Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana

GCN5-related histone acetyltransferase HOOKLESS2 regulates fungal resistance and growth in tomato

The functions of histone acetyltransferases (HATs) in the genetic control of crop traits and the underlying mechanisms are poorly understood. We studied the function of tomato HOOKLESS2 (SlHLS2), a member of the GCN5 family of HATs, through genetic, molecular and genomic approaches. Tomato hls2 mutants generated through CRISPR-cas9 gene editing show enhanced susceptibility to fungal infection, accelerated dark-induced senescence, grossly altered plant architecture, and loss of fertility accompanied by high levels of auxin accumulation. Components of the basal and induced transcriptome underlying the extensive phenotypic impact of HLS2 were uncovered. HLS2-dependent differentially expressed genes were enriched for genes implicated in photosynthesis, protein ubiquitination, oxylipin biosynthesis, autophagy, and response to biotic stimuli. In particular, induced expressions of the BTB/POZ and TAZ domain-containing protein gene (SlBT1), AUTOPHAGY-RELATED PROTEIN 11, ACYLSUGAR ACYLTRANSFERASE 3 (ASAT3), and multiple jasmonate biosynthesis genes require functional HLS2. SlHLS2 associates with the SlBT1 promoter, and histone acetylation at the chromatin of SlBT1 was reduced in the Slhls2 mutant suggesting direct regulation of SlBTB1 by HLS2. SlBTB1 is an adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB), which mediates ubiquitination and proteasomal degradation of proteins. HLS2 is degraded after fungal inoculation, which is stabilized by inhibition of the 26S proteasome. Overall, tomato HLS2 functions in pathogen responses, plant architecture, and fertility.

Roles of Histone Acetylation and Deacetylation in Root Development

Roots are usually underground plant organs, responsible for anchoring to the soil, absorbing water and nutrients, and interacting with the rhizosphere. During root development, roots respond to a variety of environmental signals, contributing to plant survival. Histone post-translational modifications play essential roles in gene expression regulation, contributing to plant responses to environmental cues. Histone acetylation is one of the most studied post-translational modifications, regulating numerous genes involved in various biological processes, including development and stress responses. Although the effect of histone acetylation on plant responses to biotic and abiotic stimuli has been extensively reviewed, no recent reviews exist focusing on root development regulation by histone acetylation. Therefore, this review brings together all the knowledge about the impact of histone acetylation on root development in several plant species, mainly focusing on Arabidopsis thaliana. Here, we summarize the role of histone acetylation and deacetylation in numerous aspects of root development, such as stem cell niche maintenance, cell division, expansion and differentiation, and developmental zone determination. We also emphasize the gaps in current knowledge and propose new perspectives for research toward deeply understanding the role of histone acetylation in root development.

Epigenetics and plant hormone dynamics: a functional and methodological perspective

Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.

Gibberellin Signaling through RGA Suppresses GCN5 Effects on Arabidopsis Developmental Stages

Histone acetyltransferases (HATs) modify the amino-terminal tails of the core histone proteins via acetylation, regulating chromatin structure and transcription. GENERAL CONTROL NON-DEREPRESSIBLE 5 (GCN5) is a HAT that specifically acetylates H3K14 residues. GCN5 has been associated with cell division and differentiation, meristem function, root, stem, foliar, and floral development, and plant environmental response. The flowers of gcn5 plants display a reduced stamen length and exhibit male sterility relative to the wild-type plants. We show that these effects may arise from gibberellin (GA)-signaling defects. The signaling pathway of bioactive GAs depends on the proteolysis of their repressors, DELLA proteins. The repressor GA (RGA) DELLA protein represses plant growth, inflorescence, and flower and seed development. Our molecular data indicate that GCN5 is required for the activation and H3K14 acetylation of genes involved in the late stages of GA biosynthesis and catabolism. We studied the genetic interaction of the RGA and GCN5; the RGA can partially suppress GCN5 action during the whole plant life cycle. The reduced elongation of the stamen filament of gcn5-6 mutants is reversed in the rga-t2;gcn5-6 double mutants. RGAs suppress the GCN5 effect on the gene expression and histone acetylation of GA catabolism and GA signaling. Interestingly, the RGA and RGL2 do not suppress ADA2b function, suggesting that ADA2b acts downstream of GA signaling and is distinct from GCN5 activity. In conclusion, we propose that the action of GCN5 on stamen elongation is partially mediated by RGA and GA signaling.

HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation

The gynoecium is critical for the reproduction of flowering plants as it contains the ovules and the tissues that foster pollen germination, growth, and guidance. These tissues, known as the reproductive tract (ReT), comprise the stigma, style, and transmitting tract (TT). The ReT and ovules originate from the carpel margin meristem (CMM) within the pistil. SHOOT MERISTEMLESS (STM) is a key transcription factor for meristem formation and maintenance. In all above-ground meristems, including the CMM, local STM downregulation is required for organ formation. However, how this downregulation is achieved in the CMM is unknown. Here, we have studied the role of HISTONE DEACETYLASE 19 (HDA19) in Arabidopsis (Arabidopsis thaliana) during ovule and ReT differentiation based on the observation that the hda19-3 mutant displays a reduced ovule number and fails to differentiate the TT properly. Fluorescence-activated cell sorting coupled with RNA-sequencing revealed that in the CMM of hda19-3 mutants, genes promoting organ development are downregulated while meristematic markers, including STM, are upregulated. HDA19 was essential to downregulate STM in the CMM, thereby allowing ovule formation and TT differentiation. STM is ectopically expressed in hda19-3 at intermediate stages of pistil development, and its downregulation by RNA interference alleviated the hda19-3 phenotype. Chromatin immunoprecipitation assays indicated that STM is a direct target of HDA19 during pistil development and that the transcription factor SEEDSTICK is also required to regulate STM via histone acetylation. Thus, we identified factors required for the downregulation of STM in the CMM, which is necessary for organogenesis and tissue differentiation.

GWAS and Meta-QTL Analysis of Yield-Related Ear Traits in Maize

Maize ear traits are an important component of yield, and the genetic basis of ear traits facilitates further yield improvement. In this study, a panel of 580 maize inbred lines were used as the study material, eight ear-related traits were measured through three years of planting, and whole genome sequencing was performed using the maize 40 K breeding chip based on genotyping by targeted sequencing (GBTS) technology. Five models were used to conduct a genome-wide association study (GWAS) on best linear unbiased estimate (BLUE) of ear traits to find the best model. The FarmCPU (Fixed and random model Circulating Probability Unification) model was the best model for this study; a total of 104 significant single nucleotide polymorphisms (SNPs) were detected, and 10 co-location SNPs were detected simultaneously in more than two environments. Through gene function annotation and prediction, a total of nine genes were identified as potentially associated with ear traits. Moreover, a total of 760 quantitative trait loci (QTL) associated with yield-related traits reported in 37 different articles were collected. Using the collected 760 QTL for meta-QTL analysis, a total of 41 MQTL (meta-QTL) associated with yield-related traits were identified, and 19 MQTL detected yield-related ear trait functional genes and candidate genes that have been reported in maize. Five significant SNPs detected by GWAS were located within these MQTL intervals, and another three significant SNPs were close to MQTL (less than 1 Mb). The results provide a theoretical reference for the analysis of the genetic basis of ear-related traits and the improvement of maize yield.

Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants

The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.

Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis

Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is lysine 27 of H3 (H3K27), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3^K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3^K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are new. They include early flowering, increased callus formation and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.

The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter

Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.

Conserved and plant-specific histone acetyltransferase complexes cooperate to regulate gene transcription and plant development

Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryza sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL and EAF6). We find that PAGA and SAGA can independently mediate moderate and high levels of histone acetylation, respectively, thereby promoting transcriptional activation. Moreover, PAGA and SAGA can also repress gene transcription via the antagonistic effect between PAGA and SAGA. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.

Histone Acetyltransferase GCN5 Affects Auxin Transport during Root Growth by Modulating Histone Acetylation and Gene Expression of PINs

General Control Non-Derepressible 5 (GCN5) is a histone acetyltransferase that targets multiple genes and is essential for the acetylation of Lysine residues in the N-terminal tail of histone H3 in Arabidopsis. GCN5 interacts with the transcriptional coactivator Alteration/Deficiency in Activation 2b (ADA2b), which enhances its activity functioning in multiprotein complexes, such as the Spt-Ada-Gcn5-Acetyltransferase complex (SAGA). Mutations in GCN5 and ADA2b result in pleiotropic phenotypes, including alterations in the growth of roots. Auxin is known to regulate root development by modulating gene expression patterns. Auxin moves polarly during plant growth via the Pin-formed (PIN) auxin efflux transport proteins. The effect of GCN5 and ADA2b on auxin distribution at different stages of early root growth (4 to 7 days post-germination) was studied using the reporter lines DR5rev::GFP and PIN1::PIN1-GFP. In wild-type plants, auxin efflux transporter PIN1 expression increases from the fourth to the seventh day of root growth. The PIN1 expression was reduced in the roots of gcn5-1 and ada2b-1 compared to the wild type. The expression of PIN1 in ada2b-1 mutants is confined only to the meristematic zone, specifically in the stele cells, whereas it is almost abolished in the elongation zone. Gene expression analysis showed that genes associated with auxin transport, PIN1, PIN3 and PIN4, are downregulated in gcn5-1 and ada2b-1 mutants relative to the wild type. As a result, auxin accumulation was also reduced in gcn5-1 and ada2b-1 compared to wild-type roots. Furthermore, acetylation of Lysine 14 of histone H3 (H3K14) was also affected in the promoter and coding region of PIN1, PIN3 and PIN4 genes during root growth of Arabidopsis in gcn5 mutants. In conclusion, GCN5 acts as a positive regulator of auxin distribution in early root growth by modulating histone H3 acetylation and the expression of auxin efflux transport genes.

