1
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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2
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Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024; 436:168341. [PMID: 37924861 DOI: 10.1016/j.jmb.2023.168341] [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: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular 'cogs' and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ∼24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (PAS) domains. PAS domains are modular, evolutionarily conserved sensory and signaling domains that typically mediate protein-protein interactions. In the mammalian circadian clock, PAS domains modulate homo and heterodimerization of several core clock proteins that assemble into transcription factors or repressors. This review will focus on the functional importance of the PAS domains in the circadian clock from a biophysical and biochemical standpoint and describe their roles in clock protein interactions and circadian timekeeping.
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Affiliation(s)
- Diksha Sharma
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States; Center for Circadian Biology, University of California San Diego, CA, United States.
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3
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light-inducible protein degradation in E. coli with the LOVdeg tag. eLife 2024; 12:RP87303. [PMID: 38270583 PMCID: PMC10945698 DOI: 10.7554/elife.87303] [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] [Indexed: 01/26/2024] Open
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
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Affiliation(s)
- Nathan Tague
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Cristian Coriano-Ortiz
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Michael B Sheets
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
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4
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Johnson LA, Mart RJ, Allemann RK. A Photoresponsive Homing Endonuclease for Programmed DNA Cleavage. ACS Synth Biol 2024; 13:195-205. [PMID: 38061193 PMCID: PMC10804406 DOI: 10.1021/acssynbio.3c00425] [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: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 01/23/2024]
Abstract
Homing endonucleases are used in a wide range of biotechnological applications including gene editing, in gene drive systems, and for the modification of DNA structures, arrays, and prodrugs. However, controlling nuclease activity and sequence specificity remain key challenges when developing new tools. Here a photoresponsive homing endonuclease was engineered for optical control of DNA cleavage by partitioning DNA binding and nuclease domains of the monomeric homing endonuclease I-TevI into independent polypeptide chains. Use of the Aureochrome1a light-oxygen-voltage domain delivered control of dimerization with light. Illumination reduced the concentration needed to achieve 50% cleavage of the homing target site by 6-fold when compared to the dark state, resulting in an up to 9-fold difference in final yields between cleavage products. I-TevI nucleases with and without a native I-TevI zinc finger motif displayed different nuclease activity and sequence preference impacting the promiscuity of the nuclease domain. By harnessing an alternative DNA binding domain, target preference was reprogrammed only when the nuclease lacked the I-TevI zinc finger motif. This work establishes a first-generation photoresponsive platform for spatiotemporal activation of DNA cleavage.
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Affiliation(s)
- Luke A. Johnson
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
| | | | - Rudolf K. Allemann
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
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5
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Jain S, Sekhar A. Transient excited states of the metamorphic protein Mad2 and their implications for function. Proteins 2024. [PMID: 38221646 DOI: 10.1002/prot.26667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/27/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
The spindle checkpoint complex is a key surveillance mechanism in cell division that prevents premature separation of sister chromatids. Mad2 is an integral component of this spindle checkpoint complex that recognizes cognate substrates such as Mad1 and Cdc20 in its closed (C-Mad2) conformation by fastening a "seatbelt" around short peptide regions that bind to the substrate recognition site. Mad2 is also a metamorphic protein that adopts not only the fold found in C-Mad2, but also a structurally distinct open conformation (O-Mad2) which is incapable of binding substrates. Here, we show using chemical exchange saturation transfer (CEST) and relaxation dispersion (CPMG) NMR experiments that Mad2 transiently populates three other higher free energy states with millisecond lifetimes, two in equilibrium with C-Mad2 (E1 and E2) and one with O-Mad2 (E3). E1 is a mimic of substrate-bound C-Mad2 in which the N-terminus of one C-Mad2 molecule inserts into the seatbelt region of a second molecule of C-Mad2, providing a potential pathway for autoinhibition of C-Mad2. E2 is the "unbuckled" conformation of C-Mad2 that facilitates the triage of molecules along competing fold-switching and substrate binding pathways. The E3 conformation that coexists with O-Mad2 shows fluctuations at a hydrophobic lock that is required for stabilizing the O-Mad2 fold and we hypothesize that E3 represents an early intermediate on-pathway towards conversion to C-Mad2. Collectively, the NMR data highlight the rugged free energy landscape of Mad2 with multiple low-lying intermediates that interlink substrate-binding and fold-switching, and also emphasize the role of molecular dynamics in its function.
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Affiliation(s)
- Shefali Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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6
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Marcus DJ, Bruchas MR. Optical Approaches for Investigating Neuromodulation and G Protein-Coupled Receptor Signaling. Pharmacol Rev 2023; 75:1119-1139. [PMID: 37429736 PMCID: PMC10595021 DOI: 10.1124/pharmrev.122.000584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 07/12/2023] Open
Abstract
Despite the fact that roughly 40% of all US Food and Drug Administration (FDA)-approved pharmacological therapeutics target G protein-coupled receptors (GPCRs), there remains a gap in our understanding of the physiologic and functional role of these receptors at the systems level. Although heterologous expression systems and in vitro assays have revealed a tremendous amount about GPCR signaling cascades, how these cascades interact across cell types, tissues, and organ systems remains obscure. Classic behavioral pharmacology experiments lack both the temporal and spatial resolution to resolve these long-standing issues. Over the past half century, there has been a concerted effort toward the development of optical tools for understanding GPCR signaling. From initial ligand uncaging approaches to more recent development of optogenetic techniques, these strategies have allowed researchers to probe longstanding questions in GPCR pharmacology both in vivo and in vitro. These tools have been employed across biologic systems and have allowed for interrogation of everything from specific intramolecular events to pharmacology at the systems level in a spatiotemporally specific manner. In this review, we present a historical perspective on the motivation behind and development of a variety of optical toolkits that have been generated to probe GPCR signaling. Here we highlight how these tools have been used in vivo to uncover the functional role of distinct populations of GPCRs and their signaling cascades at a systems level. SIGNIFICANCE STATEMENT: G protein-coupled receptors (GPCRs) remain one of the most targeted classes of proteins for pharmaceutical intervention, yet we still have a limited understanding of how their unique signaling cascades effect physiology and behavior at the systems level. In this review, we discuss a vast array of optical techniques that have been devised to probe GPCR signaling both in vitro and in vivo.
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Affiliation(s)
- David J Marcus
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
| | - Michael R Bruchas
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
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7
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light inducible protein degradation in E. coli with the LOVdeg tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530042. [PMID: 36865169 PMCID: PMC9980293 DOI: 10.1101/2023.02.25.530042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system, and introduce a powerful new tool for bacterial optogenetics.
