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Sex chromosome disorders severely compromise gametogenesis in both males and females. In oogenesis, the presence of an additional Y chromosome or the loss of an X chromosome disturbs the robust production of oocytes. Here we efficiently converted the XY chromosome set to XX without an additional Y chromosome in mouse pluripotent stem (PS) cells. In addition, this chromosomal alteration successfully eradicated trisomy 16, a model of Down’s syndrome, in PS cells. Artificially produced euploid XX PS cells differentiated into mature oocytes in culture with similar efficiency to native XX PS cells. Using this method, we differentiated induced pluripotent stem cells from the tail of a sexually mature male mouse into fully potent oocytes, which gave rise to offspring after fertilization. This study provides insights that could ameliorate infertility caused by sex chromosome or autosomal disorders, and opens the possibility of bipaternal reproduction.

Sleep problems and irritable temperaments are common among infants with autism spectrum disorders (ASDs). The prospective association between such sleep problems and irritable temperaments and ASDs needs to be determined for elucidating the mechanism and exploring the future intervention study. Thus, in this study, we investigated whether sleep quality and temperament in 1-month-old infants are associated with the onset of ASDs in 3-year-old children. We also assessed its sex-stratified associations. We conducted a longitudinal study using data from 69,751 mothers and infants from a large-cohort study, the Japan Environment and Children’s Study. We examined the prospective association between infant sleep quality and temperament at 1 month of age and ASD diagnosis by 3 years of age. Infants with longer daytime sleep had a higher risk of later ASD than those with shorter daytime sleep (risk ratio [RR]: 1.33, 95% confidence interval [CI]: 1.01–1.75). Infants who experienced intense crying had a higher risk of ASD than those who did not (RR: 1.31, 95% CI: 1.00–1.72). There was a difference in sex in the association between a bad mood and later ASD. In particular, female infants experiencing bad moods had a higher risk of ASD than others (RR: 3.59, 95% CI: 1.91–6.75). The study findings provide important information for future intervention to reduce the risk of future ASD.

During female germline development, oocytes become a highly specialized cell type and form a maternal cytoplasmic store of crucial factors. Oocyte growth is triggered at the transition from primordial to primary follicle and is accompanied by dynamic changes in gene expression1, but the gene regulatory network that controls oocyte growth remains unknown. Here we identify a set of transcription factors that are sufficient to trigger oocyte growth. By investigation of the changes in gene expression and functional screening using an in vitro mouse oocyte development system, we identified eight transcription factors, each of which was essential for the transition from primordial to primary follicle. Notably, enforced expression of these transcription factors swiftly converted pluripotent stem cells into oocyte-like cells that were competent for fertilization and subsequent cleavage. These transcription-factor-induced oocyte-like cells were formed without specification of primordial germ cells, epigenetic reprogramming or meiosis, and demonstrate that oocyte growth and lineage-specific de novo DNA methylation are separable from the preceding epigenetic reprogramming in primordial germ cells. This study identifies a core set of transcription factors for orchestrating oocyte growth, and provides an alternative source of ooplasm, which is a unique material for reproductive biology and medicine. Eight transcription factors are identified that, when overexpressed, are sufficient to grow oocyte-like cells from mouse pluripotent stem cells.

The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established and transmitted to the next generation. In the female germline, X-chromosome inactivation and reactivation are among the most prominent epigenetic reprogramming events, yet very little is known about their kinetics and biological function. Here, we investigate X-inactivation and reactivation dynamics using a tailor-made in vitro system of primordial germ cell-like cell (PGCLC) differentiation from mouse embryonic stem cells. We find that X-inactivation in PGCLCs in vitro and in germ cell-competent epiblast cells in vivo is moderate compared to somatic cells, and frequently characterized by escaping genes. X-inactivation is followed by step-wise X-reactivation, which is mostly completed during meiotic prophase I. Furthermore, we find that PGCLCs which fail to undergo X-inactivation or reactivate too rapidly display impaired meiotic potential. Thus, our data reveal fine-tuned X-chromosome remodelling as a critical feature of female germ cell development towards meiosis and oogenesis. This work was supported by the Spanish Ministry of Science, Innovation and Universities (BFU2014-55275-P, BFU2017-88407-P to B.P.), the Agencia Estatal de Investigación (AEI) (EUR2019-103817 to B.P.), the AXA Research Fund (to B.P.) and the Agencia de Gestio d’Ajuts Universitaris i de Recerca (AGAUR, 2017 SGR 346 to B.P.). We would like to thank the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership and to the “Centro de Excelencia Severo Ochoa.” We also acknowledge support of the CERCA Programme of the Generalitat de Catalunya. N.A. is supported by an EMBO postdoctoral fellowship (LTF 695-2019). J.S. and M.B. were supported by La Caixa International PhD Fellowships and J.S. by a travel grant from the Company of Biologists (Development Journal). P.A. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 751651

