1
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Gotthard G, Mous S, Weinert T, Maia RNA, James D, Dworkowski F, Gashi D, Furrer A, Ozerov D, Panepucci E, Wang M, Schertler GFX, Heberle J, Standfuss J, Nogly P. Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography. IUCRJ 2024; 11:792-808. [PMID: 39037420 PMCID: PMC11364019 DOI: 10.1107/s2052252524005608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 07/23/2024]
Abstract
Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
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Affiliation(s)
- Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Raiza Nara Antonelli Maia
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light SourcePaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Laboratory of Femtochemistry, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dmitry Ozerov
- Science ITPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Department of BiologyETH Zürich8093ZürichSwitzerland
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University in Kraków30-387KrakówPoland
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2
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Yudenko A, Bazhenov SV, Aleksenko VA, Goncharov IM, Semenov O, Remeeva A, Nazarenko VV, Kuznetsova E, Fomin VV, Konopleva MN, Al Ebrahim R, Sluchanko NN, Ryzhykau Y, Semenov YS, Kuklin A, Manukhov IV, Gushchin I. luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase. Proteins 2024. [PMID: 39171358 DOI: 10.1002/prot.26739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that the product of the luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes both in vivo in Escherichia coli and in vitro. Overall, EsLuxA is much less bright compared with luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a (β/α)8 TIM-barrel fold, characteristic for other bacterial luciferases, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for the development of new bacterial luciferases that have an advantage of being encoded by a single gene.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey V Bazhenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vladimir A Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vadim V Fomin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria N Konopleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Rahaf Al Ebrahim
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yury S Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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3
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Nikolaev A, Kuzmin A, Markeeva E, Kuznetsova E, Ryzhykau YL, Semenov O, Anuchina A, Remeeva A, Gushchin I. Reengineering of a flavin-binding fluorescent protein using ProteinMPNN. Protein Sci 2024; 33:e4958. [PMID: 38501498 PMCID: PMC10949330 DOI: 10.1002/pro.4958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/12/2024] [Accepted: 02/18/2024] [Indexed: 03/20/2024]
Abstract
Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non-proteinaceous ligand-binding protein, flavin-based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acids interacting with the chromophore (flavin mononucleotide, FMN) while letting ProteinMPNN predict the rest of the sequence. The software package suggested replacing 36-48 out of the remaining 86 amino acids so that the resulting sequences are 55%-66% identical to the original one. The three designs that we tested experimentally displayed different expression levels, yet all were able to bind FMN and displayed fluorescence, thermal stability, and other properties similar to those of CagFbFP. Our results demonstrate that ProteinMPNN can be used to generate diverging unnatural variants of fluorescent proteins, and, more generally, to reengineer proteins without losing their ligand-binding capabilities.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena Markeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
- Frank Laboratory of Neutron PhysicsJoint Institute for Nuclear ResearchDubnaRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Arina Anuchina
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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4
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Nikolaev A, Tropina EV, Boldyrev KN, Maksimov EG, Borshchevskiy V, Mishin A, Yudenko A, Kuzmin A, Kuznetsova E, Semenov O, Remeeva A, Gushchin I. Two distinct mechanisms of flavoprotein spectral tuning revealed by low-temperature and time-dependent spectroscopy. Protein Sci 2024; 33:e4851. [PMID: 38038877 PMCID: PMC10731561 DOI: 10.1002/pro.4851] [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: 07/22/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin-binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time-resolved and low-temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein-flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant. Consequently, in Q148V, excitation, emission, and phosphorescence spectra are shifted, whereas in I52V A85Q, excitation and low-temperature phosphorescence spectra are relatively unchanged, while emission spectrum is altered. We also determine the x-ray structures of the two variants to reveal the flavin environment and complement the spectroscopy data. Our findings illustrate two distinct color-tuning mechanisms of flavin-binding proteins and could be helpful for the engineering of new variants with improved optical properties.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena V. Tropina
- Institute of Spectroscopy RASTroitskMoscowRussia
- National Research University Higher School of EconomicsMoscowRussia
| | | | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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5
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Lin T, Ge Y, Gao Q, Zhang D, Chen X, Hu Y, Fan J. Backbone Cyclization of Flavin Mononucleotide-Based Fluorescent Protein Increases Fluorescence and Stability. J Microbiol Biotechnol 2023; 33:1681-1691. [PMID: 37789714 PMCID: PMC10772547 DOI: 10.4014/jmb.2305.05011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 10/05/2023]
Abstract
Flavin mononucleotide-binding proteins or domains emit cyan-green fluorescence under aerobic and anaerobic conditions, but relatively low fluorescence and less thermostability limit their application as reporters. In this work, we incorporated the codon-optimized fluorescent protein from Chlamydomonas reinhardtii with two different linkers independently into the redox-responsive split intein construct, overexpressed the precursors in hyperoxic Escherichia coli SHuffle T7 strain, and cyclized the target proteins in vitro in the presence of the reducing agent. Compared with the purified linear protein, the cyclic protein with the short linker displayed enhanced fluorescence. In contrast, cyclized protein with incorporation of the long linker including the myc-tag and human rhinovirus 3C protease cleavable sequence emitted slightly increased fluorescence compared with the protein linearized with the protease cleavage. The cyclic protein with the short linker also exhibited increased thermal stability and exopeptidase resistance. Moreover, induction of the target proteins in an oxygen-deficient culture rendered fluorescent E. coli BL21 (DE3) cells brighter than those overexpressing the linear construct. Thus, the cyclic reporter can hopefully be used in certain thermophilic anaerobes.