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8
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Kumar A, Madhurima K, Naganathan AN, Vallurupalli P, Sekhar A. Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch. Methods 2023; 218:198-209. [PMID: 37607621 PMCID: PMC7615522 DOI: 10.1016/j.ymeth.2023.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
Over 40% of eukaryotic proteomes and 15% of bacterial proteomes are predicted to be intrinsically disordered based on their amino acid sequence. Intrinsically disordered proteins (IDPs) exist as heterogeneous ensembles of interconverting conformations and pose a challenge to the structure-function paradigm by apparently functioning without possessing stable structural elements. IDPs play a prominent role in biological processes involving extensive intermolecular interaction networks and their inherently dynamic nature facilitates their promiscuous interaction with multiple structurally diverse partner molecules. NMR spectroscopy has made pivotal contributions to our understanding of IDPs because of its unique ability to characterize heterogeneity at atomic resolution. NMR methods such as Chemical Exchange Saturation Transfer (CEST) and relaxation dispersion have enabled the detection of 'invisible' excited states in biomolecules which are transiently and sparsely populated, yet central for function. Here, we develop a 1Hα CEST pulse sequence which overcomes the resonance overlap problem in the 1Hα-13Cα plane of IDPs by taking advantage of the superior resolution in the 1H-15N correlation spectrum. In this sequence, magnetization is transferred after 1H CEST using a triple resonance coherence transfer pathway from 1Hα (i) to 1HN(i + 1) during which the 15N(t1) and 1HN(t2) are frequency labelled. This approach is integrated with spin state-selective CEST for eliminating spurious dips in CEST profiles resulting from dipolar cross-relaxation. We apply this sequence to determine the excited state 1Hα chemical shifts of the intrinsically disordered DNA binding domain (CytRN) of the bacterial cytidine repressor (CytR), which transiently acquires a functional globally folded conformation. The structure of the excited state, calculated using 1Hα chemical shifts in conjunction with other excited state NMR restraints, is a three-helix bundle incorporating a helix-turn-helix motif that is vital for binding DNA.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500046, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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9
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Hetzler B, Donthamsetti P, Peitsinis Z, Stanley C, Trauner D, Isacoff EY. Optical Control of Dopamine D2-like Receptors with Cell-Specific Fast-Relaxing Photoswitches. J Am Chem Soc 2023; 145:18778-18788. [PMID: 37586061 PMCID: PMC10472511 DOI: 10.1021/jacs.3c02735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 08/18/2023]
Abstract
Dopamine D2-like receptors (D2R, D3R, and D4R) control diverse physiological and behavioral functions and are important targets for the treatment of a variety of neuropsychiatric disorders. Their complex distribution and activation kinetics in the brain make it difficult to target specific receptor populations with sufficient precision. We describe a new toolkit of light-activatable, fast-relaxing, covalently taggable chemical photoswitches that fully activate, partially activate, or block D2-like receptors. This technology combines the spatiotemporal precision of a photoswitchable ligand (P) with cell type and spatial specificity of a genetically encoded membrane anchoring protein (M) to which the P tethers. These tools set the stage for targeting endogenous D2-like receptor signaling with molecular, cellular, and spatiotemporal precision using only one wavelength of light.
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Affiliation(s)
- Belinda
E. Hetzler
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Prashant Donthamsetti
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Zisis Peitsinis
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Cherise Stanley
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Dirk Trauner
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Department
of Chemistry and Department of Systems Pharmacology and Translational
Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ehud Y. Isacoff
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
- Helen
Wills Neuroscience Institute, University
of California, Berkeley, California 94720, United States
- Weill Neurohub, University of California, Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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10
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Vide U, Kasapović D, Fuchs M, Heimböck MP, Totaro MG, Zenzmaier E, Winkler A. Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases. SCIENCE ADVANCES 2023; 9:eadh4721. [PMID: 37531459 PMCID: PMC10396304 DOI: 10.1126/sciadv.adh4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for lifestyle transitions, such as cell proliferation or apoptosis, switch-like characteristics are desirable. While nature frequently uses regulatory circuits to amplify or dampen signals, stand-alone protein switches are interesting for applications like biosensors, diagnostic tools, or optogenetics. However, such stand-alone systems frequently feature limited dynamic and operational ranges and suffer from slow response times. Here, we characterize a LOV-activated diguanylate cyclase (LadC) that offers precise temporal and spatial control of enzymatic activity with an exceptionally high dynamic range over four orders of magnitude. To establish this pronounced activation, the enzyme exhibits a two-stage activation process in which its activity is inhibited in the dark by caging its effector domains and stimulated upon illumination by the formation of an extended coiled-coil. These switch-like characteristics of the LadC system can be used to develop new optogenetic tools with tight regulation.
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Affiliation(s)
- Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Dženita Kasapović
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Maximilian Fuchs
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Martin P. Heimböck
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Massimo G. Totaro
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Elfriede Zenzmaier
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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11
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Lan TH, He L, Huang Y, Zhou Y. Optogenetics for transcriptional programming and genetic engineering. Trends Genet 2022; 38:1253-1270. [PMID: 35738948 PMCID: PMC10484296 DOI: 10.1016/j.tig.2022.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 01/24/2023]
Abstract
Optogenetics combines genetics and biophotonics to enable noninvasive control of biological processes with high spatiotemporal precision. When engineered into protein machineries that govern the cellular information flow as depicted in the central dogma, multiple genetically encoded non-opsin photosensory modules have been harnessed to modulate gene transcription, DNA or RNA modifications, DNA recombination, and genome engineering by utilizing photons emitting in the wide range of 200-1000 nm. We present herein generally applicable modular strategies for optogenetic engineering and highlight latest advances in the broad applications of opsin-free optogenetics to program transcriptional outputs and precisely manipulate the mammalian genome, epigenome, and epitranscriptome. We also discuss current challenges and future trends in opsin-free optogenetics, which has been rapidly evolving to meet the growing needs in synthetic biology and genetics research.
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Affiliation(s)
- Tien-Hung Lan
- 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
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA; Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX 77030, USA.
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12
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Britain DM, Town JP, Weiner OD. Progressive enhancement of kinetic proofreading in T cell antigen discrimination from receptor activation to DAG generation. eLife 2022; 11:e75263. [PMID: 36125261 PMCID: PMC9536835 DOI: 10.7554/elife.75263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
T cells use kinetic proofreading to discriminate antigens by converting small changes in antigen-binding lifetime into large differences in cell activation, but where in the signaling cascade this computation is performed is unknown. Previously, we developed a light-gated immune receptor to probe the role of ligand kinetics in T cell antigen signaling. We found significant kinetic proofreading at the level of the signaling lipid diacylglycerol (DAG) but lacked the ability to determine where the multiple signaling steps required for kinetic discrimination originate in the upstream signaling cascade (Tiseher and Weiner, 2019). Here, we uncover where kinetic proofreading is executed by adapting our optogenetic system for robust activation of early signaling events. We find the strength of kinetic proofreading progressively increases from Zap70 recruitment to LAT clustering to downstream DAG generation. Leveraging the ability of our system to rapidly disengage ligand binding, we also measure slower reset rates for downstream signaling events. These data suggest a distributed kinetic proofreading mechanism, with proofreading steps both at the receptor and at slower resetting downstream signaling complexes that could help balance antigen sensitivity and discrimination.
