51
|
Hierarchical control of enzymatic actuators using DNA-based switchable memories. Nat Commun 2017; 8:1117. [PMID: 29061965 PMCID: PMC5714950 DOI: 10.1038/s41467-017-01127-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/18/2017] [Indexed: 12/30/2022] Open
Abstract
Inspired by signaling networks in living cells, DNA-based programming aims for the engineering of biochemical networks capable of advanced regulatory and computational functions under controlled cell-free conditions. While regulatory circuits in cells control downstream processes through hierarchical layers of signal processing, coupling of enzymatically driven DNA-based networks to downstream processes has rarely been reported. Here, we expand the scope of molecular programming by engineering hierarchical control of enzymatic actuators using feedback-controlled DNA-circuits capable of advanced regulatory dynamics. We developed a translator module that converts signaling molecules from the upstream network to unique DNA strands driving downstream actuators with minimal retroactivity and support these findings with a detailed computational analysis. We show our modular approach by coupling of a previously engineered switchable memories circuit to downstream actuators based on β-lactamase and luciferase. To the best of our knowledge, our work demonstrates one of the most advanced DNA-based circuits regarding complexity and versatility. Naturally evolved regulatory circuits have hierarchical layers of signal generation and processing. Here, the authors emulate these networks using feedback-controlled DNA circuits that convert upstream signaling to downstream enzyme activity in a switchable memories circuit.
Collapse
|
52
|
Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biol 2017; 15:e2000841. [PMID: 29045398 PMCID: PMC5646755 DOI: 10.1371/journal.pbio.2000841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/19/2017] [Indexed: 12/28/2022] Open
Abstract
Fundamental to biological decision-making is the ability to generate bimodal expression patterns where 2 alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV's fate decision between active replication and viral latency. We find that the HIV transactivator of transcription (Tat) protein manipulates the intrinsic toggling of HIV's promoter, the long terminal repeat (LTR), to generate bimodal ON-OFF expression and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit's noncooperative "nonlatching" feedback architecture is optimized to slow the promoter's toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that nonlatching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV's decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.
Collapse
Affiliation(s)
- Brandon S. Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, California, United Sates of America
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Youfang Cao
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Maike M. K. Hansen
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (MLS); (LSW)
| | - Leor S. Weinberger
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- QB3: California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (MLS); (LSW)
| |
Collapse
|
53
|
Navlakha S, Bar-Joseph Z, Barth AL. Network Design and the Brain. Trends Cogn Sci 2017; 22:64-78. [PMID: 29054336 DOI: 10.1016/j.tics.2017.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022]
Abstract
Neural circuits have evolved to accommodate similar information processing challenges as those faced by engineered systems. Here, we compare neural versus engineering strategies for constructing networks. During circuit development, synapses are overproduced and then pruned back over time, whereas in engineered networks, connections are initially sparse and are then added over time. We provide a computational perspective on these two different approaches, including discussion of how and why they are used, insights that one can provide the other, and areas for future joint investigation. By thinking algorithmically about the goals, constraints, and optimization principles used by neural circuits, we can develop brain-derived strategies for enhancing network design, while also stimulating experimental hypotheses about circuit development and function.
Collapse
Affiliation(s)
- Saket Navlakha
- The Salk Institute for Biological Studies, Integrative Biology Laboratory, La Jolla, CA 92037, USA.
| | - Ziv Bar-Joseph
- Carnegie Mellon University, Machine Learning Department, Computational Biology Department, Pittsburgh, PA 15213, USA
| | - Alison L Barth
- Carnegie Mellon University, Center for the Neural Basis of Cognition, Department of Biological Sciences, Pittsburgh, PA 15213, USA
| |
Collapse
|
54
|
Wollman R. Single-Molecule Threshold of HIV Fate Decision. Biophys J 2017; 112:2247-2248. [PMID: 28591597 DOI: 10.1016/j.bpj.2017.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/01/2017] [Indexed: 10/19/2022] Open
Abstract
During early infection, the HIV virus makes a key decision between two states: lytic and lysogenic fate. Deterministic bistability requires combination of positive feedback and ultrasensitivity. Although HIV circuity includes positive feedback activation of the Tat transactivator, it lacks ultrasensitivity. How does the HIV circuit allow for multiple fates without ultrasensitivity? A new article suggests that HIV bistability is a result of a transient threshold that allows the kinetic trapping of the inactive state. Interestingly, the model shows that the transient threshold is a result of a single molecule threshold that occurs when the promoter toggles between inactive and active states.
Collapse
Affiliation(s)
- Roy Wollman
- Department of Integrative Biology and Physiology, Department of Chemistry and Biochemistry, and Institute of Quantiative and Computational Biology, University of California - Los Angeles, Los Angeles, California.
| |
Collapse
|
55
|
Heinen L, Heuser T, Steinschulte A, Walther A. Antagonistic Enzymes in a Biocatalytic pH Feedback System Program Autonomous DNA Hydrogel Life Cycles. NANO LETTERS 2017; 17:4989-4995. [PMID: 28656771 DOI: 10.1021/acs.nanolett.7b02165] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Enzymes regulate complex functions and active behavior in natural systems and have shown increasing prospect for developing self-regulating soft matter systems. Striving for advanced autonomous hydrogel materials with fully programmable, self-regulated life cycles, we combine two enzymes with an antagonistic pH-modulating effect in a feedback-controlled biocatalytic reaction network (BRN) and couple it to pH-responsive DNA hydrogels to realize hydrogel systems with distinct preprogrammable lag times and lifetimes in closed systems. The BRN enables precise and orthogonal internal temporal control of the "ON" and "OFF" switching times of the temporary gel state by modulation of programmable, nonlinear pH changes. The time scales are tunable by variation of the enzyme concentrations and additional buffer substances. The resulting material system operates in full autonomy after injection of the chemical fuels driving the BRN. The concept may open new applications inherent to DNA hydrogels, for instance, autonomous shape memory behavior for soft robotics. We further foresee general applicability to achieve autonomous life cycles in other pH switchable systems.
Collapse
Affiliation(s)
- Laura Heinen
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31, University of Freiburg , 79104 Freiburg, Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21, University of Freiburg , 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105, University of Freiburg , 79110 Freiburg, Germany
| | - Thomas Heuser
- DWI - Leibniz Institute for Interactive Materials , Forckenbeckstrasse 50, D-52074 Aachen, Germany
| | - Alexander Steinschulte
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, 52056 Aachen, Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31, University of Freiburg , 79104 Freiburg, Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21, University of Freiburg , 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105, University of Freiburg , 79110 Freiburg, Germany
| |
Collapse
|
56
|
Cora' D, Re A, Caselle M, Bussolino F. MicroRNA-mediated regulatory circuits: outlook and perspectives. Phys Biol 2017; 14:045001. [PMID: 28586314 DOI: 10.1088/1478-3975/aa6f21] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs have been found to be necessary for regulating genes implicated in almost all signaling pathways, and consequently their dysfunction influences many diseases, including cancer. Understanding of the complexity of the microRNA-mediated regulatory network has grown in terms of size, connectivity and dynamics with the development of computational and, more recently, experimental high-throughput approaches for microRNA target identification. Newly developed studies on recurrent microRNA-mediated circuits in regulatory networks, also known as network motifs, have substantially contributed to addressing this complexity, and therefore to helping understand the ways by which microRNAs achieve their regulatory role. This review provides a summarizing view of the state-of-the-art, and perspectives of research efforts on microRNA-mediated regulatory motifs. In this review, we discuss the topological properties characterizing different types of circuits, and the regulatory features theoretically enabled by such properties, with a special emphasis on examples of circuits typifying their biological significance in experimentally validated contexts. Finally, we will consider possible future developments, in particular regarding microRNA-mediated circuits involving long non-coding RNAs and epigenetic regulators.