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Affiliation(s)
- Tingting Lin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yuanyuan Ge
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Qing Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Di Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Xiaofeng Chen
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
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6
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Xing J, Gumerov VM, Zhulin IB. Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor. SCIENCE ADVANCES 2023; 9:eadi4517. [PMID: 37647406 PMCID: PMC10468136 DOI: 10.1126/sciadv.adi4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Signal perception is a key function in regulating biological activities and adapting to changing environments. Per-Arnt-Sim (PAS) domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity are not fully characterized. Here, we show that using sequence conservation and structural information, it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via flavin adenine dinucleotide and flavin mononucleotide cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.
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Affiliation(s)
- Jiawei Xing
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
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7
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Hocq R, Bottone S, Gautier A, Pflügl S. A fluorescent reporter system for anaerobic thermophiles. Front Bioeng Biotechnol 2023; 11:1226889. [PMID: 37476481 PMCID: PMC10355840 DOI: 10.3389/fbioe.2023.1226889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Owing to their inherent capacity to make invisible biological processes visible and quantifiable, fluorescent reporter systems have numerous applications in biotechnology. For classical fluorescent protein systems (i.e., GFP and derivatives), chromophore maturation is O2-dependent, restricting their applications to aerobic organisms. In this work, we pioneered the use of the oxygen-independent system FAST (Fluorescence Activating and absorption Shifting tag) in the thermophilic anaerobe Thermoanaerobacter kivui. We developed a modular cloning system that was used to easily clone a library of FAST expression cassettes in an E. coli-Thermoanaerobacter shuttle plasmid. FAST-mediated fluorescence was then assessed in vivo in T. kivui, and we observed bright green and red fluorescence for cells grown at 55°C. Next, we took advantage of this functional reporter system to characterize a set of homologous and heterologous promoters by quantifying gene expression, expanding the T. kivui genetic toolbox. Low fluorescence at 66°C (Topt for T. kivui) was subsequently investigated at the single-cell level using flow cytometry and attributed to plasmid instability at higher temperatures. Adaptive laboratory evolution circumvented this issue and drastically enhanced fluorescence at 66°C. Whole plasmid sequencing revealed the evolved strain carried functional plasmids truncated at the Gram-positive origin of replication, that could however not be linked to the increased fluorescence displayed by the evolved strain. Collectively, our work demonstrates the applicability of the FAST fluorescent reporter systems to T. kivui, paving the way for further applications in thermophilic anaerobes.
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Affiliation(s)
- Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sara Bottone
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Arnaud Gautier
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
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8
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Fine spectral tuning of a flavin-binding fluorescent protein for multicolor imaging. J Biol Chem 2023; 299:102977. [PMID: 36738792 PMCID: PMC10023982 DOI: 10.1016/j.jbc.2023.102977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Flavin-binding fluorescent proteins are promising genetically encoded tags for microscopy. However, spectral properties of their chromophores (riboflavin, flavin mononucleotide, and flavin adenine dinucleotide) are notoriously similar even between different protein families, which limits applications of flavoproteins in multicolor imaging. Here, we present a palette of 22 finely tuned fluorescent tags based on the thermostable LOV domain from Chloroflexus aggregans. We performed site saturation mutagenesis of three amino acid positions in the flavin-binding pocket, including the photoactive cysteine, to obtain variants with fluorescence emission maxima uniformly covering the wavelength range from 486 to 512 nm. We demonstrate three-color imaging based on spectral separation and two-color fluorescence lifetime imaging of bacteria, as well as two-color imaging of mammalian cells (HEK293T), using the proteins from the palette. These results highlight the possibility of fine spectral tuning of flavoproteins and pave the way for further applications of flavin-binding fluorescent proteins in fluorescence microscopy.