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Affiliation(s)
- Derek M Britain
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jason P Town
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Orion David Weiner
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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13
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Tan P, Hong T, Cai X, Li W, Huang Y, He L, Zhou Y. Optical control of protein delivery and partitioning in the nucleolus. Nucleic Acids Res 2022; 50:e69. [PMID: 35325178 PMCID: PMC9262612 DOI: 10.1093/nar/gkac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/12/2022] [Accepted: 03/11/2022] [Indexed: 11/14/2022] Open
Abstract
The nucleolus is a subnuclear membraneless compartment intimately involved in ribosomal RNA synthesis, ribosome biogenesis and stress response. Multiple optogenetic devices have been developed to manipulate nuclear protein import and export, but molecular tools tailored for remote control over selective targeting or partitioning of cargo proteins into subnuclear compartments capable of phase separation are still limited. Here, we report a set of single-component photoinducible nucleolus-targeting tools, designated pNUTs, to enable rapid and reversible nucleoplasm-to-nucleolus shuttling, with the half-lives ranging from milliseconds to minutes. pNUTs allow both global protein infiltration into nucleoli and local delivery of cargoes into the outermost layer of the nucleolus, the granular component. When coupled with the amyotrophic lateral sclerosis (ALS)-associated C9ORF72 proline/arginine-rich dipeptide repeats, pNUTs allow us to photomanipulate poly-proline-arginine nucleolar localization, perturb nucleolar protein nucleophosmin 1 and suppress nascent protein synthesis. pNUTs thus expand the optogenetic toolbox by permitting light-controllable interrogation of nucleolar functions and precise induction of ALS-associated toxicity in cellular models.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tingting Hong
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Xiaoli Cai
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, 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 Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
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14
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Duan T, Bian Q, Li H. Protein Hydrogels with Reversibly Patterned Multidimensional Fluorescent Images for Information Storage. Biomacromolecules 2022; 23:3009-3016. [PMID: 35749455 DOI: 10.1021/acs.biomac.2c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent polymeric hydrogels are promising soft and wet media for information storage that are desirable for lifelike biomaterials and flexible electronics. Hydrogels based on engineered proteins have attracted considerable interest. However, their potential utility as information storage media has remained largely unexplored. Here, we report a protein-based hydrogel that can serve as an information storage medium. Using LOVTRAP, which consists of protein LOV2 and its binding partner ZDark1, we developed a novel strategy to decorate/release fluorescent proteins onto/from a blank protein hydrogel slate in light-controlled and spatially defined fashions, reversibly generating fluorescent patterns such as quick response codes. To increase the information storage capacity, we further developed grayscale patterning to generate pseudo-colored multi-dimensional fluorescent images. Results of this new method demonstrate a novel reversible information storage approach in soft and wet materials and open a new avenue toward developing next-generation protein-based smart materials for information storage and anti-counterfeit applications.
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Affiliation(s)
- Tianyu Duan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Qingyuan Bian
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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15
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Dietler J, Gelfert R, Kaiser J, Borin V, Renzl C, Pilsl S, Ranzani AT, García de Fuentes A, Gleichmann T, Diensthuber RP, Weyand M, Mayer G, Schapiro I, Möglich A. Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Nat Commun 2022; 13:2618. [PMID: 35552382 PMCID: PMC9098866 DOI: 10.1038/s41467-022-30252-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins. Light-oxygen-voltage (LOV) photoreceptors perceive blue light to elicit spatio-temporally defined cellular responses, and their signalling process has been extensively characterized. Here the authors report that the light signal is still transduced in the absence of a conserved Gln residue, thought to be key.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Renate Gelfert
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Veniamin Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Renzl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | - Sebastian Pilsl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | | | | | - Tobias Gleichmann
- Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany
| | | | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121, Bonn, Germany
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany. .,Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany. .,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447, Bayreuth, Germany. .,North-Bavarian NMR Center, Universität Bayreuth, 95447, Bayreuth, Germany.
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16
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [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: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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17
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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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18
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Jaladeep A, Varghese CN, Sekhar A. Measuring radiofrequency fields in NMR spectroscopy using offset-dependent nutation profiles. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 330:107032. [PMID: 34311422 PMCID: PMC7612739 DOI: 10.1016/j.jmr.2021.107032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
The application of NMR spectroscopy for studying molecular and reaction dynamics relies crucially on the measurement of the magnitude of radiofrequency (RF) fields that are used to nutate or lock the nuclear magnetization. Here, we report a method for measuring RF field amplitudes that leverages the intrinsic modulations observed in offset-dependent NMR nutation profiles of small molecules. Such nutation profiles are exquisitely sensitive to the magnitude of the RF field, and B1 values ranging from 1 to 2000 Hz, as well the inhomogeneity in B1 distributions, can be determined with high accuracy and precision using this approach. In order to measure B1 fields associated with NMR experiments carried out on protein or nucleic acids, where these modulations are obscured by the large transverse relaxation rate constants of the analyte, our approach can be used in conjunction with a suitable external small molecule standard, expanding the scope of the method for large biomolecules.
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Affiliation(s)
- Ahallya Jaladeep
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Claris Niya Varghese
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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19
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Duan T, Bian Q, Li H. Light-Responsive Dynamic Protein Hydrogels Based on LOVTRAP. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10214-10222. [PMID: 34396769 DOI: 10.1021/acs.langmuir.1c01699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein-based hydrogels can mimic many aspects of native extracellular matrices (ECMs) and are promising biomedical materials that find various applications in cell proliferation, drug/cell delivery, and tissue engineering. To be adapted for different tasks, it is important that the mechanical and/or biochemical properties of protein-based hydrogels can be regulated by external stimuli. Light as a regulation stimulus is of advantage because it can be easily applied in demanded spatiotemporal manners. The noncovalent binding between the light-oxygen-voltage-sensing domain 2 (LOV2) and its binding partner ZDark1 (zdk1), named as LOVTRAP, is a light-responsive interaction. The binding affinity of LOVTRAP is much higher in dark than that under blue light irradiation. Taking advantage of these light-responsive interactions, herein we endeavored to use LOVTRAP as a crosslinking mechanism to engineer light-responsive protein hydrogels. Using LOV2-containing and zdk1-containing multifunctional protein building blocks, we successfully engineered a light-responsive protein hydrogel whose viscoelastic properties can change in response to light: in the dark, the hydrogel showed higher storage modulus; under blue light irradiation, the storage modulus decreased. Due to the noncovalent nature of the LOVTRAP, the engineered LOVTRAP protein hydrogels displayed shear-thinning and self-healing properties and served as an excellent injectable protein hydrogel. We anticipated that this new class of light-responsive protein hydrogels will broaden the scope of dynamic protein hydrogels and help develop other light-responsive protein hydrogels for biomedical applications.
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Affiliation(s)
- Tianyu Duan
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Qingyuan Bian
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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20
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Wichert N, Witt M, Blume C, Scheper T. Clinical applicability of optogenetic gene regulation. Biotechnol Bioeng 2021; 118:4168-4185. [PMID: 34287844 DOI: 10.1002/bit.27895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/27/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022]
Abstract
The field of optogenetics is rapidly growing in relevance and number of developed tools. Among other things, the optogenetic repertoire includes light-responsive ion channels and methods for gene regulation. This review will be confined to the optogenetic control of gene expression in mammalian cells as suitable models for clinical applications. Here optogenetic gene regulation might offer an excellent method for spatially and timely regulated gene and protein expression in cell therapeutic approaches. Well-known systems for gene regulation, such as the LOV-, CRY2/CIB-, PhyB/PIF-systems, as well as other, in mammalian cells not yet fully established systems, will be described. Advantages and disadvantages with regard to clinical applications are outlined in detail. Among the many unanswered questions concerning the application of optogenetics, we discuss items such as the use of exogenous chromophores and their effects on the biology of the cells and methods for a gentle, but effective gene transfection method for optogenetic tools for in vivo applications.