Collapse
Affiliation(s)
- Davide Cora'
- Department of Oncology, University of Torino, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Candiolo Cancer Institute-FPO, IRCCS, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Center for Molecular Systems Biology, University of Torino, Regione Gonzole 10, I-10043 Orbassano, Italy. Current address: Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Via Solaroli 17, I-28100 Novara, Italy
| | | | | | | |
Collapse
|
57
|
Shi W, Ma W, Xiong L, Zhang M, Tang C. Adaptation with transcriptional regulation. Sci Rep 2017; 7:42648. [PMID: 28233824 PMCID: PMC5324054 DOI: 10.1038/srep42648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/10/2017] [Indexed: 11/21/2022] Open
Abstract
Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.
Collapse
Affiliation(s)
- Wenjia Shi
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Wenzhe Ma
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liyang Xiong
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Mingyue Zhang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
58
|
Robust network topologies for generating oscillations with temperature-independent periods. PLoS One 2017; 12:e0171263. [PMID: 28152061 PMCID: PMC5289577 DOI: 10.1371/journal.pone.0171263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/17/2017] [Indexed: 11/26/2022] Open
Abstract
Nearly all living systems feature a temperature-independent oscillation period in circadian clocks. This ubiquitous property occurs at the system level and is rooted in the network architecture of the clock machinery. To investigate the mechanism of this prominent property of the circadian clock and provide general guidance for generating robust genetic oscillators with temperature-compensated oscillations, we theoretically explored the design principle and core network topologies preferred by oscillations with a temperature-independent period. By enumerating all topologies of genetic regulatory circuits with three genes, we obtained four network motifs, namely, a delayed negative feedback oscillator, repressilator, activator-inhibitor oscillator and substrate-depletion oscillator; hybrids of these motifs constitute the vast majority of target network topologies. These motifs are biased in their capacities for achieving oscillations and the temperature sensitivity of the period. The delayed negative feedback oscillator and repressilator are more robust for oscillations, whereas the activator-inhibitor and substrate-depletion oscillators are superior for maintaining a temperature-independent oscillation period. These results suggest that thermally robust oscillation can be more plausibly achieved by hybridizing these two categories of network motifs. Antagonistic balance and temperature insulation mechanisms for achieving temperature compensation are typically found in these topologies with temperature robustness. In the temperature insulation approach, the oscillation period relies on very few parameters, and these parameters are influenced only slightly by temperature. This approach prevents the temperature from affecting the oscillation period and generates circadian rhythms that are robust against environmental perturbations.
Collapse
|
59
|
Farhan H. Regulation of EGFR surface levels by COPII-dependent trafficking. J Cell Biol 2016; 215:441-443. [PMID: 27872251 PMCID: PMC5119945 DOI: 10.1083/jcb.201611014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/03/2016] [Indexed: 01/16/2023] Open
Abstract
Farhan discusses Scharaw et al.’s study about how the COPII machinery is used to replenish EGFR at the cell surface. Cell surface levels of epidermal growth factor receptors (EGFRs) are thought to be controlled mainly by endocytic trafficking, with biosynthetic EGFR trafficking presumed to be a constitutive and unregulated process. However, Scharaw et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201601090) demonstrate a role for inducible COPII trafficking in controlling EGFR surface levels.
Collapse
Affiliation(s)
- Hesso Farhan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway
| |
Collapse
|
60
|
Ta CH, Nie Q, Hong T. Controlling Stochasticity in Epithelial-Mesenchymal Transition Through Multiple Intermediate Cellular States. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS. SERIES B 2016; 21:2275-2291. [PMID: 29497351 PMCID: PMC5828240 DOI: 10.3934/dcdsb.2016047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is an instance of cellular plasticity that plays critical roles in development, regeneration and cancer progression. Recent studies indicate that the transition between epithelial and mesenchymal states is a multi-step and reversible process in which several intermediate phenotypes might coexist. These intermediate states correspond to various forms of stem-like cells in the EMT system, but the function of the multi-step transition or the multiple stem cell phenotypes is unclear. Here, we use mathematical models to show that multiple intermediate phenotypes in the EMT system help to attenuate the overall fluctuations of the cell population in terms of phenotypic compositions, thereby stabilizing a heterogeneous cell population in the EMT spectrum. We found that the ability of the system to attenuate noise on the intermediate states depends on the number of intermediate states, indicating the stem-cell population is more stable when it has more sub-states. Our study reveals a novel advantage of multiple intermediate EMT phenotypes in terms of systems design, and it sheds light on the general design principle of heterogeneous stem cell population.
Collapse
Affiliation(s)
- Catherine Ha Ta
- Department of Mathematics, Univ. of California Irvine Irvine, CA 92697-3875, USA
| | - Qing Nie
- Department of Mathematics, Univ. of California Irvine Irvine, CA 92697-3875, USA
| | - Tian Hong
- Department of Mathematics, Univ. of California Irvine Irvine, CA 92697-3875, USA
| |
Collapse
|
61
|
Vornanen M. The temperature dependence of electrical excitability in fish hearts. J Exp Biol 2016; 219:1941-52. [DOI: 10.1242/jeb.128439] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/17/2016] [Indexed: 01/08/2023]
Abstract
ABSTRACT
Environmental temperature has pervasive effects on the rate of life processes in ectothermic animals. Animal performance is affected by temperature, but there are finite thermal limits for vital body functions, including contraction of the heart. This Review discusses the electrical excitation that initiates and controls the rate and rhythm of fish cardiac contraction and is therefore a central factor in the temperature-dependent modulation of fish cardiac function. The control of cardiac electrical excitability should be sensitive enough to respond to temperature changes but simultaneously robust enough to protect against cardiac arrhythmia; therefore, the thermal resilience and plasticity of electrical excitation are physiological qualities that may affect the ability of fishes to adjust to climate change. Acute changes in temperature alter the frequency of the heartbeat and the duration of atrial and ventricular action potentials (APs). Prolonged exposure to new thermal conditions induces compensatory changes in ion channel expression and function, which usually partially alleviate the direct effects of temperature on cardiac APs and heart rate. The most heat-sensitive molecular components contributing to the electrical excitation of the fish heart seem to be Na+ channels, which may set the upper thermal limit for the cardiac excitability by compromising the initiation of the cardiac AP at high temperatures. In cardiac and other excitable cells, the different temperature dependencies of the outward K+ current and inward Na+ current may compromise electrical excitability at temperature extremes, a hypothesis termed the temperature-dependent depression of electrical excitation.
Collapse
Affiliation(s)
- Matti Vornanen
- University of Eastern Finland, Department of Environmental and Biological Sciences, PO Box 111, Joensuu 80101, Finland
| |
Collapse
|
62
|
Feng S, Ollivier JF, Soyer OS. Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks. PLoS Comput Biol 2016; 12:e1004918. [PMID: 27163612 PMCID: PMC4862689 DOI: 10.1371/journal.pcbi.1004918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 04/17/2016] [Indexed: 11/18/2022] Open
Abstract
Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications.
Collapse
Affiliation(s)
- Song Feng
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Orkun S. Soyer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
| |
Collapse
|
63
|
Siegal-Gaskins D, Franco E, Zhou T, Murray RM. An analytical approach to bistable biological circuit discrimination using real algebraic geometry. J R Soc Interface 2016; 12:20150288. [PMID: 26109633 DOI: 10.1098/rsif.2015.0288] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem--a tool from nineteenth-century real algebraic geometry--to comparing 'functionally equivalent' bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh-Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.
Collapse
|
64
|
He B, Tan K. Understanding transcriptional regulatory networks using computational models. Curr Opin Genet Dev 2016; 37:101-108. [PMID: 26950762 DOI: 10.1016/j.gde.2016.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 02/08/2016] [Indexed: 01/06/2023]
Abstract
Transcriptional regulatory networks (TRNs) encode instructions for animal development and physiological responses. Recent advances in genomic technologies and computational modeling have revolutionized our ability to construct models of TRNs. Here, we survey current computational methods for inferring TRN models using genome-scale data. We discuss their advantages and limitations. We summarize representative TRNs constructed using genome-scale data in both normal and disease development. We discuss lessons learned about the structure/function relationship of TRNs, based on examining various large-scale TRN models. Finally, we outline some open questions regarding TRNs, including how to improve model accuracy by integrating complementary data types, how to infer condition-specific TRNs, and how to compare TRNs across conditions and species in order to understand their structure/function relationship.
