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Andrews SS, Wiley HS, Sauro HM. Design patterns of biological cells. Bioessays 2024; 46:e2300188. [PMID: 38247191 PMCID: PMC10922931 DOI: 10.1002/bies.202300188] [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: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
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Affiliation(s)
- Steven S. Andrews
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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2
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Joshi B, Nguyen TD. Bifunctional enzyme provides absolute concentration robustness in multisite covalent modification networks. J Math Biol 2024; 88:36. [PMID: 38429564 DOI: 10.1007/s00285-024-02060-5] [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: 04/17/2023] [Revised: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 03/03/2024]
Abstract
Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions required for a network of this type to have a species with absolute concentration robustness. We find that the robustness in a substrate is endowed by its interaction with a bifunctional enzyme, which is an enzyme that has different roles when isolated versus when bound as a substrate-enzyme complex. When isolated, the bifunctional enzyme promotes production of more molecules of the robust species while when bound, the same enzyme facilitates degradation of the robust species. These dual actions produce robustness in the large class of covalent modification networks. For each network of this type, we find the network conditions for the presence of robustness, the species that has robustness, and its robustness value. The unified approach of simultaneously analyzing a large class of networks for a single property, i.e. absolute concentration robustness, reveals the underlying mechanism of the action of bifunctional enzyme while simultaneously providing a precise mathematical description of bifunctionality.
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Affiliation(s)
- Badal Joshi
- Department of Mathematics, California State University San Marcos, San Marcos, USA
| | - Tung D Nguyen
- Department of Mathematics, Texas A &M University, College Station, USA.
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3
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Kudo T, Zhao ML, Jeknić S, Kovary KM, LaGory EL, Covert MW, Teruel MN. Context-dependent regulation of lipid accumulation in adipocytes by a HIF1α-PPARγ feedback network. Cell Syst 2023; 14:1074-1086.e7. [PMID: 37995680 DOI: 10.1016/j.cels.2023.10.010] [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: 02/04/2022] [Revised: 12/03/2022] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Hypoxia-induced upregulation of HIF1α triggers adipose tissue dysfunction and insulin resistance in obese patients. HIF1α closely interacts with PPARγ, the master regulator of adipocyte differentiation and lipid accumulation, but there are conflicting results regarding how this interaction controls the excessive lipid accumulation that drives adipocyte dysfunction. To directly address these conflicts, we established a differentiation system that recapitulated prior seemingly opposing observations made across different experimental settings. Using single-cell imaging and coarse-grained mathematical modeling, we show how HIF1α can both promote and repress lipid accumulation during adipogenesis. Our model predicted and our experiments confirmed that the opposing roles of HIF1α are isolated from each other by the positive-feedback-mediated upregulation of PPARγ that drives adipocyte differentiation. Finally, we identify three factors: strength of the differentiation cue, timing of hypoxic perturbation, and strength of HIF1α expression changes that, when considered together, provide an explanation for many of the previous conflicting reports.
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Affiliation(s)
- Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Stevan Jeknić
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kyle M Kovary
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Edward L LaGory
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry and the Drukier Institute of Children's Health, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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4
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Vujovic F, Shepherd CE, Witting PK, Hunter N, Farahani RM. Redox-Mediated Rewiring of Signalling Pathways: The Role of a Cellular Clock in Brain Health and Disease. Antioxidants (Basel) 2023; 12:1873. [PMID: 37891951 PMCID: PMC10604469 DOI: 10.3390/antiox12101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Metazoan signalling pathways can be rewired to dampen or amplify the rate of events, such as those that occur in development and aging. Given that a linear network topology restricts the capacity to rewire signalling pathways, such scalability of the pace of biological events suggests the existence of programmable non-linear elements in the underlying signalling pathways. Here, we review the network topology of key signalling pathways with a focus on redox-sensitive proteins, including PTEN and Ras GTPase, that reshape the connectivity profile of signalling pathways in response to an altered redox state. While this network-level impact of redox is achieved by the modulation of individual redox-sensitive proteins, it is the population by these proteins of critical nodes in a network topology of signal transduction pathways that amplifies the impact of redox-mediated reprogramming. We propose that redox-mediated rewiring is essential to regulate the rate of transmission of biological signals, giving rise to a programmable cellular clock that orchestrates the pace of biological phenomena such as development and aging. We further review the evidence that an aberrant redox-mediated modulation of output of the cellular clock contributes to the emergence of pathological conditions affecting the human brain.
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Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Paul K. Witting
- Redox Biology Group, Charles Perkins Centre, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
| | - Ramin M. Farahani
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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5
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Pardo-Pastor C, Rosenblatt J. Piezo1 activates noncanonical EGFR endocytosis and signaling. SCIENCE ADVANCES 2023; 9:eadi1328. [PMID: 37756411 PMCID: PMC10530101 DOI: 10.1126/sciadv.adi1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
EGFR-ERK signaling controls cell cycle progression during development, homeostasis, and disease. While EGF ligand and mechanical inputs can activate EGFR-ERK signaling, the molecules linking mechanical force to this axis have remained mysterious. We previously found that stretch promotes mitosis via the stretch-activated ion channel Piezo1 and ERK signaling. Here, we show that Piezo1 provides the missing link between mechanical signals and EGFR-ERK activation. While both EGF- and Piezo1-dependent activation trigger clathrin-mediated EGFR endocytosis and ERK activation, EGF relies on canonical tyrosine autophosphorylation, whereas Piezo1 involves Src-p38 kinase-dependent serine phosphorylation. In addition, unlike EGF, ex vivo lung slices treated with Piezo1 agonist promoted cell cycle re-entry via nuclear ERK, AP-1 (FOS and JUN), and YAP accumulation, typical of regenerative and malignant signaling. Our results suggest that mechanical activation via Piezo1, Src, and p38 may be more relevant to controlling repair, regeneration, and cancer growth than tyrosine kinase signaling via canonical EGF signaling, suggesting an alternative therapeutic approach.
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Affiliation(s)
- Carlos Pardo-Pastor
- Randall Centre for Cell & Molecular Biophysics, New Hunt’s House, School of Basic & Medical Sciences, Faculty of Life Sciences & Medicine, King’s College London, SE1 1UL London, UK
| | - Jody Rosenblatt
- Randall Centre for Cell & Molecular Biophysics, New Hunt’s House, School of Basic & Medical Sciences, Faculty of Life Sciences & Medicine, King’s College London, SE1 1UL London, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, SE1 1UL London, UK
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Lima S, Blanco J, Olivieri F, Imelio JA, Nieves M, Carrión F, Alvarez B, Buschiazzo A, Marti MA, Trajtenberg F. An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis. Sci Signal 2023; 16:eabo7588. [PMID: 36693130 DOI: 10.1126/scisignal.abo7588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphorylation carries chemical information in biological systems. In two-component systems (TCSs), the sensor histidine kinase and the response regulator are connected through phosphoryl transfer reactions that may be uni- or bidirectional. Directionality enables the construction of complex regulatory networks that optimize signal propagation and ensure the forward flow of information. We combined x-ray crystallography, hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, and systems-integrative kinetic modeling approaches to study phosphoryl flow through the Bacillus subtilis thermosensing TCS DesK-DesR. The allosteric regulation of the histidine kinase DesK was critical to avoid back transfer of phosphoryl groups and futile phosphorylation-dephosphorylation cycles by isolating phosphatase, autokinase, and phosphotransferase activities. Interactions between the kinase's ATP-binding domain and the regulator's receiver domain placed the regulator in two distinct positions in the phosphotransferase and phosphatase complexes, thereby determining whether a key glutamine residue in DesK was properly situated to assist in the dephosphorylation reaction. Moreover, an energetically unfavorable phosphotransferase conformation when DesK was not phosphorylated minimized reverse phosphoryl transfer. DesR dimerization and a dissociative phosphoryl transfer reaction also enforced the direction of phosphoryl flow. Shorter or longer distances between the phosphoryl acceptor and donor residues shifted the phosphoryl transfer equilibrium by modulating the stabilizing effect of the Mg2+ cofactor. These mechanisms control the directionality of signal transmission and show how structure-encoded allostery stores and transmits information in signaling systems.
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Affiliation(s)
- Sofía Lima
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Blanco
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Olivieri
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan A Imelio
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Nieves
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Département de Microbiologie, Institut Pasteur, Paris, France
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
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Khan R, Kulasiri D, Samarasinghe S. A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: Development of an integrated mathematical model and computational experiments. J Theor Biol 2023; 556:111326. [PMID: 36279957 DOI: 10.1016/j.jtbi.2022.111326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/25/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022]
Abstract
The synaptic tagging and capture (STC) hypothesis not only explain the integration and association of synaptic activities, but also the formation of learning and memory. The synaptic pathways involved in the synaptic tagging and capture phenomenon are called STC pathways. The STC hypothesis provides a potential explanation of the neuronal and synaptic processes underlying the synaptic consolidation of memories. Several mechanisms and molecules have been proposed to explain the process of memory allocation and synaptic tags, respectively. However, a clear link between the STC hypothesis and memory allocation is still missing because the encoding of memories in neural circuits is mainly associated with strongly recurrently connected groups of neurons. To explore the mechanisms of potential synaptic tagging candidates and their involvement in the process of memory allocation, we develop a mathematical model for a single dendritic spine based on five essential criteria of a synaptic tag. By developing a mathematical model, we attempt to understand the roles of the potentially critical molecular networks underlying the STC and the essential attributes of a synaptic tag. We include essential memory molecules in the STC model that have been identified in earlier studies as crucial for STC pathways. CaMKII activation is critical for the setting of the initial tag; however, coordinated activities with other kinases and the biochemical pathways are necessary for the tag to be stable. PKA modulates NMDAR-mediated Ca2+ signalling. Similarly, PKA and ERK crosstalk is essential for Ca2+ - mediated protein synthesis during l-LTP. Our theoretical model explains the quantitative contribution of Tags and protein synthesis during l-LTP in synaptic strength.
