1
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Hong L, Zhang Z, Wang Z, Yu X, Zhang J. Phase separation provides a mechanism to drive phenotype switching. Phys Rev E 2024; 109:064414. [PMID: 39021038 DOI: 10.1103/physreve.109.064414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Phenotypic switching plays a crucial role in cell fate determination across various organisms. Recent experimental findings highlight the significance of protein compartmentalization via liquid-liquid phase separation in influencing such decisions. However, the precise mechanism through which phase separation regulates phenotypic switching remains elusive. To investigate this, we established a mathematical model that couples a phase separation process and a gene expression process with feedback. We used the chemical master equation theory and mean-field approximation to study the effects of phase separation on the gene expression products. We found that phase separation can cause bistability and bimodality. Furthermore, phase separation can control the bistable properties of the system, such as bifurcation points and bistable ranges. On the other hand, in stochastic dynamics, the droplet phase exhibits double peaks within a more extensive phase separation threshold range than the dilute phase, indicating the pivotal role of the droplet phase in cell fate decisions. These findings propose an alternative mechanism that influences cell fate decisions through the phase separation process. As phase separation is increasingly discovered in gene regulatory networks, related modeling research can help build biomolecular systems with desired properties and offer insights into explaining cell fate decisions.
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2
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Sankhe GD, Raja R, Singh DP, Bheemireddy S, Rana S, Athira PJ, Dixit NM, Saini DK. Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling. Nat Commun 2023; 14:4483. [PMID: 37491529 PMCID: PMC10368727 DOI: 10.1038/s41467-023-40095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
Bacterial two-component systems (TCSs) consist of a sensor histidine kinase (HK) that perceives a specific signal, and a cognate response regulator (RR) that modulates the expression of target genes. Positive autoregulation improves TCS sensitivity to stimuli, but may trigger disproportionately large responses to weak signals, compromising bacterial fitness. Here, we combine experiments and mathematical modelling to reveal a general design that prevents such disproportionate responses: phosphorylated HKs (HK~Ps) can be sequestered by non-cognate RRs. We study five TCSs of Mycobacterium tuberculosis and find, for all of them, non-cognate RRs that show higher affinity than cognate RRs for HK~Ps. Indeed, in vitro assays show that HK~Ps preferentially bind higher affinity non-cognate RRs and get sequestered. Mathematical modelling indicates that this sequestration would introduce a 'threshold' stimulus strength for eliciting responses, thereby preventing responses to weak signals. Finally, we construct tunable expression systems in Mycobacterium bovis BCG to show that higher affinity non-cognate RRs suppress responses in vivo.
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Affiliation(s)
- Gaurav D Sankhe
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Devendra Pratap Singh
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science, Bengaluru, India
| | - P J Athira
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Narendra M Dixit
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.
| | - Deepak Kumar Saini
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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3
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Schultz D, Stevanovic M, Tsimring LS. Optimal transcriptional regulation of dynamic bacterial responses to sudden drug exposures. Biophys J 2022; 121:4137-4152. [PMID: 36168291 PMCID: PMC9675034 DOI: 10.1016/j.bpj.2022.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Cellular responses to the presence of toxic compounds in their environment require prompt expression of the correct levels of the appropriate enzymes, which are typically regulated by transcription factors that control gene expression for the duration of the response. The characteristics of each response dictate the choice of regulatory parameters such as the affinity of the transcription factor to its binding sites and the strength of the promoters it regulates. Although much is known about the dynamics of cellular responses, we still lack a framework to understand how different regulatory strategies evolved in natural systems relate to the selective pressures acting in each particular case. Here, we analyze a dynamical model of a typical antibiotic response in bacteria, where a transcriptionally repressed enzyme is induced by a sudden exposure to the drug that it processes. We identify strategies of gene regulation that optimize this response for different types of selective pressures, which we define as a set of costs associated with the drug, enzyme, and repressor concentrations during the response. We find that regulation happens in a limited region of the regulatory parameter space. While responses to more costly (toxic) drugs favor the usage of strongly self-regulated repressors, responses where expression of enzyme is more costly favor the usage of constitutively expressed repressors. Only a very narrow range of selective pressures favor weakly self-regulated repressors. We use this framework to determine which costs and benefits are most critical for the evolution of a variety of natural cellular responses that satisfy the approximations in our model and to analyze how regulation is optimized in new environments with different demands.
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Affiliation(s)
- Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San Diego, La Jolla, California
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4
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Chaturvedi S, Pablo M, Wolf M, Rosas-Rivera D, Calia G, Kumar AJ, Vardi N, Du K, Glazier J, Ke R, Chan MF, Perelson AS, Weinberger LS. Disrupting autorepression circuitry generates "open-loop lethality" to yield escape-resistant antiviral agents. Cell 2022; 185:2086-2102.e22. [PMID: 35561685 PMCID: PMC9097017 DOI: 10.1016/j.cell.2022.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Across biological scales, gene-regulatory networks employ autorepression (negative feedback) to maintain homeostasis and minimize failure from aberrant expression. Here, we present a proof of concept that disrupting transcriptional negative feedback dysregulates viral gene expression to therapeutically inhibit replication and confers a high evolutionary barrier to resistance. We find that nucleic-acid decoys mimicking cis-regulatory sites act as "feedback disruptors," break homeostasis, and increase viral transcription factors to cytotoxic levels (termed "open-loop lethality"). Feedback disruptors against herpesviruses reduced viral replication >2-logs without activating innate immunity, showed sub-nM IC50, synergized with standard-of-care antivirals, and inhibited virus replication in mice. In contrast to approved antivirals where resistance rapidly emerged, no feedback-disruptor escape mutants evolved in long-term cultures. For SARS-CoV-2, disruption of a putative feedback circuit also generated open-loop lethality, reducing viral titers by >1-log. These results demonstrate that generating open-loop lethality, via negative-feedback disruption, may yield a class of antimicrobials with a high genetic barrier to resistance.
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Affiliation(s)
- Sonali Chaturvedi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - Michael Pablo
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marie Wolf
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Daniel Rosas-Rivera
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Giuliana Calia
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arjun J Kumar
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Noam Vardi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelvin Du
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joshua Glazier
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Matilda F Chan
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leor S Weinberger
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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5
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Ali MZ, Brewster RC. Controlling gene expression timing through gene regulatory architecture. PLoS Comput Biol 2022; 18:e1009745. [PMID: 35041641 PMCID: PMC8797265 DOI: 10.1371/journal.pcbi.1009745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 01/28/2022] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Gene networks typically involve the regulatory control of multiple genes with related function. This connectivity enables correlated control of the levels and timing of gene expression. Here we study how gene expression timing in the single-input module motif can be encoded in the regulatory DNA of a gene. Using stochastic simulations, we examine the role of binding affinity, TF regulatory function and network size in controlling the mean first-passage time to reach a fixed fraction of steady-state expression for both an auto-regulated TF gene and a target gene. We also examine how the variability in first-passage time depends on these factors. We find that both network size and binding affinity can dramatically speed up or slow down the response time of network genes, in some cases predicting more than a 100-fold change compared to that for a constitutive gene. Furthermore, these factors can also significantly impact the fidelity of this response. Importantly, these effects do not occur at “extremes” of network size or binding affinity, but rather in an intermediate window of either quantity.
