1
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Metwally H, Elbrashy MM, Ozawa T, Okuyama K, White JT, Tulyeu J, Søndergaard JN, Wing JB, Muratsu A, Matsumoto H, Ikawa M, Kishi H, Taniuchi I, Kishimoto T. Threonine phosphorylation of STAT1 restricts interferon signaling and promotes innate inflammatory responses. Proc Natl Acad Sci U S A 2024; 121:e2402226121. [PMID: 38621137 PMCID: PMC11046697 DOI: 10.1073/pnas.2402226121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/15/2024] [Indexed: 04/17/2024] Open
Abstract
Since its discovery over three decades ago, signal transducer and activator of transcription 1 (STAT1) has been extensively studied as a central mediator for interferons (IFNs) signaling and antiviral defense. Here, using genetic and biochemical assays, we unveil Thr748 as a conserved IFN-independent phosphorylation switch in Stat1, which restricts IFN signaling and promotes innate inflammatory responses following the recognition of the bacterial-derived toxin lipopolysaccharide (LPS). Genetically engineered mice expressing phospho-deficient threonine748-to-alanine (T748A) mutant Stat1 are resistant to LPS-induced lethality. Of note, T748A mice exhibited undisturbed IFN signaling, as well as total expression of Stat1. Further, the T748A point mutation of Stat1 recapitulates the safeguard effect of the genetic ablation of Stat1 following LPS-induced lethality, indicating that the Thr748 phosphorylation contributes inflammatory functionalities of Stat1. Mechanistically, LPS-induced Toll-like receptor 4 endocytosis activates a cell-intrinsic IκB kinase-mediated Thr748 phosphorylation of Stat1, which promotes macrophage inflammatory response while restricting the IFN and anti-inflammatory responses. Depletion of macrophages restores the sensitivity of the T748A mice to LPS-induced lethality. Together, our study indicates a phosphorylation-dependent modular functionality of Stat1 in innate immune responses: IFN phospho-tyrosine dependent and inflammatory phospho-threonine dependent. Better understanding of the Thr748 phosphorylation of Stat1 may uncover advanced pharmacologically targetable molecules and offer better treatment modalities for sepsis, a disease that claims millions of lives annually.
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Affiliation(s)
- Hozaifa Metwally
- Laboratory of Immune Regulation, The World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka565-0871, Japan
| | - Maha M. Elbrashy
- Laboratory of Immune Regulation, The World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka565-0871, Japan
- Biochemistry Department, Biotechnology Research Institute, National Research Center, GizaP.O. 12622, Egypt
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama930-0194, Japan
| | - Kazuki Okuyama
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
| | - Jason T. White
- Laboratory of Experimental Immunology, The World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka565-0871, Japan
| | - Janyerkye Tulyeu
- Human Immunology Team, Center for Infectious Disease Education and Research, Osaka University, Suita565-0871, Japan
| | - Jonas Nørskov Søndergaard
- Human Immunology Team, Center for Infectious Disease Education and Research, Osaka University, Suita565-0871, Japan
| | - James Badger Wing
- Laboratory of Human Single Cell Immunology, The World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka565-0871, Japan
| | - Arisa Muratsu
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Osaka565-0871, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Osaka565-0871, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka565-0871, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama930-0194, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
| | - Tadamitsu Kishimoto
- Laboratory of Immune Regulation, The World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka565-0871, Japan
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2
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Choi J, Chen W, Liao H, Li X, Shendure J. A molecular proximity sensor based on an engineered, dual-component guide RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.14.553235. [PMID: 37645782 PMCID: PMC10461971 DOI: 10.1101/2023.08.14.553235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
One of the goals of synthetic biology is to enable the design of arbitrary molecular circuits with programmable inputs and outputs. Such circuits bridge the properties of electronic and natural circuits, processing information in a predictable manner within living cells. Genome editing is a potentially powerful component of synthetic molecular circuits, whether for modulating the expression of a target gene or for stably recording information to genomic DNA. However, programming molecular events such as protein-protein interactions or induced proximity as triggers for genome editing remains challenging. Here we demonstrate a strategy termed "P3 editing", which links protein-protein proximity to the formation of a functional CRISPRCas9 dual-component guide RNA. By engineering the crRNA:tracrRNA interaction, we demonstrate that various known protein-protein interactions, as well as the chemically-induced dimerization of protein domains, can be used to activate prime editing or base editing in human cells. Additionally, we explore how P3 editing can incorporate outputs from ADAR-based RNA sensors, potentially allowing specific RNAs to induce specific genome edits within a larger circuit. Our strategy enhances the controllability of CRISPR-based genome editing, facilitating its use in synthetic molecular circuits deployed in living cells.
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Affiliation(s)
- Junhong Choi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Hanna Liao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Seattle Hub for Synthetic Biology, Seattle, WA 98195, USA
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3
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Kortemme T. De novo protein design-From new structures to programmable functions. Cell 2024; 187:526-544. [PMID: 38306980 PMCID: PMC10990048 DOI: 10.1016/j.cell.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Methods from artificial intelligence (AI) trained on large datasets of sequences and structures can now "write" proteins with new shapes and molecular functions de novo, without starting from proteins found in nature. In this Perspective, I will discuss the state of the field of de novo protein design at the juncture of physics-based modeling approaches and AI. New protein folds and higher-order assemblies can be designed with considerable experimental success rates, and difficult problems requiring tunable control over protein conformations and precise shape complementarity for molecular recognition are coming into reach. Emerging approaches incorporate engineering principles-tunability, controllability, and modularity-into the design process from the beginning. Exciting frontiers lie in deconstructing cellular functions with de novo proteins and, conversely, constructing synthetic cellular signaling from the ground up. As methods improve, many more challenges are unsolved.