Several maternal chronic diseases have been reported as risk factors for congenital anomalies of the kidney and urinary tract (CAKUT) in offspring. However, these investigations used case-control designs, and cases with isolated genitourinary CAKUT were not distinguished from cases in which CAKUT were present with extrarenal congenital anomalies (complicated CAKUT). We examined the association of maternal diseases with isolated and complicated CAKUT in offspring using data from a prospective cohort study.A nationwide prospective birth cohort study.100,239 children enrolled in the Japan Environment and Children's Study between January 2011 and March 2014 at 15 research centers. Physicians' diagnoses in mothers and children were collected from medical record transcripts and questionnaires.Medical histories of maternal noncommunicable diseases, including obesity, hypertension, diabetes mellitus, kidney disease, hyperthyroidism, hypothyroidism, psychiatric disease, epilepsy, cancer, and autoimmune disease.CAKUT diagnosed during the first 3 years of life, classified as isolated or complicated.Multivariable Poisson regression with generalized estimating equations accounting for clustering by clinical center.Among the 100,239 children, 560 (0.6%) had CAKUT, comprising 454 (81%) isolated and 106 (19%) complicated forms. The risk of isolated CAKUT was increased in children of mothers who experienced kidney disease (adjusted risk ratio [RR], 1.80 [95% CI, 1.12-2.91]) or cancer (RR, 2.11 [95% CI, 1.15-3.86]). Furthermore, the risk of complicated CAKUT was increased in children of mothers with diabetes mellitus (RR, 3.04 [95% CI, 1.64-5.61]).Lack of standardization or prespecification of clinical definitions, diagnostic criteria, measurements, and testing. Genetic testing was not performed.Isolated CAKUTs and complicated CAKUTs were associated with different maternal diseases. The results may inform clinical management of pregnancy and highlight potential differences in the genesis of isolated and complicated forms of CAKUT.

In mammals, most immature oocytes remain dormant in the primordial follicles to ensure the longevity of female reproductive life. A precise understanding of mechanisms underlying the dormancy is important for reproductive biology and medicine. In this study, by comparing mouse oogenesis in vivo and in vitro, the latter of which bypasses the primordial follicle stage, we defined the gene-expression profile representing the dormant state of oocytes. Overexpression of constitutively active FOXO3 partially reproduced the dormant state in vitro. Based on further gene-expression analysis, we found that a hypoxic condition efficiently induced the dormant state in vitro. The effect of hypoxia was severely diminished by disruption of the Foxo3 gene and inhibition of hypoxia-inducible factors. Our findings provide insights into the importance of environmental conditions and their effectors for establishing the dormant state.

In mammals, most immature oocytes remain dormant in the primordial follicles to ensure the longevity of female reproductive life. A precise understanding of mechanisms underlying the dormancy is important for reproductive biology and medicine. In this study, by comparing mouse oogenesis in vivo and in vitro, the latter of which bypasses the primordial follicle stage, we defined the gene-expression profile representing the dormant state of oocytes. Overexpression of constitutively active FOXO3 partially reproduced the dormant state in vitro. Based on further gene-expression analysis, we found that a hypoxic condition efficiently induced the dormant state in vitro. The effect of hypoxia was severely diminished by disruption of the Foxo3 gene and inhibition of hypoxia-inducible factors. Our findings provide insights into the importance of environmental conditions and their effectors for establishing the dormant state.

A set of sex chromosomes is required for gametogenesis in both males and females, as represented by sex chromosome disorders causing agametic phenotypes. Although studies using model animals have investigated the functional requirement of sex chromosomes, involvement of these chromosomes in gametogenesis remains elusive. Here, we elicit a germ cell-intrinsic effect of sex chromosomes on oogenesis, using a novel culture system in which oocytes were induced from embryonic stem cells (ESCs) harboring XX, XO or XY. In the culture system, oogenesis using XO and XY ESCs was severely disturbed, with XY ESCs being more strongly affected. The culture system revealed multiple defects in the oogenesis of XO and XY ESCs, such as delayed meiotic entry and progression, and mispairing of the homologous chromosomes. Interestingly, Eif2s3y, a Y-linked gene that promotes proliferation of spermatogonia, had an inhibitory effect on oogenesis. This led us to the concept that male and female gametogenesis appear to be in mutual conflict at an early stage. This study provides a deeper understanding of oogenesis under a sex-reversal condition., Author summary Oogenesis is a highly sex-dependent differentiation process that commences at the mid-gestation stage. Oogenesis is severely disturbed in XO and XY females, although the mechanisms underlying the disturbance are still elusive. In this study, we subjected XO and XY ES cells to an in vitro culture system, in which female (XX) ES cells differentiate into functional oocytes. Our results showed that oogenesis from XO and XY ES cells was severely disturbed due to defective processes such as delayed meiotic initiation/progression, aberrant gene expression and mispairing of homologous chromosomes. In addition, our results demonstrate that a Y-linked gene, Eif2s3y that promotes spermatogenesis, has conversely a negative impact on oogenesis. This study provides a culture system that serves as a useful model of sex reversal and contributes the concept of a substantial germ cell-intrinsic conflict between male and female gametogenesis. Further study using the culture system will reveal molecular insights into infertility with sex chromosome disorder(s).

The ultrafast structural dynamics in the electronic excited state of photoactive yellow protein (PYP) is studied by femtosecond stimulated Raman spectroscopy. Stimulated Raman spectra in the electronic excited state, S(1), can be obtained by using a Raman pump pulse in resonance with the S(1)-S(0) transition. This is confirmed by comparing the experimental results with numerical calculations based on the density matrix treatment. We also investigate the hydrogen-bonding network surrounding the wild-type (WT)-PYP chromophore in the ground and excited states by comparing its stimulated Raman spectra with those of the E46Q-PYP mutant. We focus on the relative intensity of the Raman band at 1555 cm(-1), which includes both vinyl bond C═C stretching and ring vibrations and is sensitive to the hydrogen-bonding network around the phenolic oxygen of the chromophore. The relative intensity for the WT-PYP decreases after actinic excitation within the 150 fs time resolution and reaches a similar intensity to that for E46Q-PYP. These observations indicate that the WT-PYP hydrogen-bonding network is immediately rearranged in the electronic excited state to form a structure similar to that of E46Q-PYP.

Femtosecond time-resolved mid-infrared (MIR) spectroscopy based on chirped-pulse upconversion is a promising method for observing molecular vibrational dynamics. A quantitative study on nonlinear media for upconversion is still essential for wide applications, particularly at the frequencies below 2000 cmsup-1/sup. We evaluate wide-bandgap nonlinear crystals of Li-containing ternary chalcogenides based on their performance as the upconversion medium for femtosecond MIR spectroscopy. The upconversion efficiency is measured as a function of the MIR pulse frequency and the chirped pulse energy. LiGaSsub2/subis found to be an efficient crystal for the upconversion of MIR pulses in a wide frequency range of 1100-2700 cmsup-1/sup, especially below 2000 cmsup-1/sup. By using LiGaSsub2/subas an efficient upconversion crystal, we develop a MIR pump-probe spectroscopy system with a spectral resolution of 2.5 cmsup-1/sup, a time resolution of 0.2 ps, and a probe window of 120 cmsup-1/sup. Vibrational relaxation dynamics of CO stretching modes of Mnsub2/sub(CO)sub10/subin cyclohexane and bovine serum albumin in Dsub2/subO are demonstrated with a high signal-to-noise ratio.

Perylene diimide (PDI) derivatives with cyclodextrins (PDI-CD2s) exhibit specific emission properties, which depend on the type of CDs in an aqueous solution. Herein we successfully create an emission film-kneaded PDI-CD2 derivatives via effective tumbling of the altropyranose unit. PDI-6CD2s are crosslinked with PDI between 6-amino-CDs. Although the emission intensities of PDI-6CD2s in dimethyl sulfoxide are similar regardless of the type of CD, PDI-6γCD2 has a relatively high emission intensity in aqueous solutions. In contrast, for PDIC7-3CD2s, which are linked with N,N’-bis(6-carboxylhexyl)perylene-3,4,9,10-tetracarboxyl diimide (BisC7-PDI) between 3-amino-CDs, the emission intensity of PDIC7-3βCD2 is stronger than those of PDIC7-3αCD2, PDIC7-3γCD2, and PDI-6CD2s in aqueous solutions. The selective emission behavior of PDIC7-3CD2s is due to the formation of the pseudo[1]rotaxane dimer through tumbling of the altropyranose unit in an aqueous solution. PDIC7-3βCD2 in the solid state does not demonstrate a distinctive emission due to self-quenching, whereas PDIC7-3βCD2 kneaded into the polyvinyl alcohol (PVA) film exhibits a bright yellow emission. The order of the emission intensities of PDIC7-3CD2s kneaded into PVA films is similar to those in aqueous solutions. Perylene diimide (PDI) derivatives with cyclodextrins (PDI-CD2s) exhibit specific emission properties, which depend on the type of CDs in an aqueous solution. Herein we create an emission from film kneaded PDI-CD2s derivatives via effective tumbling of the altropyranose unit. We have observed the selective emission of PDIC7-3βCD2 in aqueous solutions and prepared emission films kneaded into polyvinyl alcohol (PVA) films. The emission depends on the cavity size of the altro-CDs formed through altro-CD tumbling.

An energy transfer process was investigated using cyclodextrin-oligothiophene rotaxanes (2T-[2]rotaxane). The excited energy of 2T-[2]rotaxane is transferred to the sexithiophene derivative which is included in the cavity of β-CD stoppers of 2T-[2]rotaxane.

Picosecond time-resolved ultraviolet resonance Raman (UVRR) spectra of photoactive yellow protein (PYP) were measured. UVRR bands attributed to the vibration of tyrosine and tryptophan residues showed a spectral change upon photoreaction. It was found that the hydrogen-bond strength between the chromophore and Y42 increases in the pG* state. The ultrafast change in the tryptophan band revealed that a photoinduced structural change of the chromophore had propagated to the W119 region, located 12 A from the chromophore, within picoseconds.

Pump-dump fluorescence spectroscopy was performed for photoactive yellow protein (PYP) at room temperature. The effect of the dump pulse on the population of the potential energy surface of the electronic excited state was examined as depletion in the stationary fluorescence intensity. The dynamic behavior of the population in the electronic excited state was successfully probed in the various combinations of the pump-dump delay, the dump-pulse wavelength, the dump-pulse energy and the observation wavelength. The experimental results were compared with the results obtained by the femtosecond time-resolved fluorescence spectroscopy.

A versatile method to take femtosecond spectral snapshots of fluorescence has been developed based on a double gating technique in the combination of an optical Kerr gate and an image intensifier as an electrically driven gate set in front of a charge-coupled device detector. The application of a conventional optical-Kerr-gate method is limited to molecules with the short fluorescence lifetime up to a few hundred picoseconds, because long-lifetime fluorescence itself behaves as a source of the background signal due to insufficiency of the extinction ratio of polarizers employed for the Kerr gate. By using the image intensifier with the gate time of 200 ps, we have successfully suppressed the background signal and overcome the application limit of optical-Kerr-gate method. The system performance has been demonstrated by measuring time-resolved fluorescence spectra for laser dye solution and the riboflavin solution as a typical sample of biomolecule.

The female germ line undergoes a unique sequence of differentiation processes that confers totipotency to the egg. The reconstitution of these events in vitro using pluripotent stem cells is a key achievement in reproductive biology and regenerative medicine. Here we report successful reconstitution in vitro of the entire process of oogenesis from mouse pluripotent stem cells. Fully potent mature oocytes were generated in culture from embryonic stem cells and from induced pluripotent stem cells derived from both embryonic fibroblasts and adult tail tip fibroblasts. Moreover, pluripotent stem cell lines were re-derived from the eggs that were generated in vitro, thereby reconstituting the full female germline cycle in a dish. This culture system will provide a platform for elucidating the molecular mechanisms underlying totipotency and the production of oocytes of other mammalian species in culture.

Photonics-based frequency-domain terahertz (THz) wave measurement systems have received significant attention in both scientific and industrial fields due to their high-frequency resolution. Highly sensitive phase-measurement systems have been desired in the chemical, material, and biomedical sciences to facilitate microanalysis of materials. Here, we demonstrate a balanced self-heterodyne technique that, for the first time, simultaneously offers wide frequency tunability of more than 2.5 THz and high phase sensitivity, which is limited only by the signal-to-noise ratio (SNR) of the amplitude measurement. Using free-running lasers for THz wave generation and detection, the experimentally achieved minimum detectable optical path length change was 400±50 nm at 2 THz for a SNR of 37.7 ± 0.7 dB, even though the theoretically expected SNR-limited value was 310 ± 20 nm. The phase measurement sensitivity of our system is almost one order of magnitude better than that of the conventional systems in which limitations arise from phase instabilities in the optical components and/or laser linewidth.

We demonstrate a frequency-domain modulation spectroscopy system in the terahertz (THz) range based on the self-heterodyne technique to enhance the sensitivity of the small spectral change measurement. To evaluate the effectiveness of our system, we measured absorption of the THz wave caused by photo-induced free carriers generated in a high-resistive (4000 Ωcm) Si substrate. The 400-μm-thick Si substrate was excited by a 775-nm laser light, which was chopped at 1.7 kHz. By applying a tandem demodulation lock-in amplifier tuned at the modulation frequency of 1.7 kHz, we confirmed that the sensitivity of the amplitude absorption measurement was enhanced at least 14 dB. Our new system will pave the way for the sensitive measurement of THz spectral changes induced by photoexcitation in chemical, material, and biomedical sciences.

Time-resolved spectra of a photoactive yellow protein (PYP) containing cyano-p-coumaric acid (CHCA) were recorded. To understand the mechanism of photo-isomerization, an electron-withdrawing CN group was introduced into the PYP to alter the C[double bond, length as m-dash]C double bond character. Free CHCA chromophores in aqueous solution underwent photo-isomerization whereas PYP with a bound CHCA (PYP-CN) exhibited no photocycle at acidic or alkaline pH or in urea and other solutions. Furthermore, no photocycle was observed with PYP mutants after illumination. This phenomenon cannot be fully explained by the electron-withdrawing properties of the CN group. We conclude that the CHCA chromophore in PYP was locked in the protein cage and that the CN group interacted with the protein residues.

Vibrational energy flow in the electronic ground state of photoactive yellow protein (PYP) is studied by ultrafast infrared (IR) pump-visible probe spectroscopy. Vibrational modes of the chromophore and the surrounding protein are excited with a femtosecond IR pump pulse, and the subsequent vibrational dynamics in the chromophore are selectively probed with a visible probe pulse through changes in the absorption spectrum of the chromophore. We thus obtain the vibrational energy flow with four characteristic time constants. The vibrational excitation with an IR pulse at 1340, 1420, 1500, or 1670 cm(-1) results in ultrafast intramolecular vibrational redistribution (IVR) with a time constant of 0.2 ps. The vibrational modes excited through the IVR process relax to the initial ground state with a time constant of 6-8 ps in parallel with vibrational cooling with a time constant of 14 ps. In addition, upon excitation with an IR pulse at 1670 cm(-1), we observe the energy flow from the protein backbone to the chromophore that occurs with a time constant of 4.2 ps.

Vibrational dynamics of the chromophore in photoactive yellow protein is studied by mid-IR-pump-visible-probe spectroscopy. So-called ‘ground state intermediate’, which is believed to be a cis isomer, is directly generated by vibrational excitation.

We report a unique lambdamax shift of the absorption maximum of a photoactive yellow protein (PYP) analogue reconstituted with a fluorinated chromophore (F-PYP). The difference in lambdamax between the free chromophore and the protein was significantly larger than that with the native chromophore. We concluded that the unusual lambdamax shift is caused by the electronegative character of the fluorine atom and not by steric hindrance. This result suggests that formation of a hydrogen bond between the fluorine atom and one or more amino acid residues could neutralize its electron-withdrawing character. The properties of analogues of PYP with brominated and methylated chromophore could be explained as an effect of steric hindrance.

In order to obtain insight into the hydrogen-bonding network surrounding the chromophore in biologically photo-functional proteins, photoactive yellow protein (PYP) has been modified by a combination of a site-directed mutagenesis and a substitution of the chromophore with an analogue. Fluorescence excitation and emission spectroscopies have been performed to evaluate the inhomogeneous nature of the spectra originated from the variation of conformational substates of the modified proteins. Noticeable inhomogeneity including contributions from two distinct substates has been observed for a PYP hybrid with the E46Q mutation and a substitution of the p-coumaric acid chromophore with caffeic acid. Transient absorption spectroscopy has been also conducted to clarify whether inhomogeneity affects the recovering kinetics or not. For the PYP hybrid, a remarkable difference of the recovery time from the signaling state has been observed, depending on the wavelength of the excitation light triggering the photocycle. Although this observation is preliminary, it indicates that kinetically inhomogeneous species likely exist in the PYP hybrid.

Photoactive yellow protein (PYP) is a bacterial blue light photoreceptor, and photoexcitation of dark-state PYP (PYP(dark)) triggers a photocycle that involves several intermediate states. We report the ultraviolet resonance Raman spectra of PYP with 225-250 nm excitations and investigate protein structural changes accompanying the formation of the putative signaling state denoted PYP(M). The PYP(M)-PYP(dark) difference spectra show several features of tyrosine and tryptophan, indicating environmental changes for these amino acid residues. The tyrosine difference signals show small upshifts with intensity changes in Y8a and Y9a bands. Although there are five tyrosine residues in PYP, Tyr42 and Tyr118 are suggested to be responsible for the difference signals on the basis of a global fitting analysis of the difference spectra at different excitation wavelengths and the crystal structure of PYP(dark). A further experiment on the Thr50--Val mutant supports environmental changes in Tyr42. The observed upshift of the Y8a band suggests a weaker or broken hydrogen bond between Tyr42 and the chromophore in PYP(M). In addition, a reorientation of the OH group in Tyr42 is suggested from the upshift of the Y9a band. For tryptophan, the Raman bands of W3, W16, and W18 modes diminish in intensity upon formation of PYP(M). The loss of intensities is attributable to an exposure of tryptophan in PYP(M). PYP contains only one tryptophan (Trp119) that is located more than 10 A from the active site. Thus the observed changes are indicative of global conformational changes in protein during the transition from PYP(dark) to PYP(M). These results are in line with the currently proposed photocycle mechanism of PYP.

The blue light receptor photoactive yellow protein (PYP) displays a photocycle that involves several intermediate states. Here we report resonance Raman spectroscopic investigations of the short-lived red-shifted intermediate denoted PYP(L). We have found that the Raman bands of the carbonyl C=O stretching mode nu(11) as well as the C=C stretching mode nu(13) for the chromophore can be resolved into two peaks, and the ratio of the two components varies as a function of pH with pK(a) approximately 6. The isotope effects on the resonance Raman spectra have confirmed a deprotonated cis-chromophore for the two components. The results indicate the presence of two conformations in the active site of PYP(L). The normal coordinate calculations based on the density functional theory provide a structural model for the two conformations, where the low pH form is possibly an active structure for the protonation reaction generating a following intermediate in the photocycle.