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Affiliation(s)
- Nina Wichert
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Martin Witt
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Cornelia Blume
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Thomas Scheper
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
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21
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Farahani PE, Reed EH, Underhill EJ, Aoki K, Toettcher JE. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng 2021; 23:61-87. [PMID: 33722063 PMCID: PMC10436267 DOI: 10.1146/annurev-bioeng-083120-111648] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells receive enormous amounts of information from their environment. How they act on this information-by migrating, expressing genes, or relaying signals to other cells-comprises much of the regulatory and self-organizational complexity found across biology. The "parts list" involved in cell signaling is generally well established, but how do these parts work together to decode signals and produce appropriate responses? This fundamental question is increasingly being addressed with optogenetic tools: light-sensitive proteins that enable biologists to manipulate the interaction, localization, and activity state of proteins with high spatial and temporal precision. In this review, we summarize how optogenetics is being used in the pursuit of an answer to this question, outlining the current suite of optogenetic tools available to the researcher and calling attention to studies that increase our understanding of and improve our ability to engineer biology.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ellen H Reed
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Evan J Underhill
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
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22
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Stevens LM, Kim G, Koromila T, Steele JW, McGehee J, Stathopoulos A, Stein DS. Light-dependent N-end rule-mediated disruption of protein function in Saccharomyces cerevisiae and Drosophila melanogaster. PLoS Genet 2021; 17:e1009544. [PMID: 33999957 PMCID: PMC8158876 DOI: 10.1371/journal.pgen.1009544] [Citation(s) in RCA: 2] [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: 10/08/2020] [Revised: 05/27/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Here we describe the development and characterization of the photo-N-degron, a peptide tag that can be used in optogenetic studies of protein function in vivo. The photo-N-degron can be expressed as a genetic fusion to the amino termini of other proteins, where it undergoes a blue light-dependent conformational change that exposes a signal for the class of ubiquitin ligases, the N-recognins, which mediate the N-end rule mechanism of proteasomal degradation. We demonstrate that the photo-N-degron can be used to direct light-mediated degradation of proteins in Saccharomyces cerevisiae and Drosophila melanogaster with fine temporal control. In addition, we compare the effectiveness of the photo-N-degron with that of two other light-dependent degrons that have been developed in their abilities to mediate the loss of function of Cactus, a component of the dorsal-ventral patterning system in the Drosophila embryo. We find that like the photo-N-degron, the blue light-inducible degradation (B-LID) domain, a light-activated degron that must be placed at the carboxy terminus of targeted proteins, is also effective in eliciting light-dependent loss of Cactus function, as determined by embryonic dorsal-ventral patterning phenotypes. In contrast, another previously described photosensitive degron (psd), which also must be located at the carboxy terminus of associated proteins, has little effect on Cactus-dependent phenotypes in response to illumination of developing embryos. These and other observations indicate that care must be taken in the selection and application of light-dependent and other inducible degrons for use in studies of protein function in vivo, but importantly demonstrate that N- and C-terminal fusions to the photo-N-degron and the B-LID domain, respectively, support light-dependent degradation in vivo. Much of what we know about biological processes has come from the analysis of mutants whose loss-of-function phenotypes provide insight into their normal functions. However, for genes that are required for viability and which have multiple functions in the life of a cell or organism one can only observe mutant phenotypes produced up to the time of death. Normal functions performed in wild-type individuals later than the time of death of mutants cannot be observed. In one approach to overcoming this limitation, a class of peptide degradation signals (degrons) have been developed, which when fused to proteins-of-interest, can target those proteins for degradation in response to various stimuli (temperature, chemical agents, co-expressed proteins, or light). Here we describe a new inducible degron (the photo-N-degron or PND), which when fused to the N-terminus of a protein, can induce N-end rule-mediated degradation in response to blue-light illumination and have validated its use in both yeast and Drosophila embryos. Moreover, using the Drosophila embryonic patterning protein Cactus, we show that like the PND, the previously-described B-LID domain, but not the previously-described photosensitive degron (psd), can produce detectable light-inducible phenotypes in Drosophila embryos that are consistent with the role of Cactus in dorsal-ventral patterning.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Goheun Kim
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Theodora Koromila
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - John W. Steele
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - James McGehee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AS); (DSS)
| | - David S. Stein
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (AS); (DSS)
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23
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Light-regulated voltage-gated potassium channels for acute interrogation of channel function in neurons and behavior. PLoS One 2021; 16:e0248688. [PMID: 33755670 PMCID: PMC7987177 DOI: 10.1371/journal.pone.0248688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/03/2021] [Indexed: 01/02/2023] Open
Abstract
Voltage-gated potassium (Kv) channels regulate the membrane potential and conductance of excitable cells to control the firing rate and waveform of action potentials. Even though Kv channels have been intensely studied for over 70 year, surprisingly little is known about how specific channels expressed in various neurons and their functional properties impact neuronal network activity and behavior in vivo. Although many in vivo genetic manipulations of ion channels have been tried, interpretation of these results is complicated by powerful homeostatic plasticity mechanisms that act to maintain function following perturbations in excitability. To better understand how Kv channels shape network function and behavior, we have developed a novel optogenetic technology to acutely regulate Kv channel expression with light by fusing the light-sensitive LOV domain of Vaucheria frigida Aureochrome 1 to the N-terminus of the Kv1 subunit protein to make an Opto-Kv1 channel. Recording of Opto-Kv1 channels expressed in Xenopus oocytes, mammalian cells, and neurons show that blue light strongly induces the current expression of Opto-Kv1 channels in all systems tested. We also find that an Opto-Kv1 construct containing a dominant-negative pore mutation (Opto-Kv1(V400D)) can be used to down-regulate Kv1 currents in a blue light-dependent manner. Finally, to determine whether Opto-Kv1 channels can elicit light-dependent behavioral effect in vivo, we targeted Opto-Kv1 (V400D) expression to Kv1.3-expressing mitral cells of the olfactory bulb in mice. Exposure of the bulb to blue light for 2–3 hours produced a significant increase in sensitivity to novel odors after initial habituation to a similar odor, comparable to behavioral changes seen in Kv1.3 knockout animals. In summary, we have developed novel photoactivatable Kv channels that provide new ways to interrogate neural circuits in vivo and to examine the roles of normal and disease-causing mutant Kv channels in brain function and behavior.