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Affiliation(s)
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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4
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Abstract
Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.
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5
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Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [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: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
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Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
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6
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Scheele RA, Lindenburg LH, Petek M, Schober M, Dalby KN, Hollfelder F. Droplet-based screening of phosphate transfer catalysis reveals how epistasis shapes MAP kinase interactions with substrates. Nat Commun 2022; 13:844. [PMID: 35149678 PMCID: PMC8837617 DOI: 10.1038/s41467-022-28396-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
The combination of ultrahigh-throughput screening and sequencing informs on function and intragenic epistasis within combinatorial protein mutant libraries. Establishing a droplet-based, in vitro compartmentalised approach for robust expression and screening of protein kinase cascades (>107 variants/day) allowed us to dissect the intrinsic molecular features of the MKK-ERK signalling pathway, without interference from endogenous cellular components. In a six-residue combinatorial library of the MKK1 docking domain, we identified 29,563 sequence permutations that allow MKK1 to efficiently phosphorylate and activate its downstream target kinase ERK2. A flexibly placed hydrophobic sequence motif emerges which is defined by higher order epistatic interactions between six residues, suggesting synergy that enables high connectivity in the sequence landscape. Through positive epistasis, MKK1 maintains function during mutagenesis, establishing the importance of co-dependent residues in mammalian protein kinase-substrate interactions, and creating a scenario for the evolution of diverse human signalling networks. Here, the authors use a droplet-based screen for phosphate transfer catalysis, testing variants of the human protein kinase MKK1 for its ability to activate its downstream target ERK2. Data reveal a flexible motif in the MKK1 docking domain that promotes efficient activation of ERK2, and suggest epistasis between the residues within that sequence.
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Affiliation(s)
- Remkes A Scheele
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | | | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.,Faculty of Medicine, University of Maribor, SI-2000, Maribor, Slovenia
| | - Markus Schober
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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7
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Abstract
Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
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8
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Pillay CS, John N. Can thiol-based redox systems be utilized as parts for synthetic biology applications? Redox Rep 2021; 26:147-159. [PMID: 34378494 PMCID: PMC8366655 DOI: 10.1080/13510002.2021.1966183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Synthetic biology has emerged from molecular biology and engineering approaches and aims to develop novel, biologically-inspired systems for industrial and basic research applications ranging from biocomputing to drug production. Surprisingly, redoxin (thioredoxin, glutaredoxin, peroxiredoxin) and other thiol-based redox systems have not been widely utilized in many of these synthetic biology applications. METHODS We reviewed thiol-based redox systems and the development of synthetic biology applications that have used thiol-dependent parts. RESULTS The development of circuits to facilitate cytoplasmic disulfide bonding, biocomputing and the treatment of intestinal bowel disease are amongst the applications that have used thiol-based parts. We propose that genetically encoded redox sensors, thiol-based biomaterials and intracellular hydrogen peroxide generators may also be valuable components for synthetic biology applications. DISCUSSION Thiol-based systems play multiple roles in cellular redox metabolism, antioxidant defense and signaling and could therefore offer a vast and diverse portfolio of components, parts and devices for synthetic biology applications. However, factors limiting the adoption of redoxin systems for synthetic biology applications include the orthogonality of thiol-based components, limitations in the methods to characterize thiol-based systems and an incomplete understanding of the design principles of these systems.
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Affiliation(s)
- Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Nolyn John
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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9
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Herholt A, Sahoo VK, Popovic L, Wehr MC, Rossner MJ. Dissecting intercellular and intracellular signaling networks with barcoded genetic tools. Curr Opin Chem Biol 2021; 66:102091. [PMID: 34644670 DOI: 10.1016/j.cbpa.2021.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022]
Abstract
The power of next-generation sequencing has stimulated the development of many analysis techniques for transcriptomics and genomics. More recently, the concept of 'molecular barcoding' has broadened the spectrum of sequencing-based applications to dissect different aspects of intracellular and intercellular signaling. In these assay formats, barcode reporters replace standard reporter genes. The virtually infinitive number of expressed barcode sequences allows high levels of multiplexing, hence accelerating experimental progress. Furthermore, reporter barcodes are used to quantitatively monitor a variety of biological events in living cells which has already provided much insight into complex cellular signaling and will further increase our knowledge in the future.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Luksa Popovic
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany.
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10
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Abstract
The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
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11
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Ban D, Rice CT, McCoy MA. Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments. MAbs 2021; 13:1978132. [PMID: 34612804 PMCID: PMC8496538 DOI: 10.1080/19420862.2021.1978132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.
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Affiliation(s)
- David Ban
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Cory T Rice
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Mark A McCoy
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
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12
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Garabedian MV, Wang W, Dabdoub JB, Tong M, Caldwell RM, Benman W, Schuster BS, Deiters A, Good MC. Designer membraneless organelles sequester native factors for control of cell behavior. Nat Chem Biol 2021; 17:998-1007. [PMID: 34341589 PMCID: PMC8387445 DOI: 10.1038/s41589-021-00840-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/24/2021] [Indexed: 02/08/2023]
Abstract
Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to ninety percent of a targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division, and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.
