A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch

  1. Hélène Duplus-Bottin
  2. Martin Spichty
  3. Gérard Triqueneaux
  4. Christophe Place
  5. Philippe Emmanuel Mangeot
  6. Théophile Ohlmann
  7. Franck Vittoz
  8. Gaël Yvert  Is a corresponding author
  1. CNRS and Ecole Normale Superieure de Lyon, France
  2. INSERM and Ecole Normale Superieure de Lyon, France

Abstract

Optogenetics enables genome manipulations with high spatiotemporal resolution, opening exciting possibilities for fundamental and applied biological research. Here, we report the development of LiCre, a novel light-inducible Cre recombinase. LiCre is made of a single flavin-containing protein comprising the AsLOV2 photoreceptor domain of Avena sativa fused to a Cre variant carrying destabilizing mutations in its N-terminal and C-terminal domains. LiCre can be activated within minutes of illumination with blue light, without the need of additional chemicals. When compared to existing photoactivatable Cre recombinases based on two split units, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark. LiCre was efficient both in yeast, where it allowed us to control the production of β-carotene with light, and in human cells. Given its simplicity and performances, LiCre is particularly suited for fundamental and biomedical research, as well as for controlling industrial bioprocesses.

Data availability

Raw flow-cytometry data have been deposited in Biostudies under accession code S-BSST580. Processed data used for figures are included in the supporting files.

Article and author information

Author details

  1. Hélène Duplus-Bottin

    Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    Hélène Duplus-Bottin, A patent application covering LiCre and its potential applications has been filed. Ref: FR3079832 A1 and WO2019193205. Patent applicant: CNRS; inventors: Hélène Duplus-Bottin, Martin Spichty and Gaël Yvert..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2029-5646
  2. Martin Spichty

    Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    Martin Spichty, A patent application covering LiCre and its potential applications has been filed. Ref: FR3079832 A1 and WO2019193205. Patent applicant: CNRS; inventors: Hélène Duplus-Bottin, Martin Spichty and Gaël Yvert..
  3. Gérard Triqueneaux

    Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  4. Christophe Place

    Laboratory of Physics, CNRS UMR5672, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  5. Philippe Emmanuel Mangeot

    CIRI-Centre International de Recherche en Infectiologie, Inserm U1111, CNRS UMR5308, INSERM and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  6. Théophile Ohlmann

    CIRI-Centre International de Recherche en Infectiologie, Inserm U1111, CNRS UMR5308, INSERM and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  7. Franck Vittoz

    Laboratory of Physics, CNRS UMR5672, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  8. Gaël Yvert

    Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, CNRS and Ecole Normale Superieure de Lyon, Lyon, France
    For correspondence
    Gael.Yvert@ens-lyon.fr
    Competing interests
    Gaël Yvert, A patent application covering LiCre and its potential applications has been filed. Ref: FR3079832 A1 and WO2019193205. Patent applicant: CNRS; inventors: Hélène Duplus-Bottin, Martin Spichty and Gaël Yvert..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1955-4786

Funding

H2020 European Research Council (StG-281359 (SiGHT))

  • Gaël Yvert

Centre National de la Recherche Scientifique (MITI 80 Prime READGEN)

  • Gaël Yvert

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kevin H Gardner, CUNY Advanced Science Research Center, United States

Version history

  1. Received: July 20, 2020
  2. Accepted: February 22, 2021
  3. Accepted Manuscript published: February 23, 2021 (version 1)
  4. Version of Record published: March 26, 2021 (version 2)

Copyright

© 2021, Duplus-Bottin et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 6,602
    views
  • 782
    downloads
  • 17
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Hélène Duplus-Bottin
  2. Martin Spichty
  3. Gérard Triqueneaux
  4. Christophe Place
  5. Philippe Emmanuel Mangeot
  6. Théophile Ohlmann
  7. Franck Vittoz
  8. Gaël Yvert
(2021)
A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch
eLife 10:e61268.
https://doi.org/10.7554/eLife.61268

Share this article

https://doi.org/10.7554/eLife.61268

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Isabelle Petit-Hartlein, Annelise Vermot ... Franck Fieschi
    Research Article

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Dietmar Funck, Malte Sinn ... Jörg S Hartig
    Research Article

    Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.