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Affiliation(s)
- Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robert C. Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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6
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Zhang G, Hu S, Jia X. Highly Sensitive Whole-Cell Biosensor for Cadmium Detection Based on a Negative Feedback Circuit. Front Bioeng Biotechnol 2021; 9:799781. [PMID: 34926437 PMCID: PMC8678453 DOI: 10.3389/fbioe.2021.799781] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
Although many whole-cell biosensors (WCBs) for the detection of Cd2+ have been developed over the years, most lack sensitivity and specificity. In this paper, we developed a Cd2+ WCB with a negative feedback amplifier in P. putida KT2440. Based on the slope of the linear detection curve as a measure of sensitivity, WCB with negative feedback amplifier greatly increased the output signal of the reporter mCherry, resulting in 33% greater sensitivity than in an equivalent WCB without the negative feedback circuit. Moreover, WCB with negative feedback amplifier exhibited increased Cd2+ tolerance and a lower detection limit of 0.1 nM, a remarkable 400-fold improvement compared to the WCB without the negative feedback circuit, which is significantly below the World Health Organization standard of 27 nM (0.003 mg/L) for cadmium in drinking water. Due to the superior amplification of the output signal, WCB with negative feedback amplifier can provide a detectable signal in a much shorter time, and a fast response is highly preferable for real field applications. In addition, the WCB with negative feedback amplifier showed an unusually high specificity for Cd2+ compared to other metal ions, giving signals with other metals that were between 17.6 and 41.4 times weaker than with Cd2+. In summary, the negative feedback amplifier WCB designed in this work meets the requirements of Cd2+ detection with very high sensitivity and specificity, which also demonstrates that genetic negative feedback amplifiers are excellent tools for improving the performance of WCBs.
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Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Shuting Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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7
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Kashiwagi FM, Wendler Miranda B, de Oliveira Pedrosa F, de Souza EM, Müller-Santos M. Control of Gene Expression With Quercetin-Responsive Modular Circuits. Front Bioeng Biotechnol 2021; 9:730967. [PMID: 34604189 PMCID: PMC8481877 DOI: 10.3389/fbioe.2021.730967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Biological Sciences Undergraduate Course, Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
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8
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Wu T, Kerbler SM, Fernie AR, Zhang Y. Plant cell cultures as heterologous bio-factories for secondary metabolite production. PLANT COMMUNICATIONS 2021; 2:100235. [PMID: 34746764 PMCID: PMC8554037 DOI: 10.1016/j.xplc.2021.100235] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 05/06/2023]
Abstract
Synthetic biology has been developing rapidly in the last decade and is attracting increasing attention from many plant biologists. The production of high-value plant-specific secondary metabolites is, however, limited mostly to microbes. This is potentially problematic because of incorrect post-translational modification of proteins and differences in protein micro-compartmentalization, substrate availability, chaperone availability, product toxicity, and cytochrome p450 reductase enzymes. Unlike other heterologous systems, plant cells may be a promising alternative for the production of high-value metabolites. Several commercial plant suspension cell cultures from different plant species have been used successfully to produce valuable metabolites in a safe, low cost, and environmentally friendly manner. However, few metabolites are currently being biosynthesized using plant platforms, with the exception of the natural pigment anthocyanin. Both Arabidopsis thaliana and Nicotiana tabacum cell cultures can be developed by multiple gene transformations and CRISPR-Cas9 genome editing. Given that the introduction of heterologous biosynthetic pathways into Arabidopsis and N. tabacum is not widely used, the biosynthesis of foreign metabolites is currently limited; however, therein lies great potential. Here, we discuss the exemplary use of plant cell cultures and prospects for using A. thaliana and N. tabacum cell cultures to produce valuable plant-specific metabolites.
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Affiliation(s)
- Tong Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sandra M. Kerbler
- Leibniz-Institute für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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9
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Mittal D, Narayanan R. Resonating neurons stabilize heterogeneous grid-cell networks. eLife 2021; 10:66804. [PMID: 34328415 PMCID: PMC8357421 DOI: 10.7554/elife.66804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023] Open
Abstract
A central theme that governs the functional design of biological networks is their ability to sustain stable function despite widespread parametric variability. Here, we investigated the impact of distinct forms of biological heterogeneities on the stability of a two-dimensional continuous attractor network (CAN) implicated in grid-patterned activity generation. We show that increasing degrees of biological heterogeneities progressively disrupted the emergence of grid-patterned activity and resulted in progressively large perturbations in low-frequency neural activity. We postulated that targeted suppression of low-frequency perturbations could ameliorate heterogeneity-induced disruptions of grid-patterned activity. To test this, we introduced intrinsic resonance, a physiological mechanism to suppress low-frequency activity, either by adding an additional high-pass filter (phenomenological) or by incorporating a slow negative feedback loop (mechanistic) into our model neurons. Strikingly, CAN models with resonating neurons were resilient to the incorporation of heterogeneities and exhibited stable grid-patterned firing. We found CAN models with mechanistic resonators to be more effective in targeted suppression of low-frequency activity, with the slow kinetics of the negative feedback loop essential in stabilizing these networks. As low-frequency perturbations (1/f noise) are pervasive across biological systems, our analyses suggest a universal role for mechanisms that suppress low-frequency activity in stabilizing heterogeneous biological networks.
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Affiliation(s)
- Divyansh Mittal
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rishikesh Narayanan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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10
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Biological feedback control-Respect the loops. Cell Syst 2021; 12:477-487. [PMID: 34139160 DOI: 10.1016/j.cels.2021.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022]
Abstract
We, and all organisms, are an evolutionary masterpiece of multiscale feedback control. Feedback loops enable our cells to grow and then stop at the right size, to divide and self-repair, and to respond with agility to their changing environment. Individual cells engage in long range extracellular feedback with other cells, ensuring continued homeostasis of our tissues and organs. Many long ranging feedback loops regulate vital physiological variables. Here, I will argue that focused efforts to understand the properties and constraints of biological feedback control networks should be central to the quest of understanding life. I will also propose many pressing challenges in this field and review conceptual frameworks that might be consequential for addressing them.
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11
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Androulakis IP. Circadian rhythms and the HPA axis: A systems view. WIREs Mech Dis 2021; 13:e1518. [PMID: 33438348 DOI: 10.1002/wsbm.1518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
The circadian timing system comprises a network of time-keeping clocks distributed across a living host whose responsibility is to allocate resources and distribute functions temporally to optimize fitness. The molecular structures generating these rhythms have evolved to accommodate the rotation of the earth in an attempt to primarily match the light/dark periods during the 24-hr day. To maintain synchrony of timing across and within tissues, information from the central clock, located in the suprachiasmatic nucleus, is conveyed using systemic signals. Leading among those signals are endocrine hormones, and while the hypothalamic-pituitary-adrenal axis through the release of glucocorticoids is a major pacesetter. Interestingly, the fundamental units at the molecular and physiological scales that generate local and systemic signals share critical structural properties. These properties enable time-keeping systems to generate rhythmic signals and allow them to adopt specific properties as they interact with each other and the external environment. The purpose of this review is to provide a broad overview of these structures, discuss their functional characteristics, and describe some of their fundamental properties as these related to health and disease. This article is categorized under: Immune System Diseases > Computational Models Immune System Diseases > Biomedical Engineering.