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24
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Li L, He L, Wu B, Yu C, Zhao H, Zhou Y, Wang J, Zhu L. Structural Determinants for Light-Dependent Membrane Binding of a Photoswitchable Polybasic Domain. ACS Synth Biol 2021; 10:542-551. [PMID: 33689308 DOI: 10.1021/acssynbio.0c00571] [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: 12/12/2022]
Abstract
OptoPB is an optogenetic tool engineered by fusion of the phosphoinositide (PI)-binding polybasic domain of Rit1 (Rit-PB) to a photoreactive light-oxygen-voltage (LOV) domain. OptoPB selectively and reversibly binds the plasma membrane (PM) under blue light excitation, and in the dark, it releases back to the cytoplasm. However, the molecular mechanism of optical regulation and lipid recognition is still unclear. Here using nuclear magnetic resonance (NMR) spectroscopy, liposome pulldown assay, and surface plasmon resonance (SPR), we find that OptoPB binds to membrane mimetics containing di- or triphosphorylated phosphatidylinositols, particularly phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), an acidic phospholipid predominantly located in the eukaryotic PM. In the dark, steric hindrance prevented this protein-membrane interaction, while 470 nm blue light illumination activated it. NMR titration and site-directed mutagenesis revealed that both cationic and hydrophobic Rit-PB residues are essential to the membrane interaction, indicating that OptoPB binds the membrane via a specific PI(4,5)P2-dependent mechanism.
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Affiliation(s)
- Ling Li
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Bo Wu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuandi Yu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Hongxin Zhao
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230031, China
| | - Lei Zhu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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25
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Zhao Y, Zhang Y, Sun M, Zheng Q. A theoretical study on the signal transduction process of bacterial photoreceptor PpSB1 based on the Markov state model. Phys Chem Chem Phys 2021; 23:2398-2405. [PMID: 33458728 DOI: 10.1039/d0cp05532h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-oxygen-voltage (LOV) domains are blue light sensors and play an important role in signal transduction in many organisms. Generally, LOV domains use chromophores to absorb photons, and then photochemical reactions will occur to convert light energy into chemical energy and transduce it to the main chain of proteins. These reactions can cause conformational rearrangement of proteins, and thus leading to signal transduction. Therefore, it is important to study the signal transduction process of LOV domains for understanding the control mechanism of cellular functions. However, how small photochemical changes in the active sites of the LOV domains lead to large conformational rearrangements of proteins, which in turn lead to signal transduction, has been puzzling us for a long time. Currently, the LOV domains are mainly studied in plants. The signal transduction mechanism of LOV domains in bacteria is still unclear. In this work, the Markov state model (MSM) combined with molecular dynamics (MD) simulations was applied to investigate the signal transduction process of the LOV protein from pseudomonas putida (PpSB1-LOV). The present work will play an important role in understanding the signal transduction mechanism of PpSB1-LOV domains, which may provide theoretical basis for the design and improvement of LOV-based optogenetic tools.
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Affiliation(s)
- Yajie Zhao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People's Republic of China.
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26
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He L, Wang L, Zeng H, Tan P, Ma G, Zheng S, Li Y, Sun L, Dou F, Siwko S, Huang Y, Wang Y, Zhou Y. Engineering of a bona fide light-operated calcium channel. Nat Commun 2021; 12:164. [PMID: 33431868 PMCID: PMC7801460 DOI: 10.1038/s41467-020-20425-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
Abstract
The current optogenetic toolkit lacks a robust single-component Ca2+-selective ion channel tailored for remote control of Ca2+ signaling in mammals. Existing tools are either derived from engineered channelrhodopsin variants without strict Ca2+ selectivity or based on the stromal interaction molecule 1 (STIM1) that might crosstalk with other targets. Here, we describe the design of a light-operated Ca2+ channel (designated LOCa) by inserting a plant-derived photosensory module into the intracellular loop of an engineered ORAI1 channel. LOCa displays biophysical features reminiscent of the ORAI1 channel, which enables precise optical control over Ca2+ signals and hallmark Ca2+-dependent physiological responses. Furthermore, we demonstrate the use of LOCa to modulate aberrant hematopoietic stem cell self-renewal, transcriptional programming, cell suicide, as well as neurodegeneration in a Drosophila model of amyloidosis. Existing optogenetic methods to induce calcium mobilisation lack selectivity and specificity. Here, the authors design and engineer a single-component light-operated calcium channel to provide optical control over calcium signals and calcium-dependent physiological responses: LOCa.
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Affiliation(s)
- Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Liuqing Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hongxiang Zeng
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Sisi Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yaxin Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Fei Dou
- Beijing Key Laboratory of Genetic Engineering Drugs and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Stefan Siwko
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA. .,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA. .,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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27
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Hart JE, Gardner KH. Lighting the way: Recent insights into the structure and regulation of phototropin blue light receptors. J Biol Chem 2021; 296:100594. [PMID: 33781746 PMCID: PMC8086140 DOI: 10.1016/j.jbc.2021.100594] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The phototropins (phots) are light-activated kinases that are critical for plant physiology and the many diverse optogenetic tools that they have inspired. Phototropins combine two blue-light-sensing Light-Oxygen-Voltage (LOV) domains (LOV1 and LOV2) and a C-terminal serine/threonine kinase domain, using the LOV domains to control the catalytic activity of the kinase. While much is known about the structure and photochemistry of the light-perceiving LOV domains, particularly in how activation of the LOV2 domain triggers the unfolding of alpha helices that communicate the light signal to the kinase domain, many questions about phot structure and mechanism remain. Recent studies have made progress addressing these questions by utilizing small-angle X-ray scattering (SAXS) and other biophysical approaches to study multidomain phots from Chlamydomonas and Arabidopsis, leading to models where the domains have an extended linear arrangement, with the regulatory LOV2 domain contacting the kinase domain N-lobe. We discuss this and other advances that have improved structural and mechanistic understanding of phot regulation in this review, along with the challenges that will have to be overcome to obtain high-resolution structural information on these exciting photoreceptors. Such information will be essential to advancing fundamental understanding of plant physiology while enabling engineering efforts at both the whole plant and molecular levels.
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Affiliation(s)
- Jaynee E Hart
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, USA; PhD Programs in Biochemistry, Chemistry, and Biology, Graduate Center, City University of New York, New York, USA.
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28
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Mathony J, Niopek D. Enlightening Allostery: Designing Switchable Proteins by Photoreceptor Fusion. Adv Biol (Weinh) 2020; 5:e2000181. [PMID: 33107225 DOI: 10.1002/adbi.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Indexed: 11/05/2022]
Abstract
Optogenetics harnesses natural photoreceptors to non-invasively control selected processes in cells with previously unmet spatiotemporal precision. Linking the activity of a protein of choice to the conformational state of a photosensor domain through allosteric coupling represents a powerful method for engineering light-responsive proteins. It enables the design of compact and highly potent single-component optogenetic systems with fast on- and off-switching kinetics. However, designing protein-photoreceptor chimeras, in which structural changes of the photoreceptor are effectively propagated to the fused effector protein, is a challenging engineering problem and often relies on trial and error. Here, recent advances in the design and application of optogenetic allosteric switches are reviewed. First, an overview of existing optogenetic tools based on inducible allostery is provided and their utility for cell biology applications is highlighted. Focusing on light-oxygen-voltage domains, a widely applied class of small blue light sensors, the available strategies for engineering light-dependent allostery are presented and their individual advantages and limitations are highlighted. Finally, high-throughput screening technologies based on comprehensive insertion libraries, which could accelerate the creation of stimulus-responsive receptor-protein chimeras for use in optogenetics and beyond, are discussed.
