title: New red-fluorescent calcium indicators for optogenetics, photoactivation and multi-color imaging.
abstract: Most chemical and, with only a few exceptions, all genetically encoded fluorimetric calcium (Ca(2+)) indicators (GECIs) emit green fluorescence. Many of these probes are compatible with red-emitting cell- or organelle markers. But the bulk of available fluorescent-protein constructs and transgenic animals incorporate green or yellow fluorescent protein (GFP and YFP respectively). This is, in part, not only heritage from the tendency to aggregate of early-generation red-emitting FPs, and due to their complicated photochemistry, but also resulting from the compatibility of green-fluorescent probes with standard instrumentation readily available in most laboratories and core imaging facilities. Photochemical constraints like limited water solubility and low quantum yield have contributed to the relative paucity of red-emitting Ca(2+) probes compared to their green counterparts, too. The increasing use of GFP and GFP-based functional reporters, together with recent developments in optogenetics, photostimulation and super-resolution microscopies, has intensified the quest for red-emitting Ca(2+) probes. In response to this demand more red-emitting chemical and FP-based Ca(2+)-sensitive indicators have been developed since 2009 than in the thirty years before. In this topical review, we survey the physicochemical properties of these red-emitting Ca(2+) probes and discuss their utility for biological Ca(2+) imaging. Using the spectral separability index Xijk (Oheim M., 2010. Methods in Molecular Biology 591: 3-16) we evaluate their performance for multi-color excitation/emission experiments, involving the identification of morphological landmarks with GFP/YFP and detecting Ca(2+)-dependent fluorescence in the red spectral band. We also establish a catalog of criteria for evaluating Ca(2+) indicators that ideally should be made available for each probe. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.
authors.affiliation: CNRS, UMR 8154, Paris F-75006, France; INSERM, U603, Paris F-75006, France; University Paris Descartes, PRES Sorbonne Paris Cité, Laboratory of Neurophysiology and New Microscopies, 45 rue des Saints Pères, Paris F-75006, France. Electronic address: martin.oheim@parisdescartes.fr.
authors.forename: Martin
authors.initials: M
authors.lastname: Oheim
authors.affiliation: CNRS, UMR 8154, Paris F-75006, France; INSERM, U603, Paris F-75006, France; University Paris Descartes, PRES Sorbonne Paris Cité, Laboratory of Neurophysiology and New Microscopies, 45 rue des Saints Pères, Paris F-75006, France; University of Florence, LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors.forename: Marcel
authors.initials: M
authors.lastname: van 't Hoff
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris F-75005, France; INSERM U1024, Paris F-75005, France; CNRS UMR 8197, Paris F-75005, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Feltz
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris F-75005, France; INSERM U1024, Paris F-75005, France; CNRS UMR 8197, Paris F-75005, France.
authors.forename: Alsu
authors.initials: A
authors.lastname: Zamaleeva
authors.affiliation: UPMC Université́ Paris 06, Ecole Normale Supérieure (ENS), 24 rue Lhomond, Paris F-75005, France; CNRS UMR 7203, Paris F-75005, France.
authors.forename: Jean-Maurice
authors.initials: JM
authors.lastname: Mallet
authors.affiliation: UPMC Université́ Paris 06, Ecole Normale Supérieure (ENS), 24 rue Lhomond, Paris F-75005, France; CNRS UMR 7203, Paris F-75005, France.
authors.forename: Mayeul
authors.initials: M
authors.lastname: Collot
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001572:Benzofurans / Q000737:chemistry; D001896:Boron Compounds / Q000737:chemistry; D002118:Calcium / Q000032:analysis* / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry*; D049452:Green Fluorescent Proteins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007093:Imidazoles / Q000737:chemistry; D008164:Luminescent Proteins / Q000737:chemistry / Q000235:genetics; D057054:Molecular Imaging / Q000379:methods*; D062308:Optogenetics / Q000379:methods*; D010777:Photochemistry / Q000379:methods*; D012235:Rhodamines / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics; D000097573:Red Fluorescent Protein
chemical_list: D001426:Bacterial Proteins; D001572:Benzofurans; D001896:Boron Compounds; D002118:Calcium; D005456:Fluorescent Dyes; D049452:Green Fluorescent Proteins; D007093:Imidazoles; D008164:Luminescent Proteins; D012235:Rhodamines; D000097573:Red Fluorescent Protein; C095489:4,4-difluoro-4-bora-3a,4a-diaza-s-indacene; C054562:yellow fluorescent protein, Bacteria; C082877:fura red
keywords: Calcium; Fluorescence; Genetically encoded calcium indicator (GECI); Nanobiosensor; Spectral cross-talk