1
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Otake M, Teranishi M, Komatsu C, Hara M, Yoshiyama KO, Hidema J. Poaceae plants transfer cyclobutane pyrimidine dimer photolyase to chloroplasts for ultraviolet-B resistance. PLANT PHYSIOLOGY 2024; 195:326-342. [PMID: 38345835 PMCID: PMC11060685 DOI: 10.1093/plphys/kiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/07/2024] [Indexed: 05/02/2024]
Abstract
Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation.
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Affiliation(s)
- Momo Otake
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Chiharu Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mamoru Hara
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | | | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Sendai, Miyagi 980-8577, Japan
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2
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Abstract
Individual cell types have characteristic sizes, suggesting that size sensing mechanisms may coordinate transcription, translation, and metabolism with cell growth rates. Two types of size-sensing mechanisms have been proposed: spatial sensing of the location or dimensions of a signal, subcellular structure or organelle; or titration-based sensing of the intracellular concentrations of key regulators. Here we propose that size sensing in animal cells combines both titration and spatial sensing elements in a dynamic mechanism whereby microtubule motor-dependent localization of RNA encoding importin β1 and mTOR, coupled with regulated local protein synthesis, enable cytoskeleton length sensing for cell growth regulation.
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Affiliation(s)
- Ida Rishal
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel.
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3
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Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN. New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling. Semin Cancer Biol 2019; 54:162-173. [PMID: 29518522 PMCID: PMC6123307 DOI: 10.1016/j.semcancer.2018.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 01/04/2023]
Abstract
RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of targeting RAS directly, drugs that impact the other components of pathways where mutant RAS operates may potentially be effective. However, the system-level features, including different localizations of RAS isoforms, competition between downstream effectors, and interlocking feedback and feed-forward loops, must be understood to fully grasp the opportunities and limitations of inhibiting specific targets. Mathematical modeling can help us discern the system-level impacts of these features in normal and cancer cells. New technologies enable the acquisition of experimental data that will facilitate development of realistic models of oncogenic RAS behavior. In light of the wealth of empirical data accumulated over decades of study and the advancement of experimental methods for gathering new data, modelers now have the opportunity to advance progress toward realization of targeted treatment for mutant RAS-driven cancers.
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Affiliation(s)
- Keesha E Erickson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Richard G Posner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - William S Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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4
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Gelens L, Qian J, Bollen M, Saurin AT. The Importance of Kinase-Phosphatase Integration: Lessons from Mitosis. Trends Cell Biol 2018; 28:6-21. [PMID: 29089159 DOI: 10.1016/j.tcb.2017.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/20/2022]
Abstract
Kinases and phosphatases work antagonistically to control the behaviour of individual substrate molecules. This can be incorrectly extrapolated to imply that they also work antagonistically on the signals or processes that these molecules control. In fact, in many situations kinases and phosphatases work together to positively drive signal responses. We explain how this 'cooperativity' is critical for setting the amplitude, localisation, timing, and shape of phosphorylation signals. We use mitosis to illustrate why these properties are important for controlling mitotic entry, sister chromatid cohesion, kinetochore-microtubule attachments, the spindle assembly checkpoint, mitotic spindle elongation, and mitotic exit. These examples provide a rationale to explain how complex signalling behaviour could rely on similar types of integration within many other biological processes.
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Affiliation(s)
- Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium.
| | - Junbin Qian
- Laboratory of Biosignaling and Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling and Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Adrian T Saurin
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
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5
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Bressloff PC, Karamched BR, Lawley SD, Levien E. Diffusive transport in the presence of stochastically gated absorption. Phys Rev E 2017; 96:022102. [PMID: 28950455 DOI: 10.1103/physreve.96.022102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Indexed: 11/07/2022]
Abstract
We analyze a population of Brownian particles moving in a spatially uniform environment with stochastically gated absorption. The state of the environment at time t is represented by a discrete stochastic variable k(t)∈{0,1} such that the rate of absorption is γ[1-k(t)], with γ a positive constant. The variable k(t) evolves according to a two-state Markov chain. We focus on how stochastic gating affects the attenuation of particle absorption with distance from a localized source in a one-dimensional domain. In the static case (no gating), the steady-state attenuation is given by an exponential with length constant sqrt[D/γ], where D is the diffusivity. We show that gating leads to slower, nonexponential attenuation. We also explore statistical correlations between particles due to the fact that they all diffuse in the same switching environment. Such correlations can be determined in terms of moments of the solution to a corresponding stochastic Fokker-Planck equation.
