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Afrose SP, Roy S, Bhattacharyya P, Singh AK, Roy L, Das D. Minimal catalytic dissipative assemblies via cooperation of an amino acid, a nucleobase precursor and a cofactor. Chem Sci 2025; 16:7838-7846. [PMID: 40177318 PMCID: PMC11959741 DOI: 10.1039/d5sc00827a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Accepted: 03/20/2025] [Indexed: 04/05/2025] Open
Abstract
Functions arising from cooperation between protobiopolymers have fueled the chemical emergence of living matter, which requires a continuous supply of energy to exist in a far-from-equilibrium state. Non-equilibrium conditions imparted by available energy sources have played critical roles in the appearance of complex co-assembled architectures, which exploit the properties of different classes of biopolymers. Such co-assemblies formed from mixtures of nitrogenous heterocycles as protonucleobases and peptide precursors might have acted as early versions of catalytic machinery, capable of sustaining chemical reaction networks. Herein, we show the generation of catalytic non-equilibrium networks from a mixture of a nitrogenous heterocycle, an amino acid and a cofactor driven by an aromatic substrate. The cooperation, a result of supramolecular interactions between different components, rendered the assemblies capable of activating the cofactor towards oxidative degradation of the substrate, which resulted in autonomous disassembly (negative feedback). Furthermore, utilising promiscuous hydrolytic capability, the transient co-assemblies could metabolise a precursor to generate additional amounts of the substrate, enhancing the lifetime (positive feedback) of the assemblies.
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Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur 741246 India
| | - Soumili Roy
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur 741246 India
| | - Pratip Bhattacharyya
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur 741246 India
| | - Ajeet Kumar Singh
- Institute of Chemical Technology Mumbai, Indian Oil Odisha Campus Bhubaneswar Gajapati Nagar Bhubaneswar Odisha 751013 India
| | - Lisa Roy
- Department of Education, Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur 741246 India
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Julou T, Gervais T, de Groot D, van Nimwegen E. Growth rate controls the sensitivity of gene regulatory circuits. SCIENCE ADVANCES 2025; 11:eadu9279. [PMID: 40279435 PMCID: PMC12024649 DOI: 10.1126/sciadv.adu9279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 03/20/2025] [Indexed: 04/27/2025]
Abstract
Microbes adapt to their environments using gene regulatory switches that sense environmental signals and induce target genes in response. Mathematical modeling predicts that, because growth rate sets the intracellular dilution rate, the sensitivity of regulatory switches to chemical cues systematically decreases with growth rate. We experimentally validate that the concentration of inducer required to activate E. coli's lac operon increases quadratically with growth rate when varying nutrients but is invariant when varying growth rate through translation inhibition. We further establish that this growth-coupled sensitivity (GCS) allows bacteria to implement concentration-dependent sugar preferences, in which a new carbon source is used only if its concentration is sufficient to improve upon the current growth rate. Using microfluidics in combination with time-lapse microscopy, we validate this prediction at the single-cell level using mixtures of glucose and lactose. Overall, GCS causes cells to automatically become more sensitive to environmental signals when their growth rate decreases.
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Affiliation(s)
| | | | - Daan de Groot
- Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland
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3
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Ducharme JB, Specht JW, Bailly AR, Fennel ZJ, Nava RC, Mermier CM, Laitano O, Deyhle MR. Training Status Influences Regulation of Muscle and PBMC TLR4 Expression and Systemic Cytokine Responses to Vigorous Endurance Exercise. Med Sci Sports Exerc 2025; 57:767-780. [PMID: 39625335 DOI: 10.1249/mss.0000000000003618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
Abstract
INTRODUCTION A bout of vigorous endurance exercise transiently activates Toll-like receptor 4 (TLR4) and reduces TLR4 protein expressed on peripheral blood mononuclear cells (PBMCs). Endurance training, on the other hand, reduces TLR4-mediated signaling and minimizes the physiological stress imposed by exercise. Less is known about what occurs in skeletal muscle regarding TLR4 regulation and signaling. Therefore, this study aimed to investigate the regulation of TLR4 expressed in different tissue types (PBMCs and skeletal muscle samples) between endurance-trained and untrained men following vigorous endurance exercise and determine the effect of training status on cytokine responses associated with TLR4 activation. METHODS Endurance-trained ( n = 7) and untrained ( n = 5) men cycled for 1 h at their respiratory compensation point, with blood and skeletal muscle samples collected pre- and 3 h post-exercise. RESULTS In response to vigorous exercise, untrained men experienced a decrease in inhibitor of κBα (IκBα) protein (suggesting IκB degradation and the activation of TLR4-associated transcription factor NF-κB) and TLR4 protein levels, along with a simultaneous increase in TLR4 mRNA expression in both skeletal muscle and PBMCs. Moreover, this exercise session led to elevated levels of circulating interleukin-6, tumor necrosis factor-α, and interleukin-1β. Collectively, these results suggest a heightened TLR4-mediated signaling pathway in untrained men. However, no changes in these targets were observed in endurance-trained men, possibly indicating a potential mechanism by which regular endurance training blunts systemic inflammation. CONCLUSIONS These findings highlight the potential of endurance training to mitigate TLR4-mediated signaling, such as systemic inflammation, and shed light on the effects of exercise on TLR4 expression in PBMCs and skeletal muscle.
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Affiliation(s)
- Jeremy B Ducharme
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, NM
| | - Jonathan W Specht
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, NM
| | - Alyssa R Bailly
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, NM
| | | | | | - Christine M Mermier
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, NM
| | - Orlando Laitano
- Department of Applied Physiology & Kinesiology, University of Florida, Gainesville, FL
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Weiner AT, Nissen SB, Suyama K, Cho B, Pierre-Louis G, Axelrod JD. Cell autonomous polarization by the planar cell polarity signaling pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.09.26.559449. [PMID: 37808631 PMCID: PMC10557733 DOI: 10.1101/2023.09.26.559449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Planar Cell Polarity (PCP) signaling polarizes epithelial cells in a plane orthogonal to their apical-basal axis. A core PCP signaling module segregates two distinct molecular subcomplexes to opposite sides of cells and coordinates the direction of polarization between neighboring cells. Homodimers of the atypical cadherin Flamingo are thought to scaffold these subcomplexes and are required for intercellular polarity signaling. Feedback is required for polarization, but whether feedback requires intercellular and/or intracellular pathways is unknown, and traditional genetic tools have limited utility in dissecting these mechanisms. Using novel tools, we show that cells lacking Flamingo, or bearing a homodimerization-deficient Flamingo, do polarize, indicating that functional PCP subcomplexes form and segregate cell-autonomously. We identify feedback pathways and propose a competitive binding-based asymmetry amplifying mechanism that each operate cell-autonomously. The intrinsic logic of PCP signaling is therefore more similar to that in single cell polarizing systems than was previously recognized.
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Affiliation(s)
- Alexis T Weiner
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Silas Boye Nissen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Kaye Suyama
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bomsoo Cho
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gandhy Pierre-Louis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Developmental Biology graduate program, Stanford University, Stanford, CA, USA
| | - Jeffrey D Axelrod
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
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5
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Ryzowicz CJ, Bertram R, Karamched BR. Oscillations in delayed positive feedback systems. Phys Chem Chem Phys 2024; 26:24861-24869. [PMID: 39291452 DOI: 10.1039/d4cp01867b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Positive feedback loops exist in many biological circuits important for organismal function. In this work, we investigate how temporal delay affects the dynamics of two canonical positive feedback models. We consider models of a genetic toggle switch and a one-way switch with delay added to the feedback terms. We show that long-lasting transient oscillations exist in both models under general conditions and that the duration depends strongly on the magnitude of the delay and initial conditions. We then show the existence of long-lasting oscillations in specific biological examples: the Cdc2-Cyclin B/Wee1 system and a genetic regulatory network. Our results challenge fundamental assumptions underlying oscillatory behavior in biological systems. While generally delayed negative feedback systems are canonical in generating oscillations, we show that delayed positive feedback systems are a mechanism for generating oscillations as well.
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Affiliation(s)
| | - Richard Bertram
- Department of Mathematics, Florida State University, Tallahassee, FL 32306, USA
- Program in Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Bhargav R Karamched
- Department of Mathematics, Florida State University, Tallahassee, FL 32306, USA
- Program in Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
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O'Hearn LA. Signals of energy availability in sleep: consequences of a fat-based metabolism. Front Nutr 2024; 11:1397185. [PMID: 39267859 PMCID: PMC11390529 DOI: 10.3389/fnut.2024.1397185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024] Open
Abstract
Humans can flexibly switch between two primary metabolic modes, usually distinguished by whether substrate supply from glucose can meet energy demands or not. However, it is often overlooked that when glucose use is limited, the remainder of energy needs may still be met more or less effectively with fat and ketone bodies. Hence a fat-based metabolism marked by ketosis is often conflated with starvation and contexts of inadequate energy (including at the cellular level), even when energy itself is in ample supply. Sleep and satiation are regulated by common pathways reflecting energy metabolism. A conceptual analysis that distinguishes signals of inadequate energy in a glucose-dominant metabolism from signals of a fat-based metabolism that may well be energy sufficient allows a reexamination of experimental results in the study of sleep that may shed light on species differences and explain why ketogenic diets have beneficial effects simultaneously in the brain and the periphery. It may also help to distinguish clinically when a failure of a ketogenic diet to resolve symptoms is due to inadequate energy rather than the metabolic state itself.
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Wan W, Zhang H, Niu L, Zhang M, Xu F, Li A, Pei D, Lin M, Cheng B. TGF-β1 promotes osteogenesis of mesenchymal stem cells via integrin mediated mechanical positive autoregulation. iScience 2024; 27:110262. [PMID: 39021801 PMCID: PMC11253692 DOI: 10.1016/j.isci.2024.110262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/18/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Positive autoregulation (PAR), one type of network motifs, provides a high phenotypic heterogeneity for cells to better adapt to their microenvironments. Typical mechanosensitive proteins can also form PAR, e.g., integrin mediated PAR, but the role of such mechanical PAR in physiological development and pathological process remains elusive. In this study, we found that transforming growth factor β1 (TGF-β1) and integrin levels decrease with tissue softening after the development of paradentium in vivo in rat model of periodontitis (an inflammatory disease with bone defect). Interestingly, TGF-β1 could induce the formation of mechanical PAR involving the integrin-FAK-YAP axis in mesenchymal stem cells (MSCs) by both in vitro experiments and in silico computational model. The computational model predicted a mechanical PAR involving the bimodal distribution of focus adhesions, which enables cells to accurately perceive extracellular mechanical cues. Thus, our analysis of TGF-β1 mediated mechanosensing mechanism on MSCs may help to better understand the molecular process underlying bone regeneration.
