Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging.

Several series of near-infrared (NIR) fluorescent proteins (FPs) were recently engineered from bacterial phytochromes but were not systematically compared in neurons. To fluoresce, NIR FPs utilize an enzymatic derivative of heme, the linear tetrapyrrole biliverdin, as a chromophore whose level in neurons is poorly studied. Here, we evaluated NIR FPs of the iRFP protein family, which were reported to be the brightest in non-neuronal mammalian cells, in primary neuronal culture, in brain slices of mouse and monkey, and in mouse brain in vivo. We applied several fluorescence imaging modes, such as wide-field and confocal one-photon and two-photon microscopy, to compare photochemical and biophysical properties of various iRFPs. The iRFP682 and iRFP670 proteins exhibited the highest brightness and photostability under one-photon and two-photon excitation modes, respectively. All studied iRFPs exhibited efficient binding of the endogenous biliverdin chromophore in cultured neurons and in the mammalian brain and can be readily applied to neuroimaging.

[1]  H. Paudel,et al.  Over‐expression of heme oxygenase‐1 promotes oxidative mitochondrial damage in rat astroglia , 2006, Journal of cellular physiology.

[2]  Daria M. Shcherbakova,et al.  Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging , 2016, Nature Communications.

[3]  W. Staines,et al.  Reduction of Lipofuscin-like Autofluorescence in Fluorescently Labeled Tissue , 1999, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[4]  V. Verkhusha,et al.  Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence , 2015, Scientific Reports.

[5]  Bin Wu,et al.  Monomeric red fluorescent proteins with a large Stokes shift , 2010, Proceedings of the National Academy of Sciences.

[6]  V. Verkhusha,et al.  Advances in engineering of fluorescent proteins and photoactivatable proteins with red emission. , 2010, Current Opinion in Chemical Biology.

[7]  M. Drobizhev,et al.  Two-photon absorption standards in the 550-1600 nm excitation wavelength range. , 2008, Optics express.

[8]  Y. Jan,et al.  Rational design of a monomeric and photostable far‐red fluorescent protein for fluorescence imaging in vivo , 2016, Protein science : a publication of the Protein Society.

[9]  J. Betley,et al.  Adeno-associated viral vectors for mapping, monitoring, and manipulating neural circuits. , 2011, Human gene therapy.

[10]  Stefan R. Pulver,et al.  Independent Optical Excitation of Distinct Neural Populations , 2014, Nature Methods.

[11]  Kami Kim,et al.  Bright and stable near infra-red fluorescent protein for in vivo imaging , 2011, Nature Biotechnology.

[12]  Bin Wu,et al.  Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics. , 2011, Current opinion in cell biology.

[13]  V. Verkhusha,et al.  How to Increase Brightness of Near-Infrared Fluorescent Proteins in Mammalian Cells. , 2017, Cell chemical biology.

[14]  Brandon K. Harvey,et al.  Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue , 2015, Nature Communications.

[15]  John R. Allen,et al.  A naturally-monomeric infrared fluorescent protein for protein labeling in vivo , 2015, Nature Methods.

[16]  Xue Han,et al.  High-performance genetically targetable optical neural silencing by proton pumps , 2010 .

[17]  Joerg Bewersdorf,et al.  Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy. , 2010, Biophysical journal.

[18]  Mark A. Smith,et al.  Overexpression of Heme Oxygenase in Neuronal Cells, the Possible Interaction with Tau* , 2000, The Journal of Biological Chemistry.

[19]  Vladislav V Verkhusha,et al.  Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes. , 2017, Chemical reviews.

[20]  V. Malashkevich,et al.  Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins. , 2015, Chemistry & biology.

[21]  N. Nakatsuji,et al.  Efficient gene transfer into the embryonic mouse brain using in vivo electroporation. , 2001, Developmental biology.

[22]  V. Verkhusha,et al.  Near-infrared fluorescent proteins for multicolor in vivo imaging , 2013, Nature Methods.

[23]  Roger Y Tsien,et al.  A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein , 2016, Nature Methods.

[24]  G. Bottiroli,et al.  Autofluorescence Spectroscopy and Imaging: A Tool for Biomedical Research and Diagnosis , 2014, European journal of histochemistry : EJH.

[25]  William A. Weiss,et al.  An improved monomeric infrared fluorescent protein for neuronal and tumor brain imaging , 2014, Nature Communications.

[26]  V. Verkhusha,et al.  Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes , 2016, Scientific Reports.

[27]  M. Drobizhev,et al.  Two-photon absorption properties of fluorescent proteins , 2011, Nature Methods.

[28]  Wenzhi Sun,et al.  Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies , 2017, Journal of Neuroscience Methods.

[29]  Lihong V. Wang,et al.  Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteins , 2014, Scientific Reports.

[30]  Aleksander Rebane,et al.  Enhancement of two-photon absorption in tetrapyrrolic compounds , 2003 .

[31]  W. Denk,et al.  Two-photon targeted patching (TPTP) in vivo , 2006, Nature Protocols.

[32]  Vladislav V. Verkhusha,et al.  Engineering of Bacterial Phytochromes for Near-Infrared Imaging, Sensing, and Light-Control in Mammals , 2013 .

[33]  Stewart T. Cole,et al.  Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis , 2009, Science.

[34]  Michael Z. Lin,et al.  Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome , 2009, Science.

[35]  Vladislav V Verkhusha,et al.  Near-infrared fluorescent proteins engineered from bacterial phytochromes. , 2015, Current opinion in chemical biology.

[36]  J. Perry,et al.  Rapid, broadband two-photon-excited fluorescence spectroscopy and its application to red-emitting secondary reference compounds , 2011 .

[37]  Erik S. Welf,et al.  A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo , 2016, Nature Biotechnology.

[38]  Vladislav V Verkhusha,et al.  Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. , 2015, Annual review of biochemistry.

[39]  Karel Svoboda,et al.  ScanImage: Flexible software for operating laser scanning microscopes , 2003, Biomedical engineering online.

[40]  Lihong V. Wang,et al.  Deep-tissue photoacoustic tomography of a genetically encoded near-infrared fluorescent probe. , 2012, Angewandte Chemie.

[41]  V. Verkhusha,et al.  Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome , 2013, Nature Communications.

[42]  F. Helmchen,et al.  Specific Early and Late Oddball-Evoked Responses in Excitatory and Inhibitory Neurons of Mouse Auditory Cortex , 2015, The Journal of Neuroscience.

[43]  Seung Joong Kim,et al.  Simple rules for passive diffusion through the nuclear pore complex , 2016, The Journal of cell biology.

[44]  Kai Chen,et al.  Neurons Overexpressing Heme Oxygenase‐1 Resist Oxidative Stress‐Mediated Cell Death , 2000, Journal of neurochemistry.