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Affiliation(s)
- Paul C Bressloff
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Bhargav R Karamched
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Sean D Lawley
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Ethan Levien
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, Utah 84112, USA
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6
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Formation and maintenance of nitrogen-fixing cell patterns in filamentous cyanobacteria. Proc Natl Acad Sci U S A 2016; 113:6218-23. [PMID: 27162328 DOI: 10.1073/pnas.1524383113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen-limiting conditions, in filaments of the genus Anabaena, some cells differentiate into heterocysts, which lose the possibility to divide but are able to fix environmental nitrogen for the colony. These heterocysts form a quasiregular pattern in the filament, representing a prototype of patterning and morphogenesis in prokaryotes. Recent years have seen advances in the identification of the molecular mechanism regulating this pattern. We use these data to build a theory on heterocyst pattern formation, for which both genetic regulation and the effects of cell division and filament growth are key components. The theory is based on the interplay of three generic mechanisms: local autoactivation, early long-range inhibition, and late long-range inhibition. These mechanisms can be identified with the dynamics of hetR, patS, and hetN expression. Our theory reproduces quantitatively the experimental dynamics of pattern formation and maintenance for wild type and mutants. We find that hetN alone is not enough to play the role as the late inhibitory mechanism: a second mechanism, hypothetically the products of nitrogen fixation supplied by heterocysts, must also play a role in late long-range inhibition. The preponderance of even intervals between heterocysts arises naturally as a result of the interplay between the timescales of genetic regulation and cell division. We also find that a purely stochastic initiation of the pattern, without a two-stage process, is enough to reproduce experimental observations.
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7
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Valon L, Etoc F, Remorino A, di Pietro F, Morin X, Dahan M, Coppey M. Predictive Spatiotemporal Manipulation of Signaling Perturbations Using Optogenetics. Biophys J 2015; 109:1785-97. [PMID: 26536256 PMCID: PMC4643200 DOI: 10.1016/j.bpj.2015.08.042] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/22/2015] [Accepted: 08/03/2015] [Indexed: 11/17/2022] Open
Abstract
Recently developed optogenetic methods promise to revolutionize cell biology by allowing signaling perturbations to be controlled in space and time with light. However, a quantitative analysis of the relationship between a custom-defined illumination pattern and the resulting signaling perturbation is lacking. Here, we characterize the biophysical processes governing the localized recruitment of the Cryptochrome CRY2 to its membrane-anchored CIBN partner. We develop a quantitative framework and present simple procedures that enable predictive manipulation of protein distributions on the plasma membrane with a spatial resolution of 5 μm. We show that protein gradients of desired levels can be established in a few tens of seconds and then steadily maintained. These protein gradients can be entirely relocalized in a few minutes. We apply our approach to the control of the Cdc42 Rho GTPase activity. By inducing strong localized signaling perturbation, we are able to monitor the initiation of cell polarity and migration with a remarkable reproducibility despite cell-to-cell variability.
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Affiliation(s)
- Leo Valon
- Laboratoire Physico-Chimie, Institut Curie, Centre National de la Recherche Scientifique UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, Paris, France
| | - Fred Etoc
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York
| | - Amanda Remorino
- Laboratoire Physico-Chimie, Institut Curie, Centre National de la Recherche Scientifique UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, Paris, France
| | - Florencia di Pietro
- Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, Paris, France
| | - Xavier Morin
- Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, Paris, France
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, Centre National de la Recherche Scientifique UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, Paris, France
| | - Mathieu Coppey
- Laboratoire Physico-Chimie, Institut Curie, Centre National de la Recherche Scientifique UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, Paris, France.
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8
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Macromolecular transport in synapse to nucleus communication. Trends Neurosci 2014; 38:108-16. [PMID: 25534890 DOI: 10.1016/j.tins.2014.12.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Abstract
Local signaling events at synapses or axon terminals must be communicated to the nucleus to elicit transcriptional responses. The lengths of neuronal processes pose a significant challenge for such intracellular communication. This challenge is met by mechanisms ranging from rapid signals encoded in calcium waves to slower macromolecular signaling complexes carried by molecular motors. Here we summarize recent findings on macromolecular signaling from the synapse to the nucleus, in comparison to those employed in injury signaling along axons. A number of common themes emerge, including combinatorial signal encoding by post-translational mechanisms such as differential phosphorylation and proteolysis, and conserved roles for importins in coordinating signaling complexes. Neurons may integrate ionic flux with motor-transported signals as a temporal code for synaptic plasticity signaling.