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Affiliation(s)
- Mikael V Garabedian
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Wentao Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorge B Dabdoub
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Tong
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Reese M Caldwell
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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13
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English MA, Gayet RV, Collins JJ. Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond. Annu Rev Biochem 2021; 90:221-244. [PMID: 33784178 DOI: 10.1146/annurev-biochem-013118-111914] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's core was the modular assembly of regulators, operators, and structural genes. To illustrate the composability of these elements, Jacob and Monod linked phenotypic diversity to the architectures of regulatory circuits. In this review, we examine how the circuit blueprints imagined by Jacob and Monod laid the foundation for the first synthetic gene networks that launched the field of synthetic biology in 2000. We discuss the influences of the operon model and its broader theoretical framework on the first generation of synthetic biological circuits, which were predominantly transcriptional and posttranscriptional circuits. We also describe how recent advances in molecular biology beyond the operon model-namely, programmable DNA- and RNA-binding molecules as well as models of epigenetic and posttranslational regulation-are expanding the synthetic biology toolkit and enabling the design of more complex biological circuits.
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Affiliation(s)
- Max A English
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Raphaël V Gayet
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Microbiology Graduate Program, MIT, Cambridge, Massachusetts 02139, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Synthetic Biology Center, MIT, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
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14
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De novo design of a reversible phosphorylation-dependent switch for membrane targeting. Nat Commun 2021; 12:1472. [PMID: 33674566 PMCID: PMC7935970 DOI: 10.1038/s41467-021-21622-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells. The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.
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15
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Groseclose TM, Rondon RE, Hersey AN, Milner PT, Kim D, Zhang F, Realff MJ, Wilson CJ. Biomolecular Systems Engineering: Unlocking the Potential of Engineered Allostery via the Lactose Repressor Topology. Annu Rev Biophys 2021; 50:303-321. [PMID: 33606944 DOI: 10.1146/annurev-biophys-090820-101708] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Allosteric function is a critical component of many of the parts used to construct gene networks throughout synthetic biology. In this review, we discuss an emerging field of research and education, biomolecular systems engineering, that expands on the synthetic biology edifice-integrating workflows and strategies from protein engineering, chemical engineering, electrical engineering, and computer science principles. We focus on the role of engineered allosteric communication as it relates to transcriptional gene regulators-i.e., transcription factors and corresponding unit operations. In this review, we (a) explore allosteric communication in the lactose repressor LacI topology, (b) demonstrate how to leverage this understanding of allostery in the LacI system to engineer non-natural BUFFER and NOT logical operations, (c) illustrate how engineering workflows can be used to confer alternate allosteric functions in disparate systems that share the LacI topology, and (d) demonstrate how fundamental unit operations can be directed to form combinational logical operations.
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Affiliation(s)
- Thomas M Groseclose
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Ronald E Rondon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Ashley N Hersey
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Prasaad T Milner
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Dowan Kim
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Fumin Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Matthew J Realff
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Corey J Wilson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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16
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Gödecke N, Riedel J, Herrmann S, Behme S, Rand U, Kubsch T, Cicin-Sain L, Hauser H, Köster M, Wirth D. Synthetic rewiring and boosting type I interferon responses for visualization and counteracting viral infections. Nucleic Acids Res 2020; 48:11799-11811. [PMID: 33137201 PMCID: PMC7672444 DOI: 10.1093/nar/gkaa961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 11/12/2022] Open
Abstract
Mammalian first line of defense against viruses is accomplished by the interferon (IFN) system. Viruses have evolved numerous mechanisms to reduce the IFN action allowing them to invade the host and/or to establish latency. We generated an IFN responsive intracellular hub by integrating the synthetic transactivator tTA into the chromosomal Mx2 locus for IFN-based activation of tTA dependent expression modules. The additional implementation of a synthetic amplifier module with positive feedback even allowed for monitoring and reacting to infections of viruses that can antagonize the IFN system. Low and transient IFN amounts are sufficient to trigger these amplifier cells. This gives rise to higher and sustained—but optionally de-activatable—expression even when the initial stimulus has faded out. Amplification of the IFN response induced by IFN suppressing viruses is sufficient to protect cells from infection. Together, this interfaced sensor/actuator system provides a toolbox for robust sensing and counteracting viral infections.
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Affiliation(s)
- Natascha Gödecke
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Jan Riedel
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Sabrina Herrmann
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Sara Behme
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Ulfert Rand
- Department of Vaccinology and Applied Microbiology, Braunschweig 38124, Germany
| | - Tobias Kubsch
- Department of Vaccinology and Applied Microbiology, Braunschweig 38124, Germany
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Braunschweig 38124, Germany.,Centre for Individualised Infection Medicine (CiiM), a joint venture of Helmholtz Centre for Infection Research and Hannover Medical School, Hannover 30625, Germany
| | - Hansjörg Hauser
- Staff Unit Scientific Strategy, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Mario Köster
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Dagmar Wirth
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany.,Institute of Experimental Hematology, Medical University Hannover, Hannover 30625, Germany
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17
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Mena EL, Jevtić P, Greber BJ, Gee CL, Lew BG, Akopian D, Nogales E, Kuriyan J, Rape M. Structural basis for dimerization quality control. Nature 2020; 586:452-456. [PMID: 32814905 PMCID: PMC8024055 DOI: 10.1038/s41586-020-2636-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1. Dimerization quality control (DQC) further improves proteostasis by eliminating complexes of aberrant composition 2, yet how it detects incorrect subunits is still unknown. Here, we provide structural insight into target selection by SCFFBXL17, a DQC E3 ligase that ubiquitylates and helps degrade inactive heterodimers of BTB proteins, while sparing functional homodimers. We find that SCFFBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Complex dissociation allows SCFFBXL17 to wrap around a single BTB domain for robust ubiquitylation. SCFFBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.