Photoactive yellow protein (PYP) is a bacterial blue light receptor containing a 4-hydroxycinnamyl chromophore, and its absorption maximum is 446 nm. In a dark state, the hydroxyl group of the chromophore is deprotonated and forms hydrogen bonds with Tyr42 and Glu46. Either removal of a hydrogen bond with Tyr42 or addition of chaotropes such as thiocyanate produces a blue-shifted species called an intermediate wavelength form, in which absorption maximum ranges from 355 to 400 nm. To examine the structural origin of the intermediate wavelength form, we have performed resonance Raman investigations of wild-type PYP and some mutants (Tyr42 --Ala, Tyr42 --Phe, Glu46 --Gln, and Thr50 --Val) in the presence or absence of potassium thiocyanate. These studies show that the chromophore of the intermediate wavelength form is protonated, implying an increase in a pK(a) of the chromophore. Hence, the removal of the hydrogen bond between Tyr42 and chromophore or partial protein denaturation in the presence of thiocyanate results in a spectral blue-shift. Quantum chemical calculations based on density functional theory further support the idea that the pK(a) of the chromophore is increased by removing a hydrogen bond or by increasing the dielectric constant in the vicinity of the chromophore.

The early stage in the photo-induced dynamics of photoactive yellow protein in aqueous solution has been investigated at room temperature by the femtosecond luminescence spectroscopy using an optical Kerr-gate technique. Remarkable oscillatory components have been directly observed with the time resolution of 180 fs and the spectral resolution of 5 nm . Mapping the phase of oscillations in time at each wavelength reveals that each oscillation is restricted in the respective narrow spectral region, the period and amplitude of which are 500– 800 fs and 100– 200 cm −1 , respectively. Since the mean spectral position of each component seems to be related to the molecular vibrational energy, the oscillatory components are possibly attributed to the combination of the intramolecular vibrations of the chromophore and the surrounding protein motions.

We have investigated primary processes of ultrafast photoreactions of various photoresponsive proteins by means of fs fluorescence dynamics measurements. Based on these studies, the effects of the protein nanospace (PNS), containing the chromophore, on the dynamics and mechanisms of the ultrafast and highly efficient reactions of these proteins have been elucidated. In this article, we discuss mainly the results of our studies on ultrafast photoisomerization of photoactive yellow protein (PYP), its mutants and analogues. The chromophore of the PYP, deprotonated coumaric acid thioester (O−-phenyl-CHCH–CO–S–CH2–), fixed in PNS by hydrogen (H) bonding interactions at the head part, O−-phenyl-, and by covalent bonding at the tail part, –CO–S–, undergoes ultrafast twisting by flipping the thioester bond, owing to the intrachromophore head to tail charge transfer caused by the photoexcitation. In the site-directed mutants where the PNS structure is looser and more disordered, the photoinduced twisting reaction becomes slowed compared with the wild-type PYP and moreover, the twisting becomes much slower in the denatured PYP, showing the supreme importance of more regulated PNS for the fast twisting. We found also coherent vibrations in the fluorescence decay curves which might be coupled with the twisting. Furthermore, we found for a PYP analogue with replaced chromophore ultrafast dynamic Stokes shift of fluorescence rather than the quenching due to twisting, indicating the importance of chromophore-PNS fine adjustment for the ultrafast twisting.