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9
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Bashour KT, Tsai J, Shen K, Lee JH, Sun E, Milone MC, Dustin ML, Kam LC. Cross talk between CD3 and CD28 is spatially modulated by protein lateral mobility. Mol Cell Biol 2014; 34:955-64. [PMID: 24379441 PMCID: PMC3958039 DOI: 10.1128/mcb.00842-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/21/2013] [Accepted: 12/21/2013] [Indexed: 12/23/2022] Open
Abstract
Functional convergence of CD28 costimulation and TCR signaling is critical to T-cell activation and adaptive immunity. These receptors form complex microscale patterns within the immune synapse, although the impact of this spatial organization on cell signaling remains unclear. We investigate this cross talk using micropatterned surfaces that present ligands to these membrane proteins in order to control the organization of signaling molecules within the cell-substrate interface. While primary human CD4(+) T cells were activated by features containing ligands to both CD3 and CD28, this functional convergence was curtailed on surfaces in which engagement of these two systems was separated by micrometer-scale distances. Moreover, phosphorylated Lck was concentrated to regions of CD3 engagement and exhibited a low diffusion rate, suggesting that costimulation is controlled by a balance between the transport of active Lck to CD28 and its deactivation. In support of this model, disruption of the actin cytoskeleton increased Lck mobility and allowed functional T-cell costimulation by spatially separated CD3 and CD28. In primary mouse CD4(+) T cells, a complementary system, reducing the membrane mobility increased the sensitivity to CD3-CD28 separation. These results demonstrate a subcellular reaction-diffusion system that allows cells to sense the microscale organization of the extracellular environment.
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Affiliation(s)
- Keenan T. Bashour
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Jones Tsai
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Keyue Shen
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Joung-Hyun Lee
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Eileen Sun
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Michael C. Milone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael L. Dustin
- Molecular Pathogenesis Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
- Nuffield Department of Orthopedics and Musculoskeletal Sciences, The University of Oxford, and Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Lance C. Kam
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
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10
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Volinsky N, Kholodenko BN. Complexity of receptor tyrosine kinase signal processing. Cold Spring Harb Perspect Biol 2013; 5:a009043. [PMID: 23906711 DOI: 10.1101/cshperspect.a009043] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our knowledge of molecular mechanisms of receptor tyrosine kinase (RTK) signaling advances with ever-increasing pace. Yet our understanding of how the spatiotemporal dynamics of RTK signaling control specific cellular outcomes has lagged behind. Systems-centered experimental and computational approaches can help reveal how overlapping networks of signal transducers downstream of RTKs orchestrate specific cell-fate decisions. We discuss how RTK network regulatory structures, which involve the immediate posttranslational and delayed transcriptional controls by multiple feed forward and feedback loops together with pathway cross talk, adapt cells to the combinatorial variety of external cues and conditions. This intricate network circuitry endows cells with emerging capabilities for RTK signal processing and decoding. We illustrate how mathematical modeling facilitates our understanding of RTK network behaviors by unraveling specific systems properties, including bistability, oscillations, excitable responses, and generation of intricate landscapes of signaling activities.
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Affiliation(s)
- Natalia Volinsky
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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11
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Hwang Y, Kumar P, Barakat AI. Intracellular regulation of cell signaling cascades: how location makes a difference. J Math Biol 2013; 69:213-42. [PMID: 23774809 DOI: 10.1007/s00285-013-0701-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 06/01/2013] [Indexed: 11/26/2022]
Abstract
Organelles such as endosomes and the Golgi apparatus play a critical role in regulating signal transmission to the nucleus. Recent experiments have shown that appropriate positioning of these organelles within the intracellular space is critical for effective signal regulation. To understand the mechanism behind this observation, we consider a reaction-diffusion model of an intracellular signaling cascade and investigate the effect on the signaling of intracellular regulation in the form of a small release of phosphorylated signaling protein, kinase, and/or phosphatase. Variational analysis is applied to characterize the most effective regions for the localization of this intracellular regulation. The results demonstrate that signals reaching the nucleus are most effectively regulated by localizing the release of phosphorylated substrate protein and kinase near the nucleus. Phosphatase release, on the other hand, is nearly equally effective throughout the intracellular space. The effectiveness of the intracellular regulation is affected strongly by the characteristics of signal propagation through the cascade. For signals that are amplified as they propagate through the cascade, reactions in the upstream levels of the cascade exhibit much larger sensitivities to regulation by release of phosphorylated substrate protein and kinase than downstream reactions. On the other hand, for signals that decay through the cascade, downstream reactions exhibit larger sensitivity than upstream reactions. For regulation by phosphatase release, all reactions within the cascade show large sensitivity for amplified signals but lose this sensitivity for decaying signals. We use the analysis to develop a simple model of endosome-mediated regulation of cell signaling. The results demonstrate that signal regulation by the modeled endosome is most effective when the endosome is positioned in the vicinity of the nucleus. The present findings may explain at least in part why endosomes in many cell types localize near the nucleus.
