cells to grow and then stop at the right size, to divide and self-repair, and to respond with agility to their changing environment. Individual cells engage in long range extracellular feedback with other cells, ensuring continued homeostasis of our tissues and organs. Many long ranging feedback loops regulate vital physiological variables. Here, I will argue that focused efforts to understand the properties and constraints of biological feedback control networks should be central to the quest of understanding life. I will also propose many pressing challenges in this field and review conceptual frameworks that might be consequential for addressing them.
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2
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Patterson JO, Rees P, Nurse P. Noisy Cell-Size-Correlated Expression of Cyclin B Drives Probabilistic Cell-Size Homeostasis in Fission Yeast. Curr Biol 2019; 29:1379-1386.e4. [PMID: 30955932 PMCID: PMC6488275 DOI: 10.1016/j.cub.2019.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/07/2019] [Accepted: 03/11/2019] [Indexed: 02/08/2023]
Abstract
How cells correct deviations from a mean cell size at mitosis remains uncertain. Classical cell-size homeostasis models are the sizer, timer, and adder [1]. Sizers postulate that cells divide at some threshold size; timers, that cells grow for a set time; and adders, that cells add a constant volume before division. Here, we show that a size-based probabilistic model of cell-size control at the G2/M transition (P(Div)) can generate realistic cell-size homeostasis in silico. In fission yeast cells, Cyclin BCdc13 scales with size, and we propose that this increases the likelihood of mitotic entry, while molecular noise in its expression adds a probabilistic component to the model. Varying Cdc13 expression levels exogenously using a newly developed tetracycline inducible promoter shows that both the level and variability of its expression influence cell size at division. Our results demonstrate that as cells grow larger, their probability of dividing increases, and this is sufficient to generate cell-size homeostasis. Size-correlated Cdc13 expression forms part of the molecular circuitry of this system. A size-correlated division probability can generate cell-size homeostasis Cyclin B concentration scales noisily with size in fission yeast Cells with stochastically suprathreshold cyclin B are the ones that divide A new tetracycline inducible promoter with linear dose response is developed
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Affiliation(s)
- James O Patterson
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1ST, UK; College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea SA1 8EN, UK.
| | - Paul Rees
- College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea SA1 8EN, UK; Imaging Platform, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1ST, UK; Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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3
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Needham EJ, Parker BL, Burykin T, James DE, Humphrey SJ. Illuminating the dark phosphoproteome. Sci Signal 2019; 12:12/565/eaau8645. [PMID: 30670635 DOI: 10.1126/scisignal.aau8645] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein phosphorylation is a major regulator of protein function and biological outcomes. This was first recognized through functional biochemical experiments, and in the past decade, major technological advances in mass spectrometry have enabled the study of protein phosphorylation on a global scale. This rapidly growing field of phosphoproteomics has revealed that more than 100,000 distinct phosphorylation events occur in human cells, which likely affect the function of every protein. Phosphoproteomics has improved the understanding of the function of even the most well-characterized protein kinases by revealing new downstream substrates and biology. However, current biochemical and bioinformatic approaches have only identified kinases for less than 5% of the phosphoproteome, and functional assignments of phosphosites are almost negligible. Notably, our understanding of the relationship between kinases and their substrates follows a power law distribution, with almost 90% of phosphorylation sites currently assigned to the top 20% of kinases. In addition, more than 150 kinases do not have a single known substrate. Despite a small group of kinases dominating biomedical research, the number of substrates assigned to a kinase does not correlate with disease relevance as determined by pathogenic human mutation prevalence and mouse model phenotypes. Improving our understanding of the substrates targeted by all kinases and functionally annotating the phosphoproteome will be broadly beneficial. Advances in phosphoproteomics technologies, combined with functional screening approaches, should make it feasible to illuminate the connectivity and functionality of the entire phosphoproteome, providing enormous opportunities for discovering new biology, therapeutic targets, and possibly diagnostics.
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Affiliation(s)
- Elise J Needham
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Timur Burykin
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
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4
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Paul D, Radde N. The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs. J Theor Biol 2018; 455:86-96. [PMID: 30017944 DOI: 10.1016/j.jtbi.2018.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
Abstract
The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive. In this work we investigate the role of cascading for coping with intrinsic noise due to stochasticity in molecular reactions. We use stochastic approaches to quantify fluctuations in the terminal kinase of phosphorylation-dephosphorylation cascade motifs and demonstrate that cascading highly affects these fluctuations. We show that this purely stochastic effect can be explained by time-varying sequestration of upstream kinase molecules. In particular, we discuss conditions on time scales and parameter regimes which lead to a reduction of output fluctuations. Our results are put into biological context by adapting rate parameters of our modeling approach to biologically feasible ranges for general binding-unbinding and phosphorylation-dephosphorylation mechanisms. Overall, this study reveals a novel role of stochastic sequestration for dynamic noise filtering in signaling cascade motifs.
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Affiliation(s)
- Debdas Paul
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart 70569, Germany.
| | - Nicole Radde
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart 70569, Germany
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5
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Schwarz C, Johnson A, Kõivomägi M, Zatulovskiy E, Kravitz CJ, Doncic A, Skotheim JM. A Precise Cdk Activity Threshold Determines Passage through the Restriction Point. Mol Cell 2018; 69:253-264.e5. [PMID: 29351845 PMCID: PMC5790185 DOI: 10.1016/j.molcel.2017.12.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 11/24/2022]
Abstract
At the restriction point (R), mammalian cells irreversibly commit to divide. R has been viewed as a point in G1 that is passed when growth factor signaling initiates a positive feedback loop of Cdk activity. However, recent studies have cast doubt on this model by claiming R occurs prior to positive feedback activation in G1 or even before completion of the previous cell cycle. Here we reconcile these results and show that whereas many commonly used cell lines do not exhibit a G1 R, primary fibroblasts have a G1 R that is defined by a precise Cdk activity threshold and the activation of cell-cycle-dependent transcription. A simple threshold model, based solely on Cdk activity, predicted with more than 95% accuracy whether individual cells had passed R. That a single measurement accurately predicted cell fate shows that the state of complex regulatory networks can be assessed using a few critical protein activities.