Collapse
Affiliation(s)
- Bing He
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Tan
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
65
|
Abstract
Biological systems are complex. In particular, the interactions between molecular components often form dense networks that, more often than not, are criticized for being inscrutable 'hairballs'. We argue that one way of untangling these hairballs is through cross-disciplinary network comparison-leveraging advances in other disciplines to obtain new biological insights. In some cases, such comparisons enable the direct transfer of mathematical formalism between disciplines, precisely describing the abstract associations between entities and allowing us to apply a variety of sophisticated formalisms to biology. In cases where the detailed structure of the network does not permit the transfer of complete formalisms between disciplines, comparison of mechanistic interactions in systems for which we have significant day-to-day experience can provide analogies for interpreting relatively more abstruse biological networks. Here, we illustrate how these comparisons benefit the field with a few specific examples related to network growth, organizational hierarchies, and the evolution of adaptive systems.
Collapse
|
66
|
Villaseñor R, Kalaidzidis Y, Zerial M. Signal processing by the endosomal system. Curr Opin Cell Biol 2016; 39:53-60. [PMID: 26921695 DOI: 10.1016/j.ceb.2016.02.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/29/2016] [Accepted: 02/03/2016] [Indexed: 02/08/2023]
Abstract
Cells need to decode chemical or physical signals from their environment in order to make decisions on their fate. In the case of signalling receptors, ligand binding triggers a cascade of chemical reactions but also the internalization of the activated receptors in the endocytic pathway. Here, we highlight recent studies revealing a new role of the endosomal network in signal processing. The diversity of entry pathways and endosomal compartments is exploited to regulate the kinetics of receptor trafficking, and interactions with specific signalling adaptors and effectors. By governing the spatio-temporal distribution of signalling molecules, the endosomal system functions analogously to a digital-analogue computer that regulates the specificity and robustness of the signalling response.
Collapse
Affiliation(s)
- Roberto Villaseñor
- Roche Innovation Center Basel, Grenzacherstrasse, CH-4070 Basel, Switzerland.
| | - Yannis Kalaidzidis
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.
| | - Marino Zerial
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.
| |
Collapse
|
67
|
Suzuki Y, Lu M, Ben-Jacob E, Onuchic JN. Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays. Sci Rep 2016; 6:21037. [PMID: 26876008 PMCID: PMC4753448 DOI: 10.1038/srep21037] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/24/2023] Open
Abstract
Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.
Collapse
Affiliation(s)
- Yoko Suzuki
- Department of Physics, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.,Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA
| | - Mingyang Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA.,Department of Chemistry, Rice University, Houston, TX 77005-1827, USA.,Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005-1827, USA
| |
Collapse
|
68
|
Sumit M, Neubig RR, Takayama S, Linderman JJ. Band-pass processing in a GPCR signaling pathway selects for NFAT transcription factor activation. Integr Biol (Camb) 2015; 7:1378-86. [PMID: 26374065 PMCID: PMC4630096 DOI: 10.1039/c5ib00181a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biological processes are rhythmic and proper timing is increasingly appreciated as being critical for development and maintenance of physiological functions. To understand how temporal modulation of an input signal influences downstream responses, we employ microfluidic pulsatile stimulation of a G-protein coupled receptor, the muscarinic M3 receptor, in single cells with simultaneous real-time imaging of both intracellular calcium and NFAT nuclear localization. Interestingly, we find that reduced stimulation with pulses of ligand can give more efficient transcription factor activation, if stimuli are timed appropriately. Our experiments and computational analyses show that M3 receptor-induced calcium oscillations form a low pass filter while calcium-induced NFAT translocation forms a high pass filter. The combination acts as a band-pass filter optimized for intermediate frequencies of stimulation. We demonstrate that receptor desensitization and NFAT translocation rates determine critical features of the band-pass filter and that the band-pass may be shifted for different receptors or NFAT dynamics. As an example, we show that the two NFAT isoforms (NFAT4 and NFAT1) have shifted band-pass windows for the same receptor. While we focus specifically on the M3 muscarinic receptor and NFAT translocation, band-pass processing is expected to be a general theme that applies to multiple signaling pathways.
Collapse
Affiliation(s)
- M Sumit
- Biointerface Institute, North Campus Research Complex, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA. and Biophysics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - R R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue Street, East Lansing, MI 48824, USA
| | - S Takayama
- Biointerface Institute, North Campus Research Complex, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA. and Michigan Centre for Integrative Research in Critical Care, North Campus Research Complex, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - J J Linderman
- Department of Biomedical Engineering, University of Michigan, 1107 Carl A. Gerstacker Building, 2200, Bonisteel Blvd, Ann Arbor, MI 48109, USA. and Department of Chemical Engineering, University of Michigan, Building 26, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| |
Collapse
|
69
|
Ganter M, Kaltenbach HM, Stelling J. Predicting network functions with nested patterns. Nat Commun 2015; 5:3006. [PMID: 24398547 DOI: 10.1038/ncomms4006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 11/24/2013] [Indexed: 12/20/2022] Open
Abstract
Identifying suitable patterns in complex biological interaction networks helps understanding network functions and allows for predictions at the pattern level: by recognizing a known pattern, one can assign its previously established function. However, current approaches fail for previously unseen patterns, when patterns overlap and when they are embedded into a new network context. Here we show how to conceptually extend pattern-based approaches. We define metabolite patterns in metabolic networks that formalize co-occurrences of metabolites. Our probabilistic framework decodes the implicit information in the networks' metabolite patterns to predict metabolic functions. We demonstrate the predictive power by identifying 'indicator patterns', for instance, for enzyme classification, by predicting directions of novel reactions and of known reactions in new network contexts, and by ranking candidate network extensions for gap filling. Beyond their use in improving genome annotations and metabolic network models, we expect that the concepts transfer to other network types.
Collapse
Affiliation(s)
- Mathias Ganter
- 1] Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland [2]
| | - Hans-Michael Kaltenbach
- 1] Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland [2]
| | - Jörg Stelling
- Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland
| |
Collapse
|
70
|
Makadia HK, Schwaber JS, Vadigepalli R. Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features. PLoS Comput Biol 2015; 11:e1004563. [PMID: 26491963 PMCID: PMC4619640 DOI: 10.1371/journal.pcbi.1004563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/19/2015] [Indexed: 01/29/2023] Open
Abstract
Cell signaling dynamics and transcriptional regulatory activities are variable within specific cell types responding to an identical stimulus. In addition to studying the network interactions, there is much interest in utilizing single cell scale data to elucidate the non-random aspects of the variability involved in cellular decision making. Previous studies have considered the information transfer between the signaling and transcriptional domains based on an instantaneous relationship between the molecular activities. These studies predict a limited binary on/off encoding mechanism which underestimates the complexity of biological information processing, and hence the utility of single cell resolution data. Here we pursue a novel strategy that reformulates the information transfer problem as involving dynamic features of signaling rather than molecular abundances. We pursue a computational approach to test if and how the transcriptional regulatory activity patterns can be informative of the temporal history of signaling. Our analysis reveals (1) the dynamic features of signaling that significantly alter transcriptional regulatory patterns (encoding), and (2) the temporal history of signaling that can be inferred from single cell scale snapshots of transcriptional activity (decoding). Immediate early gene expression patterns were informative of signaling peak retention kinetics, whereas transcription factor activity patterns were informative of activation and deactivation kinetics of signaling. Moreover, the information processing aspects varied across the network, with each component encoding a selective subset of the dynamic signaling features. We developed novel sensitivity and information transfer maps to unravel the dynamic multiplexing of signaling features at each of these network components. Unsupervised clustering of the maps revealed two groups that aligned with network motifs distinguished by transcriptional feedforward vs feedback interactions. Our new computational methodology impacts the single cell scale experiments by identifying downstream snapshot measures required for inferring specific dynamical features of upstream signals involved in the regulation of cellular responses. Single cell studies have shown that differential patterns in the dynamics of signaling proteins, transcription factor activity, gene expression, etc. produce distinct downstream outcomes. The opposite also holds true where particular cellular outcomes have been found to be associated with the dynamical pattern of one or more signaling molecules. Signaling pathways, therefore, serve as signal processing units to inform specific downstream regulation. However, the functional capabilities of the dynamic aspects of signaling are not well understood. To address this issue, we developed a new approach that evaluates information processing between dynamic features in signaling patterns and transcriptional regulatory activity. Our work demonstrates that the information transfer occur through decoding of temporal history of signals rather than only through instantaneous correlations. Moreover, our results identify regulatory network motifs as the critical components in the information processing and filtering of variability in signaling dynamics to produce distinct patterns of downstream transcriptional responses. Our methodology can be broadly applied to single cell scale data on experimentally accessible downstream measures to infer dynamic aspects of upstream signaling.