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Affiliation(s)
- Jan Mathony
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany.,BZH graduate school, Heidelberg University, Im Neuheimer Feld 328, Heidelberg, 69120, Germany
| | - Dominik Niopek
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany
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29
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Tian Y, Yang S, Gao S. Advances, Perspectives and Potential Engineering Strategies of Light-Gated Phosphodiesterases for Optogenetic Applications. Int J Mol Sci 2020; 21:E7544. [PMID: 33066112 PMCID: PMC7590022 DOI: 10.3390/ijms21207544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
The second messengers, cyclic adenosine 3'-5'-monophosphate (cAMP) and cyclic guanosine 3'-5'-monophosphate (cGMP), play important roles in many animal cells by regulating intracellular signaling pathways and modulating cell physiology. Environmental cues like temperature, light, and chemical compounds can stimulate cell surface receptors and trigger the generation of second messengers and the following regulations. The spread of cAMP and cGMP is further shaped by cyclic nucleotide phosphodiesterases (PDEs) for orchestration of intracellular microdomain signaling. However, localized intracellular cAMP and cGMP signaling requires further investigation. Optogenetic manipulation of cAMP and cGMP offers new opportunities for spatio-temporally precise study of their signaling mechanism. Light-gated nucleotide cyclases are well developed and applied for cAMP/cGMP manipulation. Recently discovered rhodopsin phosphodiesterase genes from protists established a new and direct biological connection between light and PDEs. Light-regulated PDEs are under development, and of demand to complete the toolkit for cAMP/cGMP manipulation. In this review, we summarize the state of the art, pros and cons of artificial and natural light-regulated PDEs, and discuss potential new strategies of developing light-gated PDEs for optogenetic manipulation.
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Affiliation(s)
| | | | - Shiqiang Gao
- Department of Neurophysiology, Physiological Institute, University of Wuerzburg, 97070 Wuerzburg, Germany; (Y.T.); (S.Y.)
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30
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Wittmann T, Dema A, van Haren J. Lights, cytoskeleton, action: Optogenetic control of cell dynamics. Curr Opin Cell Biol 2020; 66:1-10. [PMID: 32371345 PMCID: PMC7577957 DOI: 10.1016/j.ceb.2020.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/29/2023]
Abstract
Cell biology is moving from observing molecules to controlling them in real time, a critical step towards a mechanistic understanding of how cells work. Initially developed from light-gated ion channels to control neuron activity, optogenetics now describes any genetically encoded protein system designed to accomplish specific light-mediated tasks. Recent photosensitive switches use many ingenious designs that bring spatial and temporal control within reach for almost any protein or pathway of interest. This next generation optogenetics includes light-controlled protein-protein interactions and shape-shifting photosensors, which in combination with live microscopy enable acute modulation and analysis of dynamic protein functions in living cells. We provide a brief overview of various types of optogenetic switches. We then discuss how diverse approaches have been used to control cytoskeleton dynamics with light through Rho GTPase signaling, microtubule and actin assembly, mitotic spindle positioning and intracellular transport and highlight advantages and limitations of different experimental strategies.
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Affiliation(s)
- Torsten Wittmann
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Alessandro Dema
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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31
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Lv M, Gao J, Li M, Ma R, Li F, Liu Y, Liu M, Zhang J, Yao X, Wu J, Shi Y, Tang Y, Pan Y, Zhang Z, Ruan K. Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. J Phys Chem Lett 2020; 11:7932-7938. [PMID: 32885980 DOI: 10.1021/acs.jpclett.0c02039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The first Tudor domain (Tudor1) of PHF20L1 recognizes (non)histone methylation to play versatile roles. However, the underlying ligand-recognition mechanism remains unknown as a closed state revealed in the free-form structure. NMR relaxation dispersion and molecular dynamics simulations suggest a pre-existing low-population conformation with a remarkable rearrangement of aromatic cage residues of PHF20L1 Tudor1. Such an open-form conformation is utilized to recognize lysine 142 methylated DNMT1, a cosolvent, and an NMR fragment screening hit, as revealed by the complex crystal structures. Intriguingly, the ligand binding capacity was enhanced by mutation that tunes up the open-state population only. The recognition of DNMT1 by PHF20L1 was further validated in cancer cells. This conformational selection mechanism will enable the discovery of small molecule inhibitors against the seemingly "undruggable" PHF20L1 Tudor1.
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Affiliation(s)
- Mengqi Lv
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jia Gao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingwei Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Rongsheng Ma
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yaqian Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingqing Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xuebiao Yao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jihui Wu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yajun Tang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yueyin Pan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Zhiyong Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Ke Ruan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
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32
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Lu X, Shen Y, Campbell RE. Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators. Int J Mol Sci 2020; 21:E6522. [PMID: 32906617 PMCID: PMC7555876 DOI: 10.3390/ijms21186522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022] Open
Abstract
Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).
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Affiliation(s)
- Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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33
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Goett-Zink L, Klocke JL, Bögeholz LAK, Kottke T. In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells. J Biol Chem 2020; 295:11729-11741. [PMID: 32580943 PMCID: PMC7450117 DOI: 10.1074/jbc.ra120.013091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.
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Affiliation(s)
- Lukas Goett-Zink
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Lena A K Bögeholz
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
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34
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Carrasco-López C, Zhao EM, Gil AA, Alam N, Toettcher JE, Avalos JL. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun 2020; 11:4045. [PMID: 32792484 PMCID: PMC7427095 DOI: 10.1038/s41467-020-17837-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.
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Affiliation(s)
- César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Agnieszka A Gil
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Nathan Alam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, USA.
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35
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Abstract
Light can be controlled with high spatial and temporal accuracy. Therefore, optogenetics is an attractive experimental approach to modulate intracellular cytoskeleton dynamics at much faster timescales than by genetic modification. For example, in mammalian cells, microtubules (MTs) grow tens of micrometers per minute and many intracellular MT functions are mediated by a complex of +TIP proteins that dynamically associate with growing MT plus ends. EB1 is a central component of this +TIP protein network, and we recently developed a photo-inactivated π-EB1 by inserting a blue light-sensitive LOV2/Zdk1 module between the EB1 MT-binding domain and the +TIP adaptor domain. Blue light-induced π-EB1 photodissociation results in disassembly of the +TIP complex and strongly attenuates MT growth in mammalian cells.In this chapter, we discuss theoretical and practical aspects of how to perform high-resolution live-cell microscopy in combination with π-EB1 photodissociation. However, these techniques are broadly applicable to other LOV2-based and likely other blue light-sensitive optogenetics. In addition to being a tool to investigate +TIP functions acutely and with subcellular resolution, because of its dramatic and rapid change in intracellular localization, π-EB1 can serve as a powerful tool to test and characterize optogenetic illumination setups. We describe protocols on how to achieve micrometer-scale intracellular control of π-EB1 activity using patterned illumination, and we introduce a do-it-yourself LED cube design compatible with transmitted light microscopy in multiwell plates.
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Affiliation(s)
- Jeffrey van Haren
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Lauren S Adachi
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.