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Affiliation(s)
- Clayton Schwarz
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Amy Johnson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andreas Doncic
- Department of Cell Biology & Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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6
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Oyler-Yaniv J, Oyler-Yaniv A, Shakiba M, Min NK, Chen YH, Cheng SY, Krichevsky O, Altan-Bonnet N, Altan-Bonnet G. Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation. Mol Cell 2017; 66:635-647.e7. [PMID: 28575659 PMCID: PMC6611463 DOI: 10.1016/j.molcel.2017.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/28/2017] [Accepted: 05/08/2017] [Indexed: 01/05/2023]
Abstract
Immune cells constantly survey the host for pathogens or tumors and secrete cytokines to alert surrounding cells of these threats. In vivo, activated immune cells secrete cytokines for several hours, yet an acute immune reaction occurs over days. Given these divergent timescales, we addressed how cytokine-responsive cells translate brief cytokine exposure into phenotypic changes that persist over long timescales. We studied melanoma cell responses to transient exposure to the cytokine interferon γ (IFNγ) by combining a systems-scale analysis of gene expression dynamics with computational modeling and experiments. We discovered that IFNγ is captured by phosphatidylserine (PS) on the surface of viable cells both in vitro and in vivo then slowly released to drive long-term transcription of cytokine-response genes. This mechanism introduces an additional function for PS in dynamically regulating inflammation across diverse cancer and primary cell types and has potential to usher in new immunotherapies targeting PS and inflammatory pathways.
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MESH Headings
- Animals
- Cell Communication
- Cell Line, Tumor
- Coculture Techniques
- Computational Biology
- Computer Simulation
- Databases, Genetic
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/metabolism
- Inflammation/pathology
- Inflammation Mediators/metabolism
- Interferon-gamma/immunology
- Interferon-gamma/metabolism
- Interleukin-12/immunology
- Interleukin-12/metabolism
- Interleukin-23/immunology
- Interleukin-23/metabolism
- Janus Kinases/metabolism
- Lymphocyte Activation
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Models, Biological
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/metabolism
- Phosphatidylserines/immunology
- Phosphatidylserines/metabolism
- Phosphorylation
- RAW 264.7 Cells
- Receptors, Interferon/genetics
- Receptors, Interferon/metabolism
- STAT1 Transcription Factor/metabolism
- Signal Transduction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/immunology
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Time Factors
- Transcription, Genetic
- Interferon gamma Receptor
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Affiliation(s)
- Jennifer Oyler-Yaniv
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alon Oyler-Yaniv
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Physics Department, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Mojdeh Shakiba
- Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Nina K Min
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ying-Han Chen
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Sheue-Yann Cheng
- Laboratory of Molecular Biology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Oleg Krichevsky
- Physics Department, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Kats Center for Nanoscience, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Grégoire Altan-Bonnet
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
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7
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Rodrigo G, Poyatos JF. Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits. PLoS Comput Biol 2016; 12:e1005156. [PMID: 27741249 PMCID: PMC5065233 DOI: 10.1371/journal.pcbi.1005156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/19/2016] [Indexed: 11/18/2022] Open
Abstract
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of multiple circuit copies. The result is due to the contribution of noise to the generation of autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors that correlate the responses of the redundant units (extrinsic noise or regulatory cross-talk) contribute to reduce fidelity, while those that further uncouple them (heterogeneity within the copies) can lead to stronger information gain. Overall, our study emphasizes how the interplay of signal thresholding, redundancy, and noise influences the accuracy of cellular decision making. Understanding this interplay provides a basis to explain collective cell signaling mechanisms, and to engineer robust decisions with noisy genetic circuits. There is increasing evidence that the presence of molecular noise greatly influences function in biological systems. This could imply, for instance, that genetic circuits adopt particular architectures in order to reduce noise. On the other hand, noise can be beneficial. Here, we show that this could be the case for the functioning of analog to digital genetic devices, which are commonly found in cellular decision making situations. We use the framework of information theory to illustrate first how noise can enhance information transfer in these devices. In those regimes in which noise is detrimental, we discuss how genetic redundancies allow information to be maximized, and how this effect depends on the specifics of the devices, and the interdependence among them. These results provide overall an additional rationale for genetic redundancies in genomic systems.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, CSIC–UPV, Valencia, Spain
| | - Juan F. Poyatos
- Logic of Genomic Systems Laboratory, CNB–CSIC, Madrid, Spain
- * E-mail:
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8
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Rubens JR, Selvaggio G, Lu TK. Synthetic mixed-signal computation in living cells. Nat Commun 2016; 7:11658. [PMID: 27255669 PMCID: PMC4895730 DOI: 10.1038/ncomms11658] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Living cells implement complex computations on the continuous environmental signals that they encounter. These computations involve both analogue- and digital-like processing of signals to give rise to complex developmental programs, context-dependent behaviours and homeostatic activities. In contrast to natural biological systems, synthetic biological systems have largely focused on either digital or analogue computation separately. Here we integrate analogue and digital computation to implement complex hybrid synthetic genetic programs in living cells. We present a framework for building comparator gene circuits to digitize analogue inputs based on different thresholds. We then demonstrate that comparators can be predictably composed together to build band-pass filters, ternary logic systems and multi-level analogue-to-digital converters. In addition, we interface these analogue-to-digital circuits with other digital gene circuits to enable concentration-dependent logic. We expect that this hybrid computational paradigm will enable new industrial, diagnostic and therapeutic applications with engineered cells. Digital and analogue gene circuits each have distinct advantages in natural and engineered cells. Here, Rubens et al. engineer synthetic gene circuits that implement mixed-signal digital and analogue computations in living cells.