Collapse
Affiliation(s)
- Hirenkumar K. Makadia
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - James S. Schwaber
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
71
|
Abstract
There is rapidly growing interest in learning how to engineer immune cells, such as T lymphocytes, because of the potential of these engineered cells to be used for therapeutic applications such as the recognition and killing of cancer cells. At the same time, our knowhow and capability to logically engineer cellular behavior is growing rapidly with the development of synthetic biology. Here we describe how synthetic biology approaches are being used to rationally alter the behavior of T cells to optimize them for therapeutic functions. We also describe future developments that will be important in order to construct safe and precise T cell therapeutics.
Collapse
Affiliation(s)
- Chia-Yung Wu
- Dept. of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, United States
| | - Levi J Rupp
- Dept. of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, United States
| | - Kole T Roybal
- Dept. of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, United States
| | - Wendell A Lim
- Dept. of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, United States; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, United States.
| |
Collapse
|
72
|
Ping X, Tang C. An Atlas of Network Topologies Reveals Design Principles for Caenorhabditis elegans Vulval Precursor Cell Fate Patterning. PLoS One 2015; 10:e0131397. [PMID: 26114587 PMCID: PMC4482679 DOI: 10.1371/journal.pone.0131397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/01/2015] [Indexed: 12/11/2022] Open
Abstract
The vulval precursor cell (VPC) fate patterning in Caenorhabditis elegans is a classic model experimental system for cell fate determination and patterning in development. Despite its apparent simplicity (six neighboring cells arranged in one dimension) and many experimental and computational efforts, the patterning strategy and mechanism remain controversial due to incomplete knowledge of the complex biology. Here, we carry out a comprehensive computational analysis and obtain a reservoir of all possible network topologies that are capable of VPC fate patterning under the simulation of various biological environments and regulatory rules. We identify three patterning strategies: sequential induction, morphogen gradient and lateral antagonism, depending on the features of the signal secreted from the anchor cell. The strategy of lateral antagonism, which has not been reported in previous studies of VPC patterning, employs a mutual inhibition of the 2° cell fate in neighboring cells. Robust topologies are built upon minimal topologies with basic patterning strategies and have more flexible and redundant implementations of modular functions. By simulated mutation, we find that all three strategies can reproduce experimental error patterns of mutants. We show that the topology derived by mapping currently known biochemical pathways to our model matches one of our identified functional topologies. Furthermore, our robustness analysis predicts a possible missing link related to the lateral antagonism strategy. Overall, we provide a theoretical atlas of all possible functional networks in varying environments, which may guide novel discoveries of the biological interactions in vulval development of Caenorhabditis elegans and related species.
Collapse
Affiliation(s)
- Xianfeng Ping
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail:
| |
Collapse
|
73
|
Schulze A, Gomez-Marin A, Rajendran VG, Lott G, Musy M, Ahammad P, Deogade A, Sharpe J, Riedl J, Jarriault D, Trautman ET, Werner C, Venkadesan M, Druckmann S, Jayaraman V, Louis M. Dynamical feature extraction at the sensory periphery guides chemotaxis. eLife 2015; 4. [PMID: 26077825 PMCID: PMC4468351 DOI: 10.7554/elife.06694] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/30/2015] [Indexed: 11/13/2022] Open
Abstract
Behavioral strategies employed for chemotaxis have been described across phyla, but the sensorimotor basis of this phenomenon has seldom been studied in naturalistic contexts. Here, we examine how signals experienced during free olfactory behaviors are processed by first-order olfactory sensory neurons (OSNs) of the Drosophila larva. We find that OSNs can act as differentiators that transiently normalize stimulus intensity—a property potentially derived from a combination of integral feedback and feed-forward regulation of olfactory transduction. In olfactory virtual reality experiments, we report that high activity levels of the OSN suppress turning, whereas low activity levels facilitate turning. Using a generalized linear model, we explain how peripheral encoding of olfactory stimuli modulates the probability of switching from a run to a turn. Our work clarifies the link between computations carried out at the sensory periphery and action selection underlying navigation in odor gradients. DOI:http://dx.doi.org/10.7554/eLife.06694.001 Fruit flies are attracted to the smell of rotting fruit, and use it to guide them to nearby food sources. However, this task is made more challenging by the fact that the distribution of scent or odor molecules in the air is constantly changing. Fruit flies therefore need to cope with, and exploit, this variation if they are to use odors as cues. Odor molecules bind to receptors on the surface of nerve cells called olfactory sensory neurons, and trigger nerve impulses that travel along these cells. While many studies have investigated how fruit flies can distinguish between different odors, less is known about how animals can use variation in the strength of an odor to guide them towards its source. Optogenetics is a technique that allows neuroscientists to control the activities of individual nerve cells, simply by shining light on to them. Because fruit fly larvae are almost transparent, optogenetics can be used on freely moving animals. Now, Schulze, Gomez-Marin et al. have used optogenetics in these larvae to trigger patterns of activity in individual olfactory sensory neurons that mimic the activity patterns elicited by real odors. These virtual realities were then used to study, in detail, some of the principles that control the sensory navigation of a larva—as it moves using a series of forward ‘runs’ and direction-changing ‘turns’. Olfactory sensory neurons responded most strongly whenever light levels changed rapidly in strength (which simulated a rapid change in odor concentration). On the other hand, these neurons showed relatively little response to constant light levels (i.e., constant odors). This indicates that the activity of olfactory sensory neurons typically represents the rate of change in the concentration of an odor. An independent study by Kim et al. found that olfactory sensory neurons in adult fruit flies also respond in a similar way. Schulze, Gomez-Marin et al. went on to show that the signals processed by a single type of olfactory sensory neuron could be used to predict a larva's behavior. Larvae tended to turn less when their olfactory sensory neurons were highly active. Low levels and inhibition of activity in the olfactory sensory neurons had the opposite effect; this promoted turning. It remains to be determined how this relatively simple control principle is implemented by the neural circuits that connect sensory neurons to the parts of a larva's nervous system that are involved with movement. DOI:http://dx.doi.org/10.7554/eLife.06694.002
Collapse
Affiliation(s)
- Aljoscha Schulze
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Alex Gomez-Marin
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Vani G Rajendran
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Gus Lott
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Marco Musy
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Parvez Ahammad
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ajinkya Deogade
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - James Sharpe
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Julia Riedl
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - David Jarriault
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| | - Eric T Trautman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Christopher Werner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Madhusudhan Venkadesan
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, United States
| | - Shaul Druckmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Vivek Jayaraman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Matthieu Louis
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Barcelona, Spain
| |
Collapse
|
74
|
Campbell ST, Carlson KJ, Buchholz CJ, Helmers MR, Ghosh I. Mapping the BH3 Binding Interface of Bcl-xL, Bcl-2, and Mcl-1 Using Split-Luciferase Reassembly. Biochemistry 2015; 54:2632-43. [PMID: 25844633 DOI: 10.1021/bi501505y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recognition of helical BH3 domains by Bcl-2 homology (BH) receptors plays a central role in apoptosis. The residues that determine specificity or promiscuity in this interactome are difficult to predict from structural and computational data. Using a cell free split-luciferase system, we have generated a 276 pairwise interaction map for 12 alanine mutations at the binding interface for three receptors, Bcl-xL, Bcl-2, and Mcl-1, and interrogated them against BH3 helices derived from Bad, Bak, Bid, Bik, Bim, Bmf, Hrk, and Puma. This panel, in conjunction with previous structural and functional studies, starts to provide a more comprehensive portrait of this interactome, explains promiscuity, and uncovers surprising details; for example, the Bcl-xL R139A mutation disrupts binding to all helices but the Bad-BH3 peptide, and Mcl-1 binding is particularly perturbed by only four mutations of the 12 tested (V220A, N260A, R263A, and F319A), while Bcl-xL and Bcl-2 have a more diverse set of important residues depending on the bound helix.