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Affiliation(s)
- Raheel Khan
- Centre for Advanced Computational Solutions (C-fACS), Department of Molecular Biosciences, Lincoln University, Christchurch, New Zealand
| | - D Kulasiri
- Centre for Advanced Computational Solutions (C-fACS), Department of Molecular Biosciences, Lincoln University, Christchurch, New Zealand.
| | - S Samarasinghe
- Centre for Advanced Computational Solutions (C-fACS), Department of Molecular Biosciences, Lincoln University, Christchurch, New Zealand
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8
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ADAR regulates APOL1 via A-to-I RNA editing by inhibition of MDA5 activation in a paradoxical biological circuit. Proc Natl Acad Sci U S A 2022; 119:e2210150119. [PMID: 36282916 PMCID: PMC9636950 DOI: 10.1073/pnas.2210150119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
APOL1 risk variants are associated with increased risk of kidney disease in patients of African ancestry, but not all individuals with the APOL1 high-risk genotype develop kidney disease. As APOL1 gene expression correlates closely with the degree of kidney cell injury in both cell and animal models, the mechanisms regulating APOL1 expression may be critical determinants of risk allele penetrance. The APOL1 messenger RNA includes Alu elements at the 3' untranslated region that can form a double-stranded RNA structure (Alu-dsRNA) susceptible to posttranscriptional adenosine deaminase acting on RNA (ADAR)-mediated adenosine-to-inosine (A-to-I) editing, potentially impacting gene expression. We studied the effects of ADAR expression and A-to-I editing on APOL1 levels in podocytes, human kidney tissue, and a transgenic APOL1 mouse model. In interferon-γ (IFN-γ)-stimulated human podocytes, ADAR down-regulates APOL1 by preventing melanoma differentiation-associated protein 5 (MDA5) recognition of dsRNA and the subsequent type I interferon (IFN-I) response. Knockdown experiments showed that recognition of APOL1 messenger RNA itself is an important contributor to the MDA5-driven IFN-I response. Mathematical modeling suggests that the IFN-ADAR-APOL1 network functions as an incoherent feed-forward loop, a biological circuit capable of generating fast, transient responses to stimuli. Glomeruli from human kidney biopsies exhibited widespread editing of APOL1 Alu-dsRNA, while the transgenic mouse model closely replicated the edited sites in humans. APOL1 expression in mice was inversely correlated with Adar1 expression under IFN-γ stimuli, supporting the idea that ADAR regulates APOL1 levels in vivo. ADAR-mediated A-to-I editing is an important regulator of APOL1 expression that could impact both penetrance and severity of APOL1-associated kidney disease.
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Yang M, Harrison BR, Promislow DEL. In search of a Drosophila core cellular network with single-cell transcriptome data. G3 GENES|GENOMES|GENETICS 2022; 12:6670625. [PMID: 35976114 PMCID: PMC9526075 DOI: 10.1093/g3journal/jkac212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Along with specialized functions, cells of multicellular organisms also perform essential functions common to most if not all cells. Whether diverse cells do this by using the same set of genes, interacting in a fixed coordinated fashion to execute essential functions, or a subset of genes specific to certain cells, remains a central question in biology. Here, we focus on gene coexpression to search for a core cellular network across a whole organism. Single-cell RNA-sequencing measures gene expression of individual cells, enabling researchers to discover gene expression patterns that contribute to the diversity of cell functions. Current efforts to study cellular functions focus primarily on identifying differentially expressed genes across cells. However, patterns of coexpression between genes are probably more indicative of biological processes than are the expression of individual genes. We constructed cell-type-specific gene coexpression networks using single-cell transcriptome datasets covering diverse cell types from the fruit fly, Drosophila melanogaster. We detected a set of highly coordinated genes preserved across cell types and present this as the best estimate of a core cellular network. This core is very small compared with cell-type-specific gene coexpression networks and shows dense connectivity. Gene members of this core tend to be ancient genes and are enriched for those encoding ribosomal proteins. Overall, we find evidence for a core cellular network in diverse cell types of the fruit fly. The topological, structural, functional, and evolutionary properties of this core indicate that it accounts for only a minority of essential functions.
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Affiliation(s)
- Ming Yang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Benjamin R Harrison
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
- Department of Biology, University of Washington , Seattle, WA 98195, USA
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Dynamics and Sensitivity of Signaling Pathways. CURRENT PATHOBIOLOGY REPORTS 2022; 10:11-22. [PMID: 36969954 PMCID: PMC10035447 DOI: 10.1007/s40139-022-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Purpose of Review Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets. In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer. An achievement that would facilitate the use of such models is their ability to identify controlling biochemical parameters in signaling pathways, such as molecular abundances and chemical reaction rates, because this would help determine effective points of attack by therapeutics. Recent Findings We summarize the current state of understanding the sensitivity of phosphorylation cycles with and without sequestration. We also describe some basic properties of regulatory motifs including feedback and feedforward regulation. Summary Although much recent work has focused on understanding the dynamics and particularly the sensitivity of signaling networks in eukaryotic systems, there is still an urgent need to build more scalable models of signaling networks that can appropriately represent their complexity across different cell types and tumors.
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol 2022; 18:161-170. [PMID: 34931064 PMCID: PMC8810680 DOI: 10.1038/s41589-021-00919-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.
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Imelio JA, Trajtenberg F, Buschiazzo A. Allostery and protein plasticity: the keystones for bacterial signaling and regulation. Biophys Rev 2022; 13:943-953. [PMID: 35059019 DOI: 10.1007/s12551-021-00892-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/31/2021] [Indexed: 11/25/2022] Open
Abstract
Bacteria sense intracellular and environmental signals using an array of proteins as antennas. The information is transmitted from such sensory modules to other protein domains that act as output effectors. Sensor and effector can be part of the same polypeptide or instead be separate diffusible proteins that interact specifically. The output effector modules regulate physiologic responses, allowing the cells to adapt to the varying conditions. These biological machineries are known as signal transduction systems (STSs). Despite the captivating architectural diversity exhibited by STS proteins, a universal feature is their allosteric regulation: signal binding at one site modifies the activity at a physically distant site. Allostery requires protein plasticity, precisely encoded within their 3D structures, and implicating programmed molecular motions. This review summarizes how STS proteins connect stimuli to specific responses by exploiting allostery and protein plasticity. Illustrative examples spanning a wide variety of protein folds will focus on one- and two-component systems (TCSs). The former encompass the entire transmission route within a single polypeptide, whereas TCSs have evolved as separate diffusible proteins that interact specifically, sometimes including additional intermediary proteins in the pathway. Irrespective of their structural diversity, STS proteins are able to modulate their own molecular motions, which can be relatively slow, rigid-body movements, all the way to fast fluctuations in the form of macromolecular flexibility, thus spanning a continuous protein dynamics spectrum. In sum, STSs rely on allostery to steer information transmission, going from simple two-state switching to rich multi-state conformational order/disorder transitions.
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Affiliation(s)
- J A Imelio
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - F Trajtenberg
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - A Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Microbiology, Institut Pasteur, Paris, France
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13
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Scheuer R, Dietz T, Kretz J, Hadjeras L, McIntosh M, Evguenieva-Hackenberg E. Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance. RNA Biol 2022; 19:980-995. [PMID: 35950733 PMCID: PMC9373788 DOI: 10.1080/15476286.2022.2110380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Sinorhizobium meliloti, the methionine biosynthesis genes metA and metZ are preceded by S-adenosyl-L-methionine (SAM) riboswitches of the SAM-II class. Upon SAM binding, structural changes in the metZ riboswitch were predicted to cause transcriptional termination, generating the sRNA RZ. By contrast, the metA riboswitch was predicted to regulate translation from an AUG1 codon. However, downstream of the metA riboswitch, we found a putative Rho-independent terminator and an in-frame AUG2 codon, which may contribute to metA regulation. We validated the terminator between AUG1 and AUG2, which generates the sRNA RA1 that is processed to RA2. Under high SAM conditions, the activities of the metA and metZ promoters and the steady-state levels of the read-through metA and metZ mRNAs were decreased, while the levels of the RZ and RA2 sRNAs were increased. Under these conditions, the sRNAs and the mRNAs were stabilized. Reporter fusion experiments revealed that the Shine–Dalgarno (SD) sequence in the metA riboswitch is required for translation, which, however, starts 74 nucleotides downstream at AUG2, suggesting a novel translation initiation mechanism. Further, the reporter fusion data supported the following model of RNA-based regulation: Upon SAM binding by the riboswitch, the SD sequence is sequestered to downregulate metA translation, while the mRNA is stabilized. Thus, the SAM-II riboswitches fulfil incoherent, dual regulation, which probably serves to ensure basal metA and metZ mRNA levels under high SAM conditions. This probably helps to adapt to changing conditions and maintain SAM homoeostasis.