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9
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Remeeva A, Yudenko A, Nazarenko VV, Semenov O, Smolentseva A, Bogorodskiy A, Maslov I, Borshchevskiy V, Gushchin I. Development and Characterization of Flavin-Binding Fluorescent Proteins, Part I: Basic Characterization. Methods Mol Biol 2023; 2564:121-141. [PMID: 36107340 DOI: 10.1007/978-1-0716-2667-2_6] [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] [Indexed: 06/15/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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10
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Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Microbiol Spectr 2021; 9:e0102621. [PMID: 34937179 PMCID: PMC8694187 DOI: 10.1128/spectrum.01026-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
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Smolentseva A, Goncharov IM, Yudenko A, Bogorodskiy A, Semenov O, Nazarenko VV, Borshchevskiy V, Fonin AV, Remeeva A, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species. Photochem Photobiol Sci 2021; 20:1645-1656. [PMID: 34796467 DOI: 10.1007/s43630-021-00138-3] [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: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Light-oxygen-voltage (LOV) domains are common photosensory modules that found many applications in fluorescence microscopy and optogenetics. Here, we show that the Chloroflexus aggregans LOV domain can bind different flavin species (lumichrome, LC; riboflavin, RF; flavin mononucleotide, FMN; flavin adenine dinucleotide, FAD) during heterologous expression and that its physicochemical properties depend strongly on the nature of the bound flavin. We show that whereas the dissociation constants for different chromophores are similar, the melting temperature of the protein reconstituted with single flavin species varies from ~ 60 °C for LC to ~ 81 °C for FMN, and photobleaching half-times vary almost 100-fold. These observations serve as a caution for future studies of LOV domains in non-native conditions yet raise the possibility of fine-tuning various properties of LOV-based fluorescent probes and optogenetic tools by manipulating the chromophore composition.
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Affiliation(s)
- Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, 194064, Saint Petersburg, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000, Grenoble, France.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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12
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Goncharov IM, Smolentseva A, Semenov O, Natarov I, Nazarenko VV, Yudenko A, Remeeva A, Gushchin I. High-resolution structure of a naturally red-shifted LOV domain. Biochem Biophys Res Commun 2021; 567:143-147. [PMID: 34153684 DOI: 10.1016/j.bbrc.2021.06.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/30/2022]
Abstract
LOV domains are widespread photosensory modules that have also found applications in fluorescence microscopy, optogenetics, and light-driven generation of reactive oxygen species. Many of these applications require stable proteins with altered spectra. Here, we report a flavin-based fluorescent protein CisFbFP derived from Chloroflexus islandicus LOV domain-containing protein. We show that CisFbFP is thermostable, and its absorption and fluorescence spectra are red-shifted for ∼6 nm, which has not been observed for other cysteine-substituted natural LOV domains. We also provide a crystallographic structure of CisFbFP at the resolution of 1.2 Å that reveals alterations in the active site due to replacement of conservative asparagine with a serine. Finally, we discuss the possible effects of presence of cis-proline in the Aβ-Bβ loop on the protein's structure and stability. The findings provide the basis for engineering and color tuning of LOV-based tools for molecular biology.
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Affiliation(s)
- Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Ilia Natarov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
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13
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Nexha A, Carvajal JJ, Pujol MC, Díaz F, Aguiló M. Lanthanide doped luminescence nanothermometers in the biological windows: strategies and applications. NANOSCALE 2021; 13:7913-7987. [PMID: 33899861 DOI: 10.1039/d0nr09150b] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of lanthanide-doped non-contact luminescent nanothermometers with accuracy, efficiency and fast diagnostic tools attributed to their versatility, stability and narrow emission band profiles has spurred the replacement of conventional contact thermal probes. The application of lanthanide-doped materials as temperature nanosensors, excited by ultraviolet, visible or near infrared light, and the generation of emissions lying in the biological window regions, I-BW (650 nm-950 nm), II-BW (1000 nm-1350 nm), III-BW (1400 nm-2000 nm) and IV-BW (centered at 2200 nm), are notably growing due to the advantages they present, including reduced phototoxicity and photobleaching, better image contrast and deeper penetration depths into biological tissues. Here, the different mechanisms used in lanthanide ion-doped nanomaterials to sense temperature in these biological windows for biomedical and other applications are summarized, focusing on factors that affect their thermal sensitivity, and consequently their temperature resolution. Comparing the thermometric performance of these nanomaterials in each biological window, we identified the strategies that allow boosting of their sensing properties.