Collapse
Affiliation(s)
- Sean T Campbell
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Kevin J Carlson
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Carl J Buchholz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Mark R Helmers
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| |
Collapse
|
75
|
Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Exp Biol Med (Maywood) 2015; 240:351-60. [PMID: 25710931 PMCID: PMC4436281 DOI: 10.1177/1535370214566558] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.
Collapse
Affiliation(s)
- Emma Joy Dodson
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Vered Fishbain-Yoskovitz
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| |
Collapse
|
76
|
Heng BC, Aubel D, Fussenegger M. Prosthetic gene networks as an alternative to standard pharmacotherapies for metabolic disorders. Curr Opin Biotechnol 2015; 35:37-45. [PMID: 25679308 DOI: 10.1016/j.copbio.2015.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/28/2015] [Accepted: 01/28/2015] [Indexed: 12/19/2022]
Abstract
Synthetic biology makes inroads into clinical therapy with the debut of closed-loop prosthetic gene networks specifically designed to treat human diseases. Prosthetic networks are synthetic sensor/effector devices that could functionally integrate and interface with host metabolism to monitor disease states and coordinate appropriate therapeutic responses in a self-sufficient, timely and automatic manner. Prosthetic networks hold particular promise for the current global epidemic of closely interrelated metabolic disorders encompassing obesity, type 2 diabetes, hypertension and hyperlipidaemia, which arise from the unhealthy lifestyle and dietary factors in the modern urbanised world. This review will critically examine the various attempts at constructing prosthetic gene networks for the treatment of these metabolic disorders, as well as provide insight into future developments in the field.
Collapse
Affiliation(s)
- Boon Chin Heng
- Department of Biological Sciences, Sunway University, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
| |
Collapse
|
77
|
Abstract
To what extent does the dynamical mechanism producing a specific biological phenotype bias the ability to evolve into novel phenotypes? We use the interpretation of a morphogen gradient into a single stripe of gene expression as a model phenotype. Although there are thousands of three-gene circuit topologies that can robustly develop a stripe of gene expression, the vast majority of these circuits use one of just six fundamentally different dynamical mechanisms. Here we explore the potential for gene circuits that use each of these six mechanisms to evolve novel phenotypes such as multiple stripes, inverted stripes, and gradients of gene expression. Through a comprehensive and systematic analysis, we find that circuits that use alternative mechanisms differ in the likelihood of reaching novel phenotypes through mutation. We characterize the phenotypic transitions and identify key ingredients of the evolutionary potential, such as sensitive interactions and phenotypic hubs. Finally, we provide an intuitive understanding on how the modular design of a particular mechanism favors the access to novel phenotypes. Our work illustrates how the dynamical mechanism by which an organism develops constrains how it can evolve. It is striking that these dynamical mechanisms and their impact on evolvability can be observed even for such an apparently simple patterning task, performed by just three-node circuits.
Collapse
|
78
|
van Roekel HWH, Rosier BJHM, Meijer LHH, Hilbers PAJ, Markvoort AJ, Huck WTS, de Greef TFA. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach. Chem Soc Rev 2015. [DOI: 10.1039/c5cs00361j] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli.
Collapse
Affiliation(s)
- Hendrik W. H. van Roekel
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| | - Bas J. H. M. Rosier
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| | - Lenny H. H. Meijer
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| | - Peter A. J. Hilbers
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| | - Albert J. Markvoort
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Tom F. A. de Greef
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Computational Biology Group
| |
Collapse
|
79
|
Tillmann KD, Reiterer V, Baschieri F, Hoffmann J, Millarte V, Hauser MA, Mazza A, Atias N, Legler DF, Sharan R, Weiss M, Farhan H. Regulation of Sec16 levels and dynamics links proliferation and secretion. J Cell Sci 2014; 128:670-82. [PMID: 25526736 DOI: 10.1242/jcs.157115] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We currently lack a broader mechanistic understanding of the integration of the early secretory pathway with other homeostatic processes such as cell growth. Here, we explore the possibility that Sec16A, a major constituent of endoplasmic reticulum exit sites (ERES), acts as an integrator of growth factor signaling. Surprisingly, we find that Sec16A is a short-lived protein that is regulated by growth factors in a manner dependent on Egr family transcription factors. We hypothesize that Sec16A acts as a central node in a coherent feed-forward loop that detects persistent growth factor stimuli to increase ERES number. Consistent with this notion, Sec16A is also regulated by short-term growth factor treatment that leads to increased turnover of Sec16A at ERES. Finally, we demonstrate that Sec16A depletion reduces proliferation, whereas its overexpression increases proliferation. Together with our finding that growth factors regulate Sec16A levels and its dynamics on ERES, we propose that this protein acts as an integrator linking growth factor signaling and secretion. This provides a mechanistic basis for the previously proposed link between secretion and proliferation.
Collapse
Affiliation(s)
- Kerstin D Tillmann
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland University of Konstanz, Universitätsstrasse 10, Konstanz 78464, Germany
| | - Veronika Reiterer
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland
| | - Francesco Baschieri
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland University of Konstanz, Universitätsstrasse 10, Konstanz 78464, Germany
| | - Julia Hoffmann
- Experimental Physics I, University of Bayreuth, Bayreuth 95440, Germany
| | - Valentina Millarte
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland University of Konstanz, Universitätsstrasse 10, Konstanz 78464, Germany
| | - Mark A Hauser
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland
| | - Arnon Mazza
- Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Nir Atias
- Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Daniel F Legler
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Bayreuth 95440, Germany
| | - Hesso Farhan
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland University of Konstanz, Universitätsstrasse 10, Konstanz 78464, Germany
| |
Collapse
|
80
|
Abstract
We have come a long way in the 55 years since Edmond Fischer and the late Edwin Krebs discovered that the activity of glycogen phosphorylase is regulated by reversible protein phosphorylation. Many of the fundamental molecular mechanisms that operate in biological signaling have since been characterized and the vast web of interconnected pathways that make up the cellular signaling network has been mapped in considerable detail. Nonetheless, it is important to consider how fast this field is still moving and the issues at the current boundaries of our understanding. One must also appreciate what experimental strategies have allowed us to attain our present level of knowledge. We summarize here some key issues (both conceptual and methodological), raise unresolved questions, discuss potential pitfalls, and highlight areas in which our understanding is still rudimentary. We hope these wide-ranging ruminations will be useful to investigators who carry studies of signal transduction forward during the rest of the 21st century.
