Structural changes within the bifunctional cryptochrome/photolyase CraCRY upon blue light excitation

Franz-Badur, Sophie; Penner, Alexander; Straß, Simon; Horsten, Silke von; Linne, Uwe; Essen, Lars‐Oliver

doi:10.1038/s41598-019-45885-7

Cited by 20 publications

(30 citation statements)

References 35 publications

(50 reference statements)

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“…20 The FADH• absorption spectrum was found to be in agreement with the action spectrum of aCRY in vivo and structural rearrangements in the protein moiety of aCRY were only found upon formation of the anionic fully reduced state (FADH -) as revealed by FTIR spectroscopy and hydrogen/deuterium exchange mass spectrometry on aCRY. [23][24][25] In contrast to other cryptochromes, the lifetime of the FADH• state in vitro is not influenced by oxygen levels [26][27][28] but strongly sensitive to alterations of the pH. At a pH of 6.9 a lifetime of 1340 s was reported.…”

Section: Introductionmentioning

confidence: 91%

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

2019

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Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH•) in the dark, despite a rapid FADH• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH• lifetime in the presence of 8-HDF. Millisecond time-resolved UV-vis spectroscopy showed the red light-induced formation and decay of an absorbance band at 458 nm concomitant to flavin reduction. Time-resolved FTIR spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control the flavin protonation, indicating the involvement of N395 in the stabilization of FADH•. Fluorescence spectroscopy revealed a decrease in energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to the 8-HDF deprotonation. The discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of

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Section: Introductionmentioning

confidence: 91%

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

2019

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“…The semiquinone FADH o state of Ds NewPHL is unusually stable at 4°C when compared to Mm NewPHL and other PHLs or CRYs ( 20 ) , ( 36 ). Oxidation of FADH o was barely detectable within 14 days under aerobic conditions, whereas Mm NewPHL shows FAD oxidation within five days under identical conditions.…”

Section: Resultsmentioning

confidence: 96%

“…HDX-MS was essentially carried out as described previously ( 36 ) aided by a robotic two-arm autosampler (LEAP Technologies). 7.5 μl (50 μM) Ds NewPHL were diluted with 67.5 μl of D 2 O-containing buffer (50 m m sodium phosphate, pH 8.0, 100 m m NaCl) and incubated for 10, 95, 1000 or 10 000 s at 25°C.…”

Section: Methodsmentioning

confidence: 99%

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A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA

Emmerich

Saft

Schneider

et al. 2020

Nucleic Acids Research

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Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.

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“…Phosphorylation of the mammalian CRY1 IDR stabilizes the protein [129], while phosphorylation of the CRY2 IDR destabilizes the protein and leads to its degradation [130,131]. Curiously, the C-terminal IDR of the mammalian-like CRY ortholog from the green algae Chlamydomonas reinhardtii was recently suggested to bind to its PHR upon light perception [132]. Thus, a similar mode of action might be possible for mammalian CRYs, potentially through a light dependent signalling pathway in conjunction with other photoreceptors.…”

Section: The Multivalent Role Of Protein Disorder In Cryptochrome Sigmentioning

confidence: 99%

Common Functions of Disordered Proteins across Evolutionary Distant Organisms

Wallmann

Kesten

2020

IJMS

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Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence-structure-function relationship. Hence, classic sequence-or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism. being defined by a separate set of parameters compared to their structured and globular counterparts [7]. Hence, identification of distantly related IDPs cannot rely on structure, which can help to detect relationships of folded proteins that would remain undetected by conventional sequence-based methods [8]. Methods that use antibodies to metazoan proteins to identify putative plant homologues may result in a higher incidence of artefacts when compared to folded protein targets, due to the smaller size of disordered epitopes and their comparably higher sensitivity to epitope variation [9].In contrast to folded proteins, IDPs and IDRs show an overall increased rate of evolution, while these rates can strongly vary between different parts of the IDP [10,11]. Moreover, disordered regions appear to be more permissive to mutation, further complicating sequence-function analysis. Overall, genome duplication events seem to influence the distribution of IDRs within genomes, as the amount of identical paralogous IDRs positively correlates with the number of chromosomes [12]. Interestingly, proteins can display different modes of how sequence conservation can relate to disorder as a functional feature [13]. While in some cases only the disorder itself is conserved, but not the sequence facilitating it (flexible disorder), other IDPs retain disorder together with a highly conserved sequence (constrained disorder). Short-linear motifs (SLiMs) represent conserved functional modules that can mediate low-affinity interactions and are often interspersed by regions of flexible disorder [14]. As many alignment algorithms require long stretches of sequence similarity to satisfy statistical significance, the high modality and low complexity of SLiMs can obscure the search for homologous sequences considerably. Due to their limited size (7-12 residues), these motifs can easily develop in unrelated proteins in convergent evolution. Furthermore, post-translational modifications (PTMs) that often regulate IDP function complicate the analysis, as they can drastically alter the biophysical features of a protein and phosphorylation sites display short and weakly conserved motifs that are often difficult to detect via computational sequence analysis [15].Within protein interaction networks, IDPs ofte...

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Structural changes within the bifunctional cryptochrome/photolyase CraCRY upon blue light excitation

Cited by 20 publications

References 35 publications

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA

Common Functions of Disordered Proteins across Evolutionary Distant Organisms

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