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

2020 ◽  
Vol 48 (11) ◽  
pp. 5953-5966
Author(s):  
Soonkap Kim ◽  
Sophie J M Piquerez ◽  
Juan S Ramirez-Prado ◽  
Emmanouil Mastorakis ◽  
Alaguraj Veluchamy ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Histone Modifications ◽  
Stress Responses ◽  
Target Genes ◽  
Gene Activation ◽  
Loss Of Function ◽  
Biotic And Abiotic Stress ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome

Abstract 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.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

scholarly journals Genome-wide (ChIP-seq) Identification of Target Genes Regulated by WRKY33 During Submergence Stress in Arabidopsis

2020 ◽  
Author(s):  
Zhang Junlin ◽  
Liu bao ◽  
Song Yan ◽  
Chen yang ◽  
Fu jiao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Crop Production ◽  
Target Genes ◽  
Reduction Process ◽  
Binding Motif ◽  
Genome Wide ◽  
Submergence Stress ◽  
A Genome ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Transgenic Lines

Abstract Background: Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of hypoxia signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, the transcription factor WRKY33 may regulate a series of target genes in response to submergence. Here, to determine the putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) upon 24 hours of submergence treatment.Results: Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence treatment (WRKY33BGHs). Most of the WRKY33BGHs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGHs promoters is a new cis-element, TCTCTC (we named it as “TC box”). This cis-element is different from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment.Conclusions: Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream hypoxia-related target genes via a “TC box”.

scholarly journals Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley

2021 ◽  
Vol 22 (10) ◽  
pp. 5354
Author(s):  
Jinhong Kan ◽  
Guangqi Gao ◽  
Qiang He ◽  
Qian Gao ◽  
Congcong Jiang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Loss Of Function ◽  
Biotic And Abiotic Stress ◽  
Wrky Transcription Factors ◽  
Physiological Processes ◽  
Genome Wide ◽  
Duplication Events ◽  
Cultivated Barley

The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation.

scholarly journals Genome-wide identification of miRNAs targets involved in cold response in cassava

Plant Omics ◽  
2020 ◽  
pp. 57-64
Author(s):  
Shuxia Li ◽  
Zhihao Cheng ◽  
Ming Peng
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cold Response ◽  
Mirna Targets ◽  
Genome Wide ◽  
A Genome ◽  
Growth Development

MicroRNAs (miRNAs) are recognized as essential transcriptional or post-transcriptional regulators, and play versatile roles in plants growth, development and stress responses. Cassava (Manihot esculenta) is a major root crop widely grown worldwide. Cold stress seriously affects cassava plants growth, development and yield. MiRNAs and their targets have been extensively studied in model plants, but a genome-wide identification of miRNAs’ targets is still lacking in cassava. In this study, two degradome libraries were constructed using cold-treated and control cassava seedlings to identify the roles of miRNAs and their targets in response to cold stress. Following high-throughput sequencing and comparing with miRNA database, degradome data allowed us to identify a total of 151 non-redundant miRNA-target pairs. We revealed that ~ 42% of miRNA targets are conserved across plant species. However, 83 novel miRNA targets were identified in the two libraries. Gene ontology analyses showed that many target genes involved in cellular and metabolic process. In addition, 12 miRNAs and 31 corresponding targets of them were further found to be involved in cold stress response. Particularly, miR159, 164 and 396 participated in cold stress response by up-regulating certain transcription factors that were involved in the regulation of downstream gene expression. The work helps identifing cold-responsive miRNA targets in cassava and increases the number of novel targets involved in cold stress response. Furthermore, the findings of this study might provide valuable reference and new insights for understanding the functions of miRNA in stress response in plants.

scholarly journals Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenying Xu ◽  
Tong Liu ◽  
Huiying Zhang ◽  
Hong Zhu
Keyword(s):  
Stress Responses ◽  
Expression Profiles ◽  
Pfam Domain ◽  
Vascular Plant ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Gene Structures

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

scholarly journals Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 335 ◽  
Author(s):  
Xiangshu Dong ◽  
Yanan Yang ◽  
Ziying Zhang ◽  
Ziwei Xiao ◽  
Xuehui Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Gene Expression Analysis ◽  
Target Genes ◽  
Coffea Canephora ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Cold Responses ◽  
Insight Into

WRKY transcription factors are known to play roles in diverse stress responses in plants. Low temperatures limit the geographic distribution of Coffea canephora Pierre ex A.Froehner. The WRKYs of C. canephora are still not well characterized, and the response of C. canephora WRKYs (CcWRKYs) under cold stress is still largely unknown. We identified 49 CcWRKYs from the C. canephora genome to gain insight into these mechanisms. These CcWRKYs were divided into three groups that were based on the conserved WRKY domains and zinc-finger structure. Gene expression analysis demonstrated that 14 CcWRKYs were induced during the cold acclimation stage, 17 CcWRKYs were preferentially upregulated by 4 °C treatment, and 12 CcWRKYs were downregulated by cold stress. Subsequently, we carried out a genome-wide analysis to predict 14,513 potential CcWRKY target genes in C. canephora. These isolated genes were involved in multiple biological processes, and most of them could be grouped by the response to stimulus. Among the putative CcWRKY target genes, 235 genes were categorized into response to the cold process, including carbohydrate metabolic, lipid metabolic, and photosynthesis process-related genes. Furthermore, the qRT-PCR and correlation analysis indicated that CcWRKY might control their putative targets that respond to cold stress. These results provide a basis for understanding the molecular mechanism for CcWRKY-mediated cold responses.

scholarly journals Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junlin Zhang ◽  
Bao Liu ◽  
Yan Song ◽  
Yang Chen ◽  
Jiao Fu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Crop Production ◽  
Target Genes ◽  
Reduction Process ◽  
Binding Motif ◽  
Genome Wide ◽  
Submergence Stress ◽  
A Genome ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Transgenic Lines

Abstract Background Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment. Results Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as “TC box”). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment. Conclusions Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a “TC box”.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals The Arabidopsis mediator complex subunit 8 regulates oxidative stress responses

2021 ◽  
Author(s):  
Huaming He ◽  
Jordi Denecker ◽  
Katrien Van Der Kelen ◽  
Patrick Willems ◽  
Robin Pottie ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Salicylic Acid ◽  
Jasmonic Acid ◽  
Stress Responses ◽  
Negative Regulator ◽  
Mediator Complex ◽  
Defense Gene Expression ◽  
A Genome ◽  
Oxidative Stress Responses

Abstract Signaling events triggered by hydrogen peroxide (H2O2) regulate plant growth and defense by orchestrating a genome-wide transcriptional reprogramming. However, the specific mechanisms that govern H2O2-dependent gene expression are still poorly understood. Here, we identify the Arabidopsis Mediator complex subunit MED8 as a regulator of H2O2 responses. The introduction of the med8 mutation in a constitutive oxidative stress genetic background (catalase-deficient, cat2) was associated with enhanced activation of the salicylic acid pathway and accelerated cell death. Interestingly, med8 seedlings were more tolerant to oxidative stress generated by the herbicide methyl viologen (MV) and exhibited transcriptional hyperactivation of defense signaling, in particular salicylic acid- and jasmonic acid-related pathways. The med8-triggered tolerance to MV was manipulated by the introduction of secondary mutations in salicylic acid and jasmonic acid pathways. In addition, analysis of the Mediator interactome revealed interactions with components involved in mRNA processing and microRNA biogenesis, hence expanding the role of Mediator beyond transcription. Notably, MED8 interacted with the transcriptional regulator NEGATIVE ON TATA-LESS, NOT2, to control the expression of H2O2-inducible genes and stress responses. Our work establishes MED8 as a component regulating oxidative stress responses and demonstrates that it acts as a negative regulator of H2O2-driven activation of defense gene expression.

Drosophila Gain-of-Function Mutant RTK Torso Triggers Ectopic Dpp and STAT Signaling

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 247-258 ◽  
Author(s):  
Jinghong Li ◽  
Willis X Li
Keyword(s):  
Tyrosine Kinases ◽  
Target Genes ◽  
Tor Signaling ◽  
Gain Of Function ◽  
Essential Requirement ◽  
Downstream Target ◽  
Rtk Signaling ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Overactivation of receptor tyrosine kinases (RTKs) has been linked to tumorigenesis. To understand how a hyperactivated RTK functions differently from wild-type RTK, we conducted a genome-wide systematic survey for genes that are required for signaling by a gain-of-function mutant Drosophila RTK Torso (Tor). We screened chromosomal deficiencies for suppression of a gain-of-function mutation tor (torGOF), which led to the identification of 26 genomic regions that, when in half dosage, suppressed the defects caused by torGOF. Testing of candidate genes in these regions revealed many genes known to be involved in Tor signaling (such as those encoding the Ras-MAPK cassette, adaptor and structural molecules of RTK signaling, and downstream target genes of Tor), confirming the specificity of this genetic screen. Importantly, this screen also identified components of the TGFβ (Dpp) and JAK/STAT pathways as being required for TorGOF signaling. Specifically, we found that reducing the dosage of thickveins (tkv), Mothers against dpp (Mad), or STAT92E (aka marelle), respectively, suppressed torGOF phenotypes. Furthermore, we demonstrate that in torGOF embryos, dpp is ectopically expressed and thus may contribute to the patterning defects. These results demonstrate an essential requirement of noncanonical signaling pathways for a persistently activated RTK to cause pathological defects in an organism.

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