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Affiliation(s)
- Yongyun Hwang
- Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, Cambridge, UK,
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12
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Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell 2013; 49:202-12. [PMID: 23352241 DOI: 10.1016/j.molcel.2012.12.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/30/2012] [Indexed: 12/28/2022]
Abstract
A challenge in biology is to understand how complex molecular networks in the cell execute sophisticated regulatory functions. Here we explore the idea that there are common and general principles that link network structures to biological functions, principles that constrain the design solutions that evolution can converge upon for accomplishing a given cellular task. We describe approaches for classifying networks based on abstract architectures and functions, rather than on the specific molecular components of the networks. For any common regulatory task, can we define the space of all possible molecular solutions? Such inverse approaches might ultimately allow the assembly of a design table of core molecular algorithms that could serve as a guide for building synthetic networks and modulating disease networks.
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Affiliation(s)
- Wendell A Lim
- Center for Systems and Synthetic Biology, University of California, San Francisco, CA 94158, USA.
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13
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Albus CA, Rishal I, Fainzilber M. Cell length sensing for neuronal growth control. Trends Cell Biol 2013; 23:305-10. [PMID: 23511112 DOI: 10.1016/j.tcb.2013.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/03/2013] [Accepted: 02/11/2013] [Indexed: 11/27/2022]
Abstract
Neurons exhibit great size differences, and must coordinate biosynthesis rates in cell bodies with the growth needs of different lengths of axons. Classically, axon growth has been viewed mainly as a consequence of extrinsic influences. However, recent publications have proposed at least two different intrinsic axon growth-control mechanisms. We suggest that these mechanisms form part of a continuum of axon growth-control mechanisms, wherein initial growth rates are pre-programmed by transcription factor levels, and subsequent elongating growth is dependent on feedback from intrinsic length-sensing enabled by bidirectional motor-dependent oscillating signals. This model might explain intrinsic limits on elongating neuronal growth and provides a mechanistic framework for determining the connections between genome expression and cellular growth rates in neurons.
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Affiliation(s)
- Christin A Albus
- Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
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14
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Rishal I, Kam N, Perry RBT, Shinder V, Fisher EMC, Schiavo G, Fainzilber M. A motor-driven mechanism for cell-length sensing. Cell Rep 2013; 1:608-16. [PMID: 22773964 PMCID: PMC3389498 DOI: 10.1016/j.celrep.2012.05.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Size homeostasis is fundamental in cell biology, but it is not clear how large cells such as neurons can assess their own size or length. We examined a role for molecular motors in intracellular length sensing. Computational simulations suggest that spatial information can be encoded by the frequency of an oscillating retrograde signal arising from a composite negative feedback loop between bidirectional motor-dependent signals. The model predicts that decreasing either or both anterograde or retrograde signals should increase cell length, and this prediction was confirmed upon application of siRNAs for specific kinesin and/or dynein heavy chains in adult sensory neurons. Heterozygous dynein heavy chain 1 mutant sensory neurons also exhibited increased lengths both in vitro and during embryonic development. Moreover, similar length increases were observed in mouse embryonic fibroblasts upon partial downregulation of dynein heavy chain 1. Thus, molecular motors critically influence cell-length sensing and growth control.
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Affiliation(s)
- Ida Rishal
- Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
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15
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Tănase-Nicola S, Lubensky DK. Exchange of stability as a function of system size in a nonequilibrium system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:040103. [PMID: 23214515 DOI: 10.1103/physreve.86.040103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Indexed: 06/01/2023]
Abstract
In equilibrium systems with short-ranged interactions, the relative stability of different thermodynamic states generally does not depend on system size (as long as this size is larger than the interaction range). Here, we use a large deviations approach to show that, in contrast, different states can exchange stability as system size is varied in a driven, bistable reaction-diffusion system. This striking effect is related to a shift from a spatially uniform to a nonuniform transition state and should generically be possible in a wide range of nonequilibrium physical and biological systems.