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Affiliation(s)
- Wanting Wan
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004 P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049 P.R. China
| | - Hui Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004 P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049 P.R. China
| | - Lin Niu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004 P.R. China
| | - Min Zhang
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi International Joint Research Center for Oral Diseases, Department of General Dentistry and Emergency, School of Stomatology, Fourth Military Medical University, Xi’an 710032 P.R. China
| | - Feng Xu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049 P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049 P.R. China
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004 P.R. China
| | - Dandan Pei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004 P.R. China
| | - Min Lin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049 P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049 P.R. China
| | - Bo Cheng
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049 P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049 P.R. China
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Kariya Y, Honma M. Applications of model simulation in pharmacological fields and the problems of theoretical reliability. Drug Metab Pharmacokinet 2024; 56:100996. [PMID: 38797090 DOI: 10.1016/j.dmpk.2024.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/23/2023] [Accepted: 12/31/2023] [Indexed: 05/29/2024]
Abstract
The use of mathematical models has become increasingly prevalent in pharmacological fields, particularly in drug development processes. These models are instrumental in tasks such as designing clinical trials and assessing factors like efficacy, toxicity, and clinical practice. Various types of models have been developed and documented. Nevertheless, emphasizing the reliability of parameter values is crucial, as they play a pivotal role in shaping the behavior of the system. In some instances, parameter values reported previously are treated as fixed values, which can lead to convergence towards values that deviate substantially from those found in actual biological systems. This is especially true when parameter values are determined through fitting to limited observations. To mitigate this risk, the reuse of parameter values from previous reports should be approached with a critical evaluation of their validity. Currently, there is a proposal for a simultaneous search for plausible values for all parameters using comprehensive search algorithms in both pharmacokinetic and pharmacodynamic or systems pharmacological models. Implementing these methodologies can help address issues related to parameter determination. Furthermore, integrating these approaches with methods developed in the field of machine-learning field has the potential to enhance the reliability of parameter values and the resulting model outputs.
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Affiliation(s)
- Yoshiaki Kariya
- Education Center for Medical Pharmaceutics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Laboratory of Pharmaceutical Regulatory Sciences, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Masashi Honma
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Abe Y, Sano T, Otsuka N, Ogawa M, Tanaka N. PRMT5-mediated methylation of STAT3 is required for lung cancer stem cell maintenance and tumour growth. Commun Biol 2024; 7:593. [PMID: 38760429 PMCID: PMC11101626 DOI: 10.1038/s42003-024-06290-7] [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: 06/27/2023] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
STAT3 is constitutively activated in many cancer types, including lung cancer, and can induce cancer cell proliferation and cancer stem cell (CSC) maintenance. STAT3 is activated by tyrosine kinases, such as JAK and SRC, but the mechanism by which STAT3 maintains its activated state in cancer cells remains unclear. Here, we show that PRMT5 directly methylates STAT3 and enhances its activated tyrosine phosphorylation in non-small cell lung cancer (NSCLC) cells. PRMT5 expression is also induced by STAT3, suggesting the presence of a positive feedback loop in cancer cells. Furthermore, methylation of STAT3 at arginine 609 by PRMT5 is important for its transcriptional activity and support of tumour growth and CSC maintenance. Indeed, NSCLC cells expressing the STAT3 mutant which R609 was replaced to alanine (R609K) show significantly impaired tumour growth in nude mice. Overall, our study reveals a mechanism by which STAT3 remains activated in NSCLC and provides a new target for cancer therapeutic approaches.
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Affiliation(s)
- Yoshinori Abe
- Laboratory of Molecular Analysis, Nippon Medical School, Tokyo, Japan
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Takumi Sano
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Naoki Otsuka
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Masashi Ogawa
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Nobuyuki Tanaka
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan.
- Division of Cell Physiology, Department of Physiology and Cell Biology, Graduate School of Medicine, Kobe University, Kobe, Japan.
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10
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Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. eLife 2024; 12:RP92093. [PMID: 38717010 PMCID: PMC11078544 DOI: 10.7554/elife.92093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here, I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors, and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode Caenorhabditis elegans. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
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11
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Yang X, Mao Q, Wang B. On the Question of CO's Ability to Induce HO-1 Expression in Cell Culture: A Comparative Study Using Different CO Sources. ACS Chem Biol 2024; 19:725-735. [PMID: 38340055 PMCID: PMC10949199 DOI: 10.1021/acschembio.3c00750] [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: 12/06/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
With the recognition of the endogenous signaling roles and pharmacological functions of carbon monoxide (CO), there is an increasing need to understand CO's mechanism of actions. Along this line, chemical donors have been introduced as CO surrogates for ease of delivery, dosage control, and sometimes the ability to target. Among all of the donors, two ruthenium-carbonyl complexes, CORM-2 and -3, are arguably the most commonly used tools for about 20 years in studying the mechanism of actions of CO. Largely based on data using these two CORMs, there has been a widely accepted inference that the upregulation of heme oxygenase-1 (HO-1) expression is one of the key mechanisms for CO's actions. However, recent years have seen reports of very pronounced chemical reactivities and CO-independent activities of these CORMs. We are interested in examining this question by conducting comparative studies using CO gas, CORM-2/-3, and organic CO donors in RAW264.7, HeLa, and HepG2 cell cultures. CORM-2 and CORM-3 treatment showed significant dose-dependent induction of HO-1 compared to "controls," while incubation for 6 h with 250-500 ppm CO gas did not increase the HO-1 protein expression and mRNA transcription level. A further increase of the CO concentration to 5% did not lead to HO-1 expression either. Additionally, we demonstrate that CORM-2/-3 releases minimal amounts of CO under the experimental conditions. These results indicate that the HO-1 induction effects of CORM-2/-3 are not attributable to CO. We also assessed two organic CO prodrugs, BW-CO-103 and BW-CO-111. BW-CO-111 but not BW-CO-103 dose-dependently increased HO-1 levels in RAW264.7 and HeLa cells. We subsequently studied the mechanism of induction with an Nrf2-luciferase reporter assay, showing that the HO-1 induction activity is likely due to the activation of Nrf2 by the CO donors. Overall, CO alone is unable to induce HO-1 or activate Nrf2 under various conditions in vitro. As such, there is no evidence to support attributing the HO-1 induction effect of the CO donors such as CORM-2/-3 and BW-CO-111 in cell culture to CO. This comparative study demonstrates the critical need to consider possible CO-independent effects of a chemical CO donor before attributing the observed biological effects to CO. It is also important to note that such in vitro results cannot be directly extrapolated to in vivo studies because of the increased level of complexity and the likelihood of secondary and/or synergistic effects in the latter.
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Affiliation(s)
- Xiaoxiao Yang
- Department of Chemistry and
Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Qiyue Mao
- Department of Chemistry and
Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Binghe Wang
- Department of Chemistry and
Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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12
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Wei Z, Wei H. Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation. HORTICULTURE RESEARCH 2024; 11:uhad281. [PMID: 38344650 PMCID: PMC10857936 DOI: 10.1093/hr/uhad281] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/12/2023] [Indexed: 04/29/2025]
Abstract
Wood quality is predominantly determined by the amount and the composition of secondary cell walls (SCWs). Consequently, unraveling the molecular regulatory mechanisms governing SCW formation is of paramount importance for genetic engineering aimed at enhancing wood properties. Although SCW formation is known to be governed by a hierarchical gene regulatory network (HGRN), our understanding of how a HGRN operates and regulates the formation of heterogeneous SCWs for plant development and adaption to ever-changing environment remains limited. In this review, we examined the HGRNs governing SCW formation and highlighted the significant key differences between herbaceous Arabidopsis and woody plant poplar. We clarified many confusions in existing literatures regarding the HGRNs and their orthologous gene names and functions. Additionally, we revealed many network motifs including feed-forward loops, feed-back loops, and negative and positive autoregulation in the HGRNs. We also conducted a thorough review of post-transcriptional and post-translational aspects, protein-protein interactions, and epigenetic modifications of the HGRNs. Furthermore, we summarized how the HGRNs respond to environmental factors and cues, influencing SCW biosynthesis through regulatory cascades, including many regulatory chains, wiring regulations, and network motifs. Finally, we highlighted the future research directions for gaining a further understanding of molecular regulatory mechanisms underlying SCW formation.
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Affiliation(s)
- Zhigang Wei
- Engineering Research Center of Agricultural Microbiology Technology, Ministhry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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Tuell D, Ford G, Los E, Stone W. The Role of Glutathione and Its Precursors in Type 2 Diabetes. Antioxidants (Basel) 2024; 13:184. [PMID: 38397782 PMCID: PMC10885928 DOI: 10.3390/antiox13020184] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Type 2 diabetes (T2D) is a major worldwide health crisis affecting about 6.2% of the world's population. Alarmingly, about one in five children in the USA have prediabetes. Glutathione (GSH) and its precursors play a promising role in the prevention and management of type T2D. Oxidative stress (OxS) is a probable factor in both T2D initiation and progression. GSH is the major cytosolic water-soluble chemical antioxidant and emerging evidence supports its role in improving T2D outcomes. Dietary supplementation with N-acetyl-cysteine (NAC) and/or glycine (GLY), which are GSH precursors, has also been studied for possible beneficial effects on T2D. This review will focus on the underlying pathophysiological and molecular mechanisms linking GSH and its precursors with T2D and OxS. In addition to their traditional antioxidant roles, the in vivo effects of GSH/NAC/GLY supplements will be evaluated for their potential abilities to modulate the complex pro-oxidant pathophysiological factors (e.g., hyperglycemia) driving T2D progression. Positive feedback loops that amplify OxS over long time intervals are likely to result in irreversible T2D micro- and macro-vascular damage. Most clinical studies with GSH/NAC/GLY have focused on adults or the elderly. Future research with pediatric populations should be a high priority since early intervention is critical.