The roles of epigenetic modifications in the regulation of auxin biosynthesis

Auxin is one of the most important plant growth regulators of plant morphogenesis and response to environmental stimuli. Although the biosynthesis pathway of auxin has been elucidated, the mechanisms regulating auxin biosynthesis remain poorly understood. The transcription of auxin biosynthetic genes is precisely regulated by complex signaling pathways. When the genes are expressed, epigenetic modifications guide mRNA synthesis and therefore determine protein production. Recent studies have shown that different epigenetic factors affect the transcription of auxin biosynthetic genes. In this review, we focus our attention on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis.

ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana

In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth.

Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis

Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryogenic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental processes, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin- and TSA-induced SE.

Three functionally redundant plant-specific paralogs are core subunits of the SAGA histone acetyltransferase complex in Arabidopsis

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved histone acetyltransferase complex that has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. In this study, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits but also four plant-specific subunits: three functionally redundant paralogs, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. Mutations in SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the genes encoding conserved SAGA subunits HAG1 and ADA2B, including delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. Furthermore, we demonstrated that SCS1/2A/2B are required for the function of the SAGA complex in histone acetylation, thereby promoting the transcription of development-related genes. These results together suggest that SCS1/2A/2B are core subunits of the SAGA complex in Arabidopsis. Compared with SAGA complexes in other eukaryotes, the SAGA complexes in plants have evolved unique features that are necessary for normal growth and development.

HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants

KEY MESSAGE

Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1, and analyzed loss-of-function mutants in the moss P. patens. In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pphag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mphag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.

Histone acetylation: a requirement for petunia floral scent

This article comments on: Patrick RM, Huang X-Q, Dudareva N, Li Y. 2021. Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers. Journal of Experimental Botany 72, 3704–3722.

Updated Mechanisms of GCN5-The Monkey King of the Plant Kingdom in Plant Development and Resistance to Abiotic Stresses

Histone modifications are the main epigenetic mechanisms that regulate gene expression, chromatin structure, and plant development, among which histone acetylation is one of the most important and studied epigenetic modifications. Histone acetylation is believed to enhance DNA access and promote transcription. GENERAL CONTROL NON-REPRESSIBLE 5 (GCN5), a well-known enzymatic protein responsible for the lysine acetylation of histone H3 and H4, is a universal and crucial histone acetyltransferase involved in gene transcription and plant development. Many studies have found that GCN5 plays important roles in the different development stages of Arabidopsis. In terms of exogenous stress conditions, GCN5 is also involved in the responses to heat stress, cold stress, and nutrient element deficiency by regulating the related gene expression to maintain the homeostasis of some key metabolites (e.g., cellulose) or ions (e.g., phosphate, iron); in addition, GCN5 is involved in the phytohormone pathways such as ethylene, auxin, and salicylic acid to play various roles during the plant lifecycle. Some of the pathways involved by GCN5 also interwind to regulate specific physiological processes or developmental stages. Here, interactions between various developmental events and stress-resistant pathways mediated by GCN5 are comprehensively addressed and the underlying mechanisms are discussed in the plant. Studies with some interacting factors such as ADA2b provided valuable information for the complicated histone acetylation mechanisms. We also suggest the future focuses for GCN5 functions and mechanisms such as functions in seed development/germination stages, exploration of novel interaction factors, identification of more protein substrates, and application of advanced biotechnology-CRISPR in crop genetic improvement, which would be helpful for the complete illumination of roles and mechanisms of GCN5.

The Transcriptional Adaptor Protein ADA3a Modulates Flowering of Arabidopsis thaliana

Histone acetylation is directly related to gene expression. In yeast, the acetyltransferase general control nonderepressible-5 (GCN5) targets histone H3 and associates with transcriptional co-activators alteration/deficiency in activation-2 (ADA2) and alteration/deficiency in activation-3 (ADA3) in complexes like SAGA. Arabidopsis thaliana has two genes encoding proteins, designated ADA3a and ADA3b, that correspond to yeast ADA3. We investigated the role of ADA3a and ADA3b in regulating gene expression during flowering time. Specifically, we found that knock out mutants ada3a-2 and the double mutant ada3a-2 ada3b-2 lead to early flowering compared to the wild type plants under long day (LD) conditions and after moving plants from short days to LD. Consistent with ADA3a being a repressor of floral initiation, FLOWERING LOCUS T (FT) expression was increased in ada3a mutants. In contrast, other genes involved in multiple pathways leading to floral transition, including FT repressors, players in GA signaling, and members of the SPL transcriptional factors, displayed reduced expression. Chromatin immunoprecipitation analysis revealed that ADA3a affects the histone H3K14 acetylation levels in SPL3, SPL5, RGA, GAI, and SMZ loci. In conclusion, ADA3a is involved in floral induction through a GCN5-containing complex that acetylates histone H3 in the chromatin of flowering related genes.