Collapse
|
81
|
Lück S, Thurley K, Thaben PF, Westermark PO. Rhythmic degradation explains and unifies circadian transcriptome and proteome data. Cell Rep 2014; 9:741-51. [PMID: 25373909 DOI: 10.1016/j.celrep.2014.09.021] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 07/04/2014] [Accepted: 09/11/2014] [Indexed: 12/28/2022] Open
Abstract
The rich mammalian cellular circadian output affects thousands of genes in many cell types and has been the subject of genome-wide transcriptome and proteome studies. The results have been enigmatic because transcript peak abundances do not always follow the peaks of gene-expression activity in time. We posited that circadian degradation of mRNAs and proteins plays a pivotal role in setting their peak times. To establish guiding principles, we derived a theoretical framework that fully describes the amplitudes and phases of biomolecules with circadian half-lives. We were able to explain the circadian transcriptome and proteome studies with the same unifying theory, including cases in which transcripts or proteins appeared before the onset of increased production rates. Furthermore, we estimate that 30% of the circadian transcripts in mouse liver and Drosophila heads are affected by rhythmic posttranscriptional regulation.
Collapse
Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité-Universitätsmedizin, 10115 Berlin, Germany
| | - Kevin Thurley
- Institute for Theoretical Biology, Charité-Universitätsmedizin, 10115 Berlin, Germany
| | - Paul F Thaben
- Institute for Theoretical Biology, Charité-Universitätsmedizin, 10115 Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité-Universitätsmedizin, 10115 Berlin, Germany.
| |
Collapse
|
82
|
Abstract
Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein expression levels all will affect the suitability of different strategies--such as constitutive expression or graded response--for regulating protein levels in response to environmental inputs. We propose a general framework-here specifically applied to the enzymatic regulation of metabolism in response to changing concentrations of a basic nutrient-to predict the optimal regulatory strategy given the statistics of fluctuations in the environment and measurement apparatus, respectively, and the costs associated with enzyme production. We use this framework to address three fundamental questions: (i) when a cell should prefer thresholding to a graded response; (ii) when there is a fitness advantage to implementing a Bayesian decision rule; and (iii) when retaining memory of the past provides a selective advantage. We specifically find that: (i) relative convexity of enzyme expression cost and benefit influences the fitness of thresholding or graded responses; (ii) intermediate levels of measurement uncertainty call for a sophisticated Bayesian decision rule; and (iii) in dynamic contexts, intermediate levels of uncertainty call for retaining memory of the past. Statistical properties of the environment, such as variability and correlation times, set optimal biochemical parameters, such as thresholds and decay rates in signaling pathways. Our framework provides a theoretical basis for interpreting molecular signal processing algorithms and a classification scheme that organizes known regulatory strategies and may help conceptualize heretofore unknown ones.
Collapse
|
83
|
Schaerli Y, Munteanu A, Gili M, Cotterell J, Sharpe J, Isalan M. A unified design space of synthetic stripe-forming networks. Nat Commun 2014; 5:4905. [PMID: 25247316 PMCID: PMC4172969 DOI: 10.1038/ncomms5905] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/02/2014] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
Collapse
Affiliation(s)
- Yolanda Schaerli
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andreea Munteanu
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Magüi Gili
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Cotterell
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mark Isalan
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
84
|
Ishimatsu K, Hata T, Mochizuki A, Sekine R, Yamamura M, Kiga D. General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming. ACS Synth Biol 2014; 3:638-44. [PMID: 24295073 DOI: 10.1021/sb400102w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Control of the cell-type ratio in multistable systems requires wide-range control of the initial states of cells. Here, using a synthetic circuit in E. coli, we describe the use of a simple gene-overexpression system combined with a bistable toggle switch, for the purposes of enabling the wide-range control of cellular states and thus generating arbitrary cell-type ratios. Theoretically, overexpression induction temporarily alters the bistable system to a monostable system, in which the location of the single steady state of cells can be manipulated over a wide range by regulating the overexpression levels. This induced cellular state becomes the initial state of the basal bistable system upon overexpression cessation, which restores the original bistable system. We experimentally demonstrated that the overexpression induced a monomodal cell distribution, and subsequent overexpression withdrawal generated a bimodal distribution. Furthermore, as designed theoretically, regulating the overexpression levels by adjusting the concentrations of small molecules generated arbitrary cell-type ratios.
Collapse
Affiliation(s)
- Kana Ishimatsu
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
- PRESTO, Japan
Science and Technology Agency, 7 Gobancho, Chiyodaku, Tokyo, 102-0076, Japan
| | - Takashi Hata
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
| | - Atsushi Mochizuki
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
- PRESTO, Japan
Science and Technology Agency, 7 Gobancho, Chiyodaku, Tokyo, 102-0076, Japan
- Theoretical Biology
Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan
| | - Ryoji Sekine
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
| | - Masayuki Yamamura
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
| | - Daisuke Kiga
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
- PRESTO, Japan
Science and Technology Agency, 7 Gobancho, Chiyodaku, Tokyo, 102-0076, Japan
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| |
Collapse
|
85
|
Balmer NV, Klima S, Rempel E, Ivanova VN, Kolde R, Weng MK, Meganathan K, Henry M, Sachinidis A, Berthold MR, Hengstler JG, Rahnenführer J, Waldmann T, Leist M. From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects. Arch Toxicol 2014; 88:1451-68. [PMID: 24935251 PMCID: PMC4067541 DOI: 10.1007/s00204-014-1279-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/19/2014] [Indexed: 01/17/2023]
Abstract
The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transcriptome changes could describe altered differentiation states as indirect consequence of drug exposure. We used here the developmental toxicants valproate and trichostatin A to address this question. Neurally differentiating human embryonic stem cells were treated for 6 days. Histone acetylation (primary MoA) increased quickly and returned to baseline after 48 h. Histone H3 lysine methylation at the promoter of the neurodevelopmental regulators PAX6 or OTX2 was increasingly altered over time. Methylation changes remained persistent and correlated with neurodevelopmental defects and with effects on PAX6 gene expression, also when the drug was washed out after 3-4 days. We hypothesized that drug exposures altering only acetylation would lead to reversible transcriptome changes (indicating MoA), and challenges that altered methylation would lead to irreversible developmental disturbances. Data from pulse-chase experiments corroborated this assumption. Short drug treatment triggered reversible transcriptome changes; longer exposure disrupted neurodevelopment. The disturbed differentiation was reflected by an altered transcriptome pattern, and the observed changes were similar when the drug was washed out during the last 48 h. We conclude that transcriptome data after prolonged chemical stress of differentiating cells mainly reflect the altered developmental stage of the model system and not the drug MoA. We suggest that brief exposures, followed by immediate analysis, are more suitable for information on immediate drug responses and the toxicity MoA.
Collapse
Affiliation(s)
- Nina V. Balmer
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Stefanie Klima
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Eugen Rempel
- Department of Statistics, TU Dortmund, Dortmund, Germany
| | - Violeta N. Ivanova
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | | | - Matthias K. Weng
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Kesavan Meganathan
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Margit Henry
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Michael R. Berthold
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), 44139 Dortmund, Germany
| | | | - Tanja Waldmann
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| |
Collapse
|
86
|
Stapleton AE. A biologist, a statistician, and a bioinformatician walk into a conference room… and walk out with a great metagenomics project plan. FRONTIERS IN PLANT SCIENCE 2014; 5:250. [PMID: 24917875 PMCID: PMC4042100 DOI: 10.3389/fpls.2014.00250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/15/2014] [Indexed: 06/03/2023]
|
87
|
Chylek LA, Holowka DA, Baird BA, Hlavacek WS. An Interaction Library for the FcεRI Signaling Network. Front Immunol 2014; 5:172. [PMID: 24782869 PMCID: PMC3995055 DOI: 10.3389/fimmu.2014.00172] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/31/2014] [Indexed: 12/20/2022] Open
Abstract
Antigen receptors play a central role in adaptive immune responses. Although the molecular networks associated with these receptors have been extensively studied, we currently lack a systems-level understanding of how combinations of non-covalent interactions and post-translational modifications are regulated during signaling to impact cellular decision-making. To fill this knowledge gap, it will be necessary to formalize and piece together information about individual molecular mechanisms to form large-scale computational models of signaling networks. To this end, we have developed an interaction library for signaling by the high-affinity IgE receptor, FcεRI. The library consists of executable rules for protein–protein and protein–lipid interactions. This library extends earlier models for FcεRI signaling and introduces new interactions that have not previously been considered in a model. Thus, this interaction library is a toolkit with which existing models can be expanded and from which new models can be built. As an example, we present models of branching pathways from the adaptor protein Lat, which influence production of the phospholipid PIP3 at the plasma membrane and the soluble second messenger IP3. We find that inclusion of a positive feedback loop gives rise to a bistable switch, which may ensure robust responses to stimulation above a threshold level. In addition, the library is visualized to facilitate understanding of network circuitry and identification of network motifs.
