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26 Publications

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    01/15/22 | Fluorescent chemigenetic actuators and indicators for use in living animals.
    Farrants H, Tebo AG
    Current Opinion in Pharmacology. 2022 Jan 15;62:159-167. doi: 10.1016/j.coph.2021.12.007

    Fluorescent indicators and actuators provide a means to optically observe and perturb dynamic events in living animals. Although chemistry and protein engineering have contributed many useful tools to observe and perturb cells, an emerging strategy is to use chemigenetics: systems in which a small molecule dye interacts with a genetically encoded protein domain. Here we review chemigenetic strategies that have been successfully employed in living animals as photosensitizers for photoablation experiments, fluorescent cell cycle indicators, and fluorescent indicators for studying dynamic biological signals. Although these strategies at times suffer from challenges, e.g. delivery of the small molecule and assembly of the chemigenetic unit in living animals, the advantages of using small molecules with high brightness, low photobleaching, no chromophore maturation time and expanded color palette, combined with the ability to genetically target them to specific cell types, make chemigenetic fluorescent actuators and indicators an attractive strategy for use in living animals.

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    11/30/21 | Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging.
    Benaissa H, Ounoughi K, Aujard I, Fischer E, Goïame R, Nguyen J, Tebo AG, Li C, Le Saux T, Bertolin G, Tramier M, Danglot L, Pietrancosta N, Morin X, Jullien L, Gautier A
    Nature Communications. 2021 Nov 30;12(1):6989. doi: 10.1038/s41467-021-27334-0

    Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.

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    10/31/21 | Versatile On-Demand Fluorescent Labeling of Fusion Proteins Using Fluorescence-Activating and Absorption-Shifting Tag (FAST).
    Gautier A, Jullien L, Li C, Plamont M, Tebo AG, Thauvin M, Volovitch M, Vriz S
    Methods Mol Biol. 2021;2350:253-265. doi: 10.1007/978-1-0716-1593-5_16

    Observing the localization, the concentration, and the distribution of proteins in cells or organisms is essential to understand theirs functions. General and versatile methods allowing multiplexed imaging of proteins under a large variety of experimental conditions are thus essential for deciphering the inner workings of cells and organisms. Here, we present a general method based on the non-covalent labeling of a small protein tag, named FAST (fluorescence-activating and absorption-shifting tag), with various fluorogenic ligands that light up upon labeling, which makes the simple, robust, and versatile on-demand labeling of fusion proteins in a wide range of experimental systems possible.

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    10/18/21 | The power of peer networking for improving STEM faculty job applications: a successful pilot program
    Guardia CM, Kane E, Tebo AG, Sanders AA, Kaya D, Grogan KE
    bioRxiv. 10/2021:. doi: 10.1101/2021.10.16.464662

    In order to successfully obtain a faculty position, postdoctoral fellows or ‘postdocs’, must submit an application which requires considerable time and effort to produce. These job applications are often reviewed by mentors and colleagues, but rarely are postdocs offered the opportunity to solicit feedback multiple times from reviewers with the same breadth of expertise often found on an academic search committee. To address this gap, this manuscript describes an international peer reviewing program for small groups of postdocs with a broad range of expertise to reciprocally and iteratively provide feedback to each other on their application materials. Over 145 postdocs have participated, often multiple times, over three years. A survey of participants in this program revealed that nearly all participants would recommend participation in such a program to other faculty applicants. Furthermore, this program was more likely to attract participants who struggled to find mentoring and support elsewhere, either because they changed fields or because of their identity as a woman or member of an underrepresented population in STEM. Participation in programs like this one could provide early career academics like postdocs with a diverse and supportive community of peer mentors during the difficult search for a faculty position. Such psychosocial support and encouragement has been shown to prevent attrition of individuals from these populations and programs like this one target the largest ‘leak’ in the pipeline, that of postdoc to faculty. Implementation of similar peer reviewing programs by universities or professional scientific societies could provide a valuable mechanism of support and increased chances of success for early-career academics in their search for independence.Competing Interest StatementThe authors have declared no competing interest.

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    09/06/21 | Nitrite reductase activity within an antiparallel de novo scaffold.
    Koebke KJ, Tebo AG, Manickas EC, Deb A, Penner-Hahn JE, Pecoraro VL
    JBIC Journal of Biological Inorganic Chemistry. 09/2021;26(7):855 - 862. doi: 10.1007/s00775-021-01889-1

    Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis3 binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis3 binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis3 binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.

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    03/15/21 | Enhanced Photoinduced Electron Transfer Through a Tyrosine Relay in a De Novo Designed Protein Scaffold Bearing a Photoredox Unit and a Fe <sup>II</sup> S <sub>4</sub> Site
    Tebo A, Quaranta A, Pecoraro VL, Aukauloo A
    ChemPhotoChem. 03/2021;5(7):665 - 668. doi: 10.1002/cptc.v5.710.1002/cptc.202100014

    Electron transfer (ET) processes in biology over long distances often proceed via a series of hops, which reduces the distance dependence of the rate of ET. The protein matrix itself can be involved in mediating ET directly through the participation of redox-active amino acids. We have designed an electron transfer chain incorporated into a de novo protein scaffold, which is capable of photoinduced intramolecular electron transfer between a photoredox unit and a FeIIS4 site through a tyrosine amino acid relay. The kinetics were characterized by nanosecond laser pulse photolysis and revealed that electron transfer from [RuIIIbpymal]3+ proceeds most efficiently via a tyrosine located ∼16 Å from Rubpymal (bpymal=1-((1-([2,2′-bipyridin]-4-yl)-1H-1,2,3-triazol-4-yl)methyl)-1H-pyrrole-2,5-dione). Removal of the tyrosine as the electron relay station results in a 20-fold decrease in the apparent rate constant for the electron transfer.

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    02/04/21 | Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System.
    De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P
    Angew Chemie (International Edition English). 2021 Feb 04:. doi: 10.1002/anie.202015201

    Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

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    08/01/20 | Sensing cellular biochemistry with fluorescent chemical–genetic hybrids
    Gautier A, Tebo AG
    Current Opinion in Chemical Biology. 08/2020;57:58–64. doi: 10.1016/j.cbpa.2020.04.005

    Fluorescent biosensors are powerful tools for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical–genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.

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    09/25/20 | Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins
    Zitter ED, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Meervelt LV, Dedecker P
    bioRxiv. 09/2020:2020.09.25.313528. doi: 10.1101/2020.09.25.313528

    Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

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    04/05/20 | Orthogonal fluorescent chemogenetic reporters for multicolor imaging
    Tebo AG, Moeyaert B, Thauvin M, Carlon-Andres I, Böken D, Volovitch M, Padilla-Parra S, Dedecker P, Vriz S, Gautier A
    Nature Chemical Biology. 04/2020:1–9. doi: 10.1038/s41589-020-0611-0

    Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen-activating tags based on the fluorescence-activating and absorption shifting tag (FAST) that are compatible with two-color, live-cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development and the development of split complementation systems capable of detecting multiple protein–protein interactions by live-cell fluorescence microscopy. The fluorescent chemogenetic reporters greenFAST and redFAST were engineered by protein engineering. They display orthogonal fluorogen recognition and spectral properties allowing efficient multicolor imaging of proteins in live cells and organisms.

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