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Affiliation(s)
- Albenc Nexha
- Universitat Rovira i Virgili, Departament de Química Física i Inorgànica, Física i Cristal·lografia de Materials i Nanomaterials (FiCMA-FiCNA)-EMaS, Campus Sescelades, E-43007, Tarragona, Spain.
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14
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Röllen K, Granzin J, Remeeva A, Davari MD, Gensch T, Nazarenko VV, Kovalev K, Bogorodskiy A, Borshchevskiy V, Hemmer S, Schwaneberg U, Gordeliy V, Jaeger KE, Batra-Safferling R, Gushchin I, Krauss U. The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. J Biol Chem 2021; 296:100662. [PMID: 33862085 PMCID: PMC8131319 DOI: 10.1016/j.jbc.2021.100662] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/09/2023] Open
Abstract
Photoactive biological systems modify the optical properties of their chromophores, known as spectral tuning. Determining the molecular origin of spectral tuning is instrumental for understanding the function and developing applications of these biomolecules. Spectral tuning in flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, is limited by their dependency on protein-bound flavins, whose structure and hence electronic properties cannot be altered by mutation. A blue-shifted variant of the plant-derived improved light, oxygen, voltage FbFP has been created by introducing a lysine within the flavin-binding pocket, but the molecular basis of this shift remains unconfirmed. We here structurally characterize the blue-shifted improved light, oxygen, voltage variant and construct a new blue-shifted CagFbFP protein by introducing an analogous mutation. X-ray structures of both proteins reveal displacement of the lysine away from the chromophore and opening up of the structure as instrumental for the blue shift. Site saturation mutagenesis and high-throughput screening yielded a red-shifted variant, and structural analysis revealed that the lysine side chain of the blue-shifted variant is stabilized close to the flavin by a secondary mutation, accounting for the red shift. Thus, a single additional mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography, and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools for application in life sciences.
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Affiliation(s)
- Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joachim Granzin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Thomas Gensch
- IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France; Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stefanie Hemmer
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany; DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Valentin Gordeliy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renu Batra-Safferling
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
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15
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Remeeva A, Nazarenko VV, Kovalev K, Goncharov IM, Yudenko A, Astashkin R, Gordeliy V, Gushchin I. Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures. Proteins 2021; 89:1005-1016. [PMID: 33774867 DOI: 10.1002/prot.26078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/01/2023]
Abstract
Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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16
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Schenk R, Bachmaier S, Bringaud F, Boshart M. Efficient flavinylation of glycosomal fumarate reductase by its own ApbE domain in Trypanosoma brucei. FEBS J 2021; 288:5430-5445. [PMID: 33755328 DOI: 10.1111/febs.15812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 01/26/2023]
Abstract
A subset of flavoproteins has a covalently attached flavin prosthetic group enzymatically attached via phosphoester bonding. In prokaryotes, this is catalysed by alternative pyrimidine biosynthesis E (ApbE) flavin transferases. ApbE-like domains are present in few eukaryotic taxa, for example the N-terminal domain of fumarate reductase (FRD) of Trypanosoma, a parasitic protist known as a tropical pathogen causing African sleeping sickness. We use the versatile reverse genetic tools available for Trypanosoma to investigate the flavinylation of glycosomal FRD (FRDg) in vivo in the physiological and organellar context. Using direct in-gel fluorescence detection of covalently attached flavin as proxy for activity, we show that the ApbE-like domain of FRDg has flavin transferase activity in vivo. The ApbE domain is preceded by a consensus flavinylation target motif at the extreme N terminus of FRDg, and serine 9 in this motif is essential as flavin acceptor. The preferred mode of flavinylation in the glycosome was addressed by stoichiometric expression and comparison of native and catalytically inactive ApbE domains. In addition to the trans-flavinylation activity, the ApbE domain catalyses the intramolecular cis-flavinylation with at least fivefold higher efficiency. We discuss how the higher efficiency due to unusual fusion of the ApbE domain to its substrate protein FRD may provide a selective advantage by faster FRD biogenesis during rapid metabolic adaptation of trypanosomes. The first 37 amino acids of FRDg, including the consensus motif, are sufficient as flavinylation target upon fusion to other proteins. We propose FRDg(1-37) as 4-kDa heat-stable, detergent-resistant fluorescent protein tag and suggest its use as a new tool to study glycosomal protein import.