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Ducharme JB, McKenna ZJ, Specht JW, Fennel ZJ, Berkemeier QN, Deyhle MR. Divergent mechanisms regulate TLR4 expression on peripheral blood mononuclear cells following workload-matched exercise in normoxic and hypoxic environments. J Appl Physiol (1985) 2024; 136:33-42. [PMID: 37994415 DOI: 10.1152/japplphysiol.00626.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Exercise in hypoxia increases immune responses compared with normoxic exercise, and while Toll-like receptor 4 (TLR4) is implicated in these responses, its regulation remains undefined. The purpose of this study was to 1) investigate TLR4 regulation during workload-matched endurance exercise in normoxic and hypoxic conditions in vivo and 2) determine the independent effects of hypoxia and muscle contractions on TLR4 expression in vitro. Eight recreationally active men cycled for 1 h at 65% of their V̇o2max in normoxia (630 mmHg) and in hypobaric hypoxia (440 mmHg). Exercise in normoxia decreased TLR4 expressed on peripheral blood mononuclear cells (PBMCs), had no effect on the expression of inhibitor of κBα (IκBα), and increased the concentration of soluble TLR4 (sTLR4) in circulation. In contrast, exercise in hypoxia decreased the expression of TLR4 and IκBα in PBMCs, and sTLR4 in circulation. Markers of physiological stress were higher during exercise in hypoxia, correlating with markers of intestinal barrier damage, circulating lipopolysaccharides (LPS), and a concurrent decrease in circulating sTLR4, suggesting heightened TLR4 activation, internalization, and degradation in response to escalating physiological strain. In vitro, both hypoxia and myotube contractions independently, and in combination, reduced TLR4 expressed on C2C12 myotubes, and these effects were dependent on hypoxia-inducible factor 1 (HIF-1). In summary, the regulation of TLR4 varies depending on the physiological stress during exercise. To our knowledge, our study provides the first evidence of exercise-induced effects on sTLR4 in vivo and highlights the essential role of HIF-1 in the reduction of TLR4 during contraction and hypoxia in vitro.NEW & NOTEWORTHY We provide the first evidence of exercise affecting soluble Toll-like receptor 4 (sTLR4), a TLR4 ligand decoy receptor. We found that the degree of exercise-induced physiological stress influences TLR4 regulation on peripheral blood mononuclear cells (PBMCs). Moderate-intensity exercise reduces PBMC TLR4 and increases circulating sTLR4. Conversely, workload-matched exercise in hypoxia induces greater physiological stress, intestinal barrier damage, circulating lipopolysaccharides, and reduces both TLR4 and sTLR4, suggesting heightened TLR4 activation, internalization, and degradation under increased strain.
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Affiliation(s)
- Jeremy B Ducharme
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
| | - Zachary J McKenna
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
- Institute for Exercise and Environmental Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Jonathan W Specht
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
| | - Zachary J Fennel
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
- Molecular Medicine Program, University of Utah, Salt Lake City, Utah, United States
| | - Quint N Berkemeier
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
| | - Michael R Deyhle
- Department of Health, Exercise and Sports Sciences, University of New Mexico, Albuquerque, New Mexico, United States
- Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, New Mexico, United States
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15
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Jung H. A pore-scale reactive transport modeling study for quorum sensing-driven biofilm dispersal in heterogeneous porous media. Math Biosci 2024; 367:109126. [PMID: 38070765 DOI: 10.1016/j.mbs.2023.109126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/26/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Microorganisms regulate the expression of energetically expensive phenotypes via a collective decision-making mechanism known as quorum sensing (QS). This study investigates the intricate dynamics of biofilm growth and QS-controlled biofilm dispersal in heterogeneous porous media, employing a pore-scale reactive transport modeling approach. Model simulations carried out under various fluid flow conditions and biofilm growth scenarios reveal that QS processes are influenced not only by the biomass density of biofilm colonies but also by a complex interplay between pore architecture, flow velocity, and the rates of biofilm growth and dispersal. This study demonstrates that pore architecture controls the initiation of QS processes and advection gives rise to oscillatory growth of biofilms. Such oscillation is suppressed if biofilm dynamics are in favor of sustaining a sufficiently high signal concentration, such as fast growth or slow dispersal rates. By establishing a mathematical framework, this study contributes to the fundamental understanding of QS-controlled biofilm dynamics in complex environments.
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Affiliation(s)
- Heewon Jung
- Department of Geological Sciences, Chungnam National University, Daejeon 34134, South Korea.
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16
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García-Tomsig NI, García-Rodriguez FM, Guedes-García SK, Millán V, Becker A, Robledo M, Jiménez-Zurdo JI. A double-negative feedback loop between NtrBC and a small RNA rewires nitrogen metabolism in legume symbionts. mBio 2023; 14:e0200323. [PMID: 37850753 PMCID: PMC10746234 DOI: 10.1128/mbio.02003-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Root nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.
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Affiliation(s)
- Natalia I. García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Fernando M. García-Rodriguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Sabina K. Guedes-García
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Vicenta Millán
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Marta Robledo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I. Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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17
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Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544138. [PMID: 37333369 PMCID: PMC10274868 DOI: 10.1101/2023.06.07.544138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Such stable changes can (1) alter steady-state levels while preserving the architecture, (2) induce different architectures that persist for many generations, or (3) collapse the entire architecture. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that the evolution of mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of regulatory architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode C. elegans, which range from permanent silencing to recovery from silencing within a few generations and subsequent resistance to silencing. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
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18
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Alexandris AS, Koliatsos VE. NAD +, Axonal Maintenance, and Neurological Disease. Antioxid Redox Signal 2023; 39:1167-1184. [PMID: 37503611 PMCID: PMC10715442 DOI: 10.1089/ars.2023.0350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 05/28/2023] [Indexed: 07/29/2023]
Abstract
Significance: The remarkable geometry of the axon exposes it to unique challenges for survival and maintenance. Axonal degeneration is a feature of peripheral neuropathies, glaucoma, and traumatic brain injury, and an early event in neurodegenerative diseases. Since the discovery of Wallerian degeneration (WD), a molecular program that hijacks nicotinamide adenine dinucleotide (NAD+) metabolism for axonal self-destruction, the complex roles of NAD+ in axonal viability and disease have become research priority. Recent Advances: The discoveries of the protective Wallerian degeneration slow (WldS) and of sterile alpha and TIR motif containing 1 (SARM1) activation as the main instructive signal for WD have shed new light on the regulatory role of NAD+ in axonal degeneration in a growing number of neurological diseases. SARM1 has been characterized as a NAD+ hydrolase and sensor of NAD+ metabolism. The discovery of regulators of nicotinamide mononucleotide adenylyltransferase 2 (NMNAT2) proteostasis in axons, the allosteric regulation of SARM1 by NAD+ and NMN, and the existence of clinically relevant windows of action of these signals has opened new opportunities for therapeutic interventions, including SARM1 inhibitors and modulators of NAD+ metabolism. Critical Issues: Events upstream and downstream of SARM1 remain unclear. Furthermore, manipulating NAD+ metabolism, an overdetermined process crucial in cell survival, for preventing the degeneration of the injured axon may be difficult and potentially toxic. Future Directions: There is a need for clarification of the distinct roles of NAD+ metabolism in axonal maintenance as contrasted to WD. There is also a need to better understand the role of NAD+ metabolism in axonal endangerment in neuropathies, diseases of the white matter, and the early stages of neurodegenerative diseases of the central nervous system. Antioxid. Redox Signal. 39, 1167-1184.
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Affiliation(s)
| | - Vassilis E. Koliatsos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Wang SH, Siebenhühner F, Arnulfo G, Myrov V, Nobili L, Breakspear M, Palva S, Palva JM. Critical-like Brain Dynamics in a Continuum from Second- to First-Order Phase Transition. J Neurosci 2023; 43:7642-7656. [PMID: 37816599 PMCID: PMC10634584 DOI: 10.1523/jneurosci.1889-22.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 06/07/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
The classic brain criticality hypothesis postulates that the brain benefits from operating near a continuous second-order phase transition. Slow feedback regulation of neuronal activity could, however, lead to a discontinuous first-order transition and thereby bistable activity. Observations of bistability in awake brain activity have nonetheless remained scarce and its functional significance unclear. Moreover, there is no empirical evidence to support the hypothesis that the human brain could flexibly operate near either a first- or second-order phase transition despite such a continuum being common in models. Here, using computational modeling, we found bistable synchronization dynamics to emerge through elevated positive feedback and occur exclusively in a regimen of critical-like dynamics. We then assessed bistability in vivo with resting-state MEG in healthy adults (7 females, 11 males) and stereo-electroencephalography in epilepsy patients (28 females, 36 males). This analysis revealed that a large fraction of the neocortices exhibited varying degrees of bistability in neuronal oscillations from 3 to 200 Hz. In line with our modeling results, the neuronal bistability was positively correlated with classic assessment of brain criticality across narrow-band frequencies. Excessive bistability was predictive of epileptic pathophysiology in the patients, whereas moderate bistability was positively correlated with task performance in the healthy subjects. These empirical findings thus reveal the human brain as a one-of-a-kind complex system that exhibits critical-like dynamics in a continuum between continuous and discontinuous phase transitions.SIGNIFICANCE STATEMENT In the model, while synchrony per se was controlled by connectivity, increasing positive local feedback led to gradually emerging bistable synchrony with scale-free dynamics, suggesting a continuum between second- and first-order phase transitions in synchrony dynamics inside a critical-like regimen. In resting-state MEG and SEEG, bistability of ongoing neuronal oscillations was pervasive across brain areas and frequency bands and was observed only with concurring critical-like dynamics as the modeling predicted. As evidence for functional relevance, moderate bistability was positively correlated with executive functioning in the healthy subjects, and excessive bistability was associated with epileptic pathophysiology. These findings show that critical-like neuronal dynamics in vivo involves both continuous and discontinuous phase transitions in a frequency-, neuroanatomy-, and state-dependent manner.
