HulaCCR1, a pump-like cation channelrhodopsin discovered in a lake microbiome: Figure Data

This repository contains figure data for the paper Takaramoto et al (2024) HulaCCR1, a pump-like cation channelrhodopsin discovered in a lake microbiome J Mol Biol 168844: 436.The files are as follows:<b>Figure_1a_alignment.csv</b>: Alignment of transmembrane helix 3<b>Figure_1b_for_phylogenetic_tree.meg</b>: Alignment used to generate the tree<b>Figure_2b_rhodopsin_phylogeny.newick</b>: Phylogeny of the stramenopile (and other heterotrophic flagellate) CCRs<b>Figure_2c_clade_distrbution.csv</b>: Distribution of BCCRs in the different environmental datasets containing ChRs from the mgCCR1-3 clade. CSV file with three columns: JGI GOLD analysis accession (or HulaCCR1 for our Hula Lake dataset), BCCR (sub)clade, number of genes<b>Figure_3a_difference_absorption_spectra.csv</b>: Difference UV-visible absorption spectra between before and after the hydroxylamine bleach of HulaCCR1<b>Figure_3c_photocurrents_standard_vs_NMG+.csv</b>: Photocurrents of HulaCCR1 with standard solutions and NMG+ solutions<b>Figure_3d_I-V_plot.csv</b>: I-V plot of HulaCCR1 photocurrents with different extracellular solutions<b>Figure_3e_pH_dependence.csv</b>: pH dependence of the I-V plot<b>Figure_4a_representative_traces.csv</b>: Representative photocurrent traces of HulaCCR1 with different cations<b>Figure_4b_I-V_plots.csv</b>: I-V plots of HulaCCR1 photocurrents with different extracellular cations<b>Figure_4c_Erev_permeability.csv</b>: Difference in Erev between different cations and H+ (ΔErev) and relative permeability of different cations against H+<b>Figure_5b_action_spectra.csv</b>: Normalized action spectra of the HulaCCR1 WT and E176D<b>Figure_5c_photocurrent_traces_E176.csv</b>: Photocurrent traces of the WT and E176D upon nanosecond laser flash excitation<b>Figure_5d_time_constants.csv</b>: Time constants of channel opening and closing of the HulaCCR1 WT and E176D<b>Figure_5e_photocurrent_traces_C181.csv</b>: Photocurrent traces of the HulaCCR1 WT, C181A, and C181S upon nanosecond laser flash excitation<b>Figure_5f_off-kinetics.csv</b>: Photocurrent offkinetics of HulaCCR1 WT, C303A, and ChRmine<b>Figure_5g_light-power_dependence.csv</b>: Light-power dependence of the photocurrent of HulaCCR1 WT, C303A, and ChRmine<b>Figure_6c_membrane_localization.csv</b>: Quantification of plasma membrane localization<b>Figure_6d_I-V_plot.csv</b>: I-V plot of the full length and truncated variants of HulaCCR1<b>Figure_7b_voltage_traces.csv</b>: Light stimulation of HulaCCR1-expressing hippocampal neurons: voltage traces<b>Figure_S1a_transposon_phylogeny.newick</b>: Phylogenetic tree of transposon sequences found in reference genomes and in the flanks of the contigs containing genes from the mgCCR1-3 clade<b>Figure_S1a_transposon_subclades.csv</b>: Summary of the transposon subclades identified in contigs with the genes from the mgCCR1-3 clade. For each representative sequence, numbers of fragments from each mgCCR1-3 subclade that cluster together with the representative are listed.<b>Figure_S1b_cryptist_phylogeny.newick</b>: 18S phylogeny of the Cryptista<b>Figure_S2_sintax.tsv</b>: Aggregated results of the sintax analysis<b>Figure_S4a_photocurrent_traces.csv</b>: Representative photocurrent traces of the HulaCCR1 WT and mutants<b>Figure_S4b_time_constants_E176.csv</b>: Time constants of channel opening and closing of the WT HulaCCR1 and E176D<b>Figure_S4d_action_spectra.csv</b>: Normalized action spectra of the HulaCCR1 WT and mutants<b>Figure_S4e_light-power_dependence.csv</b>: Light-power dependence of photocurrent traces of the HulaCCR1 WT, C303A, and ChRmine<b>Figure_S5b_photocurrent_traces.csv</b>: Representative photocurrent traces of the HulaCCR1 WT, E319Q, and E322Q<b>Figure_S5c_photocurrent_amplitude.csv</b>: Mean photocurrent amplitude recorded at −80 mV<b>Figure_S5d_photocurrent_traces_D2O.csv</b>: Photocurrent traces of the HulaCCR1 WT and E322Q upon nanosecond laser-flash excitation recorded in H2O/D2O solutions<b>Figure_S5e_time_constants.csv</b>: Time constants of channel opening and closing of the HulaCCR1 WT and E322Q<b>Figure_S6b_I-V_plots.csv</b>: I-V plots of the full-length HulaCCR1 and truncated variant 13-428<b>Figure_S6c_photocurrent_traces.csv</b>: Representative photocurrent traces of the full-length HulaCCR1 and truncated variant 13-428<b>Figure_S7a_fluorescence_profiles_HulaCCR1.csv</b>: Normalized fluorescence profiles of the full-length protein and the truncated variants<b>Figure_S7b_GtACR1.csv</b>: Normalized fluorescence profiles of GtACR1 WT and GtACR1 with residues 1-43 from HulaCCR1 at the N-terminus<b>Figure_S7c_photocurrent_traces.csv</b>: Representative photocurrent trances of truncated variants<b>HulaCCR1_fromColabFold.zip</b> and <b>mgCCR1_fromColabFold.zip</b>: structures of HulaCCR1 and mgCCR1 predicted with ColabFold