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Affiliation(s)
- Elijah L Mena
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA, USA.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Brandon G Lew
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA, USA.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA, USA.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemistry, University of California at Berkeley, Berkeley, CA, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA, USA.
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18
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Lemmens LM, Ottmann C, Brunsveld L. Conjugated Protein Domains as Engineered Scaffold Proteins. Bioconjug Chem 2020; 31:1596-1603. [PMID: 32374984 PMCID: PMC7303964 DOI: 10.1021/acs.bioconjchem.0c00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/05/2020] [Indexed: 01/12/2023]
Abstract
Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of libraries of engineered multidomain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multidomain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation, and hydrogel formation.
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Affiliation(s)
- Lenne
J. M. Lemmens
- Laboratory of Chemical Biology, Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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19
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Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science 2020; 366:1024-1028. [PMID: 31754004 DOI: 10.1126/science.aax8780] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
Abstract
Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we describe a generalizable computational strategy for designing sensor-actuator proteins by building binding sites de novo into heterodimeric protein-protein interfaces and coupling ligand sensing to modular actuation through split reporters. Using this approach, we designed protein sensors that respond to farnesyl pyrophosphate, a metabolic intermediate in the production of valuable compounds. The sensors are functional in vitro and in cells, and the crystal structure of the engineered binding site closely matches the design model. Our computational design strategy opens broad avenues to link biological outputs to new signals.
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Affiliation(s)
- Anum A Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Yao-Ming Huang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Mandell
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Michael Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ryan Ritterson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jenna Pellegrino
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Cody Krivacic
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Roland A Pache
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kyle A Barlow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Deborah Jeon
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. .,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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20
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An Optogenetic Method to Study Signal Transduction in Intestinal Stem Cell Homeostasis. J Mol Biol 2020; 432:3159-3176. [DOI: 10.1016/j.jmb.2020.03.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
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21
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Lee YT, He L, Zhou Y. Expanding the Chemogenetic Toolbox by Circular Permutation. J Mol Biol 2020; 432:3127-3136. [PMID: 32277990 DOI: 10.1016/j.jmb.2020.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 12/18/2022]
Abstract
To expand the repertoire of chemogenetic tools tailored for molecular and cellular engineering, we describe herein the design of cpRAPID as a circularly permuted rapamycin-inducible dimerization system composed of the canonical FK506-binding protein (FKBP) and circular permutants of FKBP12-rapamycin binding domain (cpFRB). By permuting the topology of the four helices within FRB, we have created cpFRB-FKBP pairs that respond to ligand with varying activation kinetics and dynamics. The cpRAPID system enables chemical-controllable subcellular redistribution of proteins, as well as inducible transcriptional activation when coupled with the CRISPR activation (CRISPRa) technology to induce a GFP reporter and endogenous gene expression. We have further demonstrated the use of cpRAPID to generate chemically switchable split nanobody (designated Chessbody) for ligand-gated antigen recognition in living cells. Collectively, the circular permutation approach offers a powerful means for diversifying the chemogenetics toolbox to benefit the burgeoning synthetic biology field.
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Affiliation(s)
- Yi-Tsang Lee
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX 77807, USA; Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA.
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22
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Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
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23
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Gräwe A, Ranglack J, Weyrich A, Stein V. iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains. Nucleic Acids Res 2020; 48:e24. [PMID: 31925441 PMCID: PMC7039005 DOI: 10.1093/nar/gkz1210] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/02/2023] Open
Abstract
Recent years have witnessed increasing efforts to engineer artificial biological functions through recombination of modular-organized toolboxes of protein scaffolds and parts. A critical, yet frequently neglected aspect concerns the identity of peptide linkers or spacers connecting individual domains which remain poorly understood and challenging to assemble. Addressing these limitations, iFlinkC comprises a highly scalable DNA assembly process that facilitates the combinatorial recombination of functional domains with linkers of varying length and flexibility, thereby overcoming challenges with high GC-content and the repeat nature of linker elements. The capacity of iFLinkC is demonstrated in the construction of synthetic protease switches featuring PDZ-FN3-based affinity clamps and single-chain FKBP12-FRB receptors as allosteric inputs. Library screening experiments demonstrate that linker space is highly plastic as the induction of allosterically regulated protease switches can vary from >150-fold switch-ON to >13-fold switch-OFF solely depending on the identity of the connecting linkers and relative orientation of functional domains. In addition, Pro-rich linkers yield the most potent switches contradicting the conventional use of flexible Gly-Ser linkers. Given the ease and efficiency how functional domains can be readily recombined with any type of linker, iFLinkC is anticipated to be widely applicable to the assembly of any type of fusion protein.