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Affiliation(s)
- Sheng H Wang
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Doctoral Programme Brain & Mind, University of Helsinki, 00014 Helsinki, Finland
- BioMag Laboratory, HUS Medical Imaging Center, 00290 Helsinki, Finland
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Espoo, Finland
| | - Felix Siebenhühner
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- BioMag Laboratory, HUS Medical Imaging Center, 00290 Helsinki, Finland
| | - Gabriele Arnulfo
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genoa, 16136 Genoa, Italy
| | - Vladislav Myrov
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Espoo, Finland
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Children's Sciences, University of Genoa, 16136 Genoa, Italy
- Child Neuropsychiatry Unit, Istituto Di Ricovero e Cura a Carattere Scientifico Istituto Giannina Gaslini, 16147 Genoa, Italy
- Centre of Epilepsy Surgery "C. Munari," Department of Neuroscience, Niguarda Hospital, 20162 Milan, Italy
| | - Michael Breakspear
- College of Engineering, Science and Environment, College of Health and Medicine, University of Newcastle, Callaghan, 2308 Australia
| | - Satu Palva
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Centre for Cognitive Neuroimaging, Institute of Neuroscience & Psychology, University of Glasgow, Glasgow G12 8QB, United Kingdom
| | - J Matias Palva
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Espoo, Finland
- Centre for Cognitive Neuroimaging, Institute of Neuroscience & Psychology, University of Glasgow, Glasgow G12 8QB, United Kingdom
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20
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Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
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Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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21
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Tanaka Y, Yamagishi M, Motomura Y, Kamatani T, Oguchi Y, Suzuki N, Kiniwa T, Kabata H, Irie M, Tsunoda T, Miya F, Goda K, Ohara O, Funatsu T, Fukunaga K, Moro K, Uemura S, Shirasaki Y. Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation. Commun Biol 2023; 6:915. [PMID: 37673922 PMCID: PMC10482971 DOI: 10.1038/s42003-023-05297-w] [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: 03/08/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
The decision of whether cells are activated or not is controlled through dynamic intracellular molecular networks. However, the low population of cells during the transition state of activation renders the analysis of the transcriptome of this state technically challenging. To address this issue, we have developed the Time-Dependent Cell-State Selection (TDCSS) technique, which employs live-cell imaging of secretion activity to detect an index of the transition state, followed by the simultaneous recovery of indexed cells for subsequent transcriptome analysis. In this study, we used the TDCSS technique to investigate the transition state of group 2 innate lymphoid cells (ILC2s) activation, which is indexed by the onset of interleukin (IL)-13 secretion. The TDCSS approach allowed us to identify time-dependent genes, including transiently induced genes (TIGs). Our findings of IL4 and MIR155HG as TIGs have shown a regulatory function in ILC2s activation.
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Affiliation(s)
- Yumiko Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mai Yamagishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Live Cell Diagnosis, Ltd, Saitama, Japan
| | - Yasutaka Motomura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takashi Kamatani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of AI Technology Development, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Precision Cancer Medicine, Tokyo Medical and Dental University Hospital, Tokyo, Japan
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yusuke Oguchi
- PRESTO, JST, Saitama, Japan
- RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Nobutake Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Kiniwa
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Hiroki Kabata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Misato Irie
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
| | | | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kazuyo Moro
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Yoshitaka Shirasaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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22
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Alexis E, Schulte CCM, Cardelli L, Papachristodoulou A. Regulation strategies for two-output biomolecular networks. J R Soc Interface 2023; 20:20230174. [PMID: 37528680 PMCID: PMC10394417 DOI: 10.1098/rsif.2023.0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Feedback control theory facilitates the development of self-regulating systems with desired performance which are predictable and insensitive to disturbances. Feedback regulatory topologies are found in many natural systems and have been of key importance in the design of reliable synthetic bio-devices operating in complex biological environments. Here, we study control schemes for biomolecular processes with two outputs of interest, expanding previously described concepts based on single-output systems. Regulation of such processes may unlock new design possibilities but can be challenging due to coupling interactions; also potential disturbances applied on one of the outputs may affect both. We therefore propose architectures for robustly manipulating the ratio/product and linear combinations of the outputs as well as each of the outputs independently. To demonstrate their characteristics, we apply these architectures to a simple process of two mutually activated biomolecular species. We also highlight the potential for experimental implementation by exploring synthetic realizations both in vivo and in vitro. This work presents an important step forward in building bio-devices capable of sophisticated functions.
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Affiliation(s)
- Emmanouil Alexis
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Carolin C. M. Schulte
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Luca Cardelli
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK
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23
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Irikura R, Nishizawa H, Nakajima K, Yamanaka M, Chen G, Tanaka K, Onodera M, Matsumoto M, Igarashi K. Ferroptosis model system by the re-expression of BACH1. J Biochem 2023; 174:239-252. [PMID: 37094356 DOI: 10.1093/jb/mvad036] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
Ferroptosis is a regulated cell death induced by iron-dependent lipid peroxidation. The heme-responsive transcription factor BTB and CNC homology 1 (BACH1) promotes ferroptosis by repressing the transcription of genes involved in glutathione (GSH) synthesis and intracellular labile iron metabolism, which are key regulatory pathways in ferroptosis. We found that BACH1 re-expression in Bach1-/- immortalized mouse embryonic fibroblasts (iMEFs) can induce ferroptosis upon 2-mercaptoethanol removal, without any ferroptosis inducers. In these iMEFs, GSH synthesis was reduced, and intracellular labile iron levels were increased upon BACH1 re-expression. We used this system to investigate whether the major ferroptosis regulators glutathione peroxidase 4 (Gpx4) and apoptosis-inducing factor mitochondria-associated 2 (Aifm2), the gene for ferroptosis suppressor protein 1, are target genes of BACH1. Neither Gpx4 nor Aifm2 was regulated by BACH1 in the iMEFs. However, we found that BACH1 represses AIFM2 transcription in human pancreatic cancer cells. These results suggest that the ferroptosis regulators targeted by BACH1 may vary across different cell types and animal species. Furthermore, we confirmed that the ferroptosis induced by BACH1 re-expression exhibited a propagating effect. BACH1 re-expression represents a new strategy for inducing ferroptosis after GPX4 or system Xc- suppression and is expected to contribute to future ferroptosis research.
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Key Words
- BACH1 Abbreviations: AIFM2, apoptosis-inducing factor mitochondria-associated 2; ANOVA, analysis of variance; BACH1, BTB and CNC homology 1; Bach1−/− mice, Bach1 knockout mice; BTB, Broad complex, Tramtrack, Bric-a-brac domain; bZIP, basic leucine zipper; ChIP-seq, chromatin immunoprecipitation sequencing; CNC, Cap‘n’Collar region; DAPI, 4′,6-diamidino-2-phenylindole; DFX, deferasirox; DMSO, dimethyl sulfoxide; EMT, epithelial–mesenchymal transition; Ferr-1, ferrostatin-1; FINs, ferroptosis inducers; FSP1, Ferroptosis suppressor protein 1; Fth1, ferritin heavy chain 1; Ftl, ferritin light chain; GCL, glutamate-cysteine ligase; Gclc, GCL catalytic subunit; Gclm, GCL modifier subunit; GEO, Gene Expression Omnibus; GPX4, glutathione peroxidase 4; GSH, glutathione; HO-1 (Hmox1), heme oxygenase 1; iMEFs, immortalized MEFs; KuO, Kusabira Orange; MAFK, musculoaponeurotic fibrosarcoma oncogene homolog bZIP transcription factor K; mBACH1, Bach1 gene of Mus musculus; 2-ME, 2-mercaptoethanol; MEFs, mouse embryonic fibroblasts; NRF2, nuclear factor-erythroid 2-related factor 2; NSA, necrosulfonamide; PDAC, pancreatic ductal adenocarcinoma; PI, Propidium iodide; Ptgs2, prostaglandin-endoperoxide synthase 2; RSL3, (1S,3R)-RSL3; Slc40a1, solute carrier family 40 member 1; Slc7a11, solute carrier family 7 member 11; TFRC, transferrin receptor 1; Z-VAD.FMK, Benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethylketone
- extracellular signal
- ferroptosis
- fibroblasts
- transcription
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Affiliation(s)
- Riko Irikura
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Kazuma Nakajima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Mie Yamanaka
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
- Gladstone Institute of Neurological Disease, Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Guan Chen
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masafumi Onodera
- Gene & Cell Therapy Promotion Center, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
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24
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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: 6] [Impact Index Per Article: 3.0] [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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25
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Pan TC, Chockalingam SP, Aluru M, Aluru S. MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework. Bioinformatics 2023; 39:btad373. [PMID: 37289522 PMCID: PMC10287961 DOI: 10.1093/bioinformatics/btad373] [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: 04/29/2022] [Revised: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023] Open
Abstract
MOTIVATION Gene network reconstruction from gene expression profiles is a compute- and data-intensive problem. Numerous methods based on diverse approaches including mutual information, random forests, Bayesian networks, correlation measures, as well as their transforms and filters such as data processing inequality, have been proposed. However, an effective gene network reconstruction method that performs well in all three aspects of computational efficiency, data size scalability, and output quality remains elusive. Simple techniques such as Pearson correlation are fast to compute but ignore indirect interactions, while more robust methods such as Bayesian networks are prohibitively time consuming to apply to tens of thousands of genes. RESULTS We developed maximum capacity path (MCP) score, a novel maximum-capacity-path-based metric to quantify the relative strengths of direct and indirect gene-gene interactions. We further present MCPNet, an efficient, parallelized gene network reconstruction software based on MCP score, to reverse engineer networks in unsupervised and ensemble manners. Using synthetic and real Saccharomyces cervisiae datasets as well as real Arabidopsis thaliana datasets, we demonstrate that MCPNet produces better quality networks as measured by AUPRC, is significantly faster than all other gene network reconstruction software, and also scales well to tens of thousands of genes and hundreds of CPU cores. Thus, MCPNet represents a new gene network reconstruction tool that simultaneously achieves quality, performance, and scalability requirements. AVAILABILITY AND IMPLEMENTATION Source code freely available for download at https://doi.org/10.5281/zenodo.6499747 and https://github.com/AluruLab/MCPNet, implemented in C++ and supported on Linux.
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Affiliation(s)
- Tony C Pan
- Department of Biomedical Informatics, Emory University, Woodruff Memorial Research Building 101 Woodruff Circle, 4th Floor East, Atlanta, GA 30322, United States
- Institute for Data Engineering and Science, Georgia Institute of Technology, 756 W Peachtree St NW, 12th Floor, Atlanta, GA 30332, United States
| | - Sriram P Chockalingam
- Institute for Data Engineering and Science, Georgia Institute of Technology, 756 W Peachtree St NW, 12th Floor, Atlanta, GA 30332, United States
| | - Maneesha Aluru
- School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Dr NW, Atlanta, GA 30332, United States
| | - Srinivas Aluru
- Institute for Data Engineering and Science, Georgia Institute of Technology, 756 W Peachtree St NW, 12th Floor, Atlanta, GA 30332, United States
- School of Computational Science and Engineering, Georgia Institute of Technology, 756 W Peachtree St NW, 13th Floor, Atlanta, GA 30332, United States
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26
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Wilder CL, Lefaudeux D, Mathenge R, Kishimoto K, Zuniga Munoz A, Nguyen MA, Meyer AS, Cheng QJ, Hoffmann A. A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes. Mol Syst Biol 2023; 19:e11294. [PMID: 36929731 PMCID: PMC10167482 DOI: 10.15252/msb.202211294] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Type I interferons (IFN) induce powerful antiviral and innate immune responses via the transcription factor, IFN-stimulated gene factor (ISGF3). However, in some pathological contexts, type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN-β also activates an inflammatory gene expression program in contrast to IFN-λ3, a type III IFN, which elicits only the common antiviral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis, we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus-specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK-STAT/IRF signaling network that may produce distinct biological responses and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it.