Collapse
Affiliation(s)
- Lily A Chylek
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA ; Los Alamos National Laboratory, Theoretical Division, Center for Non-linear Studies , Los Alamos, NM , USA
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - William S Hlavacek
- Los Alamos National Laboratory, Theoretical Division, Center for Non-linear Studies , Los Alamos, NM , USA
| |
Collapse
|
88
|
Zhang Y, Smolen P, Baxter DA, Byrne JH. Computational analyses of synergism in small molecular network motifs. PLoS Comput Biol 2014; 10:e1003524. [PMID: 24651495 PMCID: PMC3961176 DOI: 10.1371/journal.pcbi.1003524] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/06/2014] [Indexed: 12/21/2022] Open
Abstract
Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically) to alter the responses of the motifs to stimuli. Synergism (or antagonism) was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions. Cellular responses to stimuli are controlled by complex regulatory networks that comprise many molecular components. Understanding such networks is critical for understanding normal cellular functions and pathological conditions. Because the complexity of these networks often precludes intuitive insights, a useful approach is to study mathematical models of small network motifs having reduced complexity yet consisting of key regulatory components of the more complex networks. Computational studies have analyzed the behavior of small motifs, and have begun to describe the ways in which variations in parameters affect their functional properties. Here, we investigated how variations in pairs of parameters act synergistically (or antagonistically) to alter responses of ten common network motifs. Simulations identified parameter variations that maximized synergism, and examined the ways in which synergism was affected by stimulus protocols and motif architecture. The results have implications for the rational design of combination drug therapies where a goal is to identify drugs that when administered together have a greater effect than would be predicted by simple addition of single-drug effects (i.e., super-additive effects), thereby allowing for lower drug doses, minimizing undesirable effects.
Collapse
Affiliation(s)
- Yili Zhang
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - Paul Smolen
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - Douglas A. Baxter
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - John H. Byrne
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
89
|
Sandefur CI, Mincheva M, Schnell S. Network representations and methods for the analysis of chemical and biochemical pathways. MOLECULAR BIOSYSTEMS 2014; 9:2189-200. [PMID: 23857078 DOI: 10.1039/c3mb70052f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behaviour can be identified using network mining and functional mapping approaches.
Collapse
Affiliation(s)
- Conner I Sandefur
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center and Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | |
Collapse
|
90
|
Shreif Z, Periwal V. A network characteristic that correlates environmental and genetic robustness. PLoS Comput Biol 2014; 10:e1003474. [PMID: 24550721 PMCID: PMC3923666 DOI: 10.1371/journal.pcbi.1003474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 01/03/2014] [Indexed: 12/28/2022] Open
Abstract
As scientific advances in perturbing biological systems and technological advances in data acquisition allow the large-scale quantitative analysis of biological function, the robustness of organisms to both transient environmental stresses and inter-generational genetic changes is a fundamental impediment to the identifiability of mathematical models of these functions. An approach to overcoming this impediment is to reduce the space of possible models to take into account both types of robustness. However, the relationship between the two is still controversial. This work uncovers a network characteristic, transient responsiveness, for a specific function that correlates environmental imperturbability and genetic robustness. We test this characteristic extensively for dynamic networks of ordinary differential equations ranging up to 30 interacting nodes and find that there is a power-law relating environmental imperturbability and genetic robustness that tends to linearity as the number of nodes increases. Using our methods, we refine the classification of known 3-node motifs in terms of their environmental and genetic robustness. We demonstrate our approach by applying it to the chemotaxis signaling network. In particular, we investigate plausible models for the role of CheV protein in biochemical adaptation via a phosphorylation pathway, testing modifications that could improve the robustness of the system to environmental and/or genetic perturbation. Advances in the ways that living systems can be perturbed in order to study how they function and sharp reductions in the cost of computer resources have allowed the collection of large amounts of data. The aim of biological system modeling is to analyze this data in order to pin down the precise interactions of molecules that underlie the observed functions. This is made difficult due to two features of biological systems: (1) Living things do not show an appreciable loss of function across large ranges of environmental factors. (2) Their function is inherited from parent to child more or less unchanged in spite of random mutations in genetic sequences. We find that these two features are more correlated in a specific subset of networks and show how to use this observation to find networks in which these two features appear together. Working within this smaller space of networks may make it easier to find suitable underlying models from data.
Collapse
Affiliation(s)
- Zeina Shreif
- Laboratory of Biological Modeling, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vipul Periwal
- Laboratory of Biological Modeling, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
91
|
SANCHEZ-OSORIO ISMAEL, RAMOS FERNANDO, MAYORGA PEDRO, DANTAN EDGAR. FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEW. J Bioinform Comput Biol 2014; 12:1330003. [DOI: 10.1142/s0219720013300037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A promising alternative for unraveling the principles under which the dynamic interactions among genes lead to cellular phenotypes relies on mathematical and computational models at different levels of abstraction, from the molecular level of protein-DNA interactions to the system level of functional relationships among genes. This review article presents, under a bottom–up perspective, a hierarchy of approaches to modeling gene regulatory network dynamics, from microscopic descriptions at the single-molecule level in the spatial context of an individual cell to macroscopic models providing phenomenological descriptions at the population-average level. The reviewed modeling approaches include Molecular Dynamics, Particle-Based Brownian Dynamics, the Master Equation approach, Ordinary Differential Equations, and the Boolean logic abstraction. Each of these frameworks is motivated by a particular biological context and the nature of the insight being pursued. The setting of gene network dynamic models from such frameworks involves assumptions and mathematical artifacts often ignored by the non-specialist. This article aims at providing an entry point for biologists new to the field and computer scientists not acquainted with some recent biophysically-inspired models of gene regulation. The connections promoting intuition between different abstraction levels and the role that approximations play in the modeling process are highlighted throughout the paper.
Collapse
Affiliation(s)
- ISMAEL SANCHEZ-OSORIO
- Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico
| | - FERNANDO RAMOS
- Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico
| | - PEDRO MAYORGA
- Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico
| | - EDGAR DANTAN
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209, Mexico
| |
Collapse
|
92
|
Ying BW, Tsuru S, Seno S, Matsuda H, Yomo T. Gene expression scaled by distance to the genome replication site. MOLECULAR BIOSYSTEMS 2013; 10:375-9. [PMID: 24336896 DOI: 10.1039/c3mb70254e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A simple mode of gene expression scaled by the distance from the chromosomal location of the gene to the genome replication site oriC was determined. The common formula representing the effect of genomic position on expression capacity not only supports the multifork replication model but also provides a base correlation for theoretical simulation and synthetic constructs.
Collapse
Affiliation(s)
- Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | | | | | | | | |
Collapse
|
93
|
Tou WI, Chen CYC. May disordered protein cause serious drug side effect? Drug Discov Today 2013; 19:367-72. [PMID: 24184432 DOI: 10.1016/j.drudis.2013.10.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/23/2013] [Accepted: 10/25/2013] [Indexed: 01/16/2023]
Abstract
Insomnia is a self-reported disease where patients lose their ability to initiate and maintain sleep, leading to daytime performance impairment. Several drug targets to ameliorate insomnia symptoms have been discovered; however, these drug targets lead to serious side effects. Thus, we characterize the structural properties of these sleep-related receptors and the clock complex and discuss a possible drug design that will reduce side effects. Computational prediction shows that disordered property is shared. Over 30% of the structure of CLOCK, PER1/2/3, BMAL-1, muscarinic acetylcholine receptor-M1, melatonin receptor and casein kinase I are structurally disordered (the remaining proteins represent <30%). Investigations support the principle that the failures of insomnia drugs might be closely related to the protein architecture.