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Affiliation(s)
- Alexander Gräwe
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Jan Ranglack
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Anastasia Weyrich
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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24
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Sjölander JJ, Tarczykowska A, Picazo C, Cossio I, Redwan IN, Gao C, Solano C, Toledano MB, Grøtli M, Molin M, Sunnerhagen P. A Redox-Sensitive Thiol in Wis1 Modulates the Fission Yeast Mitogen-Activated Protein Kinase Response to H 2O 2 and Is the Target of a Small Molecule. Mol Cell Biol 2020; 40:e00346-19. [PMID: 31932483 PMCID: PMC7076255 DOI: 10.1128/mcb.00346-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/23/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022] Open
Abstract
Oxidation of a highly conserved cysteine (Cys) residue located in the kinase activation loop of mitogen-activated protein kinase kinases (MAPKK) inactivates mammalian MKK6. This residue is conserved in the fission yeast Schizosaccharomyces pombe MAPKK Wis1, which belongs to the H2O2-responsive MAPK Sty1 pathway. Here, we show that H2O2 reversibly inactivates Wis1 through this residue (C458) in vitro We found that C458 is oxidized in vivo and that serine replacement of this residue significantly enhances Wis1 activation upon addition of H2O2 The allosteric MAPKK inhibitor INR119, which binds in a pocket next to the activation loop and C458, prevented the inhibition of Wis1 by H2O2in vitro and significantly increased Wis1 activation by low levels of H2O2in vivo We propose that oxidation of C458 inhibits Wis1 and that INR119 cancels out this inhibitory effect by binding close to this residue. Kinase inhibition through the oxidation of a conserved Cys residue in MKK6 (C196) is thus conserved in the S. pombe MAPKK Wis1.
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Affiliation(s)
- Johanna J Sjölander
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Agata Tarczykowska
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Cecilia Picazo
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
- Chalmers University of Technology, Department of Biology and Biological Engineering, Gothenburg, Sweden
| | - Itziar Cossio
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Itedale Namro Redwan
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Chunxia Gao
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Carlos Solano
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Michel B Toledano
- Oxidative Stress and Cancer Laboratory, Integrative Biology and Molecular Genetics Unit, CEA Saclay, Gif-sur-Yvette, France
| | - Morten Grøtli
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Mikael Molin
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
- Chalmers University of Technology, Department of Biology and Biological Engineering, Gothenburg, Sweden
| | - Per Sunnerhagen
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
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25
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Zhan H, Xiao L, Li A, Yao L, Cai Z, Liu Y. Engineering Cellular Signal Sensors based on CRISPR-sgRNA Reconstruction Approaches. Int J Biol Sci 2020; 16:1441-1449. [PMID: 32210731 PMCID: PMC7085220 DOI: 10.7150/ijbs.42299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/24/2020] [Indexed: 11/05/2022] Open
Abstract
The discovery of the CRISPR systems has enriched the application of gene therapy and biotechnology. As a type of robust and simple toolbox, the CRISPR system has greatly promoted the development of cellular signal sensors at the genomic level. Although CRISPR systems have demonstrated that they can be used in eukaryotic and even mammalian cells after extraction from prokaryotic cells, controlling their gene-editing activity remains a challenge. Here we summarize the advantages and disadvantages of building a CRIRPR-based signal sensor through sgRNA reconstruction, as well as possible ways to reprogram the signal network of cells. We also propose how to further improve the design of the current signal sensors based on sgRNA-riboswitch. We believe that the development of these technologies and the construction of platforms can further promote the development of environment detection, disease diagnosis, and gene therapy by means of synthetic biology.
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Affiliation(s)
- Hengji Zhan
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Lulu Xiao
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Aolin Li
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
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26
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Bohnert S, Antelo L, Grünewald C, Yemelin A, Andresen K, Jacob S. Rapid adaptation of signaling networks in the fungal pathogen Magnaporthe oryzae. BMC Genomics 2019; 20:763. [PMID: 31640564 PMCID: PMC6805500 DOI: 10.1186/s12864-019-6113-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background One fundamental question in biology is how the evolution of eukaryotic signaling networks has taken place. “Loss of function” (lof) mutants from components of the high osmolarity glycerol (HOG) signaling pathway in the filamentous fungus Magnaporthe oryzae are viable, but impaired in osmoregulation. Results After long-term cultivation upon high osmolarity, stable individuals with reestablished osmoregulation capacity arise independently from each of the mutants with inactivated HOG pathway. This phenomenon is extremely reproducible and occurs only in osmosensitive mutants related to the HOG pathway – not in other osmosensitive Magnaporthe mutants. The major compatible solute produced by these adapted strains to cope with high osmolarity is glycerol, whereas it is arabitol in the wildtype strain. Genome and transcriptome analysis resulted in candidate genes related to glycerol metabolism, perhaps responsible for an epigenetic induced reestablishment of osmoregulation, since these genes do not show structural variations within the coding or promotor sequences. Conclusion This is the first report of a stable adaptation in eukaryotes by producing different metabolites and opens a door for the scientific community since the HOG pathway is worked on intensively in many eukaryotic model organisms.
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Affiliation(s)
- Stefan Bohnert
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Luis Antelo
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Christiane Grünewald
- Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany
| | - Alexander Yemelin
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Karsten Andresen
- Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany
| | - Stefan Jacob
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany. .,Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany.
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Grebennikov DS, Donets DO, Orlova OG, Argilaguet J, Meyerhans A, Bocharov GA. Mathematical Modeling of the Intracellular Regulation of Immune Processes. Mol Biol 2019. [DOI: 10.1134/s002689331905008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Santorelli M, Lam C, Morsut L. Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr Opin Biotechnol 2019; 59:130-140. [PMID: 31128430 PMCID: PMC6778502 DOI: 10.1016/j.copbio.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 12/28/2022]
Abstract
Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron et al., 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black et al., 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell-cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez et al., 2018; White et al., 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.