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Affiliation(s)
- Jacob R Rubens
- Synthetic Biology Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Microbiology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Gianluca Selvaggio
- Synthetic Biology Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Computational and System Biology Group, Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Microbiology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts 02139, USA
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9
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Abstract
Cells of a given type maintain a characteristic cell size to function efficiently in their ecological or organismal context. They achieve this through the regulation of growth rates or by actively sensing size and coupling this signal to cell division. We focus this review on potential size-sensing mechanisms, including geometric, external cue, and titration mechanisms. Mechanisms that titrate proteins against DNA are of particular interest because they are consistent with the robust correlation of DNA content and cell size. We review the literature, which suggests that titration mechanisms may underlie cell-size sensing in Xenopus embryos, budding yeast, and Escherichia coli, whereas alternative mechanisms may function in fission yeast.
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Affiliation(s)
- Amanda A Amodeo
- Department of Biology, Stanford University, Stanford, California 94305
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, California 94305
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10
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English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal 2015; 8:ra5. [PMID: 25587192 DOI: 10.1126/scisignal.2005774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Signaling pathways can behave as switches or rheostats, generating binary or graded responses to a given cell stimulus. We evaluated whether a single signaling pathway can simultaneously encode a switch and a rheostat. We found that the kinase Hog1 mediated a bifurcated cellular response: Activation and commitment to adaptation to osmotic stress are switchlike, whereas protein induction and the resolution of this commitment are graded. Through experimentation, bioinformatics analysis, and computational modeling, we determined that graded recovery is encoded through feedback phosphorylation and a gene induction program that is both temporally staggered and variable across the population. This switch-to-rheostat signaling mechanism represents a versatile stress adaptation system, wherein a broad range of inputs generate an "all-in" response that is later tuned to allow graded recovery of individual cells over time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael Malahe
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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11
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12
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Krabbenborg SO, Huskens J. Electrochemically Generated Gradients. Angew Chem Int Ed Engl 2014; 53:9152-67. [DOI: 10.1002/anie.201310349] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/06/2023]
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13
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Tsuchiya D, Yang Y, Lacefield S. Positive feedback of NDT80 expression ensures irreversible meiotic commitment in budding yeast. PLoS Genet 2014; 10:e1004398. [PMID: 24901499 PMCID: PMC4046916 DOI: 10.1371/journal.pgen.1004398] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/03/2014] [Indexed: 01/03/2023] Open
Abstract
In budding yeast, meiotic commitment is the irreversible continuation of the developmental path of meiosis. After reaching meiotic commitment, cells finish meiosis and gametogenesis, even in the absence of the meiosis-inducing signal. In contrast, if the meiosis-inducing signal is removed and the mitosis-inducing signal is provided prior to reaching meiotic commitment, cells exit meiosis and return to mitosis. Previous work has shown that cells commit to meiosis after prophase I but before entering the meiotic divisions. Since the Ndt80 transcription factor induces expression of middle meiosis genes necessary for the meiotic divisions, we examined the role of the NDT80 transcriptional network in meiotic commitment. Using a microfluidic approach to analyze single cells, we found that cells commit to meiosis in prometaphase I, after the induction of the Ndt80-dependent genes. Our results showed that high-level expression of NDT80 is important for the timing and irreversibility of meiotic commitment. A modest reduction in NDT80 levels delayed meiotic commitment based on meiotic stages, although the timing of each meiotic stage was similar to that of wildtype cells. A further reduction of NDT80 resulted in the surprising finding of inappropriately uncommitted cells: withdrawal of the meiosis-inducing signal and addition of the mitosis-inducing signal to cells at stages beyond metaphase I caused return to mitosis, leading to multi-nucleate cells. Since Ndt80 enhances its own transcription through positive feedback, we tested whether positive feedback ensured the irreversibility of meiotic commitment. Ablating positive feedback in NDT80 expression resulted in a complete loss of meiotic commitment. These findings suggest that irreversibility of meiotic commitment is a consequence of the NDT80 transcriptional positive feedback loop, which provides the high-level of Ndt80 required for the developmental switch of meiotic commitment. These results also illustrate the importance of irreversible meiotic commitment for maintaining genome integrity by preventing formation of multi-nucleate cells.
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Affiliation(s)
- Dai Tsuchiya
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Yang Yang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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14
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Johnson A, Skotheim JM. Start and the restriction point. Curr Opin Cell Biol 2013; 25:717-23. [PMID: 23916770 DOI: 10.1016/j.ceb.2013.07.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/29/2013] [Accepted: 07/15/2013] [Indexed: 02/07/2023]
Abstract
Commitment to division requires that cells sense, interpret, and respond appropriately to multiple signals. In most eukaryotes, cells commit to division in G1 before DNA replication. Beyond a point, known as Start in yeast and the restriction point in mammals, cells will proceed through the cell cycle despite changes in upstream signals. In metazoans, misregulated G1 control can lead to developmental problems or disease, so it is important to understand how cells decipher the myriad external and internal signals that contribute to the fundamental all-or-none decision to divide. Extensive study of G1 control in the budding yeast Saccharomyces cerevisiae and mammalian culture systems has revealed highly similar networks regulating commitment. However, protein sequences of functional orthologs often indicate a total lack of conservation suggesting significant evolution of G1 control. Here, we review recent studies defining the conserved and diverged features of G1 control and highlight systems-level aspects that may be common to other biological regulatory networks.