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Affiliation(s)
- Catera L Wilder
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Diane Lefaudeux
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Novadiscovery S.A.LyonFrance
| | - Raisa Mathenge
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Division of RheumatologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Kensei Kishimoto
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Department of Molecular, Cell, and Cancer BiologyUniversity of Massachusetts Chan Medical SchoolWorcesterMAUSA
| | - Alma Zuniga Munoz
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Department of Physiology and BiophysicsUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Minh A Nguyen
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Present address:
Division of Genetics and Genomics, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Aaron S Meyer
- Department of BioengineeringUniversity of CaliforniaLos AngelesCAUSA
| | - Quen J Cheng
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
- Division of Infectious Diseases, Department of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCAUSA
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27
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Chen M, Wang R. Computational analysis of synergism in small networks with different logic. J Biol Phys 2023; 49:1-27. [PMID: 36580168 PMCID: PMC9958226 DOI: 10.1007/s10867-022-09620-0] [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: 10/19/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
Cell fate decision processes are regulated by networks which contain different molecules and interactions. Different network topologies may exhibit synergistic or antagonistic effects on cellular functions. Here, we analyze six most common small networks with regulatory logic AND or OR, trying to clarify the relationship between network topologies and synergism (or antagonism) related to cell fate decisions. We systematically examine the contribution of both network topologies and regulatory logic to the cell fate synergism by bifurcation and combinatorial perturbation analysis. Initially, under a single set of parameters, the synergism of three types of networks with AND and OR logic is compared. Furthermore, to consider whether these results depend on the choices of parameter values, statistics on the synergism of five hundred parameter sets is performed. It is shown that the results are not sensitive to parameter variations, indicating that the synergy or antagonism mainly depends on the network topologies rather than the choices of parameter values. The results indicate that the topology with "Dual Inhibition" shows good synergism, while the topology with "Dual Promotion" or "Hybrid" shows antagonism. The results presented here may help us to design synergistic networks based on network structure and regulation combinations, which has promising implications for cell fate decisions and drug combinations.
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Affiliation(s)
- Menghan Chen
- Department of Mathematics, Shanghai University, Shanghai, 200444, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, 200444, China.
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28
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Le D, Akiyama T, Weiss D, Kim M. Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells. Commun Biol 2023; 6:223. [PMID: 36841892 PMCID: PMC9968327 DOI: 10.1038/s42003-023-04604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Bioactive small-molecule inhibitors represent a treasure chest for future drugs. In vitro high-throughput screening is a common approach to identify the small-molecule inhibitors that bind tightly to purified targets. Here, we investigate the inhibitor-target binding/unbinding kinetics in E. coli cells using a benzimidazole-derivative DNA inhibitor as a model system. We find that its unbinding rate is not constant but depends on cell growth rate. This dependence is mediated by the cellular activity, forming a feedback loop with the inhibitor's activity. In accordance with this feedback, we find cell-to-cell heterogeneity in inhibitor-target interaction, leading to co-existence of two distinct subpopulations: actively growing cells that dissociate the inhibitors from the targets and non-growing cells that do not. We find similar heterogeneity for other clinical DNA inhibitors. Our studies reveal a mechanism that couples inhibitor-target kinetics to cell physiology and demonstrate the significant effect of this coupling on drug efficacy.
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Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - David Weiss
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA.
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA.
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA.
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29
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Chakraborty S, Singh P, Seshasayee ASN. Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models. mSystems 2022; 7:e0090022. [PMID: 36409084 PMCID: PMC9765429 DOI: 10.1128/msystems.00900-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
Attempts to understand gene regulation by global transcription factors have largely been limited to expression studies under binary conditions of presence and absence of the transcription factor. Studies addressing genome-wide transcriptional responses to changing transcription factor concentration at high resolution are lacking. Here, we create a data set containing the entire Escherichia coli transcriptome in Luria-Bertani (LB) broth as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hill's model to accurately summarize individual gene responses into three intuitively understandable parameters, Emax, n, and k, reflecting the sensitivity, nonlinearity, and midpoint of the dynamic range. Our data show that most cAMP-regulated genes have an n of >2, with their k values centered around the wild-type concentration of cAMP. Additionally, cAMP receptor protein (CRP) affinity to a promoter is correlated with Emax but not k, hinting that a high-affinity CRP promoter need not ensure transcriptional activation at lower cAMP concentrations and instead affects the magnitude of the response. Finally, genes belonging to different functional classes are tuned to have different k, n, and Emax values. We demonstrate that phenomenological models are a better alternative for studying gene expression trends than classical clustering methods, with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network. IMPORTANCE Different genes may follow different trends in response to various transcription factor concentrations. In this study, we ask two questions: (i) what are the trends that different genes follow in response to changing transcription factor concentrations and (ii) what methods can be used to extract information from the gene trends so obtained. We demonstrate a method to analyze transcription factor concentration-dependent genome-wide expression data using phenomenological models. Conventional clustering methods and principal-component analysis (PCA) can be used to summarize trends in data but have limited interpretability. The use of phenomenological models greatly enhances the interpretability and thus utility of conventional clustering. Transformation of dose-response data into phenomenological constants opens up avenues to ask and answer many different kinds of question. We show that the phenomenological constants obtained from the model fits can be used to generate insights about network topology and allows integration of other experimental data such as chromatin immunoprecipitation sequencing (ChIP-seq) to understand the system in greater detail.
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Affiliation(s)
- Shweta Chakraborty
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | | | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
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30
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Hari K, Harlapur P, Gopalan A, Ullanat V, Duddu AS, Jolly MK. Emergent properties of coupled bistable switches. J Biosci 2022. [DOI: 10.1007/s12038-022-00310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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31
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Santiago E, Moreno DF, Acar M. Phenotypic plasticity as a facilitator of microbial evolution. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac020. [PMID: 36465837 PMCID: PMC9709823 DOI: 10.1093/eep/dvac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/27/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Tossed about by the tides of history, the inheritance of acquired characteristics has found a safe harbor at last in the rapidly expanding field of epigenetics. The slow pace of genetic variation and high opportunity cost associated with maintaining a diverse genetic pool are well-matched by the flexibility of epigenetic traits, which can enable low-cost exploration of phenotypic space and reactive tuning to environmental pressures. Aiding in the generation of a phenotypically plastic population, epigenetic mechanisms often provide a hotbed of innovation for countering environmental pressures, while the potential for genetic fixation can lead to strong epigenetic-genetic evolutionary synergy. At the level of cells and cellular populations, we begin this review by exploring the breadth of mechanisms for the storage and intergenerational transmission of epigenetic information, followed by a brief review of common and exotic epigenetically regulated phenotypes. We conclude by offering an in-depth coverage of recent papers centered around two critical issues: the evolvability of epigenetic traits through Baldwinian adaptive phenotypic plasticity and the potential for synergy between epigenetic and genetic evolution.
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Affiliation(s)
- Emerson Santiago
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - David F Moreno
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- *Correspondence address. Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA. Tel: +90 (543) 304-0388; E-mail:
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32
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Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630. Commun Biol 2022; 5:1109. [PMID: 36261484 DOI: 10.1038/s42003-022-04069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate "biological funneling" pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the β-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin.
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33
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Kariya Y, Honma M, Tokuda K, Konagaya A, Suzuki H. Utility of constraints reflecting system stability on analyses for biological models. PLoS Comput Biol 2022; 18:e1010441. [PMID: 36084151 PMCID: PMC9491612 DOI: 10.1371/journal.pcbi.1010441] [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: 12/04/2021] [Revised: 09/21/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Simulating complex biological models consisting of multiple ordinary differential equations can aid in the prediction of the pharmacological/biological responses; however, they are often hampered by the availability of reliable kinetic parameters. In the present study, we aimed to discover the properties of behaviors without determining an optimal combination of kinetic parameter values (parameter set). The key idea was to collect as many parameter sets as possible. Given that many systems are biologically stable and resilient (BSR), we focused on the dynamics around the steady state and formulated objective functions for BSR by partial linear approximation of the focused region. Using the objective functions and modified global cluster Newton method, we developed an algorithm for a thorough exploration of the allowable parameter space for biological systems (TEAPS). We first applied TEAPS to the NF-κB signaling model. This system shows a damped oscillation after stimulation and seems to fit the BSR constraint. By applying TEAPS, we found several directions in parameter space which stringently determines the BSR property. In such directions, the experimentally fitted parameter values were included in the range of the obtained parameter sets. The arachidonic acid metabolic pathway model was used as a model related to pharmacological responses. The pharmacological effects of nonsteroidal anti-inflammatory drugs were simulated using the parameter sets obtained by TEAPS. The structural properties of the system were partly extracted by analyzing the distribution of the obtained parameter sets. In addition, the simulations showed inter-drug differences in prostacyclin to thromboxane A2 ratio such that aspirin treatment tends to increase the ratio, while rofecoxib treatment tends to decrease it. These trends are comparable to the clinical observations. These results on real biological models suggest that the parameter sets satisfying the BSR condition can help in finding biologically plausible parameter sets and understanding the properties of biological systems. We propose a new method to analyze the properties of biological dynamic models, which we named TEAPS (Thorough Exploration of Allowable Parameter Space). TEAPS can thoroughly determine combinations of parameter values for ordinary differential equations with which an initial state in a certain range converges to a particular fixed point. This stable and resilient behavior is a characteristic shared with many biological systems, including metabolic systems and intracellular signaling systems. Therefore, this thorough search outlined the possible parameter space as biological systems for target models, which helps to understand the system constraints when the target systems behave dynamically. The obtained parameter space can be used as an initial space for parameter tuning. For models that include a large number of parameters, the parameter space to be searched in the parameter tuning process is too large; therefore, narrowing down the space by TEAPS potentially contributes to the analysis of the dynamics of complicated biological models. Thus, our approach can partly overcome the current problem in parameter tuning and can advance the computational dynamic analyses of biological systems.