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Affiliation(s)
- Marco Santorelli
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Calvin Lam
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, United States.
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29
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Affiliation(s)
- Yiqian Wu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
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30
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Padmanabhan S, Pérez-Castaño R, Elías-Arnanz M. B12-based photoreceptors: from structure and function to applications in optogenetics and synthetic biology. Curr Opin Struct Biol 2019; 57:47-55. [DOI: 10.1016/j.sbi.2019.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
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31
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Nance J, Frøkjær-Jensen C. The Caenorhabditis elegans Transgenic Toolbox. Genetics 2019; 212:959-990. [PMID: 31405997 PMCID: PMC6707460 DOI: 10.1534/genetics.119.301506] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022] Open
Abstract
The power of any genetic model organism is derived, in part, from the ease with which gene expression can be manipulated. The short generation time and invariant developmental lineage have made Caenorhabditis elegans very useful for understanding, e.g., developmental programs, basic cell biology, neurobiology, and aging. Over the last decade, the C. elegans transgenic toolbox has expanded considerably, with the addition of a variety of methods to control expression and modify genes with unprecedented resolution. Here, we provide a comprehensive overview of transgenic methods in C. elegans, with an emphasis on recent advances in transposon-mediated transgenesis, CRISPR/Cas9 gene editing, conditional gene and protein inactivation, and bipartite systems for temporal and spatial control of expression.
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Affiliation(s)
- Jeremy Nance
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York 10016
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), KAUST Environmental Epigenetics Program (KEEP), Thuwal 23955-6900, Saudi Arabia
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32
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Zi Z. Molecular Engineering of the TGF-β Signaling Pathway. J Mol Biol 2019; 431:2644-2654. [PMID: 31121181 DOI: 10.1016/j.jmb.2019.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Transforming growth factor beta (TGF-β) is an important growth factor that plays essential roles in regulating tissue development and homeostasis. Dysfunction of TGF-β signaling is a hallmark of many human diseases. Therefore, targeting TGF-β signaling presents broad therapeutic potential. Since the discovery of the TGF-β ligand, a collection of engineered signaling proteins have been developed to probe and manipulate TGF-β signaling responses. In this review, we highlight recent progress in the engineering of TGF-β signaling for different applications and discuss how molecular engineering approaches can advance our understanding of this important pathway. In addition, we provide a future outlook on the opportunities and challenges in the engineering of the TGF-β signaling pathway from a quantitative perspective.
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Affiliation(s)
- Zhike Zi
- Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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33
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Sambamoorthy G, Sinha H, Raman K. Evolutionary design principles in metabolism. Proc Biol Sci 2019; 286:20190098. [PMID: 30836874 PMCID: PMC6458322 DOI: 10.1098/rspb.2019.0098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 12/28/2022] Open
Abstract
Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein-protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.
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Affiliation(s)
- Gayathri Sambamoorthy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
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Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Ivarsson Y, Jemth P. Affinity and specificity of motif-based protein-protein interactions. Curr Opin Struct Biol 2018; 54:26-33. [PMID: 30368054 DOI: 10.1016/j.sbi.2018.09.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/30/2018] [Indexed: 01/02/2023]
Abstract
It is becoming increasingly clear that eukaryotic cell physiology is largely controlled by protein-protein interactions involving disordered protein regions, which usually interact with globular domains in a coupled binding and folding reaction. Several protein recognition domains are part of large families where members can interact with similar peptide ligands. Because of this, much research has been devoted to understanding how specificity can be achieved. A combination of interface complementarity, interactions outside of the core binding site, avidity from multidomain architecture and spatial and temporal regulation of expression resolves the conundrum. Here, we review recent advances in molecular aspects of affinity and specificity in such protein-protein interactions.
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Affiliation(s)
- Ylva Ivarsson
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
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36
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Stevers LM, de Vink PJ, Ottmann C, Huskens J, Brunsveld L. A Thermodynamic Model for Multivalency in 14-3-3 Protein-Protein Interactions. J Am Chem Soc 2018; 140:14498-14510. [PMID: 30296824 PMCID: PMC6213025 DOI: 10.1021/jacs.8b09618] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are at the core of molecular control over cellular function. Multivalency in PPI formation, such as via proteins with multiple binding sites and different valencies, requires fundamental understanding to address correlated challenges in pathologies and drug development. Thermodynamic binding models are needed to provide frameworks for describing multivalent PPIs. We established a model based on ditopic host-guest systems featuring the effective molarity, a hallmark property of multivalency, as a prime parameter governing the intramolecular binding in divalent interactions. By way of illustration, we study the interaction of the bivalent 14-3-3 protein scaffold with both the nonavalent CFTR and the hexavalent LRRK2 proteins, determining the underlying thermodynamics and providing insights into the role of individual sites in the context of the multivalent platform. Fitting of binding data reveals enthalpy-entropy correlation in both systems. Simulations of speciations for the entire phosphorylated protein domains reveal that the CFTR protein preferably binds to 14-3-3 by combinations including the strongest binding site pS768, but that other binding sites take over when this site is eliminated, leading to only a minor decrease in total affinity for 14-3-3. For LRRK2, two binding sites dominate the complex formation with 14-3-3, but the distantly located pS1444 site also plays a role in complex formation. Thermodynamic modeling of these multivalent PPIs allowed analyzing and predicting the effects of individual sites regarding their modulation via, for example, (de)phosphorylation or small-molecule targeting. The results specifically bring forward the potential of PPI stabilization, as an entry for drug discovery for multivalent PPIs.