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Affiliation(s)
- Amy Johnson
- Department of Biology, Stanford University, Stanford, CA 94305, United States
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15
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Wang S, Li Y, Hsu PH, Lee SY, Kim Y, Lee EYHP. Progesterone receptor A stability is mediated by glycogen synthase kinase-3β in the Brca1-deficient mammary gland. J Biol Chem 2013; 288:26265-26274. [PMID: 23880761 DOI: 10.1074/jbc.m113.476556] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Germ line mutations of the BRCA1 gene increase the risk of breast and ovarian cancer, but the basis of this tissue-specific tumor predisposition is not fully understood. Previously, we reported that the progesterone receptors are stabilized in Brca1-deficient mammary epithelial cells, and treating with anti-progesterone delays mammary tumorigenesis in Brca1/p53 conditional knock-out mice, suggesting that the progesterone has a critical role in breast carcinogenesis. To further explore how the stability of progesterone receptor is modulated, here, we have found that glycogen synthase kinase (GSK)-3β phosphorylation of progesterone receptor-A (PR-A) facilitates its ubiquitination. GSK-3β-mediated phosphorylation of serine 390 in PR-A regulates its subsequent ubiquitination and protein stability. Expression of PR-A(S390A) mutant in the human breast epithelial cells, MCF-10A, results in enhanced proliferation and formation of aberrant acini structure in the three-dimensional culture. Consistently, reduction of phosphorylation of serine 390 of PR-A and GSK-3β activity is observed in the Brca1-deficient mammary gland. Taken together, these results provide important aspects of tissue specificity of BRCA1-mediated suppression of breast carcinogenesis.
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Affiliation(s)
- Shaohui Wang
- From the Department of Biological Chemistry, University of California Irvine, Irvine, California 92697
| | - Ying Li
- Capital Medical University, Beijing 100069, China, and
| | - Pang-Hung Hsu
- the Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Sou-Ying Lee
- From the Department of Biological Chemistry, University of California Irvine, Irvine, California 92697
| | - Yoon Kim
- From the Department of Biological Chemistry, University of California Irvine, Irvine, California 92697
| | - Eva Y-H P Lee
- From the Department of Biological Chemistry, University of California Irvine, Irvine, California 92697,.
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16
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Abstract
Waddington's epigenetic landscape is probably the most famous and most powerful metaphor in developmental biology. Cells, represented by balls, roll downhill through a landscape of bifurcating valleys. Each new valley represents a possible cell fate and the ridges between the valleys maintain the cell fate once it has been chosen. Here I examine models of two important developmental processes - cell-fate induction and lateral inhibition - and ask whether the landscapes for these models at least qualitatively resemble Waddington's picture. For cell-fate induction, the answer is no. The commitment of a cell to a new fate corresponds to the disappearance of a valley from the landscape, not the splitting of one valley into two, and it occurs through a type of bifurcation - a saddle-node bifurcation - that possesses an intrinsic irreversibility that is missing from Waddington's picture. Lateral inhibition, a symmetrical cell-cell competition process, corresponds better to Waddington's picture, with one valley reversibly splitting into two through a pitchfork bifurcation. I propose an alternative epigenetic landscape that has numerous valleys and ridges right from the start, with the process of cell-fate commitment corresponding to the irreversible disappearance of some of these valleys and ridges, via cell-fate induction, complemented by the creation of new valleys and ridges through processes like cell-cell competition.
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17
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Modeling of hysteresis in gene regulatory networks. Bull Math Biol 2012; 74:1727-53. [PMID: 22588784 DOI: 10.1007/s11538-012-9733-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 04/30/2012] [Indexed: 12/26/2022]
Abstract
Hysteresis, observed in many gene regulatory networks, has a pivotal impact on biological systems, which enhances the robustness of cell functions. In this paper, a general model is proposed to describe the hysteretic gene regulatory network by combining the hysteresis component and the transient dynamics. The Bouc-Wen hysteresis model is modified to describe the hysteresis component in the mammalian gene regulatory networks. Rigorous mathematical analysis on the dynamical properties of the model is presented to ensure the bounded-input-bounded-output (BIBO) stability and demonstrates that the original Bouc-Wen model can only generate a clockwise hysteresis loop while the modified model can describe both clockwise and counter clockwise hysteresis loops. Simulation studies have shown that the hysteresis loops from our model are consistent with the experimental observations in three mammalian gene regulatory networks and two E.coli gene regulatory networks, which demonstrate the ability and accuracy of the mathematical model to emulate natural gene expression behavior with hysteresis. A comparison study has also been conducted to show that this model fits the experiment data significantly better than previous ones in the literature. The successful modeling of the hysteresis in all the five hysteretic gene regulatory networks suggests that the new model has the potential to be a unified framework for modeling hysteresis in gene regulatory networks and provide better understanding of the general mechanism that drives the hysteretic function.
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18
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Abstract
Cell size is an important adaptive trait that influences nearly all aspects of cellular physiology. Despite extensive characterization of the cell-cycle regulatory network, the molecular mechanisms coupling cell growth to division, and thereby controlling cell size, have remained elusive. Recent work in yeast has reinvigorated the size control field and suggested provocative mechanisms for the distinct functions of setting and sensing cell size. Further examination of size-sensing models based on spatial gradients and molecular titration, coupled with elucidation of the pathways responsible for nutrient-modulated target size, may reveal the fundamental principles of eukaryotic cell size control.
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19
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Denby CM, Im JH, Yu RC, Pesce CG, Brem RB. Negative feedback confers mutational robustness in yeast transcription factor regulation. Proc Natl Acad Sci U S A 2012; 109:3874-8. [PMID: 22355134 PMCID: PMC3309721 DOI: 10.1073/pnas.1116360109] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organismal fitness depends on the ability of gene networks to function robustly in the face of environmental and genetic perturbations. Understanding the mechanisms of this stability is one of the key aims of modern systems biology. Dissecting the basis of robustness to mutation has proven a particular challenge, with most experimental models relying on artificial DNA sequence variants engineered in the laboratory. In this work, we hypothesized that negative regulatory feedback could stabilize gene expression against the disruptions that arise from natural genetic variation. We screened yeast transcription factors for feedback and used the results to establish ROX1 (Repressor of hypOXia) as a model system for the study of feedback in circuit behaviors and its impact across genetically heterogeneous populations. Mutagenesis experiments revealed the mechanism of Rox1 as a direct transcriptional repressor at its own gene, enabling a regulatory program of rapid induction during environmental change that reached a plateau of moderate steady-state expression. Additionally, in a given environmental condition, Rox1 levels varied widely across genetically distinct strains; the ROX1 feedback loop regulated this variation, in that the range of expression levels across genetic backgrounds showed greater spread in ROX1 feedback mutants than among strains with the ROX1 feedback loop intact. Our findings indicate that the ROX1 feedback circuit is tuned to respond to perturbations arising from natural genetic variation in addition to its role in induction behavior. We suggest that regulatory feedback may be an important element of the network architectures that confer mutational robustness across biology.
