NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641025 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, though it remains poorly characterized in plants. Here, we describe Arabidopsis homologues of the NuA4 scaffold proteins Enhancer of Polycomb-Like1 (EPL1) and Esa1-Associated Factor1 (EAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors suggesting that NuA4 activates nuclear plastidic genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished in Atepl1 genome-wide while another active chromatin mark H3K9ac is locally enhanced. Many chloroplast-related genes depend on NuA4 as they are downregulated with loss of H4ac and H2A.Z alone. Finally, we demonstrate that NuA4 promotes deposition of H2A.Z and by doing so prevents spurious activation of stress response genes.
2021-12-02 | GSE152940 | GEO
Project description:Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like-1 (AtEPL1) and Esa1- Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes.
2021-12-20 | PXD030302 | Pride
Project description: Not available
| S-EPMC8755797 | biostudies-literature
Project description:DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2M-NM-^T. The esa1-L254P strain was compared to wild type through a series of microarrays utilizing dye swaps with and without treatment of MMS. These included synchronized cells in G1 and S phase through alpha factor treatment. Four unique microarrays were performed each with dye swaps, comparing wild type to esa1-L254P in G1 and S phase with and without treatment with MMS. As a set of controls, four microarrays were performed comparing identical strains with and without MMS in G1 or S phase.
2015-02-21 | E-GEOD-66176 | biostudies-arrayexpress
Project description:rs07-09_bou - catma1-bou - Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth. - Seeds from a heterozygous plants were grown for either 5 or 8 days after germination on synthetic medium (MS/2) without sugar under continuous light. We harvested cotyledon-stage blocked plants (bou phenotype) from three independent Petri dishes and also green seedlings with true leaves and fully developed root (heterozygotes with a wild-type phenotype) . We also grew independently Col-O plants for 5 and 8 days to compare them with the bou mutants. Keywords: gene knock in (transgenic),normal vs disease comparison,time course
2009-02-05 | GSE10399 | GEO
Project description:DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2Δ.
2015-02-21 | GSE66176 | GEO
Project description:The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale metabolic model, iSL836, predicting increased metabolic flux rates of the Wood-Ljungdahl pathway and the glycine synthase-reductase associated reactions under autotrophic conditions. Along with the observation of significant transcriptional activation of genes in the pathways, surprisingly, 13C-labeling experiments and enzyme activity assays confirmed the strain synthesizes glycine and converts into acetyl-phosphate. This study suggests the Wood-Ljungdahl and the glycine synthase-reductase pathways convert CO2 into acetyl-CoA and acetyl-phosphate, respectively. In our knowledge, this is the first report on co-utilization of the pathways under autotrophic growth in acetogen.
2019-08-01 | GSE118519 | GEO
Project description:rs07-09_bou - catma1-bou - Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth. - Seeds from a heterozygous plants were grown for either 5 or 8 days after germination on synthetic medium (MS/2) without sugar under continuous light. We harvested cotyledon-stage blocked plants (bou phenotype) from three independent Petri dishes and also green seedlings with true leaves and fully developed root (heterozygotes with a wild-type phenotype) . We also grew independently Col-O plants for 5 and 8 days to compare them with the bou mutants. Keywords: gene knock in (transgenic),normal vs disease comparison,time course 5 dye-swap - CATMA arrays
2009-02-05 | E-GEOD-10399 | biostudies-arrayexpress
Project description:Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcrip-tion. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase com-plex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an in-structive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes orig-inate from gene duplication and paralog specification. Drosophila generates the same diversi-ty by alternative splicing of a single gene.
2020-05-27 | PXD017729 | Pride
Project description:Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.
2018-07-16 | GSE97613 | GEO