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Affiliation(s)
- Loes M Stevers
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Jurriaan Huskens
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology , University of Twente , P.O. Box 217, Enschede 7500 AE , The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
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37
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Aper SJA, den Hamer A, Wouters SFA, Lemmens LJM, Ottmann C, Brunsveld L, Merkx M. Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks. ACS Synth Biol 2018; 7:2216-2225. [PMID: 30125482 PMCID: PMC6154215 DOI: 10.1021/acssynbio.8b00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14-3-3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14-3-3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14-3-3 binding site. The protease-activatable 14-3-3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14-3-3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14-3-3-templated activation of caspase-9 with a caspase-9-activatable 14-3-3 scaffold, the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14-3-3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways.
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Affiliation(s)
- Stijn J. A. Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F. A. Wouters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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38
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Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways. Proc Natl Acad Sci U S A 2018; 115:7051-7056. [PMID: 29915030 DOI: 10.1073/pnas.1718489115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane receptors regulate numerous intracellular functions. However, the molecular underpinnings remain poorly understood because most receptors initiate multiple signaling pathways through distinct interaction interfaces that are structurally uncharacterized. We present an integrated computational and experimental approach to model and rationally engineer membrane receptor-intracellular protein systems signaling with novel pathway selectivity. We targeted the dopamine D2 receptor (D2), a G-protein-coupled receptor (GPCR), which primarily signals through Gi, but triggers also the Gq and beta-arrestin pathways. Using this approach, we designed orthogonal D2-Gi complexes, which coupled with high specificity and triggered exclusively the Gi-dependent signaling pathway. We also engineered an orthogonal chimeric D2-Gs/i complex that rewired D2 signaling from a Gi-mediated inhibitory into a Gs-dependent activating pathway. Reinterpreting the evolutionary history of GPCRs in light of the designed proteins, we uncovered an unforeseen hierarchical code of GPCR-G-protein coupling selectivity determinants. The results demonstrate that membrane receptor-cytosolic protein systems can be rationally engineered to regulate mammalian cellular functions. The method should prove useful for creating orthogonal molecular switches that redirect signals at the cell surface for cell-engineering applications.
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Abstract
Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions. However, to deploy such bacteria in vivo, researchers must identify appropriate gut-adapted strains and consider performance metrics such as sensor detection thresholds, circuit computation speed, growth rate effects, and the evolutionary stability of engineered genetic systems. Other recent reviews have focused on engineering bacteria to target cancer or genetically modifying the endogenous gut microbiota in situ. Here, we develop a standard approach for engineering "smart probiotics," which both diagnose and treat disease, as well as "diagnostic gut bacteria" and "drug factory probiotics," which perform only the former and latter function, respectively. We focus on the use of cutting-edge synthetic biology tools, gut-specific design considerations, and current and future engineering challenges.
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40
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Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
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Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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41
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Giese W, Milicic G, Schröder A, Klipp E. Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction. PLoS Comput Biol 2018; 14:e1006075. [PMID: 29630597 PMCID: PMC5908195 DOI: 10.1371/journal.pcbi.1006075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/19/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023] Open
Abstract
The spatial architecture of signaling pathways and the interaction with cell size and morphology are complex, but little understood. With the advances of single cell imaging and single cell biology, it becomes crucial to understand intracellular processes in time and space. Activation of cell surface receptors often triggers a signaling cascade including the activation of membrane-attached and cytosolic signaling components, which eventually transmit the signal to the cell nucleus. Signaling proteins can form steep gradients in the cytosol, which cause strong cell size dependence. We show that the kinetics at the membrane-cytosolic interface and the ratio of cell membrane area to the enclosed cytosolic volume change the behavior of signaling cascades significantly. We suggest an estimate of average concentration for arbitrary cell shapes depending on the cell volume and cell surface area. The normalized variance, known from image analysis, is suggested as an alternative measure to quantify the deviation from the average concentration. A mathematical analysis of signal transduction in time and space is presented, providing analytical solutions for different spatial arrangements of linear signaling cascades. Quantification of signaling time scales reveals that signal propagation is faster at the membrane than at the nucleus, while this time difference decreases with the number of signaling components in the cytosol. Our investigations are complemented by numerical simulations of non-linear cascades with feedback and asymmetric cell shapes. We conclude that intracellular signal propagation is highly dependent on cell geometry and, thereby, conveys information on cell size and shape to the nucleus.
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Affiliation(s)
- Wolfgang Giese
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gregor Milicic
- Department of Mathematics, University of Salzburg, Salzburg, Austria
| | - Andreas Schröder
- Department of Mathematics, University of Salzburg, Salzburg, Austria
| | - Edda Klipp
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
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42
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Olsman N, Goentoro L. There's (still) plenty of room at the bottom. Curr Opin Biotechnol 2018; 54:72-79. [PMID: 29501949 DOI: 10.1016/j.copbio.2018.01.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/08/2018] [Accepted: 01/28/2018] [Indexed: 01/15/2023]
Abstract
Motifs, circuits, and networks are core conceptual elements in modern systems and synthetic biology. While there are still undoubtedly more fascinating computations to discover at network level, there are also rich computations that we are only beginning to uncover within the diverse molecules that constitute the networks. Here we explore some work, both new and old, that showcases the incredible computational capacity of seemingly simple molecular mechanisms. A more sophisticated understanding of computations at the molecular level will inspire the development of a more nuanced toolbox for future biological engineering.
