scholarly journals Abscisic Acid Represses Rice Lamina Joint Inclination by Antagonizing Brassinosteroid Biosynthesis and Signaling

2019 ◽  
Vol 20 (19) ◽  
pp. 4908 ◽  
Author(s):  
Qian-Feng Li ◽  
Jun Lu ◽  
Yu Zhou ◽  
Fan Wu ◽  
Hong-Ning Tong ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Interaction Network ◽  
Underlying Mechanism ◽  
Leaf Angle ◽  
Rna Seq ◽  
Regulatory Module ◽  
Promotive Effect ◽  
Transgenic Lines ◽  
Lamina Joint ◽  
Joint Inclination

Leaf angle is a key parameter that determines plant architecture and crop yield. Hormonal crosstalk involving brassinosteroid (BR) plays an essential role in leaf angle regulation in cereals. In this study, we investigated whether abscisic acid (ABA), an important stress-responsive hormone, co-regulates lamina joint inclination together with BR, and, if so, what the underlying mechanism is. Therefore, lamina joint inclination assay and RNA sequencing (RNA-Seq) analysis were performed here. ABA antagonizes the promotive effect of BR on leaf angle. Hundreds of genes responsive to both hormones that are involved in leaf-angle determination were identified by RNA-Seq and the expression of a gene subset was confirmed using quantitative real-time PCR (qRT-PCR). Results from analysis of rice mutants or transgenic lines affected in BR biosynthesis and signaling indicated that ABA antagonizes the effect of BR on lamina joint inclination by targeting the BR biosynthesis gene D11 and BR signaling genes GSK2 and DLT, thus forming a multi-level regulatory module that controls leaf angle in rice. Taken together, our findings demonstrate that BR and ABA antagonistically regulate lamina joint inclination in rice, thus contributing to the elucidation of the complex hormonal interaction network that optimizes leaf angle in rice.

scholarly journals Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiwei Chen ◽  
Longhua Zhou ◽  
Panpan Jiang ◽  
Ruiju Lu ◽  
Nigel G. Halford ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Related Protein ◽  
Rna Seq ◽  
Response Elements ◽  
Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

scholarly journals Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

2021 ◽  
Vol 11 (8) ◽  
pp. 3562
Author(s):  
Yong Jin Lee ◽  
Sang Yong Park ◽  
Dae Yeon Kim ◽  
Jae Yoon Kim
Keyword(s):  
Abscisic Acid ◽  
Differential Expression Analysis ◽  
Preharvest Sprouting ◽  
Global Changes ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Global Issue ◽  
End Use ◽  
Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

scholarly journals lncRNA CASC19 Contributes to Radioresistance of Nasopharyngeal Carcinoma by Promoting Autophagy via AMPK-mTOR Pathway

2021 ◽  
Vol 22 (3) ◽  
pp. 1407
Author(s):  
Hongxia Liu ◽  
Wang Zheng ◽  
Qianping Chen ◽  
Yuchuan Zhou ◽  
Yan Pan ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Cell Line ◽  
Malignant Tumors ◽  
Underlying Mechanism ◽  
Mtor Pathway ◽  
Rna Seq ◽  
Cellular Autophagy ◽  
First Time

Nasopharyngeal carcinoma (NPC) is one of the most frequent head and neck malignant tumors and is majorly treated by radiotherapy. However, radiation resistance remains a serious obstacle to the successful treatment of NPC. The aim of this study was to discover the underlying mechanism of radioresistance and to elucidate novel genes that may play important roles in the regulation of NPC radiosensitivity. By using RNA-seq analysis of NPC cell line CNE2 and its radioresistant cell line CNE2R, lncRNA CASC19 was screened out as a candidate radioresistance marker. Both in vitro and in vivo data demonstrated that a high expression level of CASC19 was positively correlated with the radioresistance of NPC, and the radiosensitivity of NPC cells was considerably enhanced by knockdown of CASC19. The incidence of autophagy was enhanced in CNE2R in comparison with CNE2 and another NPC cell line HONE1, and silencing autophagy with LC3 siRNA (siLC3) sensitized NPC cells to irradiation. Furthermore, CASC19 siRNA (siCASC19) suppressed cellular autophagy by inhibiting the AMPK/mTOR pathway and promoted apoptosis through the PARP1 pathway. Our results revealed for the first time that lncRNA CASC19 contributed to the radioresistance of NPC by regulating autophagy. In significance, CASC19 might be a potential molecular biomarker and a new therapeutic target in NPC.