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Affiliation(s)
- Robina Scheuer
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Theresa Dietz
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Lydia Hadjeras
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
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14
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Bogan JS. Ubiquitin-like processing of TUG proteins as a mechanism to regulate glucose uptake and energy metabolism in fat and muscle. Front Endocrinol (Lausanne) 2022; 13:1019405. [PMID: 36246906 PMCID: PMC9556833 DOI: 10.3389/fendo.2022.1019405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
In response to insulin stimulation, fat and muscle cells mobilize GLUT4 glucose transporters to the cell surface to enhance glucose uptake. Ubiquitin-like processing of TUG (Aspscr1, UBXD9) proteins is a central mechanism to regulate this process. Here, recent advances in this area are reviewed. The data support a model in which intact TUG traps insulin-responsive "GLUT4 storage vesicles" at the Golgi matrix by binding vesicle cargoes with its N-terminus and matrix proteins with its C-terminus. Insulin stimulation liberates these vesicles by triggering endoproteolytic cleavage of TUG, mediated by the Usp25m protease. Cleavage occurs in fat and muscle cells, but not in fibroblasts or other cell types. Proteolytic processing of intact TUG generates TUGUL, a ubiquitin-like protein modifier, as the N-terminal cleavage product. In adipocytes, TUGUL modifies a single protein, the KIF5B kinesin motor, which carries GLUT4 and other vesicle cargoes to the cell surface. In muscle, this or another motor may be modified. After cleavage of intact TUG, the TUG C-terminal product is extracted from the Golgi matrix by the p97 (VCP) ATPase. In both muscle and fat, this cleavage product enters the nucleus, binds PPARγ and PGC-1α, and regulates gene expression to promote fatty acid oxidation and thermogenesis. The stability of the TUG C-terminal product is regulated by an Ate1 arginyltransferase-dependent N-degron pathway, which may create a feedback mechanism to control oxidative metabolism. Although it is now clear that TUG processing coordinates glucose uptake with other aspects of physiology and metabolism, many questions remain about how this pathway is regulated and how it is altered in metabolic disease in humans.
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Affiliation(s)
- Jonathan S. Bogan
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, United States
- Yale Center for Molecular and Systems Metabolism, Yale School of Medicine, New Haven, CT, United States
- *Correspondence: Jonathan S. Bogan,
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15
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Richardson K. Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:12-17. [PMID: 34736965 DOI: 10.1016/j.pbiomolbio.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
This response aims to expand on some of the issues raised by Keith Baverstock's The Gene: An Appraisal, especially on the evolution and nature of knowledge in living things. In contrast to the simple associationism envisaged in "genetic information", it emphasises the dynamic complexity and changeability of most natural environments, and, therefore, predictability based on underlying statistical structures. That seems to be the basis of the "cognitive" functions increasingly being reported about cellular, as well as more evolved, functions, and of the autonomous agency of organisms thriving creatively in complex environments.
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16
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From spikes to intercellular waves: Tuning intercellular calcium signaling dynamics modulates organ size control. PLoS Comput Biol 2021; 17:e1009543. [PMID: 34723960 PMCID: PMC8601605 DOI: 10.1371/journal.pcbi.1009543] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/18/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
Information flow within and between cells depends significantly on calcium (Ca2+) signaling dynamics. However, the biophysical mechanisms that govern emergent patterns of Ca2+ signaling dynamics at the organ level remain elusive. Recent experimental studies in developing Drosophila wing imaginal discs demonstrate the emergence of four distinct patterns of Ca2+ activity: Ca2+ spikes, intercellular Ca2+ transients, tissue-level Ca2+ waves, and a global “fluttering” state. Here, we used a combination of computational modeling and experimental approaches to identify two different populations of cells within tissues that are connected by gap junction proteins. We term these two subpopulations “initiator cells,” defined by elevated levels of Phospholipase C (PLC) activity, and “standby cells,” which exhibit baseline activity. We found that the type and strength of hormonal stimulation and extent of gap junctional communication jointly determine the predominate class of Ca2+ signaling activity. Further, single-cell Ca2+ spikes are stimulated by insulin, while intercellular Ca2+ waves depend on Gαq activity. Our computational model successfully reproduces how the dynamics of Ca2+ transients varies during organ growth. Phenotypic analysis of perturbations to Gαq and insulin signaling support an integrated model of cytoplasmic Ca2+ as a dynamic reporter of overall tissue growth. Further, we show that perturbations to Ca2+ signaling tune the final size of organs. This work provides a platform to further study how organ size regulation emerges from the crosstalk between biochemical growth signals and heterogeneous cell signaling states. Calcium (Ca2+) is a universal second messenger that regulates a myriad of cellular processes such as cell division, cell proliferation and apoptosis. Multiple patterns of Ca2+ signaling including single-cell spikes, multicellular Ca2+ transients, large-scale Ca2+ waves, and global “fluttering” have been observed in epithelial systems during organ development. Key molecular players and biophysical mechanisms involved in formation of these patterns during organ development are not well understood. In this work, we developed a generalized multicellular model of Ca2+ that captures all the key categories of Ca2+ activity as a function of key hormonal signals. Integration of model predictions and experiments reveals two subclasses of cell populations and demonstrates that Ca2+ signaling activity at the organ scale is defined by a general decrease in gap junction communication as an organ grows. Our experiments also reveal that a “goldilocks zone” of optimal Ca2+ activity is required to achieve optimal growth at the organ level.
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17
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Law AL, Jalal S, Pallett T, Mosis F, Guni A, Brayford S, Yolland L, Marcotti S, Levitt JA, Poland SP, Rowe-Sampson M, Jandke A, Köchl R, Pula G, Ameer-Beg SM, Stramer BM, Krause M. Nance-Horan Syndrome-like 1 protein negatively regulates Scar/WAVE-Arp2/3 activity and inhibits lamellipodia stability and cell migration. Nat Commun 2021; 12:5687. [PMID: 34584076 PMCID: PMC8478917 DOI: 10.1038/s41467-021-25916-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/03/2021] [Indexed: 12/02/2022] Open
Abstract
Cell migration is important for development and its aberrant regulation contributes to many diseases. The Scar/WAVE complex is essential for Arp2/3 mediated lamellipodia formation during mesenchymal cell migration and several coinciding signals activate it. However, so far, no direct negative regulators are known. Here we identify Nance-Horan Syndrome-like 1 protein (NHSL1) as a direct binding partner of the Scar/WAVE complex, which co-localise at protruding lamellipodia. This interaction is mediated by the Abi SH3 domain and two binding sites in NHSL1. Furthermore, active Rac binds to NHSL1 at two regions that mediate leading edge targeting of NHSL1. Surprisingly, NHSL1 inhibits cell migration through its interaction with the Scar/WAVE complex. Mechanistically, NHSL1 may reduce cell migration efficiency by impeding Arp2/3 activity, as measured in cells using a Arp2/3 FRET-FLIM biosensor, resulting in reduced F-actin density of lamellipodia, and consequently impairing the stability of lamellipodia protrusions.
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Affiliation(s)
- Ah-Lai Law
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- School of Life Sciences, University of Bedfordshire, Luton, LU1 3JU, UK
| | - Shamsinar Jalal
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Tommy Pallett
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Fuad Mosis
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Ahmad Guni
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Simon Brayford
- Stramer Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Lawrence Yolland
- Stramer Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Stefania Marcotti
- Stramer Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - James A Levitt
- Ameer-Beg Group, Richard Dimbleby Cancer Research Laboratories, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Simon P Poland
- Ameer-Beg Group, Richard Dimbleby Cancer Research Laboratories, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Maia Rowe-Sampson
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Stramer Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Anett Jandke
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Robert Köchl
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Giordano Pula
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg (UKE), Martinistrasse 52, O26, 20246, Hamburg, Germany
| | - Simon M Ameer-Beg
- Ameer-Beg Group, Richard Dimbleby Cancer Research Laboratories, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Brian Marc Stramer
- Stramer Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Matthias Krause
- Krause Group, Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.
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18
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Righetti E, Kahramanoğulları O. The inverse correlation between robustness and sensitivity to autoregulation in two-component systems. Math Biosci 2021; 341:108706. [PMID: 34563549 DOI: 10.1016/j.mbs.2021.108706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
Two-component systems (TCS) are signal transduction systems in bacteria and many other organisms that relay the sensory signal to genetic components. TCS consist of two proteins: a histidine kinase and a response regulator that the histidine kinase activates. This seemingly simple machinery can generate complex regulatory dynamics that enables the level of gene expression that matches the input signal: many TCS response regulators act on their own genes as transcription factors, resulting in a positive autoregulation mechanism. This regulation, in return, modulates the transcription factor activity as a function of the input signal. Positive autoregulation does not necessarily result in positive feedback. Sensitivity to autoregulation is quantified as the output level amplification resulting from the positive autoregulation mechanism. Another structural property of these systems is formally characterized as "robustness": in a robust TCS, the output of the system is solely a function of the input signal. Thus, a robust TCS remains insensitive to fluctuations in the concentrations of its protein components and, this way, maintains the precision in the output transcription factor activity in response to input stimulus. In this paper, we show with a formal model that TCS operate on a spectrum of inverse correlation between robustness and sensitivity to autoregulation. Our model predicts that the modulation by positive autoregulation is a function of loss in TCS robustness, for example, by spontaneous dephosphorylation of the histidine kinase. Consequently, the loss in robustness provides a proportional modulation by positive autoregulation to widen the response range with a scaled amplification of the output. At the other end of the spectrum, in the presence of a strictly robust TCS machinery, amplification of the transcription factor activity by autoregulation is diminished. We show that our results are in agreement with published experimental results. Our results suggest that these TCS evolve to converge at a trade-off between robustness and positive autoregulation.
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Affiliation(s)
- Elena Righetti
- Department of Mathematics, University of Trento, Trento, Italy
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19
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Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules 2021; 11:biom11081182. [PMID: 34439849 PMCID: PMC8391864 DOI: 10.3390/biom11081182] [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] [Received: 06/30/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.