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Affiliation(s)
- Yoshiaki Kariya
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masashi Honma
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Keita Tokuda
- Department of Computer Science, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akihiko Konagaya
- Molecular Robotics Research Institute, Limited, Kyowa Create Dai-ichi, Minato-ku, Tokyo, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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34
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Gupta A, Martin-Rufino JD, Jones TR, Subramanian V, Qiu X, Grody EI, Bloemendal A, Weng C, Niu SY, Min KH, Mehta A, Zhang K, Siraj L, Al' Khafaji A, Sankaran VG, Raychaudhuri S, Cleary B, Grossman S, Lander ES. Inferring gene regulation from stochastic transcriptional variation across single cells at steady state. Proc Natl Acad Sci U S A 2022; 119:e2207392119. [PMID: 35969771 PMCID: PMC9407670 DOI: 10.1073/pnas.2207392119] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells at steady state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends from the time-invariant covariation arising from cell states, and we delineate the experimental and technical requirements for leveraging these small but meaningful cofluctuations in the presence of measurement noise. While current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs simultaneously in cells at steady state, we investigate a small-scale dataset to inform future experimental design. This study supports the potential value of mapping regulatory connections through stochastic variation, and it motivates further technological development to achieve its full potential.
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Affiliation(s)
- Anika Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Jorge D. Martin-Rufino
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Chen Weng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | | | - Kyung Hoi Min
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Kaite Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Layla Siraj
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Vijay G. Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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35
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Li Z, Gao J, Wang B, Xu J, Fu X, Han H, Wang L, Zhang W, Deng Y, Wang Y, Gong Z, Tian Y, Peng R, Yao Q. Rice carotenoid biofortification and yield improvement conferred by endosperm-specific overexpression of OsGLK1. FRONTIERS IN PLANT SCIENCE 2022; 13:951605. [PMID: 35909772 PMCID: PMC9335051 DOI: 10.3389/fpls.2022.951605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Carotenoids, indispensable isoprenoid phytonutrients, are synthesized in plastids and are known to be deficient in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthetic genes, have been performed to obtain carotenoid-enriched rice grains. Nuclear-encoded GOLDEN2-LIKE (GLK) transcription factors play important roles in the regulation of plastid and thylakoid grana development. Here, we show that endosperm-specific overexpression of rice GLK1 gene (OsGLK1) leads to enhanced carotenoid production, increased grain yield, but deteriorated grain quality in rice. Subsequently, we performed the bioengineering of carotenoids biosynthesis in rice endosperm by introducing other three carotenogenic genes, tHMG1, ZmPSY1, and PaCrtI, which encode the enzymes truncated 3-hydroxy-3-methylglutaryl-CoA reductase, phytoene synthase, and phytoene desaturase, respectively. Transgenic overexpression of all four genes (OsGLK1, tHMG1, ZmPSY1, and PaCrtI) driven by rice endosperm-specific promoter GluB-1 established a mini carotenoid biosynthetic pathway in the endosperm and exerted a roughly multiplicative effect on the carotenoid accumulation as compared with the overexpression of only three genes (tHMG1, ZmPSY1, and PaCrtI). In addition, the yield enhancement and quality reduction traits were also present in the transgenic rice overexpressing the selected four genes. Our results revealed that OsGLK1 confers favorable characters in rice endosperm and could help to refine strategies for the carotenoid and other plastid-synthesized micronutrient fortification in bioengineered plants.
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Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community. THE ISME JOURNAL 2022; 16:1004-1011. [PMID: 34759303 PMCID: PMC8940935 DOI: 10.1038/s41396-021-01148-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 09/12/2021] [Accepted: 10/22/2021] [Indexed: 01/12/2023]
Abstract
On a surface, microorganisms grow into a multi-cellular community. When a community becomes densely populated, cells migrate away to expand the community's territory. How microorganisms regulate surface motility to optimize expansion remains poorly understood. Here, we characterized surface motility of Proteus mirabilis. P. mirabilis is well known for its ability to expand its colony rapidly on a surface. Cursory visual inspection of an expanding colony suggests partial migration, i.e., one fraction of a population migrates while the other is sessile. Quantitative microscopic imaging shows that this migration pattern is determined by spatially inhomogeneous regulation of cell motility. Further analyses reveal that this spatial regulation is mediated by the Rcs system, which represses the expression of the motility regulator (FlhDC) in a nutrient-dependent manner. Alleviating this repression increases the colony expansion speed but results in a rapid drop in the number of viable cells, lowering population fitness. These findings collectively demonstrate how Rcs regulates cell motility dynamically to increase the fitness of an expanding bacterial population, illustrating a fundamental trade-off underlying bacterial colonization of a surface.
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Wiedmann F, Kraft M, Kallenberger S, Büscher A, Paasche A, Blochberger PL, Seeger T, Jávorszky N, Warnecke G, Arif R, Kremer J, Karck M, Frey N, Schmidt C. MicroRNAs Regulate TASK-1 and Are Linked to Myocardial Dilatation in Atrial Fibrillation. J Am Heart Assoc 2022; 11:e023472. [PMID: 35301863 PMCID: PMC9075420 DOI: 10.1161/jaha.121.023472] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. However, underlying molecular mechanisms are insufficiently understood. Previous studies suggested that microRNA (miRNA) dependent gene regulation plays an important role in the initiation and maintenance of AF. The 2‐pore‐domain potassium channel TASK‐1 (tandem of P domains in a weak inward rectifying K+ channel–related acid sensitive K+ channel 1) is an atrial‐specific ion channel that is upregulated in AF. Inhibition of TASK‐1 current prolongs the atrial action potential duration to similar levels as in patients with sinus rhythm. Here, we hypothesize that miRNAs might be responsible for the regulation of KCNK3 that encodes for TASK‐1. Methods and Results We selected miRNAs potentially regulating KCNK3 and studied their expression in atrial tissue samples obtained from patients with sinus rhythm, paroxysmal AF, or permanent/chronic AF. MiRNAs differentially expressed in AF were further investigated for their ability to regulate KCNK3 mRNA and TASK‐1 protein expression in human induced pluripotent stem cells, transfected with miRNA mimics or inhibitors. Thereby, we observed that miR‐34a increases TASK‐1 expression and current and further decreases the resting membrane potential of Xenopus laevis oocytes, heterologously expressing hTASK‐1. Finally, we investigated associations between miRNA expression in atrial tissues and clinical parameters of our patient cohort. A cluster containing AF stage, left ventricular end‐diastolic diameter, left ventricular end‐systolic diameter, left atrial diameter, atrial COL1A2 (collagen alpha‐2(I) chain), and TASK‐1 protein level was associated with increased expression of miR‐25, miR‐21, miR‐34a, miR‐23a, miR‐124, miR‐1, and miR‐29b as well as decreased expression of miR‐9 and miR‐485. Conclusions These results suggest an important pathophysiological involvement of miRNAs in the regulation of atrial expression of the TASK‐1 potassium channel in patients with atrial cardiomyopathy.
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Affiliation(s)
- Felix Wiedmann
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Manuel Kraft
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Stefan Kallenberger
- Digital Health Center Berlin Institute of Health (BIH) and Charité Berlin Germany.,Department of Medical Oncology National Center for Tumor DiseasesHeidelberg University Hospital Heidelberg Germany.,Health Data Science UnitMedical Faculty Heidelberg Heidelberg Germany
| | - Antonius Büscher
- Department for Cardiology II: Electrophysiology University Hospital Münster Münster Germany
| | - Amelie Paasche
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Pablo L Blochberger
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Timon Seeger
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany
| | - Natasa Jávorszky
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Gregor Warnecke
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Rawa Arif
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Jamila Kremer
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Matthias Karck
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Norbert Frey
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Constanze Schmidt
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
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LuxT Is a Global Regulator of Low-Cell-Density Behaviors, Including Type III Secretion, Siderophore Production, and Aerolysin Production, in Vibrio harveyi. mBio 2022; 13:e0362121. [PMID: 35038896 PMCID: PMC8764538 DOI: 10.1128/mbio.03621-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Quorum sensing (QS) is a chemical communication process in which bacteria produce, release, and detect extracellular signaling molecules called autoinducers. Via combined transcriptional and posttranscriptional regulatory mechanisms, QS allows bacteria to collectively alter gene expression on a population-wide scale. Recently, the TetR family transcriptional regulator LuxT was shown to control Vibrio harveyi qrr1, encoding the Qrr1 small RNA that functions at the core of the QS regulatory cascade. Here, we use RNA sequencing to reveal that, beyond the control of qrr1, LuxT is a global regulator of 414 V. harveyi genes, including those involved in type III secretion, siderophore production, and aerolysin toxin biosynthesis. Importantly, LuxT directly represses swrZ, encoding a GntR family transcriptional regulator, and LuxT control of type III secretion, siderophore, and aerolysin genes occurs by two mechanisms, one that is SwrZ dependent and one that is SwrZ independent. All of these target genes specify QS-controlled behaviors that are enacted when V. harveyi is at low cell density. Thus, LuxT and SwrZ function in parallel with QS to drive particular low-cell-density behaviors. Phylogenetic analyses reveal that luxT is highly conserved among Vibrionaceae, but swrZ is less well conserved. In a test case, we find that in Aliivibrio fischeri, LuxT also represses swrZ. SwrZ is a repressor of A. fischeri siderophore production genes. Thus, LuxT repression of swrZ drives the activation of A. fischeri siderophore gene expression. Our results indicate that LuxT is a major regulator among Vibrionaceae, and in the species that also possess swrZ, LuxT functions with SwrZ to control gene expression. IMPORTANCE Bacteria precisely tune gene expression patterns to successfully react to changes that occur in the environment. Defining the mechanisms that enable bacteria to thrive in diverse and fluctuating habitats, including in host organisms, is crucial for a deep understanding of the microbial world and also for the development of effective applications to promote or combat particular bacteria. In this study, we show that a regulator called LuxT controls over 400 genes in the marine bacterium Vibrio harveyi and that LuxT is highly conserved among Vibrionaceae species, ubiquitous marine bacteria that often cause disease. We characterize the mechanisms by which LuxT controls genes involved in virulence and nutrient acquisition. We show that LuxT functions in parallel with a set of regulators of the bacterial cell-to-cell communication process called quorum sensing to promote V. harveyi behaviors at low cell density.