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Affiliation(s)
- Robin Schenk
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Sabine Bachmaier
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Frédéric Bringaud
- CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Université de Bordeaux, France
| | - Michael Boshart
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
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17
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Cardoso
Ramos F, Cupellini L, Mennucci B. Computational Investigation of Structural and Spectroscopic Properties of LOV-Based Proteins with Improved Fluorescence. J Phys Chem B 2021; 125:1768-1777. [PMID: 33566620 PMCID: PMC7917436 DOI: 10.1021/acs.jpcb.0c10834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/27/2021] [Indexed: 01/22/2023]
Abstract
Flavin-based fluorescent proteins are a class of fluorescent reporters derived from light, oxygen, and voltage (LOV) sensing proteins. Through mutagenesis, natural LOV proteins have been engineered to obtain improved fluorescence properties. In this study, we combined extended classical Molecular Dynamics simulations and multiscale Quantum Mechanics/Molecular Mechanics methods to clarify the relationship between structural and dynamic changes induced by specific mutations and the spectroscopic response. To reach this goal we compared two LOV variants, one obtained by the single mutation needed to photochemically inactivate the natural system, and the other (iLOV) obtained through additional mutations and characterized by a significantly improved fluorescence. Our simulations confirmed the "flipping and crowding" effect induced in iLOV by the additional mutations and revealed its mechanism of action. We also showed that these mutations, and the resulting differences in the composition and flexibility of the binding pockets, are not reflected in significant shifts of the excitation and emission energies, in agreement with the similarity of the spectra measured for the two systems. However, a small but consistent reduction was found in the Stokes shift of iLOV, suggesting a reduction of the intermolecular reorganization experienced by the chromophore after excitation, which could slow down its internal conversion to the ground state and improve the fluorescence.
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Affiliation(s)
- Felipe Cardoso
Ramos
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
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18
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Pudasaini A, Green R, Song YH, Blumenfeld A, Karki N, Imaizumi T, Zoltowski BD. Steric and Electronic Interactions at Gln154 in ZEITLUPE Induce Reorganization of the LOV Domain Dimer Interface. Biochemistry 2021; 60:95-103. [PMID: 33337855 PMCID: PMC8211391 DOI: 10.1021/acs.biochem.0c00819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Plants measure light quality, intensity, and duration to coordinate growth and development with daily and seasonal changes in environmental conditions; however, the molecular details linking photochemistry to signal transduction remain incomplete. Two closely related light, oxygen, or voltage (LOV) domain-containing photoreceptor proteins, ZEITLUPE (ZTL) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), divergently regulate the protein stability of circadian clock and photoperiodic flowering components to mediate daily and seasonal development. Using structural approaches, we identified that mutations at the Gly46 position led to global rearrangements of the ZTL dimer interface in the isolated ZTL-LOV domain. Specifically, G46S and G46A variants induce a 180° rotation about the ZTL-LOV dimer interface that is coupled to ordering of N- and C-terminal signaling elements. These conformational changes hinge upon rotation of a C-terminal Gln residue (Gln154) analogous to that present in light-state structures of ZTL. In contrast to other LOV proteins, a Q154L variant retains light-state interactions with GIGANTEA (GI), thereby indicating N5 protonation is not required for ZTL signaling. The results presented herein confirm a divergent signaling mechanism within ZTL, whereby steric and electronic effects following adduct formation can be sufficient for signal propagation in LOV proteins containing a Gly residue at position 46. Examination of bacterial LOV structures with Gly residues at the equivalent position suggests that mechanisms of signal transduction in LOV proteins may be fluid across the LOV protein family.
