ABSTRACT
HISTONE MONOUBIQUITINATION1 (HUB1) and its paralog HUB2 act in a conserved heterotetrameric complex in the chromatin-mediated transcriptional modulation of developmental programs, such as flowering time, dormancy, and the circadian clock. The KHD1 and SPEN3 proteins were identified as interactors of the HUB1 and HUB2 proteins with in vitro RNA-binding activity. Mutants in SPEN3 and KHD1 had reduced rosette and leaf areas. Strikingly, in spen3 mutants, the flowering time was slightly, but significantly, delayed, as opposed to the early flowering time in the hub1-4 mutant. The mutant phenotypes in biomass and flowering time suggested a deregulation of their respective regulatory genes CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and FLOWERING LOCUS C (FLC) that are known targets of the HUB1-mediated histone H2B monoubiquitination (H2Bub). Indeed, in the spen3-1 and hub1-4 mutants, the circadian clock period was shortened as observed by luciferase reporter assays, the levels of the CCA1α and CCA1ß splice forms were altered, and the CCA1 expression and H2Bub levels were reduced. In the spen3-1 mutant, the delay in flowering time was correlated with an enhanced FLC expression, possibly due to an increased distal versus proximal ratio of its antisense COOLAIR transcript. Together with transcriptomic and double-mutant analyses, our data revealed that the HUB1 interaction with SPEN3 links H2Bub during transcript elongation with pre-mRNA processing at CCA1 Furthermore, the presence of an intact HUB1 at the FLC is required for SPEN3 function in the formation of the FLC-derived antisense COOLAIR transcripts.
Subject(s)
Arabidopsis Proteins , Gene Expression Regulation, Plant , Histones , RNA, Plant , Ubiquitin-Protein Ligases , Ubiquitination , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Circadian Clocks/genetics , Circadian Clocks/physiology , Flowers/genetics , Flowers/physiology , Gene Expression Regulation, Plant/genetics , Gene Expression Regulation, Plant/physiology , Histones/genetics , Histones/metabolism , Protein Domains/genetics , RNA Precursors/genetics , RNA Precursors/metabolism , RNA, Plant/genetics , RNA, Plant/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination/genetics , Ubiquitination/physiologyABSTRACT
The Elongator complex (hereafter Elongator) promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response and sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, including downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors. The downregulated genes LHY, HFR1 and HYH are selectively targeted by Elongator for histone H3K14 acetylation in darkness. The role of Elongator in early seedling development in darkness and light is supported by hypocotyl phenotypes of mutants defective in components of the gene network regulated by Elongator, and by double mutants between elo and mutants in light or darkness signaling components. A model is proposed in which Elongator represses the plant immune response and promotes hypocotyl elongation and photomorphogenesis via transcriptional control of positive photomorphogenesis regulators and a growth-regulatory network that converges on genes involved in cell wall biogenesis and hormone signaling.This article has an associated First Person interview with the first author of the paper.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Arabidopsis/metabolism , Darkness , Morphogenesis/radiation effects , Multiprotein Complexes/metabolism , Acetylation , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Circadian Rhythm/physiology , Epistasis, Genetic , Gene Expression Regulation, Plant , Histones/metabolism , Hypocotyl/growth & development , Models, Biological , Mutation/genetics , Phenotype , Receptors, Cell Surface/metabolism , Seedlings/growth & development , Seedlings/radiation effects , Transcriptome/geneticsABSTRACT
Cytosolic monothiol glutaredoxins (GRXs) are required in iron-sulfur (Fe-S) cluster delivery and iron sensing in yeast and mammals. In plants, it is unclear whether they have similar functions. Arabidopsis (Arabidopsis thaliana) has a sole class II cytosolic monothiol GRX encoded by GRXS17 Here, we used tandem affinity purification to establish that Arabidopsis GRXS17 associates with most known cytosolic Fe-S assembly (CIA) components. Similar to mutant plants with defective CIA components, grxs17 loss-of-function mutants showed some degree of hypersensitivity to DNA damage and elevated expression of DNA damage marker genes. We also found that several putative Fe-S client proteins directly bind to GRXS17, such as XANTHINE DEHYDROGENASE1 (XDH1), involved in the purine salvage pathway, and CYTOSOLIC THIOURIDYLASE SUBUNIT1 and CYTOSOLIC THIOURIDYLASE SUBUNIT2, both essential for the 2-thiolation step of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification of tRNAs. Correspondingly, profiling of the grxs17-1 mutant pointed to a perturbed flux through the purine degradation pathway and revealed that it phenocopied mutants in the elongator subunit ELO3, essential for the mcm5 tRNA modification step, although we did not find XDH1 activity or tRNA thiolation to be markedly reduced in the grxs17-1 mutant. Taken together, our data suggest that plant cytosolic monothiol GRXs associate with the CIA complex, as in other eukaryotes, and contribute to, but are not essential for, the correct functioning of client Fe-S proteins in unchallenged conditions.
Subject(s)
Arabidopsis Proteins/metabolism , Biosynthetic Pathways , Cytosol/metabolism , Glutaredoxins/metabolism , Iron-Sulfur Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , DNA Damage , Gene Expression Regulation, Plant , Glutaredoxins/genetics , Immunoblotting , Mutation , Plant Leaves/genetics , Plant Leaves/metabolism , Plant Roots/genetics , Plant Roots/metabolism , Plants, Genetically Modified , Protein Binding , Reverse Transcriptase Polymerase Chain Reaction , Xanthine Dehydrogenase/genetics , Xanthine Dehydrogenase/metabolismABSTRACT
Elongator (Elp) genes were identified in plants by the leaf growth-altering elo mutations in the yeast (Saccharomyces cerevisiae) gene homologs. Protein purification of the Elongator complex from Arabidopsis thaliana cell cultures confirmed its conserved structure and composition. The Elongator function in plant growth, development, and immune response is well-documented in the elp/elo mutants and correlated with the histone acetyl transferase activity of the ELP3/ELO3 subunit at the coding part of key regulatory genes of developmental and immune response pathways. Here we will focus on additional roles in transcription, such as the cytosine demethylation activity of ELP3/ELO3 at gene promoter regions and primary microRNA transcription and processing through the ELP2 subunit interaction with components of the small interference RNA machinery. Furthermore, specific interactions and upstream regulators support a role for Elongator in transcription and might reveal mechanistic insights into the specificity of the histone acetyl transferase and cytosine demethylation activities for target genes.
Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/genetics , Epigenesis, Genetic , Gene Expression Regulation, Plant , Histone Acetyltransferases/genetics , RNA-Binding Proteins/genetics , Arabidopsis/classification , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Chromatin/chemistry , Chromatin/metabolism , DNA Methylation , Histone Acetyltransferases/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Multigene Family , Phylogeny , Plant Leaves/genetics , Plant Leaves/metabolism , Promoter Regions, Genetic , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transcription, GeneticABSTRACT
In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research.