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Mahilkar A, Venkataraman P, Mall A, Saini S. Experimental Evolution of Anticipatory Regulation in Escherichia coli. Front Microbiol 2022; 12:796228. [PMID: 35087497 PMCID: PMC8787300 DOI: 10.3389/fmicb.2021.796228] [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: 10/16/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akshat Mall
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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40
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Ghafoor H, Chu H, Huang J, Chen M, Wang S, Wang J, Chao J. ZC3H4 promotes pulmonary fibrosis via an ER stress-related positive feedback loop. Toxicol Appl Pharmacol 2022; 435:115856. [PMID: 34979141 DOI: 10.1016/j.taap.2021.115856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Pulmonary fibrosis is a sequela of many pulmonary diseases, such as pneumoconiosis and idiopathic pulmonary fibrosis. The principal characteristics of pulmonary fibrosis comprise myofibroblast proliferation, alveolar damage and deposition of extracellular matrix components, which cause abnormal lung structure remodeling and an irreversible decline in lung function; however, the detailed mechanisms remain unclear. The current study focused on the role of ZC3H4, a new member of the zinc finger protein family, in SiO2-induced pulmonary fibrosis. METHODS The expression of ZC3H4 and fibroblast activation markers (COL1A1, COL3A1 and ACTA1) was measured by western blotting and immunofluorescence staining after SiO2 exposure (50 μg/cm2). The functional change in fibroblasts was studied with a scratch assay and a 3D migration assay. The CRISPR/Cas9 system was used to explore the regulatory mechanisms of ZC3H4 in pulmonary fibroblast cells. RESULTS The expression levels of ZC3H4 and sigmar1 (a key regulator of ER stress) were increased in pulmonary fibroblast cells and were associated with fibroblast activation, as indicated by the increase in COL1A1, COL3A1 and ACTA1, as well as the migration ability. SiO2-enhanced fibroblast activation was attenuated by specific knockdown of ZC3H4 and inhibition of ER stress, demonstrating that ZC3H4 activated fibroblasts via the sigmar1/ER stress pathway. Interestingly, ER stress blockade also inhibited ZC3H4 expression, indicating the positive feedback regulatory mechanism of ER stress on ZC3H4. CONCLUSIONS Our results demonstrate that ZC3H4 and sigmar1 might act as novel therapeutic targets for silicosis, providing a reference for further pulmonary fibrosis research.
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Affiliation(s)
- Hammad Ghafoor
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China; Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China; Department of Microbiology and Immunology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Han Chu
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China; Key Laboratory of Development Genes and Human Disease, Southeast University, Nanjing, Jiangsu 2100096, China
| | - Jie Huang
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China
| | - Mengling Chen
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China
| | - Sha Wang
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China
| | - Jing Wang
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China.
| | - Jie Chao
- Department of Physiology, School of Medicine, Southeast University, Nanjing, Jiangsu 2100096, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China; Key Laboratory of Development Genes and Human Disease, Southeast University, Nanjing, Jiangsu 2100096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China; School of Medicine, Xizang Minzu University, Xianyang, Shanxi 712082, China.
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41
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Lee YAL, Mousavikhamene Z, Amrithanath AK, Neidhart SM, Krishnaswamy S, Schatz GC, Odom TW. Programmable Self-Regulation with Wrinkled Hydrogels and Plasmonic Nanoparticle Lattices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2103865. [PMID: 34755454 DOI: 10.1002/smll.202103865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/25/2021] [Indexed: 06/13/2023]
Abstract
This paper describes a self-regulating system that combines wrinkle-patterned hydrogels with plasmonic nanoparticle (NP) lattices. In the feedback loop, the wrinkle patterns flatten in response to moisture, which then allows light to reach the NP lattice on the bottom layer. Upon light absorption, the NP lattice produces a photothermal effect that dries the hydrogel, and the system then returns to the initial wrinkled configuration. The timescale of this regulatory cycle can be programmed by tuning the degree of photothermal heating by NP size and substrate material. Time-dependent finite element analysis reveals the thermal and mechanical mechanisms of wrinkle formation. This self-regulating system couples morphological, optical, and thermo-mechanical properties of different materials components and offers promising design principles for future smart systems.
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Affiliation(s)
- Young-Ah Lucy Lee
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Zeynab Mousavikhamene
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | | | - Suzanne M Neidhart
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Sridhar Krishnaswamy
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - George C Schatz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Teri W Odom
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
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42
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Price CC, Mathur J, Boerckel JD, Pathak A, Shenoy VB. Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophys J 2021; 120:5074-5089. [PMID: 34627766 PMCID: PMC8633715 DOI: 10.1016/j.bpj.2021.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/26/2023] Open
Abstract
Mechanotransduction describes activation of gene expression by changes in the cell's physical microenvironment. Recent experiments show that mechanotransduction can lead to long-term "mechanical memory," in which cells cultured on stiff substrates for sufficient time (priming phase) maintain altered phenotype after switching to soft substrates (dissipation phase) as compared to unprimed controls. The timescale of memory acquisition and retention is orders of magnitude larger than the timescale of mechanosensitive cellular signaling, and memory retention time changes continuously with priming time. We develop a model that captures these features by accounting for positive reinforcement in mechanical signaling. The sensitivity of reinforcement represents the dynamic transcriptional state of the cell composed of protein lifetimes and three-dimensional chromatin organization. Our model provides a single framework connecting microenvironment mechanical history to cellular outcomes ranging from no memory to terminal differentiation. Predicting cellular memory of environmental changes can help engineer cellular dynamics through changes in culture environments.
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Affiliation(s)
- Christopher C Price
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jairaj Mathur
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri
| | - Joel D Boerckel
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amit Pathak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri.
| | - Vivek B Shenoy
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania.
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43
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Prieto TG, Baldavira CM, Machado-Rugolo J, Farhat C, Olivieri EHR, de Sá VK, da Silva ECA, Balancin ML, Ab Saber AM, Takagaki TY, Cordeiro de Lima VC, Capelozzi VL. Pulmonary Neuroendocrine Neoplasms Overexpressing Epithelial-Mesenchymal Transition Mechanical Barriers Genes Lack Immune-Suppressive Response and Present an Increased Risk of Metastasis. Front Oncol 2021; 11:645623. [PMID: 34527572 PMCID: PMC8435885 DOI: 10.3389/fonc.2021.645623] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/10/2021] [Indexed: 12/25/2022] Open
Abstract
Typical carcinoids (TC), atypical carcinoids (AC), large cell neuroendocrine carcinomas (LCNEC), and small cell lung carcinomas (SCLC) encompass a bimodal spectrum of metastatic tumors with morphological, histological and histogenesis differences, The hierarchical structure reveals high cohesiveness between neoplastic cells by mechanical desmosomes barrier assembly in carcinoid tumors and LCNEC, while SCLC does not present an organoid arrangement in morphology, the neoplastic cells are less cohesive. However, the molecular mechanisms that lead to PNENs metastasis remain largely unknown and require further study. In this work, epithelial to mesenchymal transition (EMT) transcription factors were evaluated using a set of twenty-four patients with surgically resected PNENs, including carcinomas. Twelve EMT transcription factors (BMP1, BMP7, CALD1, CDH1, COL3A1, COL5A2, EGFR, ERBB3, PLEK2, SNAI2, STEAP1, and TCF4) proved to be highly expressed among carcinomas and downregulated in carcinoid tumors, whereas upregulation of BMP1, CDH2, KRT14 and downregulation of CAV2, DSC2, IL1RN occurred in both histological subtypes. These EMT transcription factors identified were involved in proliferative signals, epithelium desmosomes assembly, and cell motility sequential steps that support PNENs invasion and metastasis in localized surgically resected primary tumor. We used a two-stage design where we first examined the candidate EMT transcription factors using a whole-genome screen, and subsequently, confirmed EMT-like changes by transmission electron microscopy and then, the EMT-related genes that were differentially expressed among PNENs subtypes were predicted through a Metascape analysis by in silico approach. A high expression of these EMT transcription factors was significantly associated with lymph node and distant metastasis. The sequential steps for invasion and metastasis were completed by an inverse association between functional barrier created by PD-L1 immunosuppressive molecule and EMT transcriptional factors. Our study implicates upregulation of EMT transcription factors to high proliferation rates, mechanical molecular barriers disassembly and increased cancer cell motility, as a critical molecular event leading to metastasis risk in PNENs thus emerging as a promising tool to select and customize therapy.
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Affiliation(s)
| | | | - Juliana Machado-Rugolo
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil.,Health Technology Assessment Center (NATS), Clinical Hospital (HCFMB), Medical School of São Paulo State University (UNESP), Botucatu, Brazil
| | - Cecília Farhat
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| | | | - Vanessa Karen de Sá
- International Center of Research/CIPE, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Marcelo Luiz Balancin
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| | | | - Teresa Yae Takagaki
- Division of Pneumology, Instituto do Coração (Incor), Medical School of University of São Paulo, São Paulo, Brazil
| | - Vladmir Cláudio Cordeiro de Lima
- Oncology, Rede D'Or São Paulo, São Paulo, Brazil.,Department of Clinical Oncology, Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, Brazil
| | - Vera Luiza Capelozzi
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
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Le D, Krasnopeeva E, Sinjab F, Pilizota T, Kim M. Active Efflux Leads to Heterogeneous Dissipation of Proton Motive Force by Protonophores in Bacteria. mBio 2021; 12:e0067621. [PMID: 34253054 PMCID: PMC8406135 DOI: 10.1128/mbio.00676-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/04/2021] [Indexed: 11/26/2022] Open
Abstract
Various toxic compounds disrupt bacterial physiology. While bacteria harbor defense mechanisms to mitigate the toxicity, these mechanisms are often coupled to the physiological state of the cells and become ineffective when the physiology is severely disrupted. Here, we characterized such feedback by exposing Escherichia coli to protonophores. Protonophores dissipate the proton motive force (PMF), a fundamental force that drives physiological functions. We found that E. coli cells responded to protonophores heterogeneously, resulting in bimodal distributions of cell growth, substrate transport, and motility. Furthermore, we showed that this heterogeneous response required active efflux systems. The analysis of underlying interactions indicated the heterogeneous response results from efflux-mediated positive feedback between PMF and protonophores' action. Our studies have broad implications for bacterial adaptation to stress, including antibiotics. IMPORTANCE An electrochemical proton gradient across the cytoplasmic membrane, alternatively known as proton motive force, energizes vital cellular processes in bacteria, including ATP synthesis, nutrient uptake, and cell division. Therefore, a wide range of organisms produce the agents that collapse the proton motive force, protonophores, to gain a competitive advantage. Studies have shown that protonophores have significant effects on microbial competition, host-pathogen interaction, and antibiotic action and resistance. Furthermore, protonophores are extensively used in various laboratory studies to perturb bacterial physiology. Here, we have characterized cell growth, substrate transport, and motility of Escherichia coli cells exposed to protonophores. Our findings demonstrate heterogeneous effects of protonophores on cell physiology and the underlying mechanism.