The Histone Acetyltransferase GCN5 and the Associated Coactivators ADA2: From Evolution of the SAGA Complex to the Biological Roles in Plants

Transcription of protein-encoding genes starts with forming a pre-initiation complex comprised of RNA polymerase II and several general transcription factors. To activate gene expression, transcription factors must overcome repressive chromatin structure, which is accomplished with multiprotein complexes. One such complex, SAGA, modifies the nucleosomal histones through acetylation and other histone modifications. A prototypical histone acetyltransferase (HAT) known as general control non-repressed protein 5 (GCN5), was defined biochemically as the first transcription-linked HAT with specificity for histone H3 lysine 14. In this review, we analyze the components of the putative plant SAGA complex during plant evolution, and current knowledge on the biological role of the key components of the HAT module, GCN5 and ADA2b in plants, will be summarized.

GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.

A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.

Multifaceted activities of the plant SAGA complex

From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.

Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.)

Plant reproductive development from the first appearance of reproductively committed axes through to floral maturation requires massive and rapid remarshalling of gene expression. In dioecious species such as poplar this is further complicated by divergent male and female developmental programs. We used seven time points in male and female balsam poplar (Populus balsamifera L.) buds and catkins representing the full annual flowering cycle, to elucidate the effects of time and sex on gene expression during reproductive development. Time (developmental stage) is dominant in patterning gene expression with the effect of sex nested within this. Here, we find (1) evidence for five successive waves of alterations to the chromatin landscape which may be important in setting the overall reproductive trajectory, regardless of sex. (2) Each individual developmental stage is further characterized by marked sex-differential gene expression. (3) Consistent sexually differentiated gene expression regardless of developmental stage reveal candidates for high-level regulators of sex and include the female-specific poplar ARR17 homologue. There is also consistent male-biased expression of the MADS-box genes PISTILLATA and APETALA3. Our work provides insights into expression trajectories shaping reproductive development, its potential underlying mechanisms, and sex-specific translation of the genome information into reproductive structures in balsam poplar.

GCN5 modulates trichome initiation in Arabidopsis by manipulating histone acetylation of core trichome initiation regulator genes

Histone acetyltransferase GCN5 affects trichome initiation via mediating the expression of some core trichome initiation regulator genes in Arabidopsis. GENERAL CONTROL NON-REPRESSED PROTEIN5 (GCN5), a histone acetyltransferase involved in the regulation of cell differentiation, organ development, secondary metabolism, and plant responses to abiotic stresses, has recently been shown to modulate trichome branching in Arabidopsis. Here, we provide evidence that GCN5 is also involved in the regulation of trichome initiation. We found that mutation of GCN5 led to increased leaf trichome density in Arabidopsis. Quantitative RT-PCR results showed that the expression of CPC, GL1, GL2, and GL3, four well-known core trichome initiation regulator genes, was decreased in the gcn5 mutants. ChIP assays indicated that these four trichome initiation regulator genes are direct targets of GCN5. Consistent with these results, GCN5-mediated H3K14/K9 acetylation levels on the TSS regions of these genes were decreased. On the other hand, leaf trichome density was reduced in plants overexpressing GCN5, and both the transcript levels and GCN5-binding enrichments of CPC, GL1, GL2, and GL3 genes were elevated. Taken together, these data suggests that GCN5 affects trichome initiation by modulating the transcription activities of trichome initiation regulator genes via H3K9/14 acetylation.

Control of stem cell activity in the carpel margin meristem (CMM) in Arabidopsis

Overview of the current understanding of the molecular mechanisms that regulate meristem activity in the CMM compared to the SAM. Meristems are undifferentiated cells responsible for post-embryonic plant development. The meristems are able to form new organs continuously by carefully balancing between stem cell proliferation and cell differentiation. The plant stem cell niche in each meristem harbors the stem cells that are important to maintain each meristem. The shoot apical meristem (SAM) produces all above-parts of a plant and the molecular mechanisms active in the SAM are actively studied since many years, and models are available. During the reproductive phase of the plant, the inflorescence meristem gives rise to floral meristems, which give rise to the flowers. During floral development, the gynoecium forms that contains a new meristem inside, called the carpel margin meristem (CMM). In Arabidopsis, the gynoecium consists out of two fused carpels, where the CMM forms along the fused carpel margins. In this review, we focus on the molecular mechanisms taking place in the CMM, and we discuss similarities and differences found in the SAM.