Spectra analysis and live-neuron imaging of cyclic AMP binding domain fusing circularly permutated GFP: Data for violet light excitable cyclic AMP indicator

Cyclic adenosine monophosphate (cyclic AMP) is a second messenger, which is involved in the regulation of various cellular processes, including neuronal firing rate, synaptic plasticity, axon formation and axon elongation in brain. Although the main molecules in the cAMP-mediated signaling pathway are well studied, the spatio-temporal dynamics of the cAMP remain to be elucidated. Live imaging is an informative tool to investigate the cell signaling dynamics. It allows continuous monitoring of a specific cell over a period of time. Thus, optical probes for cAMP are important tools for studying the dynamics of cAMP signaling. Multiple genetically encoded cAMP probes are available [1], [2], including Förster resonance energy transfer (FRET) based or circular permutated fluorescent protein (cpFP) based probes. cpFP-based probes have an advantage of easier handling than FRET-based probes caused by monomeric detection and smaller molecular size. However, there is no cAMP probe compatible with violet light excitation. Therefore, we fused violet light excitable cpGFP to cyclic nucleotide binding domain (CBD) in E. coli cAMP receptor protein. This construct successfully responded to cAMP concentration changes. We show here the spectra data and live-cell imaging data of the violet light excitable cAMP probe which can be used for multi-signal fluorescence imaging.


a b s t r a c t
Cyclic adenosine monophosphate (cyclic AMP) is a second messenger, which is involved in the regulation of various cellular processes, including neuronal firing rate, synaptic plasticity, axon formation and axon elongation in brain. Although the main molecules in the cAMP-mediated signaling pathway are well studied, the spatio-temporal dynamics of the cAMP remain to be elucidated. Live imaging is an informative tool to investigate the cell signaling dynamics. It allows continuous monitoring of a specific cell over a period of time. Thus, optical probes for cAMP are important tools for studying the dynamics of cAMP signaling. Multiple genetically encoded cAMP probes are available [1,2] , including Förster resonance energy transfer (FRET) based or circular permutated fluorescent protein (cpFP) based probes. cpFP-based probes have an advantage of easier handling than FRET-based probes caused by monomeric detection and smaller molecular size. However, there is no cAMP probe compatible with violet light excitation. Therefore, we fused violet light excitable cpGFP to cyclic nucleotide binding domain (CBD) in E. coli cAMP receptor protein. This construct successfully responded to cAMP concentration changes. We show here the spectra data and live-cell imaging data of the violet light excitable cAMP probe which can be used for multi-signal fluorescence imaging.

Value of the Data
• cAMP acts as second messengers and is widely present in many cell types such as neurons. cAMP fluorescent indicator allows continuous monitoring of a specific cell over a period of time. • Almost all other signaling fluorescent indicators including FRET-based probes use blue or green light for their excitation. Thus, this cAMP indicator construct can easily combine with other indicators. • Further mutations or modifications in this construct will expand the utility of violet excitable cAMP probe.

Data Description
The Escherichia coli ( E. coli ) CRP is a transcriptional activator which regulates many transcription units in response to intracellular concentration of cAMP. CRP is organized in two distinct domains: (i) an N-terminal CBD (residues 1-136), which contains the cyclic nucleotide-binding module and (ii) a C-terminal DNA-binding domain (DBD; residues 139-209), which contains a helix-turn-helix motif for binding to DNA [3] . So, we designed the cAMP probe for which the CBD fuses to circularly permutated GFP (cpGFP) instead of the DBD ( Fig. 1 A). Then, the CBD-cpGFP was inserted into pColdI and pAAV2-SynTetOff [5] vectors for protein expression in E. coli and hippocampal neurons, respectively ( Fig. 1 B and C). The CBD-cpGFP protein was expressed in E. coli BL21, then purified CBD-cpGFP protein was analyzed spectra using fluorescence spectrometry in the presence or absence of cAMP or cGMP ( Fig. 2 A). The CBD-cpGFP fluorescence was decreased with cAMP elevation. Fitting curve ( Fig. 2 B) indicates the K d = 4.4 μM (Hill coefficient = 0.86). The CBD-cpGFP was expressed in hippocampal neurons using rAAV vector ( Fig. 3 A). Hippocampal neurons (DIV18) were stimulated by 10 μM forskolin (agonist for adenylyl cyclase)/ 100 μM ibudilast (inhibitor for phosphodiesterase) under confocal microscopy. The CBD-cpGFP fluorescence was also decreased with cAMP elevation in hippocampal neurons ( Fig. 3 B).
The deposited data (doi: 10.17632/h5wgkrfsk4.1) contain as follows: pColdI-CBD-cpGFP.dna: SnapGene DNA file of the CBD-cpGFP in pCold I E.coli expression vector. pAAV2-SynTetOff-CBD-cpGFP.dna: SnapGene DNA file of the CBD-cpGFP in pAAV2-SynTetOff vector for neuronal expression.  CBD-cpGFP raw spectra data.xlsx: the excitation and emission spectra of the CBD-cpGFP protein in the absence or presence of cAMP. CBD-cpGFP raw dose response.xlsx: the raw dose-response data of the CBD-cpGFP for cAMP or cGMP. CBD-cpGFP raw time lapse.xlsx: the time-lapse raw data of the CBD-cpGFP expressing hippocampal neurons stimulated by the application of forskolin/ibudilast. CBD-cpGFP analyzed spectrum and dose response.JNB: SigmaPlot graph file of the normalized mean excitation and emission spectra, and the normalized dose-response data for cAMP or cGMP. CBD-cpGFP analyzed time lapse.JNB: SigmaPlot graph file of the normalized time-lapse data of the CBD-cpGFP expressing hippocampal neurons stimulated by the application of forskolin/ibudilast. CBD-cpGFP in hippocampal neurons.lsm: Zeiss image file of CBD-cpGFP expressing hippocampal neuron.