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Affiliation(s)
- Noah Olsman
- Department of Computing and Mathematical Sciences, California Institute of Technology, United States.
| | - Lea Goentoro
- Division of Biology and Biological Engineering, California Institute of Technology, United States.
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43
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Kalaivani R, Reema R, Srinivasan N. Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PLoS Comput Biol 2018; 14:e1005975. [PMID: 29438395 PMCID: PMC5826538 DOI: 10.1371/journal.pcbi.1005975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/26/2018] [Accepted: 01/13/2018] [Indexed: 11/25/2022] Open
Abstract
The conserved function of protein phosphorylation, catalysed by members of protein kinase superfamily, is regulated in different ways in different kinase families. Further, differences in activating triggers, cellular localisation, domain architecture and substrate specificity between kinase families are also well known. While the transfer of γ-phosphate from ATP to the hydroxyl group of Ser/Thr/Tyr is mediated by a conserved Asp, the characteristic functional and regulatory sites are specialized at the level of families or sub-families. Such family-specific sites of functional specialization are unknown for most families of kinases. In this work, we systematically identify the family-specific residue features by comparing the extent of conservation of physicochemical properties, Shannon entropy and statistical probability of residue distributions between families of kinases. An integrated discriminatory score, which combines these three features, is developed to demarcate the functionally specialized sites in a kinase family from other sites. We achieved an area under ROC curve of 0.992 for the discrimination of kinase families. Our approach was extensively tested on well-studied families CDK and MAPK, wherein specific protein interaction sites and substrate recognition sites were successfully detected (p-value < 0.05). We also find that the known family-specific oncogenic driver mutation sites were scored high by our method. The method was applied to all known kinases encompassing 107 families from diverse eukaryotic organisms leading to a comprehensive list of family-specific functional sites. Apart from other uses, our method facilitates identification of specific protein interaction sites and drug target sites in a kinase family.
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Affiliation(s)
- Raju Kalaivani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Raju Reema
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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44
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Akbari E, Mollica MY, Lucas CR, Bushman SM, Patton RA, Shahhosseini M, Song JW, Castro CE. Engineering Cell Surface Function with DNA Origami. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:10.1002/adma.201703632. [PMID: 29027713 PMCID: PMC5739518 DOI: 10.1002/adma.201703632] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/08/2017] [Indexed: 05/23/2023]
Abstract
A specific and reversible method is reported to engineer cell-membrane function by embedding DNA-origami nanodevices onto the cell surface. Robust membrane functionalization across epithelial, mesenchymal, and nonadherent immune cells is achieved with DNA nanoplatforms that enable functions including the construction of higher-order DNA assemblies at the cell surface and programed cell-cell adhesion between homotypic and heterotypic cells via sequence-specific DNA hybridization. It is anticipated that integration of DNA-origami nanodevices can transform the cell membrane into an engineered material that can mimic, manipulate, and measure biophysical and biochemical function within the plasma membrane of living cells.
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Affiliation(s)
- Ehsan Akbari
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Molly Y. Mollica
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Christopher R. Lucas
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Sarah M. Bushman
- Department of Biomedical Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Randy A. Patton
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Melika Shahhosseini
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Jonathan W. Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, The United States of America
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, The United States of America
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Johnson MB, March AR, Morsut L. Engineering multicellular systems: using synthetic biology to control tissue self-organization. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017; 4:163-173. [PMID: 29308442 DOI: 10.1016/j.cobme.2017.10.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marion B Johnson
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine University of Southern California Keck School of Medicine 1425 San Pablo Avenue, BCC-507, Los Angeles, 90033, USA
| | - Alexander R March
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine University of Southern California Keck School of Medicine 1425 San Pablo Avenue, BCC-507, Los Angeles, 90033, USA
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine University of Southern California Keck School of Medicine 1425 San Pablo Avenue, BCC-507, Los Angeles, 90033, USA
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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48
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Ferreira LMR, Tang Q. Generating Antigen-Specific Regulatory T Cells in the Fast Lane. Am J Transplant 2017; 17:851-853. [PMID: 28102024 DOI: 10.1111/ajt.14202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 12/23/2016] [Accepted: 01/08/2017] [Indexed: 01/25/2023]
Affiliation(s)
- L M R Ferreira
- Department of Surgery, University of California, San Francisco, San Francisco, CA.,UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Q Tang
- Department of Surgery, University of California, San Francisco, San Francisco, CA.,UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA
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Abstract
Animal cells use a conserved repertoire of intercellular signaling pathways to communicate with one another. These pathways are well-studied from a molecular point of view. However, we often lack an "operational" understanding that would allow us to use these pathways to rationally control cellular behaviors. This requires knowing what dynamic input features each pathway perceives and how it processes those inputs to control downstream processes. To address these questions, researchers have begun to reconstitute signaling pathways in living cells, analyzing their dynamic responses to stimuli, and developing new functional representations of their behavior. Here we review important insights obtained through these new approaches, and discuss challenges and opportunities in understanding signaling pathways from an operational point of view.
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Affiliation(s)
- Yaron E Antebi
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nagarajan Nandagopal
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, USA
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50
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Powell AB, Williams K, Cruz CRY. Gene-modified, cell-based therapies—an overview. Cytotherapy 2016; 18:1351-1359. [DOI: 10.1016/j.jcyt.2016.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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