DOI: 10.25338/b89k9j
title: Data from: Protein-Chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes

description: Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly
 related to the phytochromes found in a broad range of bacteria, algae, and
 plants. CBCRs can control several aspects of cyanobacterial photobiology,
 including phototaxis, motile/sessile transitions, and complementary
 chromatic acclimation. CBCRs can sense a very broad range of light, with
 different subfamilies detecting UV, violet, blue, teal, green, yellow,
 orange, red, or far-red light (375-745 nm). This dataset is associated
 with a study of red/green CBCRs, a group in which red-absorbing dark
 states give rise to green-absorbing photoproducts upon light absorption
 and subsequent 15,16-photoisomerization of the phycocyanobilin
 chromophore. Interestingly, some members of this group fail to undergo
 this reaction. By comparing a conserved lineage of these red-inactive
 CBCRs to their photoactive red/green relatives, we identified three
 residues that determine whether photoisomerization can occur: introduction
 of these three substitutions is sufficient to block photoisomerization in
 a red/green CBCR or restore it in a red-inactive one. Such engineered
 red-inactive ones also mimic other properties of naturally occuring
 red-inactive CBCRs. This study thus demonstrates that it is possible to
 engineer the fate of the excited-state population of a biological
 photoreceptor with only a few amino acid substitutions. This work used
 maximum likelihood phylogenetic analysis to identify a conserved lineage
 of red-inactive CBCRs. Chosen proteins were then obtained through
 commercial gene synthesis and recombinantly expressed in E. coli cells
 that had been engineered to product phycocaynobilin or other bilin
 chromophores. Purified proteins were then characterized using absorption,
 fluorescence, and circular dichroism (CD) spectroscopy. This dataset
 provides raw data for that analysis. Data are ogranized as a single
 gzipped tarball with an associated README file. Within the compressed
 archive, there are five subdirectories containing files for phylogenetic
 analysis, for absorption spectroscopy, for fluorescence spectroscopy, for
 CD spectroscopy, and for the sequences of the synthetic genes.
 Phylogenetic files are in CLUSTAL, PHYLIP, and Newick format (starting
 alignment in CLUSTAL format; input file for phylogenetic inference, PHYLIP
 format; output tree, Newick format). Spectroscopic data are in .csv or
 tab-delimited flat text. Synthetic gene sequences are in FASTA format.
description: Absorption spectra were collected on a Cary 50 spectrophotometer
 and were exported from the Cary software in .csv format. Those files were
 converted to unix newlines on the unix command line and are deposited here
 in that format. Processed files used for figure presentation are also
 included as tab-delimited text. Fluorescence spectra
 were collected on a QM-6/2005SE fluorimeter equipped with red-enhanced
 photomultiplier tubes (Photon Technology International 814 Series). Files
 were displayed in tabular format and copy/pasted for text export. Emission
 spectra were numerically integrated for estimation of fluorescence quantum
 yield, and the data used for quantum yield estimation are included as
 tab-delimited text along wrocessed files used for figure presentation
 (also as tab-delimited text). Circular dichroism
 spectra were collected on an Applied Photophysics Chirascan and were
 converted to tab-delimited text using the Applied Photophysics software.
 Those files were converted to unix newlines on the unix command line and
 are deposited here in that format. Processed files used for figure
 presentation are also included as tab-delimited text (compressed archive,
 .tar.gz extension). Phylogenetic data include the three
 files used in the workflow for the published phylogeny. A multiple
 sequence alignment was constructed using MAFFT v7.450 (full command-line
 settings are in the manuscript). This file is deposited here in CLUSTAL
 format (.aln extension). For use in calculating a phylogeny, this file was
 combined with structural information generated using STRIDE or DSSP on the
 command line; this was performed as described in the main manuscript. The
 resulting file is deposited here in PHYLIP format (.phy extension) and can
 be used in PhyML-structure (full command-line settings are in the
 manuscript). The output phylogeny is deposited here in Newick format (.txt
 extension). For figure preparation, the Newick file was processed in
 FigTree prior to annotation, scaling, and coloring in Adobe
 Illustrator.
description: Note that a README.txt is associated with this
 submission. Synthetic sequences are reported as the
 sequenced insert, including flanking restriction sites used in
 cloning.