Collapse
Affiliation(s)
- Weng Ieong Tou
- School of Medicine, College of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Calvin Yu-Chian Chen
- School of Medicine, College of Medicine, China Medical University, Taichung, 40402, Taiwan; Department of Biotechnology, Asia University, Taichung, 41354, Taiwan; China Medical University Beigang Hospital, Yunlin, 65152, Taiwan; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
94
|
David DJV, Wang Q, Feng JJ, Harris TJC. Bazooka inhibits aPKC to limit antagonism of actomyosin networks during amnioserosa apical constriction. Development 2013; 140:4719-29. [PMID: 24173807 DOI: 10.1242/dev.098491] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cell shape changes drive tissue morphogenesis during animal development. An important example is the apical cell constriction that initiates tissue internalisation. Apical constriction can occur through a phase of cyclic assembly and disassembly of apicomedial actomyosin networks, followed by stabilisation of these networks. Delayed negative-feedback mechanisms typically underlie cyclic behaviour, but the mechanisms regulating cyclic actomyosin networks remain obscure, as do mechanisms that transform overall network behaviour. Here, we show that a known inhibitor of apicomedial actomyosin networks in Drosophila amnioserosa cells, the Par-6-aPKC complex, is recruited to the apicomedial domain by actomyosin networks during dorsal closure of the embryo. This finding establishes an actomyosin-aPKC negative-feedback loop in the system. Additionally, we find that aPKC recruits Bazooka to the apicomedial domain, and phosphorylates Bazooka for a dynamic interaction. Remarkably, stabilising aPKC-Bazooka interactions can inhibit the antagonism of actomyosin by aPKC, suggesting that Bazooka acts as an aPKC inhibitor, and providing a possible mechanism for delaying the actomyosin-aPKC negative-feedback loop. Our data also implicate an increasing degree of Par-6-aPKC-Bazooka interactions as dorsal closure progresses, potentially explaining a developmental transition in actomyosin behaviour from cyclic to persistent networks. This later impact of aPKC inhibition is supported by mathematical modelling of the system. Overall, this work illustrates how shifting chemical signals can tune actomyosin network behaviour during development.
Collapse
Affiliation(s)
- Daryl J V David
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | | | | | | |
Collapse
|
95
|
Laufer BI, Diehl EJ, Singh SM. Neurodevelopmental epigenetic etiologies: insights from studies on mouse models of fetal alcohol spectrum disorders. Epigenomics 2013; 5:465-8. [DOI: 10.2217/epi.13.42] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Benjamin I Laufer
- Molecular Genetics Unit, Department of Biology, Western University, London, ON, N6A 5B7, Canada
| | - Eric J Diehl
- Molecular Genetics Unit, Department of Biology, Western University, London, ON, N6A 5B7, Canada
| | - Shiva M Singh
- Molecular Genetics Unit, Department of Biology, Western University, London, ON, N6A 5B7, Canada
| |
Collapse
|
96
|
Panier S, Durocher D. Push back to respond better: regulatory inhibition of the DNA double-strand break response. Nat Rev Mol Cell Biol 2013; 14:661-72. [PMID: 24002223 DOI: 10.1038/nrm3659] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single DNA lesions such as DNA double-strand breaks (DSBs) can cause cell death or trigger genome rearrangements that have oncogenic potential, and so the pathways that mend and signal DNA damage must be highly sensitive but, at the same time, selective and reversible. When initiated, boundaries must be set to restrict the DSB response to the site of the lesion. The integration of positive and, crucially, negative control points involving post-translational modifications such as phosphorylation, ubiquitylation and acetylation is key for building fast, effective responses to DNA damage and for mitigating the impact of DNA lesions on genome integrity.
Collapse
Affiliation(s)
- Stephanie Panier
- 1] The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada. [2] Present address: DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms, London EN6 3LD, UK
| | | |
Collapse
|
97
|
Kurata H, Maeda K, Onaka T, Takata T. BioFNet: biological functional network database for analysis and synthesis of biological systems. Brief Bioinform 2013; 15:699-709. [PMID: 23894104 DOI: 10.1093/bib/bbt048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. A functional network is defined as a subnetwork of biomolecules that performs a particular function. Understanding the mechanism of building functional networks would help develop a methodology for analyzing the structure of large-scale networks and design a robust biological circuit to perform a target function. We propose a biological functional network database, named BioFNet, which can cover the whole cell at the level of molecular interactions. The BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.
Collapse
|
98
|
Clarke J, Penas C, Pastori C, Komotar RJ, Bregy A, Shah AH, Wahlestedt C, Ayad NG. Epigenetic pathways and glioblastoma treatment. Epigenetics 2013; 8:785-95. [PMID: 23807265 PMCID: PMC3883781 DOI: 10.4161/epi.25440] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most common malignant adult brain tumor. Standard GBM treatment includes maximal safe surgical resection with combination radiotherapy and adjuvant temozolomide (TMZ) chemotherapy. Alarmingly, patient survival at five-years is below 10%. This is in part due to the invasive behavior of the tumor and the resulting inability to resect greater than 98% of some tumors. In fact, recurrence after such treatment may be inevitable, even in cases where gross total resection is achieved. The Cancer Genome Atlas (TCGA) research network performed whole genome sequencing of GBM tumors and found that GBM recurrence is linked to epigenetic mechanisms and pathways. Central to these pathways are epigenetic enzymes, which have recently emerged as possible new drug targets for multiple cancers, including GBM. Here we review GBM treatment, and provide a systems approach to identifying epigenetic drivers of GBM tumor progression based on temporal modeling of putative GBM cells of origin. We also discuss advances in defining epigenetic mechanisms controlling GBM initiation and recurrence and the drug discovery considerations associated with targeting epigenetic enzymes for GBM treatment.
Collapse
Affiliation(s)
- Jennifer Clarke
- Division of Biostatistics; Department of Epidemiology and Public Health; University of Miami Miller School of Medicine; Miami, FL USA
| | | | | | | | | | | | | | | |
Collapse
|
99
|
Moe-Behrens GH. The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 2013; 7:e201304003. [PMID: 24688733 PMCID: PMC3962179 DOI: 10.5936/csbj.201304003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 01/21/2023] Open
Abstract
Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
Collapse
|
100
|
Scialdone A, Mugford ST, Feike D, Skeffington A, Borrill P, Graf A, Smith AM, Howard M. Arabidopsis plants perform arithmetic division to prevent starvation at night. eLife 2013; 2:e00669. [PMID: 23805380 PMCID: PMC3691572 DOI: 10.7554/elife.00669] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/31/2013] [Indexed: 01/20/2023] Open
Abstract
Photosynthetic starch reserves that accumulate in Arabidopsis leaves during the day decrease approximately linearly with time at night to support metabolism and growth. We find that the rate of decrease is adjusted to accommodate variation in the time of onset of darkness and starch content, such that reserves last almost precisely until dawn. Generation of these dynamics therefore requires an arithmetic division computation between the starch content and expected time to dawn. We introduce two novel chemical kinetic models capable of implementing analog arithmetic division. Predictions from the models are successfully tested in plants perturbed by a night-time light period or by mutations in starch degradation pathways. Our experiments indicate which components of the starch degradation apparatus may be important for appropriate arithmetic division. Our results are potentially relevant for any biological system dependent on a food reserve for survival over a predictable time period. DOI:http://dx.doi.org/10.7554/eLife.00669.001.
Collapse
Affiliation(s)
- Antonio Scialdone
- Department of Computational and Systems Biology , John Innes Centre , Norwich , United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|