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20
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Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1. PLoS Genet 2021; 17:e1009640. [PMID: 34214075 PMCID: PMC8282090 DOI: 10.1371/journal.pgen.1009640] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/15/2021] [Accepted: 06/02/2021] [Indexed: 12/31/2022] Open
Abstract
Heterotrimeric G proteins were originally discovered through efforts to understand the effects of hormones, such as glucagon and epinephrine, on glucose metabolism. On the other hand, many cellular metabolites, including glucose, serve as ligands for G protein-coupled receptors. Here we investigate the consequences of glucose-mediated receptor signaling, and in particular the role of a Gα subunit Gpa2 and a non-canonical Gβ subunit, known as Asc1 in yeast and RACK1 in animals. Asc1/RACK1 is of particular interest because it has multiple, seemingly unrelated, functions in the cell. The existence of such “moonlighting” operations has complicated the determination of phenotype from genotype. Through a comparative analysis of individual gene deletion mutants, and by integrating transcriptomics and metabolomics measurements, we have determined the relative contributions of the Gα and Gβ protein subunits to glucose-initiated processes in yeast. We determined that Gpa2 is primarily involved in regulating carbohydrate metabolism while Asc1 is primarily involved in amino acid metabolism. Both proteins are involved in regulating purine metabolism. Of the two subunits, Gpa2 regulates a greater number of gene transcripts and was particularly important in determining the amplitude of response to glucose addition. We conclude that the two G protein subunits regulate distinct but complementary processes downstream of the glucose-sensing receptor, as well as processes that lead ultimately to changes in cell growth and metabolism. Despite the societal importance of glucose fermentation in yeast, the mechanisms by which these cells detect and respond to glucose have remained obscure. Glucose detection requires a cell surface receptor coupled to a G protein that is comprised of two subunits, rather than the more typical heterotrimer: an α subunit Gpa2 and the β subunit Asc1 (or RACK1 in humans). Asc1/RACK1 also serves as a subunit of the ribosome, where it regulates the synthesis of proteins involved in glucose fermentation. This manuscript uses global metabolomics and transcriptomics to demonstrate the distinct roles of each G protein subunit in transmitting the glucose signal. Whereas Gpa2 is primarily involved in the metabolism of carbohydrates, Asc1/RACK1 contributes to production of amino acids necessary for protein synthesis and cell division. These findings reveal the initial steps of glucose signaling and several unique and complementary functions of the G protein subunits. More broadly, the integrated approach used here is likely to guide efforts to determine the topology of complex G protein and metabolic signaling networks in humans.
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21
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Shake It Off: The Elimination of Erroneous Kinetochore-Microtubule Attachments and Chromosome Oscillation. Int J Mol Sci 2021; 22:ijms22063174. [PMID: 33804687 PMCID: PMC8003821 DOI: 10.3390/ijms22063174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/18/2021] [Indexed: 01/17/2023] Open
Abstract
Cell proliferation and sexual reproduction require the faithful segregation of chromosomes. Chromosome segregation is driven by the interaction of chromosomes with the spindle, and the attachment of chromosomes to the proper spindle poles is essential. Initial attachments are frequently erroneous due to the random nature of the attachment process; however, erroneous attachments are selectively eliminated. Proper attachment generates greater tension at the kinetochore than erroneous attachments, and it is thought that attachment selection is dependent on this tension. However, studies of meiotic chromosome segregation suggest that attachment elimination cannot be solely attributed to tension, and the precise mechanism of selective elimination of erroneous attachments remains unclear. During attachment elimination, chromosomes oscillate between the spindle poles. A recent study on meiotic chromosome segregation in fission yeast has suggested that attachment elimination is coupled to chromosome oscillation. In this review, the possible contribution of chromosome oscillation in the elimination of erroneous attachment is discussed in light of the recent finding.
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22
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Molecular switch architecture determines response properties of signaling pathways. Proc Natl Acad Sci U S A 2021; 118:2013401118. [PMID: 33688042 DOI: 10.1073/pnas.2013401118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many intracellular signaling pathways are composed of molecular switches, proteins that transition between two states-on and off Typically, signaling is initiated when an external stimulus activates its cognate receptor that, in turn, causes downstream switches to transition from off to on using one of the following mechanisms: activation, in which the transition rate from the off state to the on state increases; derepression, in which the transition rate from the on state to the off state decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several operating principles for molecular switches. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to upstream fluctuations. We demonstrate that these operating principles also hold when the models are extended to include additional features, such as receptor removal, kinetic proofreading, and cascades of switches. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.
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23
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Habtemichael EN, Li DT, Camporez JP, Westergaard XO, Sales CI, Liu X, López-Giráldez F, DeVries SG, Li H, Ruiz DM, Wang KY, Sayal BS, González Zapata S, Dann P, Brown SN, Hirabara S, Vatner DF, Goedeke L, Philbrick W, Shulman GI, Bogan JS. Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptake. Nat Metab 2021; 3:378-393. [PMID: 33686286 PMCID: PMC7990718 DOI: 10.1038/s42255-021-00359-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
TUG tethering proteins bind and sequester GLUT4 glucose transporters intracellularly, and insulin stimulates TUG cleavage to translocate GLUT4 to the cell surface and increase glucose uptake. This effect of insulin is independent of phosphatidylinositol 3-kinase, and its physiological relevance remains uncertain. Here we show that this TUG cleavage pathway regulates both insulin-stimulated glucose uptake in muscle and organism-level energy expenditure. Using mice with muscle-specific Tug (Aspscr1)-knockout and muscle-specific constitutive TUG cleavage, we show that, after GLUT4 release, the TUG C-terminal cleavage product enters the nucleus, binds peroxisome proliferator-activated receptor (PPAR)γ and its coactivator PGC-1α and regulates gene expression to promote lipid oxidation and thermogenesis. This pathway acts in muscle and adipose cells to upregulate sarcolipin and uncoupling protein 1 (UCP1), respectively. The PPARγ2 Pro12Ala polymorphism, which reduces diabetes risk, enhances TUG binding. The ATE1 arginyltransferase, which mediates a specific protein degradation pathway and controls thermogenesis, regulates the stability of the TUG product. We conclude that insulin-stimulated TUG cleavage coordinates whole-body energy expenditure with glucose uptake, that this mechanism might contribute to the thermic effect of food and that its attenuation could promote obesity.
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Affiliation(s)
- Estifanos N Habtemichael
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Evelo Biosciences, Inc., Cambridge, MA, USA
| | - Don T Li
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - João Paulo Camporez
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- University of São Paulo, São Paulo, Brazil
| | - Xavier O Westergaard
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Columbia University, New York, NY, USA
| | - Chloe I Sales
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinran Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | | | - Stephen G DeVries
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hanbing Li
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Zhejiang University of Technology, Hangzhou, China
| | - Diana M Ruiz
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Kenny Y Wang
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Bhavesh S Sayal
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sofia González Zapata
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Pamela Dann
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Stacey N Brown
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sandro Hirabara
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Institute of Physical Activity Sciences and Sports, Cruzeiro do Sul University, São Paulo, Brazil
| | - Daniel F Vatner
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Leigh Goedeke
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - William Philbrick
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Gerald I Shulman
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan S Bogan
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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24
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Wakiya M, Nishi E, Kawai S, Yamada K, Katsumata K, Hirayasu A, Itabashi Y, Yamamoto A. Chiasmata and the kinetochore component Dam1 are crucial for elimination of erroneous chromosome attachments and centromere oscillation at meiosis I. Open Biol 2021; 11:200308. [PMID: 33529549 PMCID: PMC8061696 DOI: 10.1098/rsob.200308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Establishment of proper chromosome attachments to the spindle requires elimination of erroneous attachments, but the mechanism of this process is not fully understood. During meiosis I, sister chromatids attach to the same spindle pole (mono-oriented attachment), whereas homologous chromosomes attach to opposite poles (bi-oriented attachment), resulting in homologous chromosome segregation. Here, we show that chiasmata that link homologous chromosomes and kinetochore component Dam1 are crucial for elimination of erroneous attachments and oscillation of centromeres between the spindle poles at meiosis I in fission yeast. In chiasma-forming cells, Mad2 and Aurora B kinase, which provides time for attachment correction and destabilizes erroneous attachments, respectively, caused elimination of bi-oriented attachments of sister chromatids, whereas in chiasma-lacking cells, they caused elimination of mono-oriented attachments. In chiasma-forming cells, in addition, homologous centromere oscillation was coordinated. Furthermore, Dam1 contributed to attachment elimination in both chiasma-forming and chiasma-lacking cells, and drove centromere oscillation. These results demonstrate that chiasmata alter attachment correction patterns by enabling error correction factors to eliminate bi-oriented attachment of sister chromatids, and suggest that Dam1 induces elimination of erroneous attachments. The coincidental contribution of chiasmata and Dam1 to centromere oscillation also suggests a potential link between centromere oscillation and attachment elimination.
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Affiliation(s)
- Misuzu Wakiya
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Eriko Nishi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Shinnosuke Kawai
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.,Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kohei Yamada
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kazuhiro Katsumata
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ami Hirayasu
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yuta Itabashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ayumu Yamamoto
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.,Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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25
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Muldoon JJ, Kandula V, Hong M, Donahue PS, Boucher JD, Bagheri N, Leonard JN. Model-guided design of mammalian genetic programs. SCIENCE ADVANCES 2021; 7:eabe9375. [PMID: 33608279 PMCID: PMC7895425 DOI: 10.1126/sciadv.abe9375] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/06/2021] [Indexed: 06/10/2023]
Abstract
Genetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multifunctional proteins integrating both transcriptional and posttranslational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.
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Affiliation(s)
- J J Muldoon
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - V Kandula
- Honors Program in Medical Education, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - M Hong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - P S Donahue
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - J D Boucher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - N Bagheri
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Chemistry of Life Processes Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
- Departments of Biology and Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - J N Leonard
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Chemistry of Life Processes Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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26
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Marmor-Kollet H, Siany A, Kedersha N, Knafo N, Rivkin N, Danino YM, Moens TG, Olender T, Sheban D, Cohen N, Dadosh T, Addadi Y, Ravid R, Eitan C, Toth Cohen B, Hofmann S, Riggs CL, Advani VM, Higginbottom A, Cooper-Knock J, Hanna JH, Merbl Y, Van Den Bosch L, Anderson P, Ivanov P, Geiger T, Hornstein E. Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis. Mol Cell 2020; 80:876-891.e6. [PMID: 33217318 PMCID: PMC7816607 DOI: 10.1016/j.molcel.2020.10.032] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/30/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
Stress granules (SGs) are cytoplasmic assemblies of proteins and non-translating mRNAs. Whereas much has been learned about SG formation, a major gap remains in understanding the compositional changes SGs undergo during normal disassembly and under disease conditions. Here, we address this gap by proteomic dissection of the SG temporal disassembly sequence using multi-bait APEX proximity proteomics. We discover 109 novel SG proteins and characterize distinct SG substructures. We reveal dozens of disassembly-engaged proteins (DEPs), some of which play functional roles in SG disassembly, including small ubiquitin-like modifier (SUMO) conjugating enzymes. We further demonstrate that SUMOylation regulates SG disassembly and SG formation. Parallel proteomics with amyotrophic lateral sclerosis (ALS)-associated C9ORF72 dipeptides uncovered attenuated DEP recruitment during SG disassembly and impaired SUMOylation. Accordingly, SUMO activity ameliorated C9ORF72-ALS-related neurodegeneration in Drosophila. By dissecting the SG spatiotemporal proteomic landscape, we provide an in-depth resource for future work on SG function and reveal basic and disease-relevant mechanisms of SG disassembly.
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Affiliation(s)
- Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aviad Siany
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nancy Kedersha
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Naama Knafo
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Thomas G Moens
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daoud Sheban
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Revital Ravid
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Beata Toth Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarah Hofmann
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Claire L Riggs
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Vivek M Advani
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Paul Anderson
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tamar Geiger
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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27
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Lin J, Chen K, Chen W, Yao Y, Ni S, Ye M, Zhuang G, Hu M, Gao J, Gao C, Liu Y, Yang M, Zhang Z, Zhang X, Huang J, Chen F, Sun L, Zhang X, Yu S, Chen Y, Jiang Y, Wang S, Yang X, Liu K, Zhou HM, Ji Z, Deng H, Haque ME, Li J, Mi LZ, Li Y, Yang Y. Paradoxical Mitophagy Regulation by PINK1 and TUFm. Mol Cell 2020; 80:607-620.e12. [PMID: 33113344 DOI: 10.1016/j.molcel.2020.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 01/19/2023]
Abstract
Aberrant mitophagy has been implicated in a broad spectrum of disorders. PINK1, Parkin, and ubiquitin have pivotal roles in priming mitophagy. However, the entire regulatory landscape and the precise control mechanisms of mitophagy remain to be elucidated. Here, we uncover fundamental mitophagy regulation involving PINK1 and a non-canonical role of the mitochondrial Tu translation elongation factor (TUFm). The mitochondrion-cytosol dual-localized TUFm interacts with PINK1 biochemically and genetically, which is an evolutionarily conserved Parkin-independent route toward mitophagy. A PINK1-dependent TUFm phosphoswitch at Ser222 determines conversion from activating to suppressing mitophagy. PINK1 modulates differential translocation of TUFm because p-S222-TUFm is restricted predominantly to the cytosol, where it inhibits mitophagy by impeding Atg5-Atg12 formation. The self-antagonizing feature of PINK1/TUFm is critical for the robustness of mitophagy regulation, achieved by the unique kinetic parameters of p-S222-TUFm, p-S65-ubiquitin, and their common kinase PINK1. Our findings provide new mechanistic insights into mitophagy and mitophagy-associated disorders.
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Affiliation(s)
- Jingjing Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Kai Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yizhou Yao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Shiwei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Meina Ye
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Guifeng Zhuang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Minhuang Hu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jun Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Caixi Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yan Liu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mingjuan Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zhenkun Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaohui Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jiexiang Huang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Fei Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Ling Sun
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xi Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Suhong Yu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yating Jiang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shujuan Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaozhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ke Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - M Emdadul Haque
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, PO Box 17666, United Arab Emirates
| | - Junxiang Li
- AgeCode R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yuexi Li
- Huadong Research Institute for Medicine and Biotechniques, 293 East Zhongshan Road, Nanjing 210002, China.
| | - Yufeng Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China.
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28
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Gurska D, Vargas Jentzsch IM, Panfilio KA. Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium. Commun Biol 2020; 3:552. [PMID: 33020571 PMCID: PMC7536231 DOI: 10.1038/s42003-020-01250-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 08/21/2020] [Indexed: 02/03/2023] Open
Abstract
Insect Hox3/zen genes represent an evolutionary hotspot for changes in function and copy number. Single orthologues are required either for early specification or late morphogenesis of the extraembryonic tissues, which protect the embryo. The tandemly duplicated zen paralogues of the beetle Tribolium castaneum present a unique opportunity to investigate both functions in a single species. We dissect the paralogues' expression dynamics (transcript and protein) and transcriptional targets (RNA-seq after RNAi) throughout embryogenesis. We identify an unexpected role of Tc-Zen2 in repression of Tc-zen1, generating a negative feedback loop that promotes developmental progression. Tc-Zen2 regulation is dynamic, including within co-expressed multigene loci. We also show that extraembryonic development is the major event within the transcriptional landscape of late embryogenesis and provide a global molecular characterization of the extraembryonic serosal tissue. Altogether, we propose that paralogue mutual regulation arose through multiple instances of zen subfunctionalization, leading to their complementary extant roles.
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Affiliation(s)
- Daniela Gurska
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Iris M Vargas Jentzsch
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Kristen A Panfilio
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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29
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Tran AP, Ali Al-Radhawi M, Kareva I, Wu J, Waxman DJ, Sontag ED. Delicate Balances in Cancer Chemotherapy: Modeling Immune Recruitment and Emergence of Systemic Drug Resistance. Front Immunol 2020; 11:1376. [PMID: 32695118 PMCID: PMC7338613 DOI: 10.3389/fimmu.2020.01376] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/29/2020] [Indexed: 01/21/2023] Open
Abstract
Metronomic chemotherapy can drastically enhance immunogenic tumor cell death. However, the mechanisms responsible are still incompletely understood. Here, we develop a mathematical model to elucidate the underlying complex interactions between tumor growth, immune system activation, and therapy-mediated immunogenic cell death. Our model is conceptually simple, yet it provides a surprisingly excellent fit to empirical data obtained from a GL261 SCID mouse glioma model treated with cyclophosphamide on a metronomic schedule. The model includes terms representing immune recruitment as well as the emergence of drug resistance during prolonged metronomic treatments. Strikingly, a single fixed set of parameters, adjusted neither for individuals nor for drug schedule, recapitulates experimental data across various drug regimens remarkably well, including treatments administered at intervals ranging from 6 to 12 days. Additionally, the model predicts peak immune activation times, rediscovering experimental data that had not been used in parameter fitting or in model construction. Notably, the validated model suggests that immunostimulatory and immunosuppressive intermediates are responsible for the observed phenomena of resistance and immune cell recruitment, and thus for variation of responses with respect to different schedules of drug administration.
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Affiliation(s)
- Anh Phong Tran
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - M Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, United States
| | - Irina Kareva
- Mathematical and Computational Sciences Center, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, United States
| | - Junjie Wu
- Clinical Research Institute, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, United States
| | - Eduardo D Sontag
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, United States
- Department of Bioengineering, Northeastern University, Boston, MA, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA, United States
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30
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From cancer to rejuvenation: incomplete regeneration as the missing link (part II: rejuvenation circle). Future Sci OA 2020; 6:FSO610. [PMID: 32983567 PMCID: PMC7491027 DOI: 10.2144/fsoa-2020-0085] [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] [Indexed: 12/13/2022] Open
Abstract
In the first part of our study, we substantiated that the embryonic reontogenesis and malignant growth (disintegrating growth) pathways are the same, but occur at different stages of ontogenesis, this mechanism is carried out in opposite directions. Cancer has been shown to be epigenetic-blocked redifferentiation and unfinished somatic embryogenesis. We formulated that only this approach of aging elimination has real prospects for a future that is fraught with cancer, as we will be able to convert this risk into a rejuvenation process through the continuous cycling of cell dedifferentiation-differentiation processes (permanent remorphogenesis). Here, we continue to develop the idea of looped ontogenesis and formulate the concept of the rejuvenation circle.
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31
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Cook SL, Franke MC, Sievert EP, Sciammas R. A Synchronous IRF4-Dependent Gene Regulatory Network in B and Helper T Cells Orchestrating the Antibody Response. Trends Immunol 2020; 41:614-628. [PMID: 32467029 DOI: 10.1016/j.it.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022]
Abstract
Control of diverse pathogens requires an adaptive antibody response, dependent on cellular division of labor to allocate antigen-dependent B- and CD4+ T-cell fates that collaborate to control the quantity and quality of antibody. This is orchestrated by the dynamic action of key transcriptional regulators mediating gene expression programs in response to pathogen-specific environmental inputs. We describe a conserved, likely ancient, gene regulatory network that intriguingly operates contemporaneously in B and CD4+ T cells to control their cell fate dynamics and thus, the character of the antibody response. The remarkable output of this network derives from graded expression, designated by antigen receptor signal strength, of a pivotal transcription factor that regulates alternate cell fate choices.