scholarly journals Whole Transcriptome Analysis of Hypertension Induced Cardiac Injury Using Deep Sequencing

2016 ◽  
Vol 38 (2) ◽  
pp. 670-682 ◽  
Author(s):  
Tao-Tao Li ◽  
Xiao-Yan Li ◽  
Li-Xin Jia ◽  
Jing Zhang ◽  
Wen-Mei Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Cell Activation ◽  
Critical Role ◽  
Cardiac Injury ◽  
Interaction Network ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Cardiac Inflammation ◽  
Molecular Events ◽  
Focal Adhesion Protein

Background/Aims: Hypertension plays a critical role in the cardiac inflammation and injury. However, the mechanism of how hypertension causes the cardiac injury at a molecular level remains to be elucidated. Methods: RNA-Seq has been demonstrated to be an effective approach for transcriptome analysis, which is essential to reveal the molecular constituents of cells and tissues. In this study, we investigated the global molecular events associated with the mechanism of hypertension induced cardiac injury using RNA-Seq analysis. Results: Our results showed that totally 1,801 genes with different expression variations were identified after Ang II infusion at 1, 3 and 7 days. Go analysis showed that the top 5 high enrichment Go terms were response to stress, response to wounding, cellular component organization, cell activation and defense response. KEGG pathway analysis revealed the top 5 significantly overrepresented pathways were associated with ECM-receptor interaction, focal adhesion, protein digestion and absorption, phagosome and asthma. Moreover, protein-protein interaction network analysis indicated that ubiquitin C may play a key role in the processes of hypertension-induced cardiac injury. Conclusion: Our study provides a comprehensive understanding of the transcriptome events in hypertension-induced cardiac pathology.

Analysis of Expression Profiles of mRNA and lncRNA in Oviduct During Estrus Phase of Sheep (Ovis Aries) with Two Fecundity (FecB Gene) Genotypes

2021 ◽  
Author(s):  
Weihao Chen ◽  
Zhifeng Li ◽  
Wei Sun ◽  
Mingxing Chu
Keyword(s):  
Embryo Development ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Functional Enrichment ◽  
Saga Complex ◽  
Rna Seq ◽  
Estrus Phase

Abstract Background:In sheep, FecB is the essential biomarker of the fertility, previous researches have provided a detailed insight on the regulation involved estrus phase and FecB in the reproductive-related tissues including hypothalamus, pituitary, and ovary. However, as the host of embryo development and connection between the ovary and the uterus, little is known about the interaction between mRNAs and lncRNAs in sheep oviduct. In the present study, RNA-Seq was performed to identify the transcriptomic profiles of mRNAs and lncRNAs in oviduct during estrus phase of sheep with FecBBB/++ genotypes.Results:In total, 21,863 lncRNAs and 43,674 mRNAs were identified, 57 DE lncRNAs and 637 DE mRNAs were revealed in the comparisons between follicular phase and luteal phase, 26 DE lncRNAs and 421 DE lncRNAs were revealed in the comparisons between FecB BB genotype and FecB ++ genotype. Functional enrichment analysis suggested that GO and KEGG terms related to reproduction such as SAGA complex, ATP-binding cassette (ABC), Nestin, and Hippo signalling pathway. DE-interaction network suggested that LNC_018420 maybe the key regulators related to embryo development in sheep oviduct.Conclusion:This was the first study to reveal the transcriptomic profiles of mRNAs and lncRNAs in the oviduct of FecB BB/++ sheep at estrus phase using RNA-Seq. Our findings can provide new understanding on the molecular mechanisms of mRNAs and lncRNAs underlying sheep embryo development and also opening new lines of investigation in sheep reproduction.

scholarly journals Rice OsHSFA3 Gene Improves Drought Tolerance by Modulating Polyamine Biosynthesis Depending on Abscisic Acid and ROS Levels

2020 ◽  
Vol 21 (5) ◽  
pp. 1857 ◽  
Author(s):  
Ming-Dong Zhu ◽  
Meng Zhang ◽  
Du-Juan Gao ◽  
Kun Zhou ◽  
Shan-Jun Tang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Drought Tolerance ◽  
Functional Characterization ◽  
Activity Levels ◽  
Enzymatic Antioxidants ◽  
Heat Shock Factors ◽  
Polyