Search results for "Deinococcus"
showing 10 items of 30 documents
Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage
2018
WOS:000452343100012; International audience; Background: Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. Methods: Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coif and DR. slip knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette. Results: DR1533 contains an N-terminal SRA…
The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension.
2022
AbstractSignal transduction typically starts with either ligand binding or cofactor activation, eventually affecting biological activities in the cell. In red light-sensing phytochromes, isomerization of the bilin chromophore results in regulation of the activity of diverse output modules. During this process, several structural elements and chemical events influence signal propagation. In our study, we have studied the full-length bacteriophytochrome from Deinococcus radiodurans as well as a previously generated optogenetic tool where the native histidine kinase output module has been replaced with an adenylate cyclase. We show that the composition of the output module influences the stabi…
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
2019
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
2021
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP a…
ERA-experiment “space biochemistry”
1995
Abstract The general goal of the experiment was to study the response of anhydrobiotic (metabolically dormant) microorganisms (spores of Bacillus subtilis, cells of Deinococcus radiodurans, conidia of Aspergillus species) and cellular constituents (plasmid DNA, proteins, purple membranes, amino acids, urea) to the extremely dehydrating conditions of open space, in some cases in combination with irradiation by solar UV-light. Methods of investigation included viability tests, analysis of DNA damages (strand breaks, DNA-protein cross-links) and analysis of chemical effects by spectroscopic, electrophoretic and chromatographic methods. The decrease in viability of the microorganisms was as exp…
The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser
2019
Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The chan…
Removal of Chromophore-proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor
2015
Genetically encoded fluorescent markers have revolutionized cell and molecular biology due to their biological compatibility, controllable spatiotemporal expression, and photostability. To achieve in vivo imaging in whole animals, longer excitation wavelength probes are needed due to the superior ability of near infrared light to penetrate tissues unimpeded by absorbance from biomolecules or autofluorescence of water. Derived from near infrared-absorbing bacteriophytochromes, phytofluors are engineered to fluoresce in this region of the electromagnetic spectrum, although high quantum yield remains an elusive goal. An invariant aspartate residue is of utmost importance for photoconversion in…
Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome
2022
Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory …
The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study.
2021
AbstractSolvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation…
UV-Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes
2019
Red‐light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large‐scale secondary and tertiary changes which follow small‐scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore‐binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemi…