Janne A. Ihalainen

Signal amplification and transduction in phytochrome photosensors

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi. Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain. Structures of photosensory cores are reported in the resting state and conformational responses to light activation have been proposed in the vicinity of the chromophore. However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved ‘tongue’, which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an ångstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.

Pigment organization and energy transfer dynamics in isolated photosystem I (PSI) complexes from Arabidopsis thaliana depleted of the PSI-G, PSI-K, PSI-L, or PSI-N subunit

Green plant photosystem I (PSI) consists of at least 18 different protein subunits. The roles of some of these protein subunits are not well known, in particular those that do not occur in the well characterized PSI complexes from cyanobacteria. We investigated the spectroscopic properties and excited-state dynamics of isolated PSI-200 particles from wild-type and mutant Arabidopsis thaliana plants devoid of the PSI-G, PSI-K, PSI-L, or PSI-N subunit. Pigment analysis and a comparison of the 5 K absorption spectra of the various particles suggests that the PSI-L and PSI-H subunits together bind approximately five chlorophyll a molecules with absorption maxima near 688 and 667 nm, that the PSI-G subunit binds approximately two red-shifted beta-carotene molecules, that PSI-200 particles without PSI-K lack a part of the peripheral antenna, and that the PSI-N subunit does not bind pigments. Measurements of fluorescence decay kinetics at room temperature with picosecond time resolution revealed lifetimes of ~0.6, 5, 15, 50, 120, and 5000 ps in all particles. The 5- and 15-ps phases could, at least in part, be attributed to the excitation equilibration between bulk and red chlorophyll forms, though the 15-ps phase also contains a contribution from trapping by charge separation. The 50- and 120-ps phases predominantly reflect trapping by charge separation. We suggest that contributions from the core antenna dominate the 15-ps trapping phase, that those from the peripheral antenna proteins Lhca2 and Lhca3 dominate the 50-ps phase, and that those from Lhca1 and Lhca4 dominate the 120-ps phase. In the PSI-200 particles without PSI-K or PSI-G protein, more excitations are trapped in the 15-ps phase and less in 50- and 120-ps phases, which is in agreement with the notion that these subunits are involved in the interaction between the core and peripheral antenna proteins.

2D-IR study of a photoswitchable isotope-labeled alpha-helix.

A series of photoswitchable, alpha-helical peptides were studied using two-dimensional infrared spectroscopy (2D-IR). Single-isotope labeling with (13)C(18)O at various positions in the sequence was employed to spectrally isolate particular backbone positions. We show that a single (13)C(18)O label can give rise to two bands along the diagonal of the 2D-IR spectrum, one of which is from an amide group that is hydrogen-bonded internally, or to a solvent molecule, and the other from a non-hydrogen-bonded amide group. The photoswitch enabled examination of both the folded and unfolded state of the helix. For most sites, unfolding of the peptide caused a shift of intensity from the hydrogen-bonded peak to the non-hydrogen-bonded peak. The relative intensity of the two diagonal peaks gives an indication of the fraction of molecules hydrogen-bonded at a certain location along the sequence. As this fraction varies quite substantially along the helix, we conclude that the helix is not uniformly folded. Furthermore, the shift in hydrogen bonding is much smaller than the change of helicity measured by CD spectroscopy, indicating that non-native hydrogen-bonded or mis-folded loops are formed in the unfolded ensemble.

Origins of fluorescence in evolved bacteriophytochromes.

Background: Near-infrared (NIR) fluorescent bacteriophytochromes are valuable for optical imaging in mammals. Results: Reversal of one position in the fluorescent phytochrome variant IFP1.4 led to the brightest monomeric NIR phytofluor known. Conclusion: Crystallography shows that limiting motion and changing polarity in the chromophore binding pocket increase fluorescence. Significance: Understanding the source of increased fluorescence in NIR fluorescent phytofluors is essential for further improving these novel imaging tools. Use of fluorescent proteins to study in vivo processes in mammals requires near-infrared (NIR) biomarkers that exploit the ability of light in this range to penetrate tissue. Bacteriophytochromes (BphPs) are photoreceptors that couple absorbance of NIR light to photoisomerization, protein conformational changes, and signal transduction. BphPs have been engineered to form NIR fluorophores, including IFP1.4, Wi-Phy, and the iRFP series, initially by replacement of Asp-207 by His. This position was suggestive because its main chain carbonyl is within hydrogen-bonding distance to pyrrole ring nitrogens of the biliverdin chromophore, thus potentially functioning as a crucial transient proton sink during photoconversion. To explain the origin of fluorescence in these phytofluors, we solved the crystal structures of IFP1.4 and a comparison non-fluorescent monomeric phytochrome DrCBDmon. Met-186 and Val-288 in IFP1.4 are responsible for the formation of a tightly packed hydrophobic hub around the biliverdin D ring. Met-186 is also largely responsible for the blue-shifted IFP1.4 excitation maximum relative to the parent BphP. The structure of IFP1.4 revealed decreased structural heterogeneity and a contraction of two surface regions as direct consequences of side chain substitutions. Unexpectedly, IFP1.4 with Asp-207 reinstalled (IFPrev) has a higher fluorescence quantum yield (∼9%) than most NIR phytofluors published to date. In agreement, fluorescence lifetime measurements confirm the exceptionally long excited state lifetimes, up to 815 ps, in IFP1.4 and IFPrev. Our research helps delineate the origin of fluorescence in engineered BphPs and will facilitate the wide-spread adoption of phytofluors as biomarkers.

Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells

Bioactive glasses are known for their ability to induce osteogenic differentiation of stem cells. To elucidate the mechanism of the osteoinductivity in more detail, we studied whether ionic extracts prepared from a commercial glass S53P4 and from three experimental glasses (2-06, 1-06 and 3-06) are alone sufficient to induce osteogenic differentiation of human adipose stem cells. Cells were cultured using basic medium or osteogenic medium as extract basis. Our results indicate that cells stay viable in all the glass extracts for the whole culturing period, 14 days. At 14 days the mineralization in osteogenic medium extracts was excessive compared to the control. Parallel to the increased mineralization we observed a decrease in the cell amount. Raman and Laser Induced Breakdown Spectroscopy analyses confirmed that the mineral consisted of calcium phosphates. Consistently, the osteogenic medium extracts also increased osteocalcin production and collagen Type-I accumulation in the extracellular matrix at 13 days. Of the four osteogenic medium extracts, 2-06 and 3-06 induced the best responses of osteogenesis. However, regardless of the enhanced mineral formation, alkaline phosphatase activity was not promoted by the extracts. The osteogenic medium extracts could potentially provide a fast and effective way to differentiate human adipose stem cells in vitro.

Design, synthesis, and biological evaluation of nonsteroidal cycloalkane[d]isoxazole-containing androgen receptor modulators.

We report here the design, preparation, and systematic evaluation of a novel cycloalkane[d]isoxazole pharmacophoric fragment-containing androgen receptor (AR) modulators. Cycloalkane[d]isoxazoles form new core structures that interact with the hydrophobic region of the AR ligand-binding domain. To systematize and rationalize the structure-activity relationship of the new fragment, we used molecular modeling to design a molecular library containing over 40 cycloalkane[d]isoxazole derivatives. The most potent compound, 4-(3a,4,5,6,7,7a-hexahydrobenzo[d]isoxazol-3-yl)-2-(trifluoromethyl)benzonitrile (6a), exhibits antiandrogenic activity significantly greater than that of the most widely used antiandrogenic prostate cancer drugs bicalutamide (1) and hydroxyflutamide (2) in reporter gene assays measuring the transcriptional activity of AR (decreasing approximately 90% of the total AR activity) and in competitive AR ligand-binding assays (showing over four times higher potency to inhibit radioligand binding in comparison to bicalutamide). Notably, 6a maintains its antiandrogenic activity with AR mutants W741L and T877A commonly observed and activated by bicalutamide and hydroxyflutamide, respectively, in prostate cancer patients.

Light-induced Changes in the Dimerization Interface of Bacteriophytochromes *

Background: Bacteriophytochromes are dimeric histidine kinases, but the functional role of their dimerization interfaces is unclear. Results: The phytochrome from Deinococcus radiodurans has two dimerization interfaces, which are critical for thermal back reversion and are altered by illumination. Conclusion: The dimerization interfaces cause strain in the structure. Significance: A functional role for the dimerization interfaces is proposed. Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximately equal contributions. The existence of both dimerization interfaces is critical for thermal reversion back to the resting state. We also find that a mutant in which the interactions between the GAF domains were removed monomerizes under red light. This implies that the interactions between the HK domains are significantly altered by photoconversion. The results suggest functional importance of the dimerization interfaces in bacteriophytochromes.

Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans

Fluorescent proteins are versatile tools for molecular imaging. In this study, we report a detailed analysis of the absorption and fluorescence properties of the chromophore-binding domain from Deinococcus radiodurans and its D207H mutant. Using single photon counting and transient absorption techniques, the average excited state lifetime of both studied systems was about 370 ps. The D207H mutation slightly changed the excited state decay profile but did not have a considerable effect on the average decay time of the system or the shape of the absorption and emission spectra of the biliverdin chromophore. We confirmed that the fluorescence properties of both samples are very similar in vivo and in vitro. However, we found that the paraformaldehyde fixation of the Escherichia coli cells containing the recombinant phytochrome protein significantly changed the fluorescence properties of the chromophore-binding domain. The biliverdin fluorescence was diminished almost completely, and the fluorescence originated only from the protoporphyrin molecules. Our results emphasize that the effect of protoporphyrin IXa should not be ignored in the fluorescence experiments with phytochrome systems while designing better red fluorescence markers for cellular imaging.

Structural photoactivation of a full-length bacterial phytochrome

Time-resolved x-ray solution scattering reveals the conformational signaling mechanism of a bacterial phytochrome. Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro- and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.

Functional Rearrangement of the Light-Harvesting Antenna upon State Transitions in a Green Alga

State transitions in the green alga Chlamydomonas reinhardtii serve to balance excitation energy transfer to photosystem I (PSI) and to photosystem II (PSII) and possibly play a role as a photoprotective mechanism. Thus, light-harvesting complex II (LHCII) can switch between the photosystems consequently transferring more excitation energy to PSII (state 1) or to PSI (state 2) or can end up in LHCII-only domains. In this study, low-temperature (77 K) steady-state and time-resolved fluorescence measured on intact cells of Chlamydomonas reinhardtii shows that independently of the state excitation energy transfer from LHCII to PSI or to PSII occurs on two main timescales of <15 ps and ∼ 100 ps. Moreover, in state 1 almost all LHCIIs are functionally connected to PSII, whereas the transition from state 1 to a state 2 chemically locked by 0.1 M sodium fluoride leads to an almost complete functional release of LHCIIs from PSII. About 2/3 of the released LHCIIs transfer energy to PSI and ∼ 1/3 of the released LHCIIs form a component designated X-685 peaking at 685 nm that decays with time constants of 0.28 and 5.8 ns and does not transfer energy to PSI or to PSII. A less complete state 2 was obtained in cells incubated under anaerobic conditions without chemical locking. In this state about half of all LHCIIs remained functionally connected to PSII, whereas the remaining half became functionally connected to PSI or formed X-685 in similar amounts as with chemical locking. We demonstrate that X-685 originates from LHCII domains not connected to a photosystem and that its presence introduces a change in the interpretation of 77 K steady-state fluorescence emission measured upon state transitions in Chalamydomonas reinhardtii.