Phototransformation of the Red Light Sensor Cyanobacterial Phytochrome 2 from Synechocystis Species Depends on Its Tongue Motifs

Abstract

Background: Phytochromes are bilin-dependent red/far red photoreceptors. Results: Late processes of the P r 3 P fr photoconversion involve large scale conformational changes within the tongue region. Conclusion: Early intermediates lumi-R and R1 affect only the chromophore and its nearest surroundings, whereas late R2 formation recruits the Trp motifs in the peripheral tongue. Significance: The conserved motifs of the tongue region are important for photoconversion and presumably for signaling.

Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353

“…We also identified two knotless Phys, Mbl0113 and Mbl3828, which possess distinct domain structures (Table 2) and photochemical properties (Fig. 6) relative to SyCph2, the single knotless Phy in Synechocystis 6803 (48). These studies also expand our knowledge of both the diversity and spectral tuning of dual Cys CBCR GAFs.…”

“…4). To gain insight into the chromophore binding pockets and chromophore-protein interactions in these new proteins, we leveraged crystal structures of GAF domains from SyCph1, SyCph2, and a red-absorbing dark state (Pr) of AnPixJg2, and a green-absorbing photoproduct (Pg) of TePixJ (3,47,48). Notably, we chose to use the AnPixJg2 structure (Protein Data Bank code 3W2Z) to map these amino acid residues onto the conserved GAF domain fold that surrounds the PCB chromophore (Fig.…”

“…Both N-terminal GGDEF and EAL domains contain well conserved GGDEF and EAL motifs, suggesting that only the N-terminal guanylate cyclase is red/farred light regulated. We predict that c-di-GMP signaling in Microcoleus B353, presumably responsible for cell growth and phototactic movement responses, will be red/far-red dependent, rather than blue/green sensitive as seen in Synechocystis 6803 (48,49).…”

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

“…In support of this hairpin conformational switch, mutational studies on several Phys showed that the hairpin/GAF domain interactions are critical to Phy chemistry despite limited contact with the chromophore. For example, single amino acid substitutions within the PRXSF, WGG, and HbXE motifs either preclude photoconversion of Pr to Pfr, or enhance or stall thermal reversion if the Pfr state was generated, consistent with their predicted ability to impact the hairpin/GAF domain interface as Pr or Pfr (Essen et al, 2008;Anders et al, 2013Anders et al, , 2014Burgie et al, 2014aBurgie et al, , 2014b.…”

Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes

“…Most of the knowledge in molecular phytochrome research was obtained from cyanobacterial phytochromes and bacteriophytochromes which employ phycocyanobilin (PCB) and biliverdin (BV) as chromophores, respectively (Rockwell and Lagarias, 2010 ). These phytochromes are more tractable than plant phytochromes and thus, the first three-dimensional (3D) structures at atomic resolution were obtained from these representatives of the superfamily (Wagner et al, 2005 , 2007 ; Yang et al, 2007 , 2008 , 2009 , 2011 ; Essen et al, 2008 ; Malliet et al, 2011 ; Bellini and Papiz, 2012 ; Anders et al, 2013 , 2014 ; Takala et al, 2014 ). Crystallographic studies of a bacteriophytochrome also revealed the protein structural changes implicated in regulating the output module (Takala et al, 2014 ) that is typically a histidine kinase-like region.…”