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36
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Kumar A, Narayanan V, Sekhar A. Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy. Biochemistry 2019; 59:57-73. [PMID: 31682116 DOI: 10.1021/acs.biochem.9b00827] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Vaishali Narayanan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
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37
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Tischer DK, Weiner OD. Light-based tuning of ligand half-life supports kinetic proofreading model of T cell signaling. eLife 2019; 8:42498. [PMID: 30947808 PMCID: PMC6488292 DOI: 10.7554/elife.42498] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/03/2019] [Indexed: 11/30/2022] Open
Abstract
T cells are thought to discriminate self from foreign peptides by converting small differences in ligand binding half-life into large changes in cell signaling. Such a kinetic proofreading model has been difficult to test directly, as existing methods of altering ligand binding half-life also change other potentially important biophysical parameters, most notably the mechanical stability of the receptor-ligand interaction. Here we develop an optogenetic approach to specifically tune the binding half-life of a chimeric antigen receptor without changing other binding parameters and provide direct evidence of kinetic proofreading in T cell signaling. This half-life discrimination is executed in the proximal signaling pathway, downstream of ZAP70 recruitment and upstream of diacylglycerol accumulation. Our methods represent a general tool for temporal and spatial control of T cell signaling and extend the reach of optogenetics to probe pathways where the individual molecular kinetics, rather than the ensemble average, gates downstream signaling.
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Affiliation(s)
- Doug K Tischer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Orion David Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
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38
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Dagliyan O, Hahn KM. Controlling protein conformation with light. Curr Opin Struct Biol 2019; 57:17-22. [PMID: 30849716 DOI: 10.1016/j.sbi.2019.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022]
Abstract
Optogenetics, genetically encoded engineering of proteins to respond to light, has enabled precise control of the timing and localization of protein activity in live cells and for specific cell types in animals. Light-sensitive ion channels have become well established tools in neurobiology, and a host of new methods have recently enabled the control of other diverse protein structures as well. This review focuses on approaches to switch proteins between physiologically relevant, naturally occurring conformations using light, accomplished by incorporating light-responsive engineered domains that sterically and allosterically control the active site.
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Affiliation(s)
- Onur Dagliyan
- Department of Neurobiology, Harvard Medical School, United States.
| | - Klaus M Hahn
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, United States.
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Insights into histidine kinase activation mechanisms from the monomeric blue light sensor EL346. Proc Natl Acad Sci U S A 2019; 116:4963-4972. [PMID: 30808807 DOI: 10.1073/pnas.1813586116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translation of environmental cues into cellular behavior is a necessary process in all forms of life. In bacteria, this process frequently involves two-component systems in which a sensor histidine kinase (HK) autophosphorylates in response to a stimulus before subsequently transferring the phosphoryl group to a response regulator that controls downstream effectors. Many details of the molecular mechanisms of HK activation are still unclear due to complications associated with the multiple signaling states of these large, multidomain proteins. To address these challenges, we combined complementary solution biophysical approaches to examine the conformational changes upon activation of a minimal, blue-light-sensing histidine kinase from Erythrobacter litoralis HTCC2594, EL346. Our data show that multiple conformations coexist in the dark state of EL346 in solution, which may explain the enzyme's residual dark-state activity. We also observe that activation involves destabilization of the helices in the dimerization and histidine phosphotransfer-like domain, where the phosphoacceptor histidine resides, and their interactions with the catalytic domain. Similar light-induced changes occur to some extent even in constitutively active or inactive mutants, showing that light sensing can be decoupled from activation of kinase activity. These structural changes mirror those inferred by comparing X-ray crystal structures of inactive and active HK fragments, suggesting that they are at the core of conformational changes leading to HK activation. More broadly, our findings uncover surprising complexity in this simple system and allow us to outline a mechanism of the multiple steps of HK activation.
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40
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Fleming CL, Grøtli M, Andréasson J. On‐Command Regulation of Kinase Activity using Photonic Stimuli. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cassandra L. Fleming
- Department of Chemistry and Molecular BiologyUniversity of Gothenburg SE-41296 Göteborg Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular BiologyUniversity of Gothenburg SE-41296 Göteborg Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chemistry and BiochemistryChalmers University of Technology SE-41296 Göteborg Sweden
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Nguyen NT, Ma G, Lin E, D'Souza B, Jing J, He L, Huang Y, Zhou Y. CRAC channel-based optogenetics. Cell Calcium 2018; 75:79-88. [PMID: 30199756 DOI: 10.1016/j.ceca.2018.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/31/2018] [Indexed: 01/28/2023]
Abstract
Store-operated Ca²+ entry (SOCE) constitutes a major Ca2+ influx pathway in mammals to regulate a myriad of physiological processes, including muscle contraction, synaptic transmission, gene expression, and metabolism. In non-excitable cells, the Ca²+ release-activated Ca²+ (CRAC) channel, composed of ORAI and stromal interaction molecules (STIM), constitutes a prototypical example of SOCE to mediate Ca2+ entry at specialized membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and the plasma membrane (PM). The key steps of SOCE activation include the oligomerization of the luminal domain of the ER-resident Ca2+ sensor STIM1 upon Ca²+ store depletion, subsequent signal propagation toward the cytoplasmic domain to trigger a conformational switch and overcome the intramolecular autoinhibition, and ultimate exposure of the minimal ORAI-activating domain to directly engage and gate ORAI channels in the plasma membrane. This exquisitely coordinated cellular event is also facilitated by the C-terminal polybasic domain of STIM1, which physically associates with negatively charged phosphoinositides embedded in the inner leaflet of the PM to enable efficient translocation of STIM1 into ER-PM MCSs. Here, we present recent progress in recapitulating STIM1-mediated SOCE activation by engineering CRAC channels with optogenetic approaches. These STIM1-based optogenetic tools make it possible to not only mechanistically recapture the key molecular steps of SOCE activation, but also remotely and reversibly control Ca²+-dependent cellular processes, inter-organellar tethering at MCSs, and transcriptional reprogramming when combined with CRISPR/Cas9-based genome-editing tools.
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Affiliation(s)
- Nhung Thi Nguyen
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Eena Lin
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Brendan D'Souza
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Ji Jing
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine, Texas A&M University, Temple, TX 76504, USA.
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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43
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Affiliation(s)
- Mareike Daniela Hoffmann
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Felix Bubeck
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Roland Eils
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
- Digital Health Center; Berlin Institute of Health (BIH) and Charité-University Medicine Berlin; 10117 Berlin Germany
- Health Data Science Unit; University Hospital Heidelberg; 10117 Heidelberg Germany
| | - Dominik Niopek
- Department of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
- Synthetic Biology Group; Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant); University of Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
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44
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Nedrud D, Schmidt D. Combinatorial Assembly of Lumitoxins. Methods Mol Biol 2018; 1684:193-209. [PMID: 29058193 DOI: 10.1007/978-1-4939-7362-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ion channels are among the most important proteins in neuroscience and serve as drug targets for many brain disorders. During development, learning, disease progression, and other processes, the activity levels of specific ion channels are tuned in a cell-type specific manner. However, it is difficult to assess how cell-specific changes in ion channel activity alter emergent brain functions. We have developed a protein architecture for fully genetically encoded light-activated modulation of endogenous ion channel activity. Fusing a genetically encoded photoswitch and an ion channel-modulating peptide toxin in a computationally designed fashion, this reagent, which we call Lumitoxins, can mediate light-modulation of specific endogenous ion channel activities in targeted cells. The modular lumitoxin architecture may be useful in a diversity of neuroscience tools. Here, we delineate how to construct lumitoxin genes from synthesized components, and provide a general outline for how to test their function in mammalian cell culture.