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Affiliation(s)
- Charles M. Denby
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220; and
| | - Joo Hyun Im
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220; and
| | | | | | - Rachel B. Brem
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220; and
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20
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Hsu C, Scherrer S, Buetti-Dinh A, Ratna P, Pizzolato J, Jaquet V, Becskei A. Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution. Nat Commun 2012; 3:682. [PMID: 22353713 PMCID: PMC3293423 DOI: 10.1038/ncomms1687] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 01/17/2012] [Indexed: 01/18/2023] Open
Abstract
During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit.
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Affiliation(s)
- Chieh Hsu
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland
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21
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Pfeuty B, Bodart JF, Blossey R, Lefranc M. A dynamical model of oocyte maturation unveils precisely orchestrated meiotic decisions. PLoS Comput Biol 2012; 8:e1002329. [PMID: 22238511 PMCID: PMC3252271 DOI: 10.1371/journal.pcbi.1002329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/11/2011] [Indexed: 12/04/2022] Open
Abstract
Maturation of vertebrate oocytes into haploid gametes relies on two consecutive meioses without intervening DNA replication. The temporal sequence of cellular transitions driving eggs from G2 arrest to meiosis I (MI) and then to meiosis II (MII) is controlled by the interplay between cyclin-dependent and mitogen-activated protein kinases. In this paper, we propose a dynamical model of the molecular network that orchestrates maturation of Xenopus laevis oocytes. Our model reproduces the core features of maturation progression, including the characteristic non-monotonous time course of cyclin-Cdks, and unveils the network design principles underlying a precise sequence of meiotic decisions, as captured by bifurcation and sensitivity analyses. Firstly, a coherent and sharp meiotic resumption is triggered by the concerted action of positive feedback loops post-translationally activating cyclin-Cdks. Secondly, meiotic transition is driven by the dynamic antagonism between positive and negative feedback loops controlling cyclin turnover. Our findings reveal a highly modular network in which the coordination of distinct regulatory schemes ensures both reliable and flexible cell-cycle decisions. In the life cycle of sexual organisms, a specialized cell division -meiosis- reduces the number of chromosomes in gametes or spores while fertilization or mating restores the original number. The essential feature that distinguishes meiosis from mitosis (the usual division) is the succession of two rounds of division following a single DNA replication, as well as the arrest at the second division in the case of oocyte maturation. The fact that meiosis and mitosis are similar but different raises several interesting questions: What is the meiosis-specific dynamics of cell-cycle regulators? Are there mechanisms which guarantee the occurence of two and only two rounds of division despite the presence of intrinsic and extrinsic noises ? The study of a model of the molecular network that underlies the meiotic maturation process in Xenopus oocytes provides unexpected answers to these questions. On the one hand, the modular organization of this network ensures separate controls of the first and second divisions. On the other hand, regulatory synergies ensure that these two stages are precisely and reliably sequenced during meiosis. We conclude that cells have evolved a sophisticated regulatory network to achieve a robust, albeit flexible, meiotic dynamics.
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Affiliation(s)
- Benjamin Pfeuty
- Laboratoire de Physique des Lasers, Atomes, et Molécules, CNRS, UMR8523, Université Lille 1 Sciences et Technologies, Villeneuve d'Ascq, France.
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22
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Chatterjee S, Kumar D. Unraveling the design principle for motif organization in signaling networks. PLoS One 2011; 6:e28606. [PMID: 22164309 PMCID: PMC3228783 DOI: 10.1371/journal.pone.0028606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/11/2011] [Indexed: 11/21/2022] Open
Abstract
Cellular signaling networks display complex architecture. Defining the design principle of this architecture is crucial for our understanding of various biological processes. Using a mathematical model for three-node feed-forward loops, we identify that the organization of motifs in specific manner within the network serves as an important regulator of signal processing. Further, incorporating a systemic stochastic perturbation to the model we could propose a possible design principle, for higher-order organization of motifs into larger networks in order to achieve specific biological output. The design principle was then verified in a large, complex human cancer signaling network. Further analysis permitted us to classify signaling nodes of the network into robust and vulnerable nodes as a result of higher order motif organization. We show that distribution of these nodes within the network at strategic locations then provides for the range of features displayed by the signaling network.
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Affiliation(s)
- Samrat Chatterjee
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dhiraj Kumar
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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23
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Eser U, Falleur-Fettig M, Johnson A, Skotheim JM. Commitment to a cellular transition precedes genome-wide transcriptional change. Mol Cell 2011; 43:515-27. [PMID: 21855792 DOI: 10.1016/j.molcel.2011.06.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/13/2011] [Accepted: 06/17/2011] [Indexed: 01/13/2023]
Abstract
In budding yeast, commitment to cell division corresponds to activating the positive feedback loop of G1 cyclins controlled by the transcription factors SBF and MBF. This pair of transcription factors has over 200 targets, implying that cell-cycle commitment coincides with genome-wide changes in transcription. Here, we find that genes within this regulon have a well-defined distribution of transcriptional activation times. Combinatorial use of SBF and MBF results in a logical OR function for gene expression and partially explains activation timing. Activation of G1 cyclin expression precedes the activation of the bulk of the G1/S regulon, ensuring that commitment to cell division occurs before large-scale changes in transcription. Furthermore, we find similar positive feedback-first regulation in the yeasts S. bayanus and S. cerevisiae, as well as human cells. The widespread use of the feedback-first motif in eukaryotic cell-cycle control, implemented by nonorthologous proteins, suggests its frequent deployment at cellular transitions.
