Metal A and Metal B Sites of Nuclear RNA Polymerases Pol IV and Pol V Are Required for siRNA-Dependent DNA Methylation and Gene Silencing

Plants are unique among eukaryotes in having five multi-subunit nuclear RNA polymerases: the ubiquitous RNA polymerases I, II and III plus two plant-specific activities, nuclear RNA polymerases IV and V (previously known as Polymerases IVa and IVb). Pol IV and Pol V are not required for viability but play non-redundant roles in small interfering RNA (siRNA)-mediated pathways, including a pathway that silences retrotransposons and endogenous repeats via siRNA-directed DNA methylation. RNA polymerase activity has not been demonstrated for Polymerases IV or V in vitro, making it unclear whether they are catalytically active enzymes. Their largest and second-largest subunit sequences have diverged considerably from Pol I, II and III in the vicinity of the catalytic center, yet retain the invariant Metal A and Metal B amino acid motifs that bind magnesium ions essential for RNA polymerization. By using site-directed mutagenesis in conjunction with in vivo functional assays, we show that the Metal A and Metal B motifs of Polymerases IV and V are essential for siRNA production, siRNA-directed DNA methylation, retrotransposon silencing, and the punctate nuclear localization patterns typical of both polymerases. Collectively, these data show that the minimal core sequences of polymerase active sites, the Metal A and B sites, are essential for Pol IV and Pol V biological functions, implying that both are catalytically active

Maize ABP9 enhances tolerance to multiple stresses in transgenic Arabidopsis by modulating ABA signaling and cellular levels of reactive oxygen species

The phytohormone abscisic acid (ABA) and reactive oxygen species (ROS) play critical roles in mediating abiotic stress responses in plants. It is well known that ABA is involved in the modulation of ROS levels by regulating ROS-producing and ROS-scavenging genes, but the molecular mechanisms underlying this regulation are poorly understood. Here we show that the expression of maize ABP9 gene, which encodes a bZIP transcription factor capable of binding to the ABRE2 motif in the maize Cat1 promoter, is induced by ABA, H2O2, drought and salt. Constitutive expression of ABP9 in transgenic Arabidopsis leads to remarkably enhanced tolerance to multiple stresses including drought, high salt, freezing temperature and oxidative stresses. ABP9 expressing Arabidopsis plants also exhibit increased sensitivity to exogenously applied ABA during seed germination, root growth and stomatal closure and improved water-conserving capacity. Moreover, constitutive expression of ABP9 causes reduced cellular levels of ROS, alleviated oxidative damage and reduced cell death, accompanied by elevated expression of many stress/ABA responsive genes including those for scavenging and regulating ROS. Taken together, these results suggest that ABP9 may play a pivotal role in plant tolerance to abiotic stresses by fine tuning ABA signaling and control of ROS accumulation

An insertional mutagenesis programme with an enhancer trap for the identification and tagging of genes involved in abiotic stress tolerance in the tomato wild-related species Solanum pennellii

Salinity and drought have a huge impact on agriculture since there are few areas free of these abiotic stresses and the problem continues to increase. In tomato, the most important horticultural crop worldwide, there are accessions of wild-related species with a high degree of tolerance to salinity and drought. Thus, the finding of insertional mutants with other tolerance levels could lead to the identification and tagging of key genes responsible for abiotic stress tolerance. To this end, we are performing an insertional mutagenesis programme with an enhancer trap in the tomato wild-related species Solanum pennellii. First, we developed an efficient transformation method which has allowed us to generate more than 2,000 T-DNA lines. Next, the collection of S. pennelli T0 lines has been screened in saline or drought conditions and several presumptive mutants have been selected for their salt and drought sensitivity. Moreover, T-DNA lines with expression of the reporter uidA gene in specific organs, such as vascular bundles, trichomes and stomata, which may play key roles in processes related to abiotic stress tolerance, have been identified. Finally, the growth of T-DNA lines in control conditions allowed us the identification of different development mutants. Taking into account that progenies from the lines are being obtained and that the collection of T-DNA lines is going to enlarge progressively due to the high transformation efficiency achieved, there are great possibilities for identifying key genes involved in different tolerance mechanisms to salinity and drought

The prevalence of galaxy overdensities around UV-luminous Lyman α emitters in the Epoch of Reionization

ABSTRACT Before the end of the Epoch of Reionization, the Hydrogen in the Universe was predominantly neutral. This leads to a strong attenuation of Ly α lines of z ≳ 6 galaxies in the intergalactic medium. Nevertheless, Ly α has been detected up to very high redshifts (z ∼ 9) for several especially UV luminous galaxies. Here, we test to what extent the galaxy’s local environment might impact the Ly α transmission of such sources. We present an analysis of dedicated Hubble Space Telescope (HST) imaging in the CANDELS/EGS field to search for fainter neighbours around three of the most UV luminous and most distant spectroscopically confirmed Ly α emitters: EGS-zs8-1, EGS-zs8-2, and EGSY-z8p7 at zspec = 7.73, 7.48, and 8.68, respectively. We combine the multiwavelength HST imaging with Spitzer data to reliably select z ∼ 7–9 galaxies around the central, UV-luminous sources. In all cases, we find a clear enhancement of neighbouring galaxies compared to the expected number in a blank field (by a factor ∼3–9×). Our analysis thus reveals ubiquitous overdensities around luminous Ly α emitting sources in the heart of the cosmic reionization epoch. We show that our results are in excellent agreement with expectations from the Dragons simulation, confirming the theoretical prediction that the first ionized bubbles preferentially formed in overdense regions. While three UV luminous galaxies already have spectroscopic redshifts, the majority of the remaining fainter, surrounding sources are yet to be confirmed via spectroscopy. JWST follow-up observations of the neighbouring galaxies identified here will thus be needed to confirm their physical association and to map out the ionized regions produced by these sources.</jats:p

A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.

Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish

The prevalence of galaxy overdensities around UV-luminous Lyman α emitters in the Epoch of Reionization

Before the end of the Epoch of Reionization, the Hydrogen in the Universe was predominantly neutral. This leads to a strong attenuation of Ly α lines of z ≳ 6 galaxies in the intergalactic medium. Nevertheless, Ly α has been detected up to very high redshifts (z ∼9) for several especially UV luminous galaxies. Here, we test to what extent the galaxy's local environment might impact the Ly α transmission of such sources. We present an analysis of dedicated Hubble Space Telescope (HST) imaging in the CANDELS/EGS field to search for fainter neighbours around three of the most UV luminous and most distant spectroscopically confirmed Ly α emitters: EGS-zs8-1, EGS-zs8-2, and EGSY-z8p7 at zspec = 7.73, 7.48, and 8.68, respectively. We combine the multiwavelength HST imaging with Spitzer data to reliably select z ∼7-9 galaxies around the central, UV-luminous sources. In all cases, we find a clear enhancement of neighbouring galaxies compared to the expected number in a blank field (by a factor ∼3-9×). Our analysis thus reveals ubiquitous overdensities around luminous Ly α emitting sources in the heart of the cosmic reionization epoch. We show that our results are in excellent agreement with expectations from the Dragons simulation, confirming the theoretical prediction that the first ionized bubbles preferentially formed in overdense regions. While three UV luminous galaxies already have spectroscopic redshifts, the majority of the remaining fainter, surrounding sources are yet to be confirmed via spectroscopy. JWST follow-up observations of the neighbouring galaxies identified here will thus be needed to confirm their physical association and to map out the ionized regions produced by these sources