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Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, Georgia, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Ekaterina Krasnopeeva
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Faris Sinjab
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, Georgia, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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Abegaz F, Martines ACMF, Vieira-Lara MA, Rios-Morales M, Reijngoud DJ, Wit EC, Bakker BM. Bistability in fatty-acid oxidation resulting from substrate inhibition. PLoS Comput Biol 2021; 17:e1009259. [PMID: 34383741 PMCID: PMC8396765 DOI: 10.1371/journal.pcbi.1009259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/27/2021] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
In this study we demonstrated through analytic considerations and numerical studies that the mitochondrial fatty-acid β-oxidation can exhibit bistable-hysteresis behavior. In an experimentally validated computational model we identified a specific region in the parameter space in which two distinct stable and one unstable steady state could be attained with different fluxes. The two stable states were referred to as low-flux (disease) and high-flux (healthy) state. By a modular kinetic approach we traced the origin and causes of the bistability back to the distributive kinetics and the conservation of CoA, in particular in the last rounds of the β-oxidation. We then extended the model to investigate various interventions that may confer health benefits by activating the pathway, including (i) activation of the last enzyme MCKAT via its endogenous regulator p46-SHC protein, (ii) addition of a thioesterase (an acyl-CoA hydrolysing enzyme) as a safety valve, and (iii) concomitant activation of a number of upstream and downstream enzymes by short-chain fatty-acids (SCFA), metabolites that are produced from nutritional fibers in the gut. A high concentration of SCFAs, thioesterase activity, and inhibition of the p46Shc protein led to a disappearance of the bistability, leaving only the high-flux state. A better understanding of the switch behavior of the mitochondrial fatty-acid oxidation process between a low- and a high-flux state may lead to dietary and pharmacological intervention in the treatment or prevention of obesity and or non-alcoholic fatty-liver disease.
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Affiliation(s)
- Fentaw Abegaz
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Statistics and Probability Unit, University of Groningen, Groningen, The Netherlands
| | - Anne-Claire M. F. Martines
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A. Vieira-Lara
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melany Rios-Morales
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ernst C. Wit
- Statistics and Probability Unit, University of Groningen, Groningen, The Netherlands
- Institute of Computational Science, Università della Svizzera italiana, Lugano, Switzerland
| | - Barbara M. Bakker
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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47
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Akiyama T, Kim M. Stochastic response of bacterial cells to antibiotics: its mechanisms and implications for population and evolutionary dynamics. Curr Opin Microbiol 2021; 63:104-108. [PMID: 34325154 DOI: 10.1016/j.mib.2021.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/20/2022]
Abstract
The effectiveness of antibiotics against bacterial infections has been declining due to the emergence of resistance. Precisely understanding the response of bacteria to antibiotics is critical to maximizing antibiotic-induced bacterial eradication while minimizing the emergence of antibiotic resistance. Cell-to-cell heterogeneity in antibiotic susceptibility is observed across various bacterial species for a wide range of antibiotics. Heterogeneity in antibiotic susceptibility is not always due to the genetic differences. Rather, it can be caused by non-genetic mechanisms such as stochastic gene expression and biased partitioning upon cell division. Heterogeneous susceptibility leads to the stochastic growth and death of individual cells and stochastic fluctuations in population size. These fluctuations have important implications for the eradication of bacterial populations and the emergence of genotypic resistance.
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Affiliation(s)
- Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA; Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA; Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA; Emory Antibiotic Resistance Center, Emory University, Atlanta, GA, 30322, USA.
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48
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Naren N, Zhang XX. Role of a local transcription factor in governing cellular carbon/nitrogen homeostasis in Pseudomonas fluorescens. Nucleic Acids Res 2021; 49:3204-3216. [PMID: 33675669 PMCID: PMC8034625 DOI: 10.1093/nar/gkab091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Autoactivation of two-component systems (TCSs) can increase the sensitivity to signals but inherently cause a delayed response. Here, we describe a unique negative feedback mechanism enabling the global NtrB/NtrC regulator to rapidly respond to nitrogen starvation over the course of histidine utilization (hut) in Pseudomonas fluorescens. NtrBC directly activates transcription of hut genes, but overexpression will produce excess ammonium leading to NtrBC inactivation. To prevent this from occurring, the histidine-responsive repressor HutC fine-tunes ntrBC autoactivation: HutC and NtrC bind to the same operator site in the ntrBC promoter. This newly discovered low-affinity binding site shows little sequence similarity with the consensus sequence that HutC recognizes for substrate-specific induction of hut operons. A combination of genetic and transcriptomic analysis indicated that both ntrBC and hut promoter activities cannot be stably maintained in the ΔhutC background when histidine fluctuates at high concentrations. Moreover, the global carbon regulator CbrA/CbrB is involved in directly activating hut transcription while de-repressing hut translation via the CbrAB-CrcYZ-Crc/Hfq regulatory cascade. Together, our data reveal that the local transcription factor HutC plays a crucial role in governing NtrBC to maintain carbon/nitrogen homeostasis through the complex interactions between two TCSs (NtrBC and CbrAB) at the hut promoter.
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Affiliation(s)
- Naran Naren
- School of Natural and Computational Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University at Albany, Auckland 0745, New Zealand
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49
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Kim H, Lee K, Kim JM, Kim MY, Kim JR, Lee HW, Chung YW, Shin HI, Kim T, Park ES, Rho J, Lee SH, Kim N, Lee SY, Choi Y, Jeong D. Selenoprotein W ensures physiological bone remodeling by preventing hyperactivity of osteoclasts. Nat Commun 2021; 12:2258. [PMID: 33859201 PMCID: PMC8050258 DOI: 10.1038/s41467-021-22565-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
Selenoproteins containing selenium in the form of selenocysteine are critical for bone remodeling. However, their underlying mechanism of action is not fully understood. Herein, we report the identification of selenoprotein W (SELENOW) through large-scale mRNA profiling of receptor activator of nuclear factor (NF)-κΒ ligand (RANKL)-induced osteoclast differentiation, as a protein that is downregulated via RANKL/RANK/tumour necrosis factor receptor-associated factor 6/p38 signaling. RNA-sequencing analysis revealed that SELENOW regulates osteoclastogenic genes. SELENOW overexpression enhances osteoclastogenesis in vitro via nuclear translocation of NF-κB and nuclear factor of activated T-cells cytoplasmic 1 mediated by 14-3-3γ, whereas its deficiency suppresses osteoclast formation. SELENOW-deficient and SELENOW-overexpressing mice exhibit high bone mass phenotype and osteoporosis, respectively. Ectopic SELENOW expression stimulates cell-cell fusion critical for osteoclast maturation as well as bone resorption. Thus, RANKL-dependent repression of SELENOW regulates osteoclast differentiation and blocks osteoporosis caused by overactive osteoclasts. These findings demonstrate a biological link between selenium and bone metabolism. Selenoproteins containing selenium have a variety of physiological functions including redox homeostasis and thyroid hormone metabolism. Here, the authors show that RANKL-dependent repression of selenoprotein W regulates cell fusion during osteoclast differentiation and bone remodelling in mice.
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Affiliation(s)
- Hyunsoo Kim
- Department of Microbiology, Laboratory of Bone Metabolism and Control, Yeungnam University College of Medicine, Daegu, Korea.,Departments of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Kyunghee Lee
- Department of Microbiology, Laboratory of Bone Metabolism and Control, Yeungnam University College of Medicine, Daegu, Korea
| | - Jin Man Kim
- Department of Microbiology, Laboratory of Bone Metabolism and Control, Yeungnam University College of Medicine, Daegu, Korea
| | - Mi Yeong Kim
- Department of Microbiology, Laboratory of Bone Metabolism and Control, Yeungnam University College of Medicine, Daegu, Korea
| | - Jae-Ryong Kim
- Department of Biochemistry and Molecular Biology, Smart-aging Convergence Research Center, Yeungnam University College of Medicine, Daegu, Korea
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Youn Wook Chung
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hong-In Shin
- IHBR, Department of Oral Pathology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Taesoo Kim
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea
| | - Eui-Soon Park
- Department of Microbiology and BK21 Bio Brain Center, Chungnam National University, Daejeon, Korea
| | - Jaerang Rho
- Department of Microbiology and BK21 Bio Brain Center, Chungnam National University, Daejeon, Korea
| | - Seoung Hoon Lee
- Department of Oral Microbiology and Immunology, Wonkwang University School of Dentistry, Iksan, Korea
| | - Nacksung Kim
- National Research Laboratory for Regulation of Bone Metabolism and Disease, Chonnam National University Medical School, Gwangju, Korea
| | - Soo Young Lee
- Division of Life and Pharmaceutical Sciences, Department of Life Science, Center for Cell Signaling & Drug Discovery Research, College of Natural Sciences, Ewha Womans University, Seoul, Korea
| | - Yongwon Choi
- Departments of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Daewon Jeong
- Department of Microbiology, Laboratory of Bone Metabolism and Control, Yeungnam University College of Medicine, Daegu, Korea.
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50
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Jiang Y, Hao N. Memorizing environmental signals through feedback and feedforward loops. Curr Opin Cell Biol 2021; 69:96-102. [PMID: 33549848 PMCID: PMC8058236 DOI: 10.1016/j.ceb.2020.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
Cells in diverse organisms can store the information of previous environmental conditions for long periods of time. This form of cellular memory adjusts the cell's responses to future challenges, providing fitness advantages in fluctuating environments. Many biological functions, including cellular memory, are mediated by specific recurring patterns of interactions among proteins and genes, known as 'network motifs.' In this review, we focus on three well-characterized network motifs - negative feedback loops, positive feedback loops, and feedforward loops, which underlie different types of cellular memories. We describe the latest studies identifying these motifs in various molecular processes and discuss how the topologies and dynamics of these motifs can enable memory encoding and storage.
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Affiliation(s)
- Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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