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Affiliation(s)
- Umut Eser
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
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24
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Xie L, Xie L, Kinnings SL, Bourne PE. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol 2011; 52:361-79. [PMID: 22017683 DOI: 10.1146/annurev-pharmtox-010611-134630] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polypharmacology, which focuses on designing therapeutics to target multiple receptors, has emerged as a new paradigm in drug discovery. Polypharmacological effects are an attribute of most, if not all, drug molecules. The efficacy and toxicity of drugs, whether designed as single- or multitarget therapeutics, result from complex interactions between pharmacodynamic, pharmacokinetic, genetic, epigenetic, and environmental factors. Ultimately, to predict a drug response phenotype, it is necessary to understand the change in information flow through cellular networks resulting from dynamic drug-target interactions and the impact that this has on the complete biological system. Although such is a future objective, we review recent progress and challenges in computational techniques that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes.
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Affiliation(s)
- Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, New York 10065, USA.
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25
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Recent progress in the application of microfluidic systems and gold nanoparticles in immunoassays. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4338-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Gautier A, Deiters A, Chin JW. Light-activated kinases enable temporal dissection of signaling networks in living cells. J Am Chem Soc 2011; 133:2124-7. [PMID: 21271704 PMCID: PMC3048767 DOI: 10.1021/ja1109979] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report a general strategy for creating protein kinases in mammalian cells that are poised for very rapid activation by light. By photoactivating a caged version of MEK1, we demonstrate the specific, rapid, and receptor independent activation of an artificial subnetwork within the Raf/MEK/ERK pathway. Time-lapse microscopy allowed us to precisely characterize the kinetics of elementary steps in the signaling cascade and provided insight into adaptive feedback and rate-determining processes in the pathway.
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Affiliation(s)
- Arnaud Gautier
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, United Kingdom
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27
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Affiliation(s)
- Xiaoli Liao
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
| | - Rafe T Petty
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
| | - Milan Mrksich
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
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28
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29
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Abstract
We develop a novel method for Western blot based on microfluidics, incorporating the internal molecular weight marker, loading control, and antibody titration in the same protocol. Compared with the conventional method which could detect only one protein, the microfluidic Western blot could analyze at least 10 proteins simultaneously from a single sample, and it requires only about 1% of the amount of antibody used in conventional Western blot.
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30
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Iadevaia S, Lu Y, Morales FC, Mills GB, Ram PT. Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. Cancer Res 2010; 70:6704-14. [PMID: 20643779 PMCID: PMC2932856 DOI: 10.1158/0008-5472.can-10-0460] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Targeted therapeutics hold tremendous promise in inhibiting cancer cell proliferation. However, targeting proteins individually can be compensated for by bypass mechanisms and activation of regulatory loops. Designing optimal therapeutic combinations must therefore take into consideration the complex dynamic networks in the cell. In this study, we analyzed the insulin-like growth factor (IGF-1) signaling network in the MDA-MB231 breast cancer cell line. We used reverse-phase protein array to measure the transient changes in the phosphorylation of proteins after IGF-1 stimulation. We developed a computational procedure that integrated mass action modeling with particle swarm optimization to train the model against the experimental data and infer the unknown model parameters. The trained model was used to predict how targeting individual signaling proteins altered the rest of the network and identify drug combinations that minimally increased phosphorylation of other proteins elsewhere in the network. Experimental testing of the modeling predictions showed that optimal drug combinations inhibited cell signaling and proliferation, whereas nonoptimal combination of inhibitors increased phosphorylation of nontargeted proteins and rescued cells from cell death. The integrative approach described here is useful for generating experimental intervention strategies that could optimize drug combinations and discover novel pharmacologic targets for cancer therapy.
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Affiliation(s)
- Sergio Iadevaia
- To whom correspondence should be addressed. Mailing address: 7435 Fannin St, Unit 950, P.O. Box 301429. or ; phone: 1-713-563-2848; fax: 1-713-563-4235
| | | | | | | | - Prahlad T. Ram
- To whom correspondence should be addressed. Mailing address: 7435 Fannin St, Unit 950, P.O. Box 301429. or ; phone: 1-713-563-2848; fax: 1-713-563-4235
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31
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Bodart JFL. Extracellular-regulated kinase-mitogen-activated protein kinase cascade: unsolved issues. J Cell Biochem 2010; 109:850-7. [PMID: 20082320 DOI: 10.1002/jcb.22477] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This review point out several aspects regarding the mitogen-activated protein kinase (MAPK)/extracellular-regulated kinase (Erk) network, which are still pending issues in the understanding how this pathway integrate information to drive cell fates. Focusing on the role of Erk during cell cycle, it has to be underlined that Erk downstream effectors, which are required for mitosis progression and contribute to aneuploidy during tumorigenesis, remain to be determined. In addition to the identity of the terminal enzymes or effectors of Erk, it has to be stressed that the dynamic nature of the Erk signal is itself a key factor in cell phenotype decisions. Development of biophotonics strategies for monitoring the Erk network at the spatiotemporal level in living cells, as well as computational and hypothesis-driven approaches, are called to unravel the principles by which signaling networks create biochemical and biological specificities. Finally, Erk dynamics might also be impacted by other post-translational modification than phosphorylation, such as O-GlcNAcylation.
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Affiliation(s)
- Jean-François L Bodart
- Laboratoire de Régulation des Signaux de Division, University of Lille 1, EA4020, Building SN3, Room 304, F-59655 Villeneuve d'Ascq cedex, France.
