Structural determinants for NF-Y/DNA interaction at the CCAAT box

The recently determined crystal structures of the sequence-specific transcription factor NF-Y have illuminated the structural mechanism underlying transcription at the CCAAT box. NF-Y is a trimeric protein complex composed by the NF-YA, NF-YB, and NF-YC subunits. NF-YB and NF-YC contain a histone-like domain and assemble on a head-to-tail fashion to form a dimer, which provides the structural scaffold for the DNA sugar-phosphate backbone binding (mimicking the nucleosome H2A/H2B\ue2\u80\u93DNA assembly) and for the interaction with NF-YA. The NF-YA subunit hosts two structurally extended \uce\ub1-helices; one is involved in NF-YB/NF-YC binding and the other inserts deeply into the DNA minor groove, providing exquisite sequence-specificity for recognition and binding of the CCAAT box. The analysis of these structural data is expected to serve as a powerful guide for future experiments aimed at understanding the role of post-translational modification at NF-Y regulation sites and to unravel the three-dimensional architecture of higher order complexes formed between NF-Y and other transcription factors that act synergistically for transcription activation. Moreover, these structures represent an excellent starting point to challenge the formation of a stable hybrid nucleosome between NF-Y and core histone proteins, and to rationalize the fine molecular details associated with the wide combinatorial association of plant NF-Y subunits

Fusicoccin activates KAT1 channels by stabilizing their interaction with 14-3-3 proteins

Plants acquire potassium (K+) ions for cell growth and movement via regulated diffusion through K+ channels. Here, we present crystallographic and functional data showing that the K+ inward rectifier KAT1 (K+ Arabidopsis thaliana 1) channel is regulated by 14-3-3 proteins and further modulated by the phytotoxin fusicoccin, in analogy to the H+-ATPase. We identified a 14-3-3 mode III binding site at the very C terminus of KAT1 and cocrystallized it with tobacco (Nicotiana tabacum) 14-3-3 proteins to describe the protein complex at atomic detail. Validation of this interaction by electrophysiology shows that 14-3-3 binding augments KAT1 conductance by increasing the maximal current and by positively shifting the voltage dependency of gating. Fusicoccin potentiates the 14-3-3 effect on KAT1 activity by stabilizing their interaction. Crystal structure of the ternary complex reveals a noncanonical binding site for the toxin that adopts a novel conformation. The structural insights underscore the adaptability of fusicoccin, predicting more potential targets than so far anticipated. The data further advocate a common mechanism of regulation of the proton pump and a potassium channel, two essential elements in K+ uptake in plant cells

Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR

This is the final version. Available from Oxford University Press via the DOI in this record.Atomic coordinates and structure factors for the reported apo-PdxR crystal structure have been deposited with the RCSB Protein Data Bank (PDB) under accession number 7PQ9. The cryo-EM maps of the holo-PdxR–DNA complex in the open, half-closed, and closed (C1 and C2 symmetry) conformation and the relative coordinates generated and analysed in the current study have been deposited in the Electron Microscopy Data Bank (EMDB) and in the PDB under accession code EMD-14960 (PDB 7ZTH), EMD-14778 (PDB 7ZLA), EMD-14852 (PDB 7ZPA) and EMD-14801 (PDB 7ZN5), respectively.Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.Italian MIUR-PRIN 2020POR FESR Lazio 2014–2020Sapienza University of RomeDefence Science and Technology Laboratory (DSTL)Istituto Pasteur Italia – Fondazione Cenci Bolognett

The miniJPAS survey: Identification and characterization of the emission line galaxies down to z<0.35z < 0.35 in the AEGIS field

The Javalambre-Physics of the Accelerating Universe Astrophysical Survey (J-PAS) is expected to map thousands of square degrees of the northern sky with 56 narrowband filters in the upcoming years. This will make J-PAS a very competitive and unbiased emission line survey compared to spectroscopic or narrowband surveys with fewer filters. The miniJPAS survey covered 1 deg$^2$, and it used the same photometric system as J-PAS, but the observations were carried out with the pathfinder J-PAS camera. In this work, we identify and characterize the sample of emission line galaxies (ELGs) from miniJPAS with a redshift lower than $0.35$. Using a method based on artificial neural networks, we detect the ELG population and measure the equivalent width and flux of the $H\alpha$, $H\beta$, [OIII], and [NII] emission lines. We explore the ionization mechanism using the diagrams [OIII]/H$\beta$ versus [NII]/H$\alpha$ (BPT) and EW(H$\alpha$) versus [NII]/H$\alpha$ (WHAN). We identify 1787 ELGs ($83$%) from the parent sample (2154 galaxies) in the AEGIS field. For the galaxies with reliable EW values that can be placed in the WHAN diagram (2000 galaxies in total), we obtained that $72.8 \pm 0.4$%, $17.7 \pm 0.4$% , and $9.4 \pm 0.2$% are star-forming (SF), active galactic nucleus (Seyfert), and quiescent galaxies, respectively. Based on the flux of $H\alpha$ we find that the star formation main sequence is described as $\log$ SFR $[M_\mathrm{\odot} \mathrm{yr}^{-1}] = 0.90^{+ 0.02}_{-0.02} \log M_{\star} [M_\mathrm{\odot}] -8.85^{+ 0.19}_{-0.20}$ and has an intrinsic scatter of $0.20^{+ 0.01}_{-0.01}$. The cosmic evolution of the SFR density ($\rho_{\text{SFR}}$) is derived at three redshift bins: $0 < z \leq 0.15$, $0.15 < z \leq 0.25$, and $0.25 < z \leq 0.35$, which agrees with previous results that were based on measurements of the $H\alpha$ emission line.Comment: 22 pages, 19 figure

J-NEP: 60-band photometry and photometric redshifts for the James Webb Space Telescope North Ecliptic Pole Time-Domain Field

The J-PAS survey will observe ~1/3 of the northern sky with a set of 56 narrow-band filters using the dedicated 2.55 m JST telescope at the Javalambre Astrophysical Observatory. Prior to the installation of the main camera, in order to demonstrate the scientific potential of J-PAS, two small surveys were performed with the single-CCD Pathfinder camera: miniJPAS (~1 deg2 along the Extended Groth Strip), and J-NEP (~0.3 deg2 around the JWST North Ecliptic Pole Time Domain Field), including all 56 J-PAS filters as well as u, g, r, and i. J-NEP is ~0.5-1.0 magnitudes deeper than miniJPAS, providing photometry for 24,618 r-band detected sources and photometric redshifts (photo-z) for the 6,662 sources with r<23. In this paper we describe the photometry and photo-z of J-NEP and demonstrate a new method for the removal of systematic offsets in the photometry based on the median colours of galaxies, dubbed "galaxy locus recalibration". This method does not require spectroscopic observations except in a few reference pointings and, unlike previous methods, is applicable to the whole J-PAS survey. We use a spectroscopic sample of 787 galaxies to test the photo-z performance for J-NEP and in comparison to miniJPAS. We find that the deeper J-NEP observations result in a factor ~1.5-2 decrease in sigma_NMAD (a robust estimate of the standard deviation of the photo-z error) and the outlier rate relative to miniJPAS for r>21.5 sources, but no improvement in brighter ones. We find the same relation between sigma_NMAD and odds in J-NEP and miniJPAS, suggesting sigma_NMAD can be predicted for any set of J-PAS sources from their odds distribution alone, with no need for additional spectroscopy to calibrate the relation. We explore the causes for photo-z outliers and find that colour-space degeneracy at low S/N, photometry artifacts, source blending, and exotic spectra are the most important factors.Comment: 16 pages, 25 figures, accepted for publication in Astronomy and Astrophysic

TOPz: Photometric redshifts for J-PAS

The importance of photometric galaxy redshift estimation is rapidly increasing with the development of specialised powerful observational facilities. We develop a new photometric redshift estimation workflow TOPz to provide reliable and efficient redshift estimations for the upcoming large-scale survey J-PAS which will observe 8500 deg2 of the northern sky through 54 narrow-band filters. TOPz relies on template-based photo-z estimation with some added J-PAS specific features and possibilities. We present TOPz performance on data from the miniJPAS survey, a precursor to the J-PAS survey with an identical filter system. First, we generated spectral templates based on the miniJPAS sources using the synthetic galaxy spectrum generation software CIGALE. Then we applied corrections to the input photometry by minimising systematic offsets from the template flux in each filter. To assess the accuracy of the redshift estimation, we used spectroscopic redshifts from the DEEP2, DEEP3, and SDSS surveys, available for 1989 miniJPAS galaxies with r < 22 magAB. We also tested how the choice and number of input templates, photo-z priors, and photometric corrections affect the TOPz redshift accuracy. The general performance of the combination of miniJPAS data and the TOPz workflow fulfills the expectations for J-PAS redshift accuracy. Similarly to previous estimates, we find that 38.6% of galaxies with r < 22 mag reach the J-PAS redshift accuracy goal of dz/(1 + z) < 0.003. Limiting the number of spectra in the template set improves the redshift accuracy up to 5%, especially for fainter, noise-dominated sources. Further improvements will be possible once the actual J-PAS data become available.Comment: 20 pages, 24 figure

Black hole virial masses from single-epoch photometry:the miniJPAS test case

Precise measurements of black hole (BH) masses are essential to understanding the coevolution of these sources and their host galaxies. In this work, we develop a novel approach to compute BH virial masses using measurements of continuum luminosities and emission line widths from partially-overlapping, narrow-band observations of quasars; we refer to this technique as single-epoch photometry. This novel method relies on forward-modelling quasar observations to estimate the previous properties, which enables accurate measurements of emission line widths even for lines poorly resolved by narrow-band data. We assess the performance of this technique using quasars from the Sloan Digital Sky Survey (SDSS) observed by the miniJPAS survey, a proof-of-concept project of the J-PAS collaboration covering $\simeq1\,\mathrm{deg}^2$ of the northern sky using the 56 J-PAS narrow-band filters. We find remarkable agreement between BH masses from single-epoch SDSS spectra and single-epoch miniJPAS photometry, with no systematic difference between these and a scatter ranging from 0.4 to 0.07 dex for masses from $\log(M_\mathrm{BH}/\mathrm{M}_\odot)\simeq8$ to 9.75, respectively. Reverberation mapping studies show that single-epoch masses approximately present 0.4 dex precision, letting us conclude that our novel technique delivers BH masses with only mildly worse precision than single-epoch spectroscopy. The J-PAS survey will soon start observing thousands of square degrees without any source preselection other than the photometric depth in the detection band, and thus single-epoch photometry has the potential to provide details on the physical properties of quasar populations not satisfying the preselection criteria of previous spectroscopic surveys

The miniJPAS survey:Photometric redshift catalogue

MiniJPAS is a ∼1 deg2 imaging survey of the AEGIS field in 60 bands, performed to demonstrate the scientific potential of the upcoming Javalambre-Physics of the Accelerating Universe Astrophysical Survey (J-PAS). Full coverage of the 3800-9100 Å range with 54 narrow-band filters, in combination with 6 optical broad-band filters, allows for extremely accurate photometric redshifts (photo-z), which, applied over areas of thousands of square degrees, will enable new applications of the photo-z technique, such as measurement of baryonic acoustic oscillations. In this paper we describe the method we used to obtain the photo-z that is included in the publicly available miniJPAS catalogue, and characterise the photo-z performance. We built photo-spectra with 100 Å resolution based on forced-aperture photometry corrected for point spread function. Systematic offsets in the photometry were corrected by applying magnitude shifts obtained through iterative fitting with stellar population synthesis models. We computed photo-z with a customised version of LEPHARE, using a set of templates that is optimised for the J-PAS filter-set. We analysed the accuracy of miniJPAS photo-z and their dependence on multiple quantities using a subsample of 5266 galaxies with spectroscopic redshifts from SDSS and DEEP, which we find to be representative of the whole r 0.03), regardless of the magnitude, redshift, or spectral type of the sources. We show that the two main summary statistics characterising the photo-z accuracy for a population of galaxies (σNMAD and η) can be predicted by the distribution of odds in this population, and we use this to estimate the statistics for the whole miniJPAS sample. At r 0.82 with η = 0.05, at the cost of decreasing the density of selected galaxies to n ∼5200 deg-2 (∼2600 of which have |Δz| <0.003). © ESO 2021

The miniJPAS survey: A search for extreme emission-line galaxies

This is an Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Context. Galaxies with extreme emission lines (EELGs) may play a key role in the evolution of the Universe, as well as in our understanding of the star formation process itself. For this reason an accurate determination of their spatial density and fundamental properties in different epochs of the Universe will constitute a unique perspective towards a comprehensive picture of the interplay between star formation and mass assembly in galaxies. In addition to this, EELGs are also interesting in order to explain the reionization of the Universe, since their interstellar medium (ISM) could be leaking ionizing photons, and thus they could be low z, analogous of extreme galaxies at high z. Aims. This paper presents a method to obtain a census of EELGs over a large area of the sky by detecting galaxies with rest-frame equivalent widths ≥300 Å in the emission lines [O II]λλ3727,3729Å, [O III]λ5007Å, and Hα. For this, we aim to use the J-PAS survey, which will image an area of ≈8000 deg2 with 56 narrow band filters in the optical. As a pilot study, we present a methodology designed to select EELGs on the miniJPAS images, which use the same filter dataset as J-PAS, and thus will be exportable to this larger survey. Methods. We make use of the miniJPAS survey data, conceived as a proof of concept of J-PAS, and covering an area of ≈1 deg2. Objects were detected in the rSDSS images and selected by imposing a condition on the flux in a given narrow-band J-PAS filter with respect to the contiguous ones, which is analogous to requiring an observed equivalent width larger than 300 Å in a certain emission line within the filter bandwidth. The selected sources were then classified as galaxies or quasi-stellar objects (QSOs) after a comparison of their miniJPAS fluxes with those of a spectral database of objects known to present strong emission lines. This comparison also provided a redshift for each source, which turned out to be consistent with the spectroscopic redshifts when available (|Δz/(1 + zspec)| ≤ 0.01). Results. The selected candidates were found to show a compact appearance in the optical images, some of them even being classified as point-like sources according to their stellarity index. After discarding sources classified as QSOs, a total of 17 sources turned out to exhibit EW0 ≥ 300 Å in at least one emission line, thus constituting our final list of EELGs. Our counts are fairly consistent with those of other samples of EELGs in the literature, although there are some differences, which were expected due to biases resulting from different selection criteria. © J. Iglesias-Páramo et al. 2022.This work has been partially funded by projects PID2019-107408GB-C44 from the Spanish PNAYA, co-funded with FEDER, and grand P18-FR-2664, funded by Junta de Andalucía. We acknowledge financial support from the State Agency for Research of the Spanish MCIU through the “Center of Excellence Severo Ochoa” award to the Instituto de Astrofísica de Andalucía (SEV-2017-0709). RGD and LADG acknowledge financial support from the State Agency for Research of the Spanish MCIU through the “Center of Excellence Severo Ochoa” award to the Instituto de Astrofísica de Andalucía (SEV-2017-0709), and PID2019-109067-GB100. IM acknowledges financial support from the State Agency for Research of the Spanish MCIU through the PID2019-106027GB-C41. JCM acknowledges partial support from the Spanish Ministry of Science, Innovation and Universities (MCIU/AEI/FEDER, UE) through the grant PGC2018-097585-B-C22. SDP is grateful to the Fonds de Recherche du Québec – Nature et Technologies. LSJ acknowledges the support of CNPq (304819/2017-4) and FAPESP (2019/10923-5). JAFO acknowledges the financial support from the Spanish Ministry of Science and Innovation and the European Union – NextGenerationEU through the Recovery and Resilience Facility project ICTS-MRR-2021-03- CEFCA. Funding for the J-PAS Project has been provided by the Governments of España and Aragón though the Fondo de Inversión de Teruel, European FEDER funding and the MINECO and by the Brazilian agencies FINEP, FAPESP, FAPERJ and by the National Observatory of Brazil. Based on observations made with the JST/T250 telescope and PathFinder camera for the miniJPAS project at the Observatorio Astrofísico de Javalambre (OAJ), in Teruel, owned, managed, and operated by the Centro de Estudios de Física del Cosmos de Aragón (CEFCA). We acknowledge the OAJ Data Processing and Archiving Unit (UPAD) for reducing and calibrating the OAJ data used in this work. Funding for OAJ, UPAD, and CEFCA has been provided by the Governments of Spain and Aragón through the Fondo de Inversiones de Teruel; the Aragón Government through the Research Groups E96, E103, and E16_17R; the Spanish Ministry of Science, Innovation and Universities (MCIU/AEI/FEDER, UE) with grant PGC2018-097585-B-C21; the Spanish Ministry of Economy and Competitiveness (MINECO/FEDER, UE) under AYA2015-66211-C2-1-P, AYA2015-66211-C2-2, AYA2012-30789, and ICTS-2009-14; and European FEDER funding (FCDD10-4E-867, FCDD13-4E-2685). This research has made use of the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. Funding for SDSS-IV has been provided by the Alfred P. Sloan Foundation, the Participating Institutions, the National Science Foundation, and the U.S. Department of Energy Office of Science. The SDSS-IV web site is https://www.sdss.org/. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 898633.Peer reviewe

Structure and kinetic properties of human d-aspartate oxidase, the enzyme-controlling d-aspartate levels in brain

d-Amino acids are the \u201cwrong\u201d enantiomers of amino acids as they are not used in proteins synthesis but evolved in selected functions. On this side, d-aspartate (d-Asp) plays several significant roles in mammals, especially as an agonist of N-methyl-d-aspartate receptors (NMDAR), and is involved in relevant diseases, such as schizophrenia and Alzheimer's disease. In vivo modulation of d-Asp levels represents an intriguing task to cope with such pathological states. As little is known about d-Asp synthesis, the only option for modulating the levels is via degradation, which is due to the flavoenzyme d-aspartate oxidase (DASPO). Here we present the first three-dimensional structure of a DASPO enzyme (from human) which belongs to the d-amino acid oxidase family. Notably, human DASPO differs from human d-amino acid oxidase (attributed to d-serine degradation, the main coagonist of NMDAR) showing peculiar structural features (a specific active site charge distribution), oligomeric state and kinetic mechanism, and a higher FAD affinity and activity. These results provide useful insights into the structure-function relationships of human DASPO: modulating its activity represents now a feasible novel therapeutic target