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Affiliation(s)
- Ioannis P Androulakis
- Biomedical Engineering Department, Chemical & Biochemical Engineering Department, Rutgers University, New Brunswick, New Jersey.,Department of Surgery, Rutgers-Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
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12
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Roy B, Granas D, Bragg F, Cher JAY, White MA, Stormo GD. Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation. Commun Biol 2020; 3:761. [PMID: 33311538 PMCID: PMC7732827 DOI: 10.1038/s42003-020-01494-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 11/15/2020] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional autoregulation of gene expression is common in bacteria but many fewer examples are known in eukaryotes. We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins by overexpressing a non-regulatable version of a gene and observing the effects on the expression of the GFP-fused version. We tested 95 ribosomal protein genes and found a wide continuum of effects, with 30% showing at least a 3-fold reduction in expression. Two genes, RPS22B and RPL1B, showed over a 10-fold repression. In both cases the cis-regulatory segment resides in the 5’ UTR of the gene as shown by placing that segment of the mRNA upstream of GFP alone and demonstrating it is sufficient to cause repression of GFP when the protein is over-expressed. Further analyses showed that the intron in the 5’ UTR of RPS22B is required for regulation, presumably because the protein inhibits splicing that is necessary for translation. The 5’ UTR of RPL1B contains a sequence and structure motif that is conserved in the binding sites of Rpl1 orthologs from bacteria to mammals, and mutations within the motif eliminate repression. Here, the authors screen for feedback regulation of ribosomal proteins by overexpressing a non- regulatable version of a gene and observing its effects on the expression of the GFP-fused version. They find that 30% show at least a 3-fold reduction in expression and two genes show a 10-fold reduction with the regulatory site being in the 5’ untranslated region of the gene.
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Affiliation(s)
- Basab Roy
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - David Granas
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Fredrick Bragg
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Jonathan A Y Cher
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Michael A White
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gary D Stormo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA.
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13
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Binary Expression Enhances Reliability of Messaging in Gene Networks. ENTROPY 2020; 22:e22040479. [PMID: 33286254 PMCID: PMC7516962 DOI: 10.3390/e22040479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023]
Abstract
The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter of a gene (the source) is communicated by the amounts of transcription factors that it expresses (the message) to modulate the state of the promoter and expression levels of another gene (the receptor). The reliability of the gene network dynamics can be quantified by Shannon's entropy of the message and the mutual information between the message and the promoter state. Here we consider a stochastic model for a binary gene and use its exact steady state solutions to calculate the entropy and mutual information. We show that a slow switching promoter with long and equally standing ON and OFF states maximizes the mutual information and reduces entropy. That is a binary gene expression regime generating a high variance message governed by a bimodal probability distribution with peaks of the same height. Our results indicate that Shannon's theory can be a powerful framework for understanding how bursty gene expression conciliates with the striking spatio-temporal precision exhibited in pattern formation of developing organisms.
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14
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Gao R, Stock AM. Overcoming the Cost of Positive Autoregulation by Accelerating the Response with a Coupled Negative Feedback. Cell Rep 2019; 24:3061-3071.e6. [PMID: 30208328 PMCID: PMC6194859 DOI: 10.1016/j.celrep.2018.08.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/06/2018] [Accepted: 08/08/2018] [Indexed: 12/13/2022] Open
Abstract
A fundamental trade-off between rapid response and optimal expression of genes below cytotoxic levels exists for many signaling circuits, particularly for positively autoregulated systems with an inherent response delay. Here, we describe a regulatory scheme in the E. coli PhoB-PhoR two-component system, which overcomes the cost of positive feedback and achieves both fast and optimal steadystate response for maximal fitness across different environments. Quantitation of the cellular activities enables accurate modeling of the response dynamics to describe how requirements for optimal protein concentrations place limits on response speed. An observed fast response that exceeds the limit led to the prediction and discovery of a coupled negative autoregulation, which allows fast gene expression without increasing steady-state levels. We demonstrate the fitness advantages for the coupled feedbacks in both dynamic and stable environments. Such regulatory schemes offer great flexibility for accurate control of gene expression levels and dynamics upon environmental changes. Positive autoregulation of transcription produces a delayed response. Gao and Stock describe the limit of response delay caused by requirements of optimal protein levels in the PhoBR twocomponent system. Coupled negative autoregulation is discovered to allow a strong promoter for fast response without incurring cost of increasing protein expression levels.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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15
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Rogan PK. Multigene signatures of responses to chemotherapy derived by biochemically-inspired machine learning. Mol Genet Metab 2019; 128:45-52. [PMID: 31451418 DOI: 10.1016/j.ymgme.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 01/08/2023]
Abstract
Pharmacogenomic responses to chemotherapy drugs can be modeled by supervised machine learning of expression and copy number of relevant gene combinations. Such biochemical evidence can form the basis of derived gene signatures using cell line data, which can subsequently be examined in patients that have been treated with the same drugs. These gene signatures typically contain elements of multiple biochemical pathways which together comprise multiple origins of drug resistance or sensitivity. The signatures can capture variation in these responses to the same drug among different patients.
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Affiliation(s)
- Peter K Rogan
- Departments of Biochemistry, Oncology, and Computer Science, University of Western Ontario, London, ON N6A 2C1, UK.
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16
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Ueda Y, Yanagisawa S. Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3709-3717. [PMID: 30949701 DOI: 10.1093/jxb/erz148] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/19/2019] [Indexed: 05/20/2023]
Abstract
Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.
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Affiliation(s)
- Yoshiaki Ueda
- Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo
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17
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Boczek E, Gaglia G, Olshina M, Sarraf S. The first Autumn School on Proteostasis: from molecular mechanisms to organismal consequences. Cell Stress Chaperones 2019; 24:481-492. [PMID: 31073902 PMCID: PMC6527634 DOI: 10.1007/s12192-019-00998-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The first Autumn School on Proteostasis was held at the Mediterranean Institute for Life Sciences (MedILS) in Split, Croatia, from November 12th-16th, 2018, bringing together 44 graduate students and postdoctoral fellows and 22 principal investigators from around the world. This meeting was geared towards providing students with an in-depth understanding of the field of proteostasis, with the aim of broadening their perspectives of the field. Session topics covered multiple aspects of cellular and organismal proteostasis, including fundamental principles, responses to heat shock, aging and disease, and protein folding, misfolding, and degradation. The structure of the meeting and the restricted number of participants afforded the students and postdocs the opportunity to interact with principal investigators to discuss not only their latest research, but also their career prospects and progression in a close, supportive environment.
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Affiliation(s)
- Edgar Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giorgio Gaglia
- Brigham Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Maya Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shireen Sarraf
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD USA
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18
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Sabino AU, Vasconcelos MFS, Sittoni MY, Lautenschlager WW, Queiroga AS, Morais MCC, Ramos AF. Lessons and perspectives for applications of stochastic models in biological and cancer research. Clinics (Sao Paulo) 2018; 73:e536s. [PMID: 30281699 PMCID: PMC6131223 DOI: 10.6061/clinics/2018/e536s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 11/18/2022] Open
Abstract
The effects of randomness, an unavoidable feature of intracellular environments, are observed at higher hierarchical levels of living matter organization, such as cells, tissues, and organisms. Additionally, the many compounds interacting as a well-orchestrated network of reactions increase the difficulties of assessing these systems using only experiments. This limitation indicates that elucidation of the dynamics of biological systems is a complex task that will benefit from the establishment of principles to help describe, categorize, and predict the behavior of these systems. The theoretical machinery already available, or ones to be discovered to help solve biological problems, might play an important role in these processes. Here, we demonstrate the application of theoretical tools by discussing some biological problems that we have approached mathematically: fluctuations in gene expression and cell proliferation in the context of loss of contact inhibition. We discuss the methods that have been employed to provide the reader with a biologically motivated phenomenological perspective of the use of theoretical methods. Finally, we end this review with a discussion of new research perspectives motivated by our results.
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Affiliation(s)
- Alan U Sabino
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Miguel FS Vasconcelos
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Misaki Yamada Sittoni
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Alexandre S Queiroga
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Mauro CC Morais
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Alexandre F Ramos
- Escola de Artes Ciências e Humanidades (EACH), Universidade de Sao Paulo, Sao Paulo, SP, BR
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
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19
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Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design. ACS Synth Biol 2018; 7:1507-1518. [PMID: 29733627 DOI: 10.1021/acssynbio.7b00440] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs. Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict NAR function in TX-TL. We transfer successful network designs into Escherichia coli and show that our sRNA transcriptional network reduces both network response time and steady-state gene expression. This work broadens our ability to construct increasingly sophisticated RNA genetic networks with predictable function.