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32
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Pandurangan S, Gakkhar S. Lose and gain: impacts of ERK5 and JNK cascades on each other. SYSTEMS AND SYNTHETIC BIOLOGY 2010; 4:125-32. [PMID: 21629392 PMCID: PMC2923301 DOI: 10.1007/s11693-010-9061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/15/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
Abstract
UNLABELLED Kinase cascades in ERK5 (Extracellular signal-regulated kinases) and JNK (c-Jun N-terminal kinases) signaling pathways mediate the sensing and processing of stimuli. Cross-talks between signaling cascades is a likely phenomenon that can cause apparently different biological responses from a single pathway, on its activation. Feedback loops have the potential to greatly alter the properties of a pathway and its response to stimuli. Based on enzyme kinetic reactions, mathematical models have been developed to predict and analyze the impacts of cross-talks and feedback loops in ERK5 and JNK cascades. It has been observed that, there is no significant impact on neither ERK5 activation nor JNKs' activation due to cross-talks between them. But it is due to cross-talks and feedback loops in ERK5 and JNK cascade, ERK5 gets activated in a transient manner in the absence of input signals. Planning to obtain the parameter values from the experimentalist and the result should be validated by experimental verification. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11693-010-9061-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sundaramurthy Pandurangan
- Department of Mathematics, Indian Institute of Technology Roorkee, Roorkee, 247667 Uttarakhand India
- National Center for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore, 560 065 India
| | - Sunita Gakkhar
- Department of Mathematics, Indian Institute of Technology Roorkee, Roorkee, 247667 Uttarakhand India
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33
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Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M. A global protein kinase and phosphatase interaction network in yeast. Science 2010; 328:1043-6. [PMID: 20489023 PMCID: PMC3983991 DOI: 10.1126/science.1176495] [Citation(s) in RCA: 526] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The interactions of protein kinases and phosphatases with their regulatory subunits and substrates underpin cellular regulation. We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. The KPI network contained many dense local regions of interactions that suggested new functions. Notably, the cell cycle phosphatase Cdc14 associated with multiple kinases that revealed roles for Cdc14 in mitogen-activated protein kinase signaling, the DNA damage response, and metabolism, whereas interactions of the target of rapamycin complex 1 (TORC1) uncovered new effector kinases in nitrogen and carbon metabolism. An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses.
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Affiliation(s)
- Ashton Breitkreutz
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Hyungwon Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey R. Sharom
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Lorrie Boucher
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Victor Neduva
- Wellcome Trust Centre for Cell Biology and School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK
| | - Brett Larsen
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Zhen-Yuan Lin
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Bobby-Joe Breitkreutz
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Chris Stark
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Guomin Liu
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Jessica Ahn
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Danielle Dewar-Darch
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Teresa Reguly
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Xiaojing Tang
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
| | - Ricardo Almeida
- Wellcome Trust Centre for Cell Biology and School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK
| | - Zhaohui Steve Qin
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tony Pawson
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mike Tyers
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario, M5S 1A8, Canada
- Wellcome Trust Centre for Cell Biology and School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK
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34
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Buchert M, Athineos D, Abud HE, Burke ZD, Faux MC, Samuel MS, Jarnicki AG, Winbanks CE, Newton IP, Meniel VS, Suzuki H, Stacker SA, Näthke IS, Tosh D, Huelsken J, Clarke AR, Heath JK, Sansom OJ, Ernst M. Genetic dissection of differential signaling threshold requirements for the Wnt/beta-catenin pathway in vivo. PLoS Genet 2010; 6:e1000816. [PMID: 20084116 PMCID: PMC2800045 DOI: 10.1371/journal.pgen.1000816] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 12/15/2009] [Indexed: 12/29/2022] Open
Abstract
Contributions of null and hypomorphic alleles of Apc in mice produce both developmental and pathophysiological phenotypes. To ascribe the resulting genotype-to-phenotype relationship unambiguously to the Wnt/β-catenin pathway, we challenged the allele combinations by genetically restricting intracellular β-catenin expression in the corresponding compound mutant mice. Subsequent evaluation of the extent of resulting Tcf4-reporter activity in mouse embryo fibroblasts enabled genetic measurement of Wnt/β-catenin signaling in the form of an allelic series of mouse mutants. Different permissive Wnt signaling thresholds appear to be required for the embryonic development of head structures, adult intestinal polyposis, hepatocellular carcinomas, liver zonation, and the development of natural killer cells. Furthermore, we identify a homozygous Apc allele combination with Wnt/β-catenin signaling capacity similar to that in the germline of the Apcmin mice, where somatic Apc loss-of-heterozygosity triggers intestinal polyposis, to distinguish whether co-morbidities in Apcmin mice arise independently of intestinal tumorigenesis. Together, the present genotype–phenotype analysis suggests tissue-specific response levels for the Wnt/β-catenin pathway that regulate both physiological and pathophysiological conditions. Germline or somatic mutations in genes are the underlying cause of many human diseases, most notably cancer. Interestingly though, even in situations where every cell of every tissue of an organism carries the same mutation (as is the case for germline mutations), some tissues are more susceptible to the development of disease over time than others. For example, in familial adenomatous polyposis (FAP), affected persons carry different germline mutations in the APC gene and are prone to developing cancers of the colon and the rectum—and, less frequently, cancers in other tissues such as stomach, liver, and bones. Here we utilize a panel of mutant mice with truncating or hypomorphic mutations in the Apc gene, resulting in different levels of activation of the Wnt/β-catenin pathway. Our results reveal that different pathophysiological outcomes depend on different permissive signaling thresholds in embryonic, intestinal, and liver tissues. Importantly, we demonstrate that reducing Wnt pathway activation by 50% is enough to prevent the manifestation of embryonic abnormalities and disease in the adult mouse. This raises the possibility of developing therapeutic strategies that modulate the activation levels of this pathway rather than trying to “repair” the mutation in the gene itself.
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Affiliation(s)
- Michael Buchert
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Dimitris Athineos
- The Beatson Institute Cancer Research, Garscube Estate, Glasgow, United Kingdom
| | - Helen E. Abud
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
- Department of Anatomy and Cell Biology, University of Melbourne, Melbourne, Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Zoe D. Burke
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maree C. Faux
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Michael S. Samuel
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
- The Beatson Institute Cancer Research, Garscube Estate, Glasgow, United Kingdom
| | - Andrew G. Jarnicki
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | | | - Ian P. Newton
- Cell and Developmental Biology, University of Dundee, Dundee, United Kingdom
| | - Valerie S. Meniel
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom
| | - Hiromu Suzuki
- First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan
| | - Steven A. Stacker
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Inke S. Näthke
- Cell and Developmental Biology, University of Dundee, Dundee, United Kingdom
| | - David Tosh
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Joerg Huelsken
- Ecole Polytechnique Fédérale de Lausanne, Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland
| | - Alan R. Clarke
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom
| | - Joan K. Heath
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
| | - Owen J. Sansom
- The Beatson Institute Cancer Research, Garscube Estate, Glasgow, United Kingdom
- * E-mail: (ME); (OS)
| | - Matthias Ernst
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
- * E-mail: (ME); (OS)
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Russo C, Beaujois R, Bodart JF, Blossey R. Kicked by Mos and tuned by MPF-the initiation of the MAPK cascade in Xenopus oocytes. HFSP JOURNAL 2009; 3:428-40. [PMID: 20514133 DOI: 10.2976/1.3265771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 09/24/2009] [Indexed: 11/19/2022]
Abstract
The mitogen-activated protein kinase (MAPK) cascade is a paradigmatic signaling cascade, which plays a crucial role in many aspects of cellular events. The main initiator of the cascade in Xenopus oocytes is the oncoprotein Mos. After activation of the cascade, Mos activity is stabilized by MAPK via a feedback loop. Mos concentration levels are, however, not controlled by MAPK alone. In this paper we show, by imposing either a sustained or a peaked activity of M-phase promoting factor (MPF) (Cdc2-cyclin B), how the latter regulates the dynamics of Mos. Our experiments are supported by a detailed kinetic model for the Mos-MPF-MAPK network, which takes into account the three different phosphorylation states of Mos and, as a consequence, allows us to determine the time evolution of Mos under control of MPF. Our work opens a path toward a more complete and biologically realistic quantitative understanding of the dynamic interdependence of Mos and MPF in Xenopus oocytes.
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Pomerening JR. Positive-feedback loops in cell cycle progression. FEBS Lett 2009; 583:3388-96. [PMID: 19818353 DOI: 10.1016/j.febslet.2009.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 09/28/2009] [Accepted: 10/01/2009] [Indexed: 01/19/2023]
Abstract
A positive-feedback loop is a simple motif that is ubiquitous to the modules and networks that comprise cellular signaling systems. Signaling behaviors that are synonymous with positive feedback include amplification and rapid switching, maintenance, and the coherence of outputs. Recent advances have been made towards understanding how positive-feedback loops function, as well as their mechanistic basis in controlling eukaryotic cell cycle progression. Some of these advances will be reviewed here, including: how cyclin controls passage through Start and maintains coherence of G1/S regulon expression in yeast; how Polo-like kinase 1 activation is driven by Bora and Aurora A, and its expression is stimulated by Forkhead Box M1 in mammalian cells; and how some of the various dynamic behaviors of spindle assembly and anaphase onset can be produced.
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Affiliation(s)
- Joseph R Pomerening
- Department of Biology, Interdisciplinary Program in Biochemistry, Indiana University, 212 S. Hawthorne Drive Simon Hall Room 043F, Bloomington, IN 47405-7003, United States.
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37
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Growth control and ribosome biogenesis. Curr Opin Cell Biol 2009; 21:855-63. [PMID: 19796927 DOI: 10.1016/j.ceb.2009.09.002] [Citation(s) in RCA: 274] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 09/02/2009] [Accepted: 09/02/2009] [Indexed: 12/27/2022]
Abstract
Ribosomes provide the basis for protein production and this drives cell growth. Recent studies, both in yeast and in higher eukaryotes, are beginning to reveal new mechanisms underlying the elaborate control of ribosome biogenesis, which requires coordinate regulation of all three RNA polymerases. Transcription of ribosomal RNA is finely tuned to cellular energy status and linked to the production of ribosomal proteins. Several autoregulatory mechanisms controlling various aspects of ribosome biogenesis have been uncovered and reveal new connections to cell-cycle and cell-size control. Ribosome biogenesis has now been clearly linked to disease, particularly to cancer and anemia, and also to aging. A challenge for future studies will be to elucidate further the molecular mechanisms underlying these connections.
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39
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Abstract
The association of receptors and solute transporters with components of the endocytic machinery regulates their surface levels, and thereby cellular sensitivity to cytokines, ligands and nutrients in the extracellular environment. Most transmembrane receptors and solute transporters are glycoproteins, and the Asn (N)-linked oligosaccharides (N-glycans) can bind animal lectins, forming multivalent lattices or microdomains that regulate glycoprotein mobility in the plane of membrane. The N-glycan number (sequence-encoded NXS/T) and context-dependent Golgi N-glycan branching cooperate to regulate glycoprotein affinities for the galectin family of lectins. Galectin-3 binding reduces EGF receptor trafficking into clathrin-coated pits and caveolae lipid rafts, decreases ligand-independent receptor activation and promotes alpha5beta1 integrin remodelling in focal adhesions. N-glycan branching in the medial Golgi increases glycan affinity for galectins, and the Golgi pathway is sensitive to uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) supply, in turn hexosamine pathway metabolites (fructose-6-P, glutamine and acetyl-CoA). Thus, lattice avidity and cellular responsiveness to extracellular cues are regulated in an adaptive manner by metabolism and Golgi modification to glycoproteins. Computational modelling of the hexosamine/Golgi/lattice has provided new insight on cell surface adaptation in cancer and autoimmune disease.
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Affiliation(s)
- James W Dennis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue R988, Toronto, ON, Canada M5G 1X5.
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40
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Skotheim JM. Cell signaling. To divide or not to divide. Science 2009; 324:476-7. [PMID: 19390035 DOI: 10.1126/science.1173769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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