PYP (photoactive yellow protein) is a photoreceptor protein, which is activated upon photo-isomerization of the p-coumaric acid chromophore and is inactivated as the chromophore is thermally back-isomerized within a second (in PYP(M)-to-PYP(dark) conversion). Here we have examined the mechanism of the rapid thermal isomerization by analyzing mutant PYPs of Met100, which was previously shown to play a major role in facilitating the reaction [Devanathan, S. et al. (1998) Biochemistry 37, 11563-11568]. The mutation to Lys, Leu, Ala, or Glu decelerated the dark state recovery by one to three orders of magnitude. By evaluating temperature-dependence of the kinetics, it was found that the retardation resulted unequivocally from elevations of activation enthalpy (DeltaH( double dagger )) but not the other parameters such as activation entropy or heat capacity changes. Another effect exerted by the mutations was an up-shift of the apparent pK(a) of the chromophore [the pK(a) of a titratable group (X) that controls the pK(a) of the chromophore] in the PYP(M)-decay process. The pK(a) up-shift and the DeltaH( double dagger ) elevation show an approximately linear correlation. We, therefore, postulate that the role of Met100 is to reduce the energy barrier of the PYP(M)-decay process by an indirect interaction through X and that the process is thereby facilitated.

Light-activation of the PAS domain protein photoactive yellow protein (PYP) is believed to trigger a negative phototactic response in the phototropic bacterium Halorhodospira halophila. To investigate transient conformational changes of the PYP photocycle, we utilized the PYP mutant M100L that displays an increased lifetime of the putative signaling-state photointermediate PYP(M) by 3 orders of magnitude, as previously reported for the M100A mutant [Devanathan, S., Genick, U. K., Canestrelli, I. L., Meyer, T. E., Cusanovich, M. A., Getzoff, E. D., and Tollin, G. Biochemistry (1998) 37, 11563-11568]. The FTIR difference spectrum of PYP(M) and the ground state of M100L demonstrated extensive peptide-backbone structural changes as observed in the FTIR difference spectrum of the wild-type protein and PYP(M). The conformational change investigated by CD spectroscopy in the far-UV region showed reduction of the alpha-helical content by approximately 40%, indicating a considerable amount of changes in the secondary structure. The optical activity of the p-coumaric acid chromophore completely vanished upon PYP(M) in contrast to the dark state, indicating deformation of the binding pocket structure in PYP(M). The tertiary structural changes were further monitored by small-angle X-ray scattering measurements, which demonstrated a significant increase of the radius of gyration of the molecule by approximately 5% in PYP(M). These structural changes were reversed concomitantly with the chromophore anionization upon the dark state recovery. The observed changes of the quantities provided a more vivid view of the structural changes of the mutant PYP in going from PYP(M) to PYP(dark), which can be regarded as a process of folding of the secondary and the tertiary structures of the "PAS" domain structure, coupled with the p-coumaric acid chromophore deprotonation and isomerization.

Model compounds of PYP chromophore were synthesized and characterized to investigate the role of the Cys69 residue in the active center, which has the intramolecular NHOC hydrogen bond to the conjugated carbonyl oxygen and thioester linkage of the chromophore. The results of UV-vis and (13)C NMR spectroscopy of the model compounds indicated that they delocalized the negative charge of the chromophore and increased the contribution of the quinoid-like resonance structure in the phenolate anion state. Thus, the Cys69 residue plays an important role in the regulation of the color and the stabilization of the chromophore anion in the active center.

The ultrafast photo-induced dynamics of wild-type photoactive yellow protein and its site-directed mutant of E46Q in aqueous solution was studied at room temperature by femtosecond fluorescence spectroscopy using the optical Kerr-gate method. The vibronic structure appears, depending on the excitation photon energy, in the time-resolved fluorescence spectra just after photoexcitation, which winds with time and disappears on a time scale of sub-picoseconds. This result indicates that the wavepacket is localized in the electronic excited state followed by dumped oscillations and broadening, and also that the initial condition of the wavepacket prepared depending on the excitation photon energy affects much the following ultrafast dynamics in the electronic excited state.

The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180 fs time resolution and 5 nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120 cm(-1). In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm(-1), which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.

Pump-dump fluorescence spectroscopy was performed for photoactive yellow protein (PYP) at room temperature. The effect of the dump pulse on the population of the potential energy surface of the electronic excited state was examined as depletion in the stationary fluorescence intensity. The dynamic behavior of the population in the electronic excited state was successfully probed in the various combinations of the pump-dump delay, the dump-pulse wavelength, the dump-pulse energy and the observation wavelength. The experimental results were compared with the results obtained by the femtosecond time-resolved fluorescence spectroscopy.