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20
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Li C, Cesbron F, Oehler M, Brunner M, Höfer T. Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation. Cell Syst 2018; 6:409-423.e11. [PMID: 29454937 DOI: 10.1016/j.cels.2018.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/16/2017] [Accepted: 01/11/2018] [Indexed: 01/17/2023]
Abstract
Gene regulation is a complex non-equilibrium process. Here, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive, active, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First, for transcription factors (TFs) that regulate transcription burst frequency, as opposed to amplitude or duration, weak TF binding is sufficient to elicit strong transcriptional responses. Second, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates, not different TF occupancy, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total, our work demonstrates the relevance of a kinetic, non-equilibrium framework for understanding transcriptional regulation.
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Affiliation(s)
- Congxin Li
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, Heidelberg University, 69120 Heidelberg, Germany
| | - François Cesbron
- Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Oehler
- Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Brunner
- Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, Heidelberg University, 69120 Heidelberg, Germany.
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21
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Ledezma-Tejeida D, Ishida C, Collado-Vides J. Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli. Front Microbiol 2017; 8:1466. [PMID: 28824593 PMCID: PMC5540944 DOI: 10.3389/fmicb.2017.01466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/20/2017] [Indexed: 11/13/2022] Open
Abstract
In the face of changes in their environment, bacteria adjust gene expression levels and produce appropriate responses. The individual layers of this process have been widely studied: the transcriptional regulatory network describes the regulatory interactions that produce changes in the metabolic network, both of which are coordinated by the signaling network, but the interplay between them has never been described in a systematic fashion. Here, we formalize the process of detection and processing of environmental information mediated by individual transcription factors (TFs), utilizing a concept termed genetic sensory response units (GENSOR units), which are composed of four components: (1) a signal, (2) signal transduction, (3) genetic switch, and (4) a response. We used experimentally validated data sets from two databases to assemble a GENSOR unit for each of the 189 local TFs of Escherichia coli K-12 contained in the RegulonDB database. Further analysis suggested that feedback is a common occurrence in signal processing, and there is a gradient of functional complexity in the response mediated by each TF, as opposed to a one regulator/one pathway rule. Finally, we provide examples of other GENSOR unit applications, such as hypothesis generation, detailed description of cellular decision making, and elucidation of indirect regulatory mechanisms.
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Affiliation(s)
- Daniela Ledezma-Tejeida
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Cecilia Ishida
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
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22
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Sturrock M, Li S, Shahrezaei V. The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression. J Theor Biol 2017; 424:55-72. [DOI: 10.1016/j.jtbi.2017.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 01/11/2023]
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23
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Turonova H, Haddad N, Hernould M, Chevret D, Pazlarova J, Tresse O. Profiling of Campylobacter jejuni Proteome in Exponential and Stationary Phase of Growth. Front Microbiol 2017; 8:913. [PMID: 28572800 PMCID: PMC5435804 DOI: 10.3389/fmicb.2017.00913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022] Open
Abstract
Campylobacter jejuni has been reported as a major cause of bacterial food-borne enteritides in developed countries during the last decade. Despite its fastidious growth requirements, including low level of oxygen and high level of CO2, this pathogen is able to persist in the environment without permanent loss of its viability and virulence. As C. jejuni is not able to multiply outside a host, the cells spend significant amount of time in stationary phase of growth. The entry into the stationary phase is often correlated to resistance to various stresses in bacteria. The switching between exponential and stationary phases is frequently mediated by the regulator sigma S (RpoS). However, this factor is absent in C. jejuni and molecular mechanisms responsible for transition of cells to the stationary phase remain elusive. In this work, proteomic profiles of cells from exponential and stationary phases were compared using 2-D electrophoresis (2DE) fingerprinting combined with mass spectrometry analysis and qRT-PCR. The identified proteins, whose expression differed between the two phases, are mostly involved in protein biosynthesis, carbon metabolism, stress response and motility. Altered expression was observed also in the pleiotropic regulator CosR that was over-expressed during stationary phase. A shift between transcript and protein level evolution of CosR throughout the growth of C. jejuni was observed using qRT-PCR and (2DE). From these data, we hypothesized that CosR could undergo a negative autoregulation in stationary phase. A consensus sequence resulting from promoter sequence alignment of genes potentially regulated by CosR, including its own upstream region, among C. jejuni strains is proposed. To verify experimentally the potential autoregulation of CosR at the DNA level, electrophoretic mobility shift assay was performed with DNA fragments of CosR promoter region and rCosR. Different migration pattern of the promoter fragments indicates the binding capacity of CosR, suggesting its auto-regulation potential.
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Affiliation(s)
- Hana Turonova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and TechnologyPrague, Czechia
| | - Nabila Haddad
- SECALIM UMR1014, Institut National de la Recherche AgronomiqueNantes, France
| | - Mathieu Hernould
- SECALIM UMR1014, Institut National de la Recherche AgronomiqueNantes, France
| | - Didier Chevret
- UMR1319 MICALIS, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche AgronomiqueJouy-en-Josas, France
| | - Jarmila Pazlarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and TechnologyPrague, Czechia
| | - Odile Tresse
- SECALIM UMR1014, Institut National de la Recherche AgronomiqueNantes, France
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24
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Jensch A, Thomaseth C, Radde NE. Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines. BMC SYSTEMS BIOLOGY 2017; 11:11. [PMID: 28122551 PMCID: PMC5267478 DOI: 10.1186/s12918-017-0392-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprises several of these motifs, whose functioning depends on the cell line at hand and on the particular context. The maintainance of specificity of the response of the MAPK module to distinct stimuli has become a key paradigm especially in PC-12 cells, where the same module leads to different cell fates, depending on the stimulating growth factor. This cell fate is regulated by differences in the ERK (MAPK) activation profile, which shows a transient response upon stimulation with EGF, while the response is sustained in case of NGF. This behavior was explained by different effective network topologies. It is widely believed that this sustained response requires a bistable system. RESULTS In this study we present a sampling-based Bayesian model analysis on a dataset, in which PC-12 cells have been stimulated with different growth factors. This is combined with novel analysis methods to investigate the role of feedback interconnections to shape ERK response. Results strongly suggest that, besides bistability, an additional effect called quasi-bistability can contribute to explain the observed responses of the system to different stimuli. Quasi-bistability is the ability of a monostable system to maintain two distinct states over a long time period upon a transient signal, which is also related to positive feedback, but cannot be detected by standard steady state analysis methods. CONCLUSIONS Although applied on a specific example, our framework is generic enough to be also relevant for other regulatory network modeling studies that comprise positive feedback to explain cellular decision making processes. Overall, this study advices to focus not only on steady states, but also to take transient behavior into account in the analysis.
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Affiliation(s)
- Antje Jensch
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany
| | - Caterina Thomaseth
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany
| | - Nicole E Radde
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany.