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Affiliation(s)
- Sorin Tănase-Nicola
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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16
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Polyansky A, Zagrovic B. Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation. J Phys Chem Lett 2012; 3:973-976. [PMID: 23914287 PMCID: PMC3726239 DOI: 10.1021/jz300103p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 03/22/2012] [Indexed: 06/02/2023]
Abstract
We use explicit-solvent, molecular dynamics simulations to study the change in polar properties of a solvent-accessible surface for proteins undergoing phosphorylation. We analyze eight different pairs of proteins representing different structural classes in native and phosphorylated states and estimate the polarity of their surface using the molecular hydrophobicity potential approach. Whereas the phosphorylation-induced hydrophobicity change in the vicinity of phosphosites does not vary strongly among the studied proteins, the equivalent change for complete proteins covers a surprisingly wide range of effects including even an increase in the overall hydrophobicity in some cases. Importantly, the observed changes are strongly related to electrostatic properties of proteins, such as the net charge per residue, the distribution of charged side-chain contacts, and the isoelectric point. These features predefine the level of surface hydrophobicity change upon phosphorylation and may thus contribute to the phosphorylation-induced alteration of the interactions between a protein and its environment.
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Affiliation(s)
- Anton
A. Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute
of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
- Mediterranean Institute for Life Sciences, Split, Croatia
- Department of Physics, Faculty of Science, University of Split, Split, Croatia
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17
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Nguyen LK, Matallanas D, Croucher DR, von Kriegsheim A, Kholodenko BN. Signalling by protein phosphatases and drug development: a systems-centred view. FEBS J 2012; 280:751-65. [PMID: 22340367 DOI: 10.1111/j.1742-4658.2012.08522.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein modification cycles catalysed by opposing enzymes, such as kinases and phosphatases, form the backbone of signalling networks. Although, historically, kinases have been at the research forefront, a systems-centred approach reveals predominant roles for phosphatases in controlling the network response times and spatio-temporal profiles of signalling activities. Emerging evidence suggests that phosphatase kinetics are critical for network function and cell-fate decisions. Protein phosphatases operate as both immediate and delayed regulators of signal transduction, capable of attenuating or amplifying signalling. This versatility of phosphatase action emphasizes the need for systems biology approaches to understand cellular signalling networks and predict the cellular outcomes of combinatorial drug interventions.
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Affiliation(s)
- Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Ireland
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18
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Tsyganov MA, Kolch W, Kholodenko BN. The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. MOLECULAR BIOSYSTEMS 2012; 8:730-43. [DOI: 10.1039/c2mb05375f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Schwartz PA, Murray BW. Protein kinase biochemistry and drug discovery. Bioorg Chem 2011; 39:192-210. [PMID: 21872901 DOI: 10.1016/j.bioorg.2011.07.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 12/19/2022]
Abstract
Protein kinases are fascinating biological catalysts with a rapidly expanding knowledge base, a growing appreciation in cell regulatory control, and an ascendant role in successful therapeutic intervention. To better understand protein kinases, the molecular underpinnings of phosphoryl group transfer, protein phosphorylation, and inhibitor interactions are examined. This analysis begins with a survey of phosphate group and phosphoprotein properties which provide context to the evolutionary selection of phosphorylation as a central mechanism for biological regulation of most cellular processes. Next, the kinetic and catalytic mechanisms of protein kinases are examined with respect to model aqueous systems to define the elements of catalysis. A brief structural biology overview further delves into the molecular basis of catalysis and regulation of catalytic activity. Concomitant with a prominent role in normal physiology, protein kinases have important roles in the disease state. To facilitate effective kinase drug discovery, classic and emerging approaches for characterizing kinase inhibitors are evaluated including biochemical assay design, inhibitor mechanism of action analysis, and proper kinetic treatment of irreversible inhibitors. As the resulting protein kinase inhibitors can modulate intended and unintended targets, profiling methods are discussed which can illuminate a more complete range of an inhibitor's biological activities to enable more meaningful cellular studies and more effective clinical studies. Taken as a whole, a wealth of protein kinase biochemistry knowledge is available, yet it is clear that a substantial extent of our understanding in this field remains to be discovered which should yield many new opportunities for therapeutic intervention.
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Affiliation(s)
- Phillip A Schwartz
- Pfizer Worldwide Research and Development, La Jolla, Pfizer Inc., San Diego, CA 92121, United States
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