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Affiliation(s)
- Sarah L Cook
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA.
| | - Marissa C Franke
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Evelyn P Sievert
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
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32
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Vashishtha S, Broderick G, Craddock TJA, Barnes ZM, Collado F, Balbin EG, Fletcher MA, Klimas NG. Leveraging Prior Knowledge to Recover Characteristic Immune Regulatory Motifs in Gulf War Illness. Front Physiol 2020; 11:358. [PMID: 32411011 PMCID: PMC7198798 DOI: 10.3389/fphys.2020.00358] [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: 01/21/2019] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Potentially linked to the basic physiology of stress response, Gulf War Illness (GWI) is a debilitating condition presenting with complex immune, endocrine and neurological symptoms. Here we interrogate the immune response to physiological stress by measuring 16 blood-borne immune markers at 8 time points before, during and after maximum exercise challenge in n = 12 GWI veterans and n = 11 healthy veteran controls deployed to the same theater. Immune markers were combined into functional sets and the dynamics of their joint expression described as classical rate equations. These empirical networks were further informed structurally by projection onto prior knowledge networks mined from the literature. Of the 49 literature-informed immune signaling interactions, 21 were found active in the combined exercise response data. However, only 4 signals were common to both subject groups while 7 were uniquely active in GWI and 10 uniquely active in healthy veterans. Feedforward mediation of IL-23 and IL-17 by IL-6 and IL-10 emerged as distinguishing control elements that were characteristically active in GWI versus healthy subjects. Simulated restructuring of the regulatory circuitry in GWI as a result of applying an IL-6 receptor antagonist in combination with either a Th1 (IL-2, IFNγ, and TNFα) or IL-23 receptor antagonist predicted a partial rescue of immune response elements previously associated with illness severity. Overall, results suggest that pharmacologically altering the topology of the immune response circuitry identified as active in GWI can inform on strategies that while not curative, may nonetheless deliver a reduction in symptom burden. A lasting and more complete remission in GWI may therefore require manipulation of a broader physiology, namely one that includes endocrine oversight of immune function.
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Affiliation(s)
- Saurabh Vashishtha
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States.,Department of Biomedical Engineering, Kate Gleason College of Engineering, Rochester Institute of Technology, Rochester, NY, United States
| | - Travis J A Craddock
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Zachary M Barnes
- Diabetes Research Institute, University of Miami, Miami, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Fanny Collado
- Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Elizabeth G Balbin
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Mary Ann Fletcher
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
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33
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Guan S, Xu L, Zhang Q, Shi H. Trade-offs between effectiveness and cost in bifunctional enzyme circuit with concentration robustness. Phys Rev E 2020; 101:012409. [PMID: 32069674 DOI: 10.1103/physreve.101.012409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 01/01/2023]
Abstract
A fundamental trade-off in biological systems is whether they consume resources to perform biological functions or save resources. Bacteria need to reliably and rapidly respond to input signals by using limited cellular resources. However, excessive resource consumption will become a burden for bacteria growth. To investigate the relationship between functional effectiveness and resource cost, we study the ubiquitous bifunctional enzyme circuit, which is robust to fluctuations in protein concentration and responds quickly to signal changes. We show that trade-off relationships exist between functional effectiveness and protein cost. Expressing more proteins of the circuit increases concentration robustness and response speed but affects bacterial growth. In particular, our study reveals a general relationship between free-energy dissipation rate, response speed, and concentration robustness. The dissipation of free energy plays an important role in the concentration robustness and response speed. High robustness can only be achieved with a large amount of free-energy consumption and protein cost. In addition, the noise of the output increases with increasing protein cost, while the noise of the response time decreases with increasing protein cost. We also calculate the trade-off relationships in the EnvZ-OmpR system and the nitrogen assimilation system, which both have the bifunctional enzyme. Similar results indicate that these relationships are mainly derived from the specific feature of the bifunctional enzyme circuits and are not relevant to the details of the models. According to the trade-off relationships, bacteria take a compromise solution that reliably performs biological functions at a reasonable cost.
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Affiliation(s)
- Shaohua Guan
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liufang Xu
- Department of Physics and Biophysics & Complex System Center, Jilin University, Changchun 130012, Jilin, China
| | - Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Evidence of Robustness in a Two-Component System Using a Synthetic Circuit. J Bacteriol 2020; 202:JB.00672-19. [PMID: 31792012 DOI: 10.1128/jb.00672-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023] Open
Abstract
Variation in the concentration of biological components is inescapable for any cell. Robustness in any biological circuit acts as a cushion against such variation and enables the cells to produce homogeneous output despite the fluctuation. The two-component system (TCS) with a bifunctional sensor kinase (that possesses both kinase and phosphatase activities) is proposed to be a robust circuit. Few theoretical models explain the robustness of a TCS, although the criteria and extent of robustness by these models differ. Here, we provide experimental evidence to validate the extent of the robustness of a TCS signaling pathway. We have designed a synthetic circuit in Escherichia coli using a representative TCS of Mycobacterium tuberculosis, MprAB, and monitored the in vivo output signal by systematically varying the concentration of either of the components or both. We observed that the output of the TCS is robust if the concentration of MprA is above a threshold value. This observation is further substantiated by two in vitro assays, in which we estimated the phosphorylated MprA pool or MprA-dependent transcription yield by varying either of the components of the TCS. This synthetic circuit could be used as a model system to analyze the relationship among different components of gene regulatory networks.IMPORTANCE Robustness in essential biological circuits is an important feature of the living organism. A few pieces of evidence support the existence of robustness in vivo in the two-component system (TCS) with a bifunctional sensor kinase (SK). The assays were done under physiological conditions in which the SK was much lower than the response regulator (RR). Here, using a synthetic circuit, we varied the concentrations of the SK and RR of a representative TCS to monitor output robustness in vivo. In vitro assays were also performed under conditions where the concentration of the SK was greater than that of the RR. Our results demonstrate the extent of output robustness in the TCS signaling pathway with respect to the concentrations of the two components.
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Trajtenberg F, Buschiazzo A. Protein Dynamics in Phosphoryl-Transfer Signaling Mediated by Two-Component Systems. Methods Mol Biol 2020; 2077:1-18. [PMID: 31707648 DOI: 10.1007/978-1-4939-9884-5_1] [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] [Indexed: 01/25/2023]
Abstract
The ability to perceive the environment, an essential attribute in living organisms, is linked to the evolution of signaling proteins that recognize specific signals and execute predetermined responses. Such proteins constitute concerted systems that can be as simple as a unique protein, able to recognize a ligand and exert a phenotypic change, or extremely complex pathways engaging dozens of different proteins which act in coordination with feedback loops and signal modulation. To understand how cells sense their surroundings and mount specific adaptive responses, we need to decipher the molecular workings of signal recognition, internalization, transfer, and conversion into chemical changes inside the cell. Protein allostery and dynamics play a central role. Here, we review recent progress on the study of two-component systems, important signaling machineries of prokaryotes and lower eukaryotes. Such systems implicate a sensory histidine kinase and a separate response regulator protein. Both components exploit protein flexibility to effect specific conformational rearrangements, modulating protein-protein interactions, and ultimately transmitting information accurately. Recent work has revealed how histidine kinases switch between discrete functional states according to the presence or absence of the signal, shifting key amino acid positions that define their catalytic activity. In concert with the cognate response regulator's allosteric changes, the phosphoryl-transfer flow during the signaling process is exquisitely fine-tuned for proper specificity, efficiency and directionality.
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Affiliation(s)
- Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Département de Microbiologie, Institut Pasteur, Paris, France.
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Belyaeva OV, Adams MK, Popov KM, Kedishvili NY. Generation of Retinaldehyde for Retinoic Acid Biosynthesis. Biomolecules 2019; 10:biom10010005. [PMID: 31861321 PMCID: PMC7022914 DOI: 10.3390/biom10010005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
The concentration of all-trans-retinoic acid, the bioactive derivative of vitamin A, is critically important for the optimal performance of numerous physiological processes. Either too little or too much of retinoic acid in developing or adult tissues is equally harmful. All-trans-retinoic acid is produced by the irreversible oxidation of all-trans-retinaldehyde. Thus, the concentration of retinaldehyde as the immediate precursor of retinoic acid has to be tightly controlled. However, the enzymes that produce all-trans-retinaldehyde for retinoic acid biosynthesis and the mechanisms responsible for the control of retinaldehyde levels have not yet been fully defined. The goal of this review is to summarize the current state of knowledge regarding the identities of physiologically relevant retinol dehydrogenases, their enzymatic properties, and tissue distribution, and to discuss potential mechanisms for the regulation of the flux from retinol to retinaldehyde.
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Affiliation(s)
- Olga V. Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
- Correspondence: ; Tel.: +1-205-996-4024
| | - Mark K. Adams
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA;
| | - Kirill M. Popov
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
| | - Natalia Y. Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
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Rodrigo G. Insights about collective decision-making at the genetic level. Biophys Rev 2019; 12:19-24. [PMID: 31845181 DOI: 10.1007/s12551-019-00608-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
By living in a collective, individuals can share and aggregate information to base their decisions on the many rather than on the one, thereby increasing accuracy. But a collective can also be defined at the molecular level. In the following, we reason that genes, by working collectively, share fundamental features with social organisms, which ends, without invoking cognition, in wiser responses. For that, we compile into a single picture the terms redundancy, stochastic resonance, intrinsic and extrinsic noise, and cross-regulation.