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Affiliation(s)
- Ashutosh Pudasaini
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Robert Green
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Young Hun Song
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Abby Blumenfeld
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Brian D. Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA Center for Drug Discovery, Design and Delivery, Southern Methodist University,corresponding author: Brian D. Zoltowski, Associate Professor, Department of Chemistry, Southern Methodist University, Dallas, TX 75275-0314, t. 214-768-2640, f. 214-768-4089,
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19
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Yudenko A, Smolentseva A, Maslov I, Semenov O, Goncharov IM, Nazarenko VV, Maliar NL, Borshchevskiy V, Gordeliy V, Remeeva A, Gushchin I. Rational Design of a Split Flavin-Based Fluorescent Reporter. ACS Synth Biol 2021; 10:72-83. [PMID: 33325704 DOI: 10.1021/acssynbio.0c00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nina L. Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38044 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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20
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Anderson NT, Weyant KB, Mukherjee A. Characterization of flavin binding in oxygen-independent fluorescent reporters. AIChE J 2020; 66. [PMID: 34305141 DOI: 10.1002/aic.17083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent proteins based on light, oxygen, and voltage (LOV) sensing photoreceptors are among the few reporter gene technologies available for studying living systems in oxygen-free environments that render reporters based on the green fluorescent protein nonfluorescent. LOV reporters develop fluorescence by binding flavin mononucleotide (FMN), which they endogenously obtain from cells. As FMN is essential to cell physiology as well as for determining fluorescence in LOV proteins, it is important to be able to study and characterize flavin binding in LOV reporters. To this end, we report a method for reversibly separating FMN from two commonly used LOV reporters to prepare stable and soluble apoproteins. Using fluorescence titration, we measured the equilibrium dissociation constant for binding with all three cellular flavins: FMN, flavin adenine dinucleotide, and riboflavin. Finally, we exploit the riboflavin affinity of apo LOV reporters, identified in this work, to develop a fluorescence turn-on biosensor for vitamin B2.
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Affiliation(s)
- Nolan T. Anderson
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
| | - Kevin B. Weyant
- Smith School of Chemical & Biomolecular Engineering Cornell University Ithaca New York 14853 USA
| | - Arnab Mukherjee
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
- Department of Chemistry University of California Santa Barbara California 93106 USA
- Neuroscience Research Institute University of California Santa Barbara California 93106 USA
- Center for Bioengineering University of California Santa Barbara California 93106 USA
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21
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Kim NM, Sinnott RW, Sandoval NR. Transcription factor-based biosensors and inducible systems in non-model bacteria: current progress and future directions. Curr Opin Biotechnol 2020; 64:39-46. [DOI: 10.1016/j.copbio.2019.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
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22
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Effects of Proline Substitutions on the Thermostable LOV Domain from Chloroflexus aggregans. CRYSTALS 2020. [DOI: 10.3390/cryst10040256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Light-oxygen-voltage (LOV) domains are ubiquitous photosensory modules found in proteins from bacteria, archaea and eukaryotes. Engineered versions of LOV domains have found widespread use in fluorescence microscopy and optogenetics, with improved versions being continuously developed. Many of the engineering efforts focused on the thermal stabilization of LOV domains. Recently, we described a naturally thermostable LOV domain from Chloroflexus aggregans. Here we show that the discovered protein can be further stabilized using proline substitution. We tested the effects of three mutations, and found that the melting temperature of the A95P mutant is raised by approximately 2 °C, whereas mutations A56P and A58P are neutral. To further evaluate the effects of mutations, we crystallized the variants A56P and A95P, while the variant A58P did not crystallize. The obtained crystal structures do not reveal any alterations in the proteins other than the introduced mutations. Molecular dynamics simulations showed that mutation A58P alters the structure of the respective loop (Aβ-Bβ), but does not change the general structure of the protein. We conclude that proline substitution is a viable strategy for the stabilization of the Chloroflexus aggregans LOV domain. Since the sequences and structures of the LOV domains are overall well-conserved, the effects of the reported mutations may be transferable to other proteins belonging to this family.
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23
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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24
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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25
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Polverini E, Schackert FK, Losi A. Interplay among the “flipping” glutamine, a conserved phenylalanine, water and hydrogen bonds within a blue-light sensing LOV domain. Photochem Photobiol Sci 2020; 19:892-904. [DOI: 10.1039/d0pp00082e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A combined photoacoustics and molecular dynamics approach highlights the crucial role of a conserved phenyalanine in photosensing LOV domains.
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Affiliation(s)
- Eugenia Polverini
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Florian Karl Schackert
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Aba Losi
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
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