Plasmid Construction
Green fluorescent cAMP indicators were constructed as follows: cAMP-binding domains of E. coli (DH5a) CRP (a.a. 1-134, GenBank Accession Number KP670514) were PCR amplified ( Pfx50 , ThermoFisher). cpGFP of GEX-GECO [4] was also PCR amplified. These PCR products were inserted into subcloning vector pBluescript II KS( + ) (Agilent), followed by sequence analysis. cpGFP was fused to the Xho I site attached to the C-terminal of CBD. CBD-cpGFP construct was inserted into pCold I (TaKaRa) and pAAV2-SynTetOff [5] for protein expression in E. coli and hippocampal neurons, respectively.

Bacterial Protein Expression and Purification
E. coli BL21 (BioDynamics) transformed with histidine tag containing pCold I-CBD-cpGFP was grown at 37 °C until OD 600 ≈0.4 in 50 mL LB medium supplemented with 100 μg/mL ampicillin, and protein expression was induced by adding 0.5 mM IPTG and incubating for an additional 20-24 h at 15 °C. Protein-expressing E. coli was collected and lysed with 3 mL BugBuster solution (Merck) for 30 min at 4 °C, followed by binding with 300 μL cobalt resin (ABT) with 30 mL buffer containing (in mM) 50 Na-phosphate, 300 NaCl, and 10 imidazole for 1 h at 4 °C. Proteinbinding resin was washed thrice with the buffer (30 mL) using centrifuge. Protein was eluted with 3 mL elution buffer containing (in mM) 50 Na-phosphate, 300 NaCl, and 150 imidazole. Subsequently, protein was concentrated and its buffer replaced to phosphate buffered saline by 10,0 0 0 MW cut ultrafiltration (VIVASPIN 6, sartorius). The concentrated protein solutions were stored at 4 °C under dark conditions.

Optical Properties Analysis
Purified CBD-cpGFP protein was suspended in the buffer containing 50 mM HEPES pH 7.0, 5 mM ascorbic acid, 4 mM Glutathione and 0.1% bovine serum albumin. The fluorescence spectra were measured using a fluorescence spectrophotometer (FP-6500, JASCO).

Primary Hippocampal Culture
Hippocampi were dissected from ICR embryos at E17. Hippocampal neurons were dissociated by using Neuron Dissociation Solutions (Fujifilm) and plated on coverslips coated with poly-Dlysine at a density of 3 × 10 4 cells/cm 2 in Neurobasal plus medium supplemented with B27 (Thermo Fisher) and 2 mM L-alanyl-L-glutamine. Dissociated neurons were maintained at 37 °C in 5% CO 2 for 3 weeks.

Live-Cell Imaging
Time-lapse images were taken using a confocal microscopy (LSM710, Zeiss) with a 20 ×, 0.8 N.A. dry objective lens. 405 nm laser was used for excitation of cpGFP. Emission was collected between 489 nm and 538 nm. Time-lapse images were performed in Hank's balanced salt solution (Fujifilm) with/without 10 μM forskolin (Fujifilm) and 100 μM ibudilast (Fujifilm), and acquired every 1 s using Zen 2009 software (Zeiss).

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.