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Affiliation(s)
- Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - U. Valencia, 46980, Paterna, Spain.
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38
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The Emerging Landscape of p53 Isoforms in Physiology, Cancer and Degenerative Diseases. Int J Mol Sci 2019; 20:ijms20246257. [PMID: 31835844 PMCID: PMC6941119 DOI: 10.3390/ijms20246257] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
p53, first described four decades ago, is now established as a master regulator of cellular stress response, the “guardian of the genome”. p53 contributes to biological robustness by behaving in a cellular-context dependent manner, influenced by several factors (e.g., cell type, active signalling pathways, the type, extent and intensity of cellular damage, cell cycle stage, nutrient availability, immune function). The p53 isoforms regulate gene transcription and protein expression in response to the stimuli so that the cell response is precisely tuned to the cell signals and cell context. Twelve isoforms of p53 have been described in humans. In this review, we explore the interactions between p53 isoforms and other proteins contributing to their established cellular functions, which can be both tumour-suppressive and oncogenic in nature. Evidence of p53 isoform in human cancers is largely based on RT-qPCR expression studies, usually investigating a particular type of isoform. Beyond p53 isoform functions in cancer, it is implicated in neurodegeneration, embryological development, progeroid phenotype, inflammatory pathology, infections and tissue regeneration, which are described in this review.
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Li DT, Habtemichael EN, Julca O, Sales CI, Westergaard XO, DeVries SG, Ruiz D, Sayal B, Bogan JS. GLUT4 Storage Vesicles: Specialized Organelles for Regulated Trafficking. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2019; 92:453-470. [PMID: 31543708 PMCID: PMC6747935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Fat and muscle cells contain a specialized, intracellular organelle known as the GLUT4 storage vesicle (GSV). Insulin stimulation mobilizes GSVs, so that these vesicles fuse at the cell surface and insert GLUT4 glucose transporters into the plasma membrane. This example is likely one instance of a broader paradigm for regulated, non-secretory exocytosis, in which intracellular vesicles are translocated in response to diverse extracellular stimuli. GSVs have been studied extensively, yet these vesicles remain enigmatic. Data support the view that in unstimulated cells, GSVs are present as a pool of preformed small vesicles, which are distinct from endosomes and other membrane-bound organelles. In adipocytes, GSVs contain specific cargoes including GLUT4, IRAP, LRP1, and sortilin. They are formed by membrane budding, involving sortilin and probably CHC22 clathrin in humans, but the donor compartment from which these vesicles form remains uncertain. In unstimulated cells, GSVs are trapped by TUG proteins near the endoplasmic reticulum - Golgi intermediate compartment (ERGIC). Insulin signals through two main pathways to mobilize these vesicles. Signaling by the Akt kinase modulates Rab GTPases to target the GSVs to the cell surface. Signaling by the Rho-family GTPase TC10α stimulates Usp25m-mediated TUG cleavage to liberate the vesicles from the Golgi. Cleavage produces a ubiquitin-like protein modifier, TUGUL, that links the GSVs to KIF5B kinesin motors to promote their movement to the cell surface. In obesity, attenuation of these processes results in insulin resistance and contributes to type 2 diabetes and may simultaneously contribute to hypertension and dyslipidemia in the metabolic syndrome.
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Affiliation(s)
- Don T. Li
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT,Department of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT
| | - Estifanos N. Habtemichael
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Omar Julca
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Chloe I. Sales
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Xavier O. Westergaard
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Stephen G. DeVries
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Diana Ruiz
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Bhavesh Sayal
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT
| | - Jonathan S. Bogan
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, Yale University, New Haven, CT,Department of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT,To whom all correspondence should be addressed: Jonathan S. Bogan, Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, P.O. Box 208020, New Haven, CT 06520-8020; Tel: 203-785-6319; Fax: 203-785-6462;
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Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019; 16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Cellular behavior is controlled by the interplay of diverse biomolecules. Most
experimental methods, however, can monitor only a single molecule class or
reaction type at a time. We developed an in vitro Nuclear Magnetic Resonance
spectroscopy (NMR) approach, which permitted dynamic quantification of an entire
“heterotypic” network – simultaneously monitoring three
distinct molecule classes (metabolites, proteins, RNA) and all elementary
reaction types (bimolecular interactions, catalysis, unimolecular changes).
Focusing on an 8-reaction co-transcriptional RNA folding network, in a single
sample we recorded over 35 time-points with over 170 observables each, and
accurately determined 5 core reaction constants in multiplex. This
reconstruction revealed unexpected cross-talk between the different reactions.
We further observed dynamic phase-separation in a system of five distinct RNA
binding domains in the course of the RNA transcription reaction. Our Systems NMR
approach provides a deeper understanding of biological network dynamics by
combining the dynamic resolution of biochemical assays and the multiplexing
ability of “omics”.
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Affiliation(s)
- Yaroslav Nikolaev
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
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41
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Buschiazzo A, Trajtenberg F. Two-Component Sensing and Regulation: How Do Histidine Kinases Talk with Response Regulators at the Molecular Level? Annu Rev Microbiol 2019; 73:507-528. [PMID: 31226026 DOI: 10.1146/annurev-micro-091018-054627] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Perceiving environmental and internal information and reacting in adaptive ways are essential attributes of living organisms. Two-component systems are relevant protein machineries from prokaryotes and lower eukaryotes that enable cells to sense and process signals. Implicating sensory histidine kinases and response regulator proteins, both components take advantage of protein phosphorylation and flexibility to switch conformations in a signal-dependent way. Dozens of two-component systems act simultaneously in any given cell, challenging our understanding about the means that ensure proper connectivity. This review dives into the molecular level, attempting to summarize an emerging picture of how histidine kinases and cognate response regulators achieve required efficiency, specificity, and directionality of signaling pathways, properties that rely on protein:protein interactions. α helices that carry information through long distances, the fine combination of loose and specific kinase/regulator interactions, and malleable reaction centers built when the two components meet emerge as relevant universal principles.
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Affiliation(s)
- Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; , .,Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris 75015, France
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; ,
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42
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Bonnaffoux A, Herbach U, Richard A, Guillemin A, Gonin-Giraud S, Gros PA, Gandrillon O. WASABI: a dynamic iterative framework for gene regulatory network inference. BMC Bioinformatics 2019; 20:220. [PMID: 31046682 PMCID: PMC6498543 DOI: 10.1186/s12859-019-2798-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used for gene regulatory network inference, with both successes and limitations. RESULTS In the present work we propose an iterative algorithm called WASABI, dedicated to inferring a causal dynamical network from time-stamped single-cell data, which tackles some of the limitations associated with current approaches. We first introduce the concept of waves, which posits that the information provided by an external stimulus will affect genes one-by-one through a cascade, like waves spreading through a network. This concept allows us to infer the network one gene at a time, after genes have been ordered regarding their time of regulation. We then demonstrate the ability of WASABI to correctly infer small networks, which have been simulated in silico using a mechanistic model consisting of coupled piecewise-deterministic Markov processes for the proper description of gene expression at the single-cell level. We finally apply WASABI on in vitro generated data on an avian model of erythroid differentiation. The structure of the resulting gene regulatory network sheds a new light on the molecular mechanisms controlling this process. In particular, we find no evidence for hub genes and a much more distributed network structure than expected. Interestingly, we find that a majority of genes are under the direct control of the differentiation-inducing stimulus. CONCLUSIONS Together, these results demonstrate WASABI versatility and ability to tackle some general gene regulatory networks inference issues. It is our hope that WASABI will prove useful in helping biologists to fully exploit the power of time-stamped single-cell data.
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Affiliation(s)
- Arnaud Bonnaffoux
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, Lyon, France
- Cosmotech, Lyon, France
| | - Ulysse Herbach
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, Lyon, France
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5208, Institut Camille Jordan, Villeurbanne, France
| | - Angélique Richard
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
| | - Anissa Guillemin
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
| | - Sandrine Gonin-Giraud
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
| | | | - Olivier Gandrillon
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, Lyon, France
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43
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Ye Y, Kang X, Bailey J, Li C, Hong T. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol 2019; 15:e1006855. [PMID: 30845219 PMCID: PMC6424469 DOI: 10.1371/journal.pcbi.1006855] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/19/2019] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
Multistep cell fate transitions with stepwise changes of transcriptional profiles are common to many developmental, regenerative and pathological processes. The multiple intermediate cell lineage states can serve as differentiation checkpoints or branching points for channeling cells to more than one lineages. However, mechanisms underlying these transitions remain elusive. Here, we explored gene regulatory circuits that can generate multiple intermediate cellular states with stepwise modulations of transcription factors. With unbiased searching in the network topology space, we found a motif family containing a large set of networks can give rise to four attractors with the stepwise regulations of transcription factors, which limit the reversibility of three consecutive steps of the lineage transition. We found that there is an enrichment of these motifs in a transcriptional network controlling the early T cell development, and a mathematical model based on this network recapitulates multistep transitions in the early T cell lineage commitment. By calculating the energy landscape and minimum action paths for the T cell model, we quantified the stochastic dynamics of the critical factors in response to the differentiation signal with fluctuations. These results are in good agreement with experimental observations and they suggest the stable characteristics of the intermediate states in the T cell differentiation. These dynamical features may help to direct the cells to correct lineages during development. Our findings provide general design principles for multistep cell linage transitions and new insights into the early T cell development. The network motifs containing a large family of topologies can be useful for analyzing diverse biological systems with multistep transitions. The functions of cells are dynamically controlled in many biological processes including development, regeneration and disease progression. Cell fate transition, or the switch of cellular functions, often involves multiple steps. The intermediate stages of the transition provide the biological systems with the opportunities to regulate the transitions in a precise manner. These transitions are controlled by key regulatory genes of which the expression shows stepwise patterns, but how the interactions of these genes can determine the multistep processes was unclear. Here, we present a comprehensive analysis on the design principles of gene circuits that govern multistep cell fate transition. We found a large network family with common structural features that can generate systems with the ability to control three consecutive steps of the transition. We found that this type of networks is enriched in a gene circuit controlling the development of T lymphocyte, a crucial type of immune cells. We performed mathematical modeling using this gene circuit and we recapitulated the stepwise and irreversible loss of stem cell properties of the developing T lymphocytes. Our findings can be useful to analyze a wide range of gene regulatory networks controlling multistep cell fate transitions.