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Affiliation(s)
- David Nedrud
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology and Development, University of Minnesota-Twin Cities, 321 Church Street SE, 6-160 Jackson, Minneapolis, MN, 55455, USA.
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45
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Dagliyan O, Tarnawski M, Chu PH, Shirvanyants D, Schlichting I, Dokholyan NV, Hahn KM. Engineering extrinsic disorder to control protein activity in living cells. Science 2017; 354:1441-1444. [PMID: 27980211 DOI: 10.1126/science.aah3404] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 11/16/2016] [Indexed: 11/03/2022]
Abstract
Optogenetic and chemogenetic control of proteins has revealed otherwise inaccessible facets of signaling dynamics. Here, we use light- or ligand-sensitive domains to modulate the structural disorder of diverse proteins, thereby generating robust allosteric switches. Sensory domains were inserted into nonconserved, surface-exposed loops that were tight and identified computationally as allosterically coupled to active sites. Allosteric switches introduced into motility signaling proteins (kinases, guanosine triphosphatases, and guanine exchange factors) controlled conversion between conformations closely resembling natural active and inactive states, as well as modulated the morphodynamics of living cells. Our results illustrate a broadly applicable approach to design physiological protein switches.
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Affiliation(s)
- Onur Dagliyan
- Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Miroslaw Tarnawski
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Pei-Hsuan Chu
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Shirvanyants
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Nikolay V Dokholyan
- Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Klaus M Hahn
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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46
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Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
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47
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Wang H, Hahn KM. LOVTRAP: A Versatile Method to Control Protein Function with Light. ACTA ACUST UNITED AC 2016; 73:21.10.1-21.10.14. [PMID: 27906450 DOI: 10.1002/cpcb.12] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a detailed procedure for the use of LOVTRAP, an approach to reversibly sequester and release proteins from cellular membranes using light. In the application described here, proteins that act at the plasma membrane are held at mitochondria in the dark, and reversibly released by irradiation. The technique relies on binding of an engineered Zdk domain to a LOV2 domain, with affinity <30 nM in the dark and >500 nM upon irradiation between 400 and 500 nm. LOVTRAP can be applied to diverse proteins, as it requires attaching only one member of the Zdk/LOV2 pair to the target protein, and the other to the membrane where the target protein is to be sequestered. Light-induced protein release occurs in less than a second, and the half-life of return can be adjusted using LOV point mutations (∼2 to 500 sec). © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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48
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Tan P, He L, Han G, Zhou Y. Optogenetic Immunomodulation: Shedding Light on Antitumor Immunity. Trends Biotechnol 2016; 35:215-226. [PMID: 27692897 DOI: 10.1016/j.tibtech.2016.09.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/28/2022]
Abstract
Microbial opsin-based optogenetic tools have been transformative for neuroscience. To extend optogenetic approaches to the immune system to remotely control immune responses with superior spatiotemporal precision, pioneering tools have recently been crafted to modulate lymphocyte trafficking, inflammasome activation, dendritic cell (DC) maturation, and antitumor immunity through the photoactivation of engineered chemokine receptors and calcium release-activated calcium channels. We highlight herein some conceptual design strategies for installing light sensitivities into the immune signaling network and, in parallel, we propose potential solutions for in vivo optogenetic applications in living organisms with near-infrared light-responsive upconversion nanomaterials. Moreover, to move beyond proof-of-concept into translational applications, we discuss future prospects for integrating personalized immunoengineering with optogenetics to overcome critical hurdles in cancer immunotherapy.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Gang Han
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA; Department of Medical Physiology, College of Medicine, Texas A&M University Health Science Center, Temple, TX 76504, USA.
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49
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Konold PE, Mathes T, Weiβenborn J, Groot ML, Hegemann P, Kennis JTM. Unfolding of the C-Terminal Jα Helix in the LOV2 Photoreceptor Domain Observed by Time-Resolved Vibrational Spectroscopy. J Phys Chem Lett 2016; 7:3472-6. [PMID: 27537211 DOI: 10.1021/acs.jpclett.6b01484] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Light-triggered reactions of biological photoreceptors have gained immense attention for their role as molecular switches in their native organisms and for optogenetic application. The light, oxygen, and voltage 2 (LOV2) sensing domain of plant phototropin binds a C-terminal Jα helix that is docked on a β-sheet and unfolds upon light absorption by the flavin mononucleotide (FMN) chromophore. In this work, the signal transduction pathway of LOV2 from Avena sativa was investigated using time-resolved infrared spectroscopy from picoseconds to microseconds. In D2O buffer, FMN singlet-to-triplet conversion occurs in 2 ns and formation of the covalent cysteinyl-FMN adduct in 10 μs. We observe a two-step unfolding of the Jα helix: The first phase occurs concomitantly with Cys-FMN covalent adduct formation in 10 μs, along with hydrogen-bond rupture of the FMN C4═O with Gln-513, motion of the β-sheet, and an additional helical element. The second phase occurs in approximately 240 μs. The final spectrum at 500 μs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
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Affiliation(s)
- Patrick E Konold
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - Tilo Mathes
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - Jörn Weiβenborn
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - Marie Louise Groot
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
| | - Peter Hegemann
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081HV Amsterdam, The Netherlands
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50
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Aper SJ, Merkx M. Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn(2+) Sensor into a Light-Responsive Zn(2+) Binding Protein. ACS Synth Biol 2016; 5:698-709. [PMID: 27031076 DOI: 10.1021/acssynbio.6b00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein-based sensors and switches provide attractive tools for the real-time monitoring and control of molecular processes in complex biological environments. Fluorescent sensor proteins have been developed for a wide variety of small molecules, but the construction of genetically encoded light-responsive ligand binding proteins remains mostly unexplored. Here we present a generic approach to reengineer a previously developed FRET-based Zn(2+) sensor into a light-activatable Zn(2+) binding protein using a design strategy based on mutually exclusive domain interactions. These so-called VividZn proteins consist of two light-responsive Vivid domains that homodimerize upon illumination with blue light, thus preventing the binding of Zn(2+) between two Zn(2+) binding domains, Atox1 and WD4. Following optimization of the linker between WD4 and the N-terminus of one of the Vivid domains, VividZn variants were obtained that show a 9- to 55-fold decrease in Zn(2+) affinity upon illumination, which is fully reversible following dark adaptation. The Zn(2+) affinities of the switch could be rationally tuned between 1 pM and 2 nM by systematic variation of linker length and mutation of one of the Zn(2+) binding residues. Similarly, introduction of mutations in the Vivid domains allowed tuning of the switching kinetics between 10 min and 7 h. Low expression levels in mammalian cells precluded the demonstration of light-induced perturbation of cytosolic Zn(2+) levels. Nonetheless, our results firmly establish the use of intramolecular Vivid dimerization as an attractive light-sensitive input module to rationally engineer light-responsive protein switches based on mutually exclusive domain interactions.
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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
| | - 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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