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25
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Rodrigo G, Bajic D, Elola I, Poyatos JF. Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. Sci Rep 2016; 6:36196. [PMID: 27796341 PMCID: PMC5086920 DOI: 10.1038/srep36196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 01/15/2023] Open
Abstract
By integrating positive and negative feedback loops, biological systems establish intricate gene expression patterns linked to multistability, pulsing, and oscillations. This depends on the specific characteristics of each interlinked feedback, and thus one would expect additional expression programs to be found. Here, we investigate one such program associated with an antagonistic positive and negative transcriptional autoregulatory motif derived from the multiple antibiotic resistance (mar) system of Escherichia coli. We studied the dynamics of the system by combining a predictive mathematical model with high-resolution experimental measures of the response both at the population and single-cell level. We show that in this motif the weak positive autoregulation does not slow down but rather enhances response speedup in combination with a strong negative feedback loop. This balance of feedback strengths anticipates a homogeneous population phenotype, which we corroborate experimentally. Theoretical analysis also emphasized the specific molecular properties that determine the dynamics of the mar phenotype. More broadly, response acceleration could provide a rationale for the presence of weak positive feedbacks in other biological scenarios exhibiting these interlinked regulatory architectures.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Cellular de Plantas, CSIC–UPV, 46022 Valencia, Spain
| | - Djordje Bajic
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
| | - Ignacio Elola
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
| | - Juan F. Poyatos
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
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26
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Pires JC, Conant GC. Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes. Annu Rev Genet 2016; 50:113-131. [PMID: 27617972 DOI: 10.1146/annurev-genet-120215-035400] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complex manner in which organisms respond to changes in their gene dosage has long fascinated geneticists. Oddly, although the existence of dominance implies that dosage reductions often have mild phenotypes, extra copies of whole chromosomes (aneuploidy) are generally strongly deleterious. Even more paradoxically, an extra copy of the genome is better tolerated than is aneuploidy. We review the resolution of this paradox, highlighting the roles of biochemistry, protein aggregation, and disruption of cellular microstructure in that explanation. Returning to life's curious combination of robustness and sensitivity to dosage changes, we argue that understanding how biological robustness evolved makes these observations less inexplicable. We propose that noise in gene expression and evolutionary strategies for its suppression play a role in generating dosage phenotypes. Finally, we outline an unappreciated mechanism for the preservation of duplicate genes, namely preservation to limit expression noise, arguing that it is particularly relevant in polyploid organisms.
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Affiliation(s)
- J Chris Pires
- Division of Biological Sciences.,Informatics Institute, and
| | - Gavin C Conant
- Informatics Institute, and.,Division of Animal Sciences, University of Missouri, Columbia, Missouri, 65211-5300;
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27
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Marciano DC, Lua RC, Herman C, Lichtarge O. Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness. PHYSICAL REVIEW LETTERS 2016; 116:258104. [PMID: 27391757 PMCID: PMC5152588 DOI: 10.1103/physrevlett.116.258104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 05/05/2023]
Abstract
Negative autoregulation is universally found across organisms. In the bacterium Escherichia coli, transcription factors often repress their own expression to form a negative feedback network motif that enables robustness to changes in biochemical parameters. Here we present a simple phenomenological model of a negative feedback transcription factor repressing both itself and another target gene. The strength of the negative feedback is characterized by three parameters: the cooperativity in self-repression, the maximal expression rate of the transcription factor, and the apparent dissociation constant of the transcription factor binding to its own promoter. Analysis of the model shows that the target gene levels are robust to mutations in the transcription factor, and that the robustness improves as the degree of cooperativity in self-repression increases. The prediction is tested in the LexA transcriptional network of E. coli by altering cooperativity in self-repression and promoter strength. Indeed, we find robustness is correlated with the former. Considering the proposed importance of gene regulation in speciation, parameters governing a transcription factor's robustness to mutation may have significant influence on a cell or organism's capacity to evolve.
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Affiliation(s)
- David C. Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rhonald C. Lua
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Corresponding author.
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28
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Chauhan R, Ravi J, Datta P, Chen T, Schnappinger D, Bassler KE, Balázsi G, Gennaro ML. Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis. Nat Commun 2016; 7:11062. [PMID: 27029515 PMCID: PMC4821874 DOI: 10.1038/ncomms11062] [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: 05/14/2015] [Accepted: 02/15/2016] [Indexed: 01/26/2023] Open
Abstract
Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics. Sigma factors are regulatory proteins that reprogram the bacterial RNA polymerase in response to stress conditions to transcribe certain genes, including those for other sigma factors. Here, Chauhan et al. describe the complete sigma factor regulatory network of the pathogen Mycobacterium tuberculosis.
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Affiliation(s)
- Rinki Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Janani Ravi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Pratik Datta
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Tianlong Chen
- Department of Physics, University of Houston, Houston, Texas 77204-5005, USA.,Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5002, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Kevin E Bassler
- Department of Physics, University of Houston, Houston, Texas 77204-5005, USA.,Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5002, USA.,Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Gábor Balázsi
- Laufer Center for Physical &Quantitative Biology and Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
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29
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Noise Expands the Response Range of the Bacillus subtilis Competence Circuit. PLoS Comput Biol 2016; 12:e1004793. [PMID: 27003682 PMCID: PMC4803322 DOI: 10.1371/journal.pcbi.1004793] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 02/05/2016] [Indexed: 12/01/2022] Open
Abstract
Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins. While some circuits act to reduce this noise, others appear to exploit it. A striking example is the competence circuit in Bacillus subtilis, which exhibits much larger noise in the duration of its competence events than a synthetically constructed analog that performs the same function. Here, using stochastic modeling and fluorescence microscopy, we show that this larger noise allows cells to exit terminal phenotypic states, which expands the range of stress levels to which cells are responsive and leads to phenotypic heterogeneity at the population level. This is an important example of how noise confers a functional benefit in a genetic decision-making circuit. Fluctuations, or “noise”, in the response of a system is usually thought to be harmful. However, it is becoming increasingly clear that in single-celled organisms, noise can sometimes help cells survive. This is because noise can enhance the diversity of responses within a cell population. In this study, we identify a novel benefit of noise in the competence response of a population of Bacillus subtilis bacteria, where competence is the ability of bacteria to take in DNA from their environment when under stress. We use computational modeling and experiments to show that noise increases the range of stress levels for which these bacteria exhibit a highly dynamic response, meaning that they are neither unresponsive, nor permanently in the competent state. Since a dynamic response is thought to be optimal for survival, this study suggests that noise is exploited to increase the fitness of the bacterial population.
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Hong T, Fung ES, Zhang L, Huynh G, Monuki ES, Nie Q. Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling. J R Soc Interface 2016; 12:rsif.2015.0258. [PMID: 25972436 DOI: 10.1098/rsif.2015.0258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Temporal dynamics of morphogen-driven signalling events are critical for proper embryonic development. During development, cells translate extracellular bone morphogenetic protein (BMP) gradients, often subject to noise, into graded intracellular tail-phosphorylated SMAD (TP-SMAD) levels. Using modelling and experimental approaches, we found that BMPs induce TP-SMAD responses in neural precursor cells in a concentration-dependent manner, which are semi-adaptive within a specific intermediate range of BMP concentration. These semi-adaptive TP-SMAD responses involve an intrinsically slow deactivation of BMP receptors, which attenuates noise by prolonging SMAD deactivation time after BMP withdrawal, but increases response time. Interestingly, negative feedback on BMP receptors is also required for semi-adaptation, which benefits both noise attenuation and response time, and therefore balances the trade-off seen with slow BMP receptor deactivation. These results highlight the rich dynamics of SMAD regulation in response to graded BMP concentration, and elucidate general design principles for balancing noise attenuation and activation speed in signalling systems.
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Affiliation(s)
- Tian Hong
- Department of Mathematics, University of California, Irvine, CA, USA Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ernest S Fung
- Center for Complex Biological Systems, University of California, Irvine, CA, USA Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Lei Zhang
- Beijing International Center for Mathematical Research, Peking University, Beijing, China
| | - Grace Huynh
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Edwin S Monuki
- Center for Complex Biological Systems, University of California, Irvine, CA, USA Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA, USA Center for Complex Biological Systems, University of California, Irvine, CA, USA
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31
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Prajapat MK, Jain K, Choudhury D, Raj N, Saini S. Revisiting demand rules for gene regulation. MOLECULAR BIOSYSTEMS 2016; 12:421-30. [DOI: 10.1039/c5mb00693g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Starting with Savageau's pioneering work regarding demand rules for gene regulation from the 1970s, here, we choose the simplest transcription network and ask: how does the cell choose a particular regulatory topology from all available possibilities?
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Affiliation(s)
| | - Kirti Jain
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai - 400076
- India
| | - Debika Choudhury
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai - 400076
- India
| | - Nikhil Raj
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai - 400076
- India
| | - Supreet Saini
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai - 400076
- India
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32
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An Autogenously Regulated Expression System for Gene Therapeutic Ocular Applications. Sci Rep 2015; 5:17105. [PMID: 26597678 PMCID: PMC4656984 DOI: 10.1038/srep17105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022] Open
Abstract
The future of treating inherited and acquired genetic diseases will be defined by our ability to introduce transgenes into cells and restore normal physiology. Here we describe an autogenous transgene regulatory system (ARES), based on the bacterial lac repressor, and demonstrate its utility for controlling the expression of a transgene in bacteria, eukaryotic cells, and in the retina of mice. This ARES system is inducible by the small non-pharmacologic molecule, Isopropyl β-D-1-thiogalactopyranoside (IPTG) that has no off-target effects in mammals. Following subretinal injection of an adeno-associated virus (AAV) vector encoding ARES, luciferase expression can be reversibly controlled in the murine retina by oral delivery of IPTG over three induction-repression cycles. The ability to induce transgene expression repeatedly via administration of an oral inducer in vivo, suggests that this type of regulatory system holds great promise for applications in human gene therapy.
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33
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Phaiboun A, Zhang Y, Park B, Kim M. Survival kinetics of starving bacteria is biphasic and density-dependent. PLoS Comput Biol 2015; 11:e1004198. [PMID: 25838110 PMCID: PMC4383377 DOI: 10.1371/journal.pcbi.1004198] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
In the lifecycle of microorganisms, prolonged starvation is prevalent and sustaining life during starvation periods is a vital task. In the literature, it is commonly assumed that survival kinetics of starving microbes follows exponential decay. This assumption, however, has not been rigorously tested. Currently, it is not clear under what circumstances this assumption is true. Also, it is not known when such survival kinetics deviates from exponential decay and if it deviates, what underlying mechanisms for the deviation are. Here, to address these issues, we quantitatively characterized dynamics of survival and death of starving E. coli cells. The results show that the assumption--starving cells die exponentially--is true only at high cell density. At low density, starving cells persevere for extended periods of time, before dying rapidly exponentially. Detailed analyses show intriguing quantitative characteristics of the density-dependent and biphasic survival kinetics, including that the period of the perseverance is inversely proportional to cell density. These characteristics further lead us to identification of key underlying processes relevant for the perseverance of starving cells. Then, using mathematical modeling, we show how these processes contribute to the density-dependent and biphasic survival kinetics observed. Importantly, our model reveals a thrifty strategy employed by bacteria, by which upon sensing impending depletion of a substrate, the limiting substrate is conserved and utilized later during starvation to delay cell death. These findings advance quantitative understanding of survival of microbes in oligotrophic environments and facilitate quantitative analysis and prediction of microbial dynamics in nature. Furthermore, they prompt revision of previous models used to analyze and predict population dynamics of microbes.
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Affiliation(s)
- Andy Phaiboun
- Department of Physics, Emory University, Atlanta, Georgia, United States of America
| | - Yiming Zhang
- Department of Physics, Emory University, Atlanta, Georgia, United States of America
| | - Boryung Park
- Department of Physics, Emory University, Atlanta, Georgia, United States of America
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, Georgia, United States of America
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, United States of America
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34
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Niklas KJ, Bondos SE, Dunker AK, Newman SA. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Front Cell Dev Biol 2015; 3:8. [PMID: 25767796 PMCID: PMC4341551 DOI: 10.3389/fcell.2015.00008] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/26/2015] [Indexed: 11/16/2022] Open
Abstract
Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM). Consequently, many transcription factors do not have fixed cis-acting regulatory targets, and developmental determination by GRNs alone is untenable. Modeling these phenomena requires a multi-scale approach to explain how GRNs operationally interact with the intra- and intercellular environments. Evidence shows that AS, IDP, and PTM complicate gene expression and act synergistically to facilitate and promote time- and cell-specific protein modifications involved in cell signaling and cell fate specification and thereby disrupt a strict deterministic GRN-phenotype mapping. The combined effects of AS, IDP, and PTM give proteomes physiological plasticity, adaptive responsiveness, and developmental versatility without inefficiently expanding genome size. They also help us understand how protein functionalities can undergo major evolutionary changes by buffering mutational consequences.
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Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College Station, TX, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University Indianapolis, IN, USA
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College Valhalla, NY, USA
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35
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Iyer-Biswas S, Jayaprakash C. Mixed Poisson distributions in exact solutions of stochastic autoregulation models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:052712. [PMID: 25493821 DOI: 10.1103/physreve.90.052712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Indexed: 06/04/2023]
Abstract
In this paper we study the interplay between stochastic gene expression and system design using simple stochastic models of autoactivation and autoinhibition. Using the Poisson representation, a technique whose particular usefulness in the context of nonlinear gene regulation models we elucidate, we find exact results for these feedback models in the steady state. Further, we exploit this representation to analyze the parameter spaces of each model, determine which dimensionless combinations of rates are the shape determinants for each distribution, and thus demarcate where in the parameter space qualitatively different behaviors arise. These behaviors include power-law-tailed distributions, bimodal distributions, and sub-Poisson distributions. We also show how these distribution shapes change when the strength of the feedback is tuned. Using our results, we reexamine how well the autoinhibition and autoactivation models serve their conventionally assumed roles as paradigms for noise suppression and noise exploitation, respectively.
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Affiliation(s)
| | - C Jayaprakash
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
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36
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Witters D, Sun B, Begolo S, Rodriguez-Manzano J, Robles W, Ismagilov RF. Digital biology and chemistry. LAB ON A CHIP 2014; 14:3225-32. [PMID: 24889331 DOI: 10.1039/c4lc00248b] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This account examines developments in "digital" biology and chemistry within the context of microfluidics, from a personal perspective. Using microfluidics as a frame of reference, we identify two areas of research within digital biology and chemistry that are of special interest: (i) the study of systems that switch between discrete states in response to changes in chemical concentration of signals, and (ii) the study of single biological entities such as molecules or cells. In particular, microfluidics accelerates analysis of switching systems (i.e., those that exhibit a sharp change in output over a narrow range of input) by enabling monitoring of multiple reactions in parallel over a range of concentrations of signals. Conversely, such switching systems can be used to create new kinds of microfluidic detection systems that provide "analog-to-digital" signal conversion and logic. Microfluidic compartmentalization technologies for studying and isolating single entities can be used to reconstruct and understand cellular processes, study interactions between single biological entities, and examine the intrinsic heterogeneity of populations of molecules, cells, or organisms. Furthermore, compartmentalization of single cells or molecules in "digital" microfluidic experiments can induce switching in a range of reaction systems to enable sensitive detection of cells or biomolecules, such as with digital ELISA or digital PCR. This "digitizing" offers advantages in terms of robustness, assay design, and simplicity because quantitative information can be obtained with qualitative measurements. While digital formats have been shown to improve the robustness of existing chemistries, we anticipate that in the future they will enable new chemistries to be used for quantitative measurements, and that digital biology and chemistry will continue to provide further opportunities for measuring biomolecules, understanding natural systems more deeply, and advancing molecular and cellular analysis. Microfluidics will impact digital biology and chemistry and will also benefit from them if it becomes massively distributed.
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Affiliation(s)
- Daan Witters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
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37
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Marciano DC, Lua RC, Katsonis P, Amin SR, Herman C, Lichtarge O. Negative feedback in genetic circuits confers evolutionary resilience and capacitance. Cell Rep 2014; 7:1789-95. [PMID: 24910431 DOI: 10.1016/j.celrep.2014.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/04/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022] Open
Abstract
Natural selection for specific functions places limits upon the amino acid substitutions a protein can accept. Mechanisms that expand the range of tolerable amino acid substitutions include chaperones that can rescue destabilized proteins and additional stability-enhancing substitutions. Here, we present an alternative mechanism that is simple and uses a frequently encountered network motif. Computational and experimental evidence shows that the self-correcting, negative-feedback gene regulation motif increases repressor expression in response to deleterious mutations and thereby precisely restores repression of a target gene. Furthermore, this ability to rescue repressor function is observable across the Eubacteria kingdom through the greater accumulation of amino acid substitutions in negative-feedback transcription factors compared to genes they control. We propose that negative feedback represents a self-contained genetic canalization mechanism that preserves phenotype while permitting access to a wider range of functional genotypes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Rhonald C Lua
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shivas R Amin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Biology Department, University of St. Thomas, Houston, TX 77006, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
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38
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Charlebois DA, Balázsi G, Kærn M. Coherent feedforward transcriptional regulatory motifs enhance drug resistance. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052708. [PMID: 25353830 PMCID: PMC5749921 DOI: 10.1103/physreve.89.052708] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 05/25/2023]
Abstract
Fluctuations in gene expression give identical cells access to a spectrum of phenotypes that can serve as a transient, nongenetic basis for natural selection by temporarily increasing drug resistance. In this study, we demonstrate using mathematical modeling and simulation that certain gene regulatory network motifs, specifically coherent feedforward loop motifs, can facilitate the development of nongenetic resistance by increasing cell-to-cell variability and the time scale at which beneficial phenotypic states can be maintained. Our results highlight how regulatory network motifs enabling transient, nongenetic inheritance play an important role in defining reproductive fitness in adverse environments and provide a selective advantage subject to evolutionary pressure.
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Affiliation(s)
- Daniel A Charlebois
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario, Canada K1N 6N5 and Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Gábor Balázsi
- Department of Systems Biology-Unit 950, University of Texas MD Anderson Cancer Center, 7435 Fannin Street, Houston, Texas 77054, USA
| | - Mads Kærn
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario, Canada K1N 6N5 and Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5 and Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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39
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Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer. PLoS Genet 2014; 10:e1004171. [PMID: 24586200 PMCID: PMC3937220 DOI: 10.1371/journal.pgen.1004171] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 12/26/2013] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major force driving bacterial evolution. Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. This ability, however, poses specific requisites on plasmid physiology, in particular the need to overcome a multilevel selection process with opposing demands. We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria. Transcriptional analysis by fluorescence expression profiling and quantitative PCR revealed a regulatory network controlled by six transcriptional repressors. The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops. Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection. In the environment, bacteria often evolve by the acquisition of new genes from different species. Plasmids are small DNA molecules that mediate horizontal gene transfer in bacteria, thus they are fundamental agents for the spread of antibiotic resistances. Plasmids replicate inside the bacterial cytoplasm, and propagate infectiously by contact. Plasmids control these two ways of multiplication, but like many other symbionts they suffer from a tradeoff. If plasmids become very infective, they can spread fast and successfully, but this damages the bacterial hosts they depend upon. If, on the contrary, plasmids become very mild, the host is able to grow better but the ability of plasmids to infect new hosts is hampered. We have studied the regulatory mechanisms plasmids use to overcome this paradox. We discovered that negative feedback, a regulatory motif ubiquitous in the plasmid network, allows transient activation of plasmid functions immediately after plasmids invade a new host. This might be an adaptive strategy for plasmids to be highly infective without damaging their hosts, and it illustrates a natural mechanism for DNA transplantation that could be implemented in synthetic genomic transplants.
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40
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Abstract
Herein, I track the evolution of synthetic biology from its earliest incarnations more than 50 years ago, through the DIYbio revolution, to the next 50 years.
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Affiliation(s)
- Roy D Sleator
- Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland
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41
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Koulnis M, Porpiglia E, Hidalgo D, Socolovsky M. Erythropoiesis: from molecular pathways to system properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 844:37-58. [PMID: 25480636 DOI: 10.1007/978-1-4939-2095-2_3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Erythropoiesis is regulated through a long-range negative feedback loop, whereby tissue hypoxia stimulates erythropoietin (Epo) secretion, which promotes an increase in erythropoietic rate. However, this long-range feedback loop, by itself, cannot account for the observed system properties of erythropoiesis, namely, a wide dynamic range, stability in the face of random perturbations, and a rapid stress response. Here, we show that three Epo-regulated erythroblast survival pathways each give rise to distinct system properties. The induction of Bcl-xL by signal transducer and activator of transcription 5 (Stat5) is responsive to the rate of change in Epo levels, rather than to its absolute level, and is therefore maximally but transiently activated in acute stress. By contrast, Epo-mediated suppression of the pro-survival Fas and Bim pathways is proportional to the levels of stress/Epo and persists throughout chronic stress. Together, these elements operate in a manner reminiscent of a "proportional-integral-derivative (PID)" feedback controller frequently found in engineering applications. A short-range negative autoregulatory loop within the early erythroblast compartment, operated by Fas/FasL, filters out random noise and controls a reserve pool of early erythroblasts that is poised to accelerate the response to acute stress. Both these properties have previously been identified as inherent to negative regulatory motifs. Finally, we show that signal transduction by Stat5 combines binary and graded modalities, thereby increasing signaling fidelity over the wide dynamic range of Epo found in health and disease.
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Affiliation(s)
- Miroslav Koulnis
- Department of Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Lazare Research Building (LRB) Room 440A, 01605, Worcester, MA, USA,
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42
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Transcription factor binding kinetics constrain noise suppression via negative feedback. Nat Commun 2013; 4:1864. [PMID: 23673649 DOI: 10.1038/ncomms2867] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/15/2013] [Indexed: 11/08/2022] Open
Abstract
Negative autoregulation, where a transcription factor regulates its own expression by preventing transcription, is commonly used to suppress fluctuations in gene expression. Recent single molecule in vivo imaging has shown that it takes significant time for a transcription factor molecule to bind its chromosomal binding site. Given the slow association kinetics, transcription factor mediated feedback cannot at the same time be fast and strong. Here we show that with a limited association rate follows an optimal transcription factor binding strength where noise is maximally suppressed. At the optimal binding strength the binding site is free a fixed fraction of the time independent of the transcription factor concentration. One consequence is that high-copy number transcription factors should bind weakly to their operators, which is observed for transcription factors in Escherichia coli. The results demonstrate that a binding site's strength may be uncorrelated to its functional importance.
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43
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44
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Vodovotz Y, An G, Androulakis IP. A Systems Engineering Perspective on Homeostasis and Disease. Front Bioeng Biotechnol 2013; 1:6. [PMID: 25022216 PMCID: PMC4090890 DOI: 10.3389/fbioe.2013.00006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 08/16/2013] [Indexed: 01/06/2023] Open
Abstract
Engineered systems are coupled networks of interacting sub-systems, whose dynamics are constrained to requirements of robustness and flexibility. They have evolved by design to optimize function in a changing environment and maintain responses within ranges. Analysis, synthesis, and design of complex supply chains aim to identify and explore the laws governing optimally integrated systems. Optimality expresses balance between conflicting objectives while resiliency results from dynamic interactions among elements. Our increasing understanding of life’s multi-scale architecture suggests that living systems share similar characteristics with much to be learned about biological complexity from engineered systems. If health reflects a dynamically stable integration of molecules, cell, tissues, and organs; disease indicates displacement compensated for and corrected by activation and combination of feedback mechanisms through interconnected networks. In this article, we draw analogies between concepts in systems engineering and conceptual models of health and disease; establish connections between these concepts and physiologic modeling; and describe how these mirror onto the physiological counterparts of engineered systems.
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Affiliation(s)
- Yoram Vodovotz
- Department of Surgery, University of Pittsburgh , Pittsburgh, PA , USA ; Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh , Pittsburgh, PA , USA
| | - Gary An
- Department of Surgery, The University of Chicago , Chicago, IL , USA
| | - Ioannis P Androulakis
- Department of Biomedical Engineering, Rutgers University , Piscataway, NJ , USA ; Department of Chemical and Biochemical Engineering, Rutgers University , Piscataway, NJ , USA ; Department of Surgery, Rutgers Robert Wood Johnson Medical School , New Brunswick, NJ , USA
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45
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Scazzocchio C. In praise of erroneous hypotheses. Fungal Genet Biol 2013; 58-59:126-31. [PMID: 23973960 DOI: 10.1016/j.fgb.2013.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/18/2022]
Abstract
In the sixties Cove and Pateman discovered that mutants of Aspergillus nidulans lacking nitrate reductase activity were constitutive for the expression of genes induced by nitrate and dependent on the transcription factor NirA. They proposed that the nitrate protein acted as a repressor, preventing the transcription factor activity of NirA. Nitrate-mediated regulation behaved similarly in other organisms. This "autogenous regulation hypothesis" has recently shown to be erroneous, in the very organism for which it was first proposed. Nevertheless this erroneous hypothesis have led to a thorough dissection of the process of regulation of nitrate assimilation and more importantly to a hypothesis bearing on the origin of metabolite-responsive transcription factors. In this article I discuss the heuristic value and evolutionary importance of autogenous regulation.
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Affiliation(s)
- Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France.
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46
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Network nonlinearities in drug treatment. Interdiscip Sci 2013; 5:85-94. [PMID: 23740389 DOI: 10.1007/s12539-013-0165-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/25/2012] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
Abstract
Despite major achievements in the understanding of human disease, there is a general perception that the drug development industry has failed to meet the expectations that recent advances in biotechnology should drive. One of the potential sources of failure of many next generation drugs is that their targets are embedded in highly nonlinear signaling pathways and gene networks with multiple negative and positive feedback loops of regulation. There is increasing evidence that this complex network shapes the response to external perturbations in the form of drug treatment, originating bistability, hypersensitivity, robustness, complex dose-response curves or schedule dependent activity. This review focuses on the effect of nonlinearities on signaling and gene networks involved in human disease, using tools from Nonlinear Dynamics to discuss the implications and to overcome the effects of the nonlinearities on regulatory networks.
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Williams K, Savageau MA, Blumenthal RM. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res 2013; 41:6045-57. [PMID: 23630319 PMCID: PMC3695507 DOI: 10.1093/nar/gkt324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Restriction–modification (RM) systems are extremely widespread among bacteria and archaea, and are often specified by mobile genetic elements. In type II RM systems, where the restriction endonuclease (REase) and protective DNA methyltransferase (MTase) are separate proteins, a major regulatory challenge is delaying expression of the REase relative to the MTase after RM genes enter a new host cell. Basic understanding of this regulation is available for few RM systems, and detailed understanding for none. The PvuII RM system is one of a large subset in which the central regulatory role is played by an activator–repressor protein (called C, for controller). REase expression depends upon activation by C, whereas expression of the MTase does not. Thus delay of REase expression depends on the rate of C-protein accumulation. This is a nonlinear process, as C also activates transcription of its own gene. Mathematical modeling of the PvuII system led to the unexpected predictions of responsiveness to a factor not previously studied in RM system control—gene copy number—and of a hysteretic response. In this study, those predictions have been confirmed experimentally. The results may apply to many other C-regulated RM systems, and help explain their ability to spread so widely.
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Affiliation(s)
- Kristen Williams
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, University of Toledo, Toledo, OH 43614, USA
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Abstract
Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools that facilitate the analysis of dynamic biological systems. This paper depicts major developments in BST up to the current state of the art in 2012. It discusses its rationale, describes the typical strategies and methods of designing, diagnosing, analyzing, and utilizing BST models, and reviews areas of application. The paper is intended as a guide for investigators entering the fascinating field of biological systems analysis and as a resource for practitioners and experts.
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Tiwari A, Igoshin OA. Coupling between feedback loops in autoregulatory networks affects bistability range, open-loop gain and switching times. Phys Biol 2012; 9:055003. [PMID: 23011599 DOI: 10.1088/1478-3975/9/5/055003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Biochemical regulatory networks governing diverse cellular processes such as stress-response, differentiation and cell cycle often contain coupled feedback loops. We aim at understanding how features of feedback architecture, such as the number of loops, the sign of the loops and the type of their coupling, affect network dynamical performance. Specifically, we investigate how bistability range, maximum open-loop gain and switching times of a network with transcriptional positive feedback are affected by additive or multiplicative coupling with another positive- or negative-feedback loop. We show that a network's bistability range is positively correlated with its maximum open-loop gain and that both quantities depend on the sign of the feedback loops and the type of feedback coupling. Moreover, we find that the addition of positive feedback could decrease the bistability range if we control the basal level in the signal-response curves of the two systems. Furthermore, the addition of negative feedback has the capacity to increase the bistability range if its dissociation constant is much lower than that of the positive feedback. We also find that the addition of a positive feedback to a bistable network increases the robustness of its bistability range, whereas the addition of a negative feedback decreases it. Finally, we show that the switching time for a transition from a high to a low steady state increases with the effective fold change in gene regulation. In summary, we show that the effect of coupled feedback loops on the bistability range and switching times depends on the underlying mechanistic details.
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Affiliation(s)
- Abhinav Tiwari
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, TX 77005, USA
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Riccione KA, Smith RP, Lee AJ, You L. A synthetic biology approach to understanding cellular information processing. ACS Synth Biol 2012; 1:389-402. [PMID: 23411668 PMCID: PMC3568971 DOI: 10.1021/sb300044r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The survival of cells and organisms requires proper responses to environmental signals. These responses are governed by cellular networks, which serve to process diverse environmental cues. Biological networks often contain recurring network topologies called "motifs". It has been recognized that the study of such motifs allows one to predict the response of a biological network and thus cellular behavior. However, studying a single motif in complete isolation of all other network motifs in a natural setting is difficult. Synthetic biology has emerged as a powerful approach to understanding the dynamic properties of network motifs. In addition to testing existing theoretical predictions, construction and analysis of synthetic gene circuits has led to the discovery of novel motif dynamics, such as how the combination of simple motifs can lead to autonomous dynamics or how noise in transcription and translation can affect the dynamics of a motif. Here, we review developments in synthetic biology as they pertain to increasing our understanding of cellular information processing. We highlight several types of dynamic behaviors that diverse motifs can generate, including the control of input/output responses, the generation of autonomous spatial and temporal dynamics, as well as the influence of noise in motif dynamics and cellular behavior.
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Affiliation(s)
| | - Robert P Smith
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Anna J Lee
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
- Center for Systems Biology, Duke University, Durham, NC 27708, USA
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