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Affiliation(s)
- Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Xin Kang
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Jordan Bailey
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America.,National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, United States of America
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44
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Qian J, Gelens L, Bollen M. Coordination of Timers and Sensors in Cell Signaling. Bioessays 2019; 41:e1800217. [PMID: 30730051 DOI: 10.1002/bies.201800217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/12/2018] [Indexed: 02/06/2023]
Abstract
Timers and sensors are common devices that make our daily life safer, more convenient, and more efficient. In a cellular context, they arguably play an even more crucial role as they ensure the survival of cells in the presence of various extrinsic and intrinsic stresses. Biological timers and sensors generate distinct signaling profiles, enabling them to produce different types of cellular responses. Recent data suggest that they can work together to guarantee correct timing and responsiveness. By exploring examples of cellular stress signaling from mitosis, DNA damage, and hypoxia, the authors discuss the common architecture of timer-sensor integration, and how its added features contribute to the generation of desired signaling profiles when dealing with stresses of variable duration and strength. The authors propose timer-sensor integration as a widespread mechanism with profound biological implications and therapeutic potential.
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Affiliation(s)
- Junbin Qian
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium.,VIB Center for Cancer Biology, 3000, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
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45
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Gao XJ, Chong LS, Kim MS, Elowitz MB. Programmable protein circuits in living cells. Science 2018; 361:1252-1258. [PMID: 30237357 DOI: 10.1126/science.aat5062] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
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Affiliation(s)
- Xiaojing J Gao
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucy S Chong
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Kim
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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46
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Saurin AT. Kinase and Phosphatase Cross-Talk at the Kinetochore. Front Cell Dev Biol 2018; 6:62. [PMID: 29971233 PMCID: PMC6018199 DOI: 10.3389/fcell.2018.00062] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/31/2018] [Indexed: 01/26/2023] Open
Abstract
Multiple kinases and phosphatases act on the kinetochore to control chromosome segregation: Aurora B, Mps1, Bub1, Plk1, Cdk1, PP1, and PP2A-B56, have all been shown to regulate both kinetochore-microtubule attachments and the spindle assembly checkpoint. Given that so many kinases and phosphatases converge onto two key mitotic processes, it is perhaps not surprising to learn that they are, quite literally, entangled in cross-talk. Inhibition of any one of these enzymes produces secondary effects on all the others, which results in a complicated picture that is very difficult to interpret. This review aims to clarify this picture by first collating the direct effects of each enzyme into one overarching schematic of regulation at the Knl1/Mis12/Ndc80 (KMN) network (a major signaling hub at the outer kinetochore). This schematic will then be used to discuss the implications of the cross-talk that connects these enzymes; both in terms of why it may be needed to produce the right type of kinetochore signals and why it nevertheless complicates our interpretations about which enzymes control what processes. Finally, some general experimental approaches will be discussed that could help to characterize kinetochore signaling by dissociating the direct from indirect effect of kinase or phosphatase inhibition in vivo. Together, this review should provide a framework to help understand how a network of kinases and phosphatases cooperate to regulate two key mitotic processes.
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Affiliation(s)
- Adrian T. Saurin
- Jacqui Wood Cancer Centre, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
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Habtemichael EN, Li DT, Alcázar-Román A, Westergaard XO, Li M, Petersen MC, Li H, DeVries SG, Li E, Julca-Zevallos O, Wolenski JS, Bogan JS. Usp25m protease regulates ubiquitin-like processing of TUG proteins to control GLUT4 glucose transporter translocation in adipocytes. J Biol Chem 2018; 293:10466-10486. [PMID: 29773651 DOI: 10.1074/jbc.ra118.003021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/09/2018] [Indexed: 12/14/2022] Open
Abstract
Insulin stimulates the exocytic translocation of specialized vesicles in adipocytes, which inserts GLUT4 glucose transporters into the plasma membrane to enhance glucose uptake. Previous results support a model in which TUG (Tether containing a UBX domain for GLUT4) proteins trap these GLUT4 storage vesicles at the Golgi matrix and in which insulin triggers endoproteolytic cleavage of TUG to translocate GLUT4. Here, we identify the muscle splice form of Usp25 (Usp25m) as a protease required for insulin-stimulated TUG cleavage and GLUT4 translocation in adipocytes. Usp25m is expressed in adipocytes, binds TUG and GLUT4, dissociates from TUG-bound vesicles after insulin addition, and colocalizes with TUG and insulin-responsive cargoes in unstimulated cells. Previous results show that TUG proteolysis generates the ubiquitin-like protein, TUGUL (for TUGubiquitin-like). We now show that TUGUL modifies the kinesin motor protein, KIF5B, and that TUG proteolysis is required to load GLUT4 onto these motors. Insulin stimulates TUG proteolytic processing independently of phosphatidylinositol 3-kinase. In nonadipocytes, TUG cleavage can be reconstituted by transfection of Usp25m, but not the related Usp25a isoform, together with other proteins present on GLUT4 vesicles. In rodents with diet-induced insulin resistance, TUG proteolysis and Usp25m protein abundance are reduced in adipose tissue. These effects occur soon after dietary manipulation, prior to the attenuation of insulin signaling to Akt. Together with previous data, these results support a model whereby insulin acts through Usp25m to mediate TUG cleavage, which liberates GLUT4 storage vesicles from the Golgi matrix and activates their microtubule-based movement to the plasma membrane. This TUG proteolytic pathway for insulin action is independent of Akt and is impaired by nutritional excess.
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Affiliation(s)
| | - Don T Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Departments of Cell Biology and
| | - Abel Alcázar-Román
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Xavier O Westergaard
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Muyi Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Max C Petersen
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,Cellular and Molecular Physiology, Yale University School of Medicine
| | - Hanbing Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Institute of Pharmacology, Department of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Stephen G DeVries
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Eric Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Omar Julca-Zevallos
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Departments of Cell Biology and
| | - Joseph S Wolenski
- the Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, and
| | - Jonathan S Bogan
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and .,the Departments of Cell Biology and
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48
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Li P, Markson JS, Wang S, Chen S, Vachharajani V, Elowitz MB. Morphogen gradient reconstitution reveals Hedgehog pathway design principles. Science 2018; 360:543-548. [PMID: 29622726 DOI: 10.1126/science.aao0645] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/22/2018] [Indexed: 12/30/2022]
Abstract
In developing tissues, cells estimate their spatial position by sensing graded concentrations of diffusible signaling proteins called morphogens. Morphogen-sensing pathways exhibit diverse molecular architectures, whose roles in controlling patterning dynamics and precision have been unclear. In this work, combining cell-based in vitro gradient reconstitution, genetic rewiring, and mathematical modeling, we systematically analyzed the distinctive architectural features of the Sonic Hedgehog pathway. We found that the combination of double-negative regulatory logic and negative feedback through the PTCH receptor accelerates gradient formation and improves robustness to variation in the morphogen production rate compared with alternative designs. The ability to isolate morphogen patterning from concurrent developmental processes and to compare the patterning behaviors of alternative, rewired pathway architectures offers a powerful way to understand and engineer multicellular patterning.
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Affiliation(s)
- Pulin Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joseph S Markson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sheng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Siheng Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vipul Vachharajani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. .,Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
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49
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Angeles-Albores D, Puckett Robinson C, Williams BA, Wold BJ, Sternberg PW. Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements. Proc Natl Acad Sci U S A 2018; 115:E2930-E2939. [PMID: 29531064 PMCID: PMC5879656 DOI: 10.1073/pnas.1712387115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1-dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.
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Affiliation(s)
- David Angeles-Albores
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
| | - Carmie Puckett Robinson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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50
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Roybal KT, Lim WA. Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. Annu Rev Immunol 2018; 35:229-253. [PMID: 28446063 DOI: 10.1146/annurev-immunol-051116-052302] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The ability of immune cells to survey tissues and sense pathologic insults and deviations makes them a unique platform for interfacing with the body and disease. With the rapid advancement of synthetic biology, we can now engineer and equip immune cells with new sensors and controllable therapeutic response programs to sense and treat diseases that our natural immune system cannot normally handle. Here we review the current state of engineered immune cell therapeutics and their unique capabilities compared to small molecules and biologics. We then discuss how engineered immune cells are being designed to combat cancer, focusing on how new synthetic biology tools are providing potential ways to overcome the major roadblocks for treatment. Finally, we give a long-term vision for the use of synthetic biology to engineer immune cells as a general sensor-response platform to precisely detect disease, to remodel disease microenvironments, and to treat a potentially wide range of challenging diseases.
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Affiliation(s)
- Kole T Roybal
- Parker Institute for Cancer Immunotherapy, Department of Microbiology and Immunology, University of California, San Francisco, California 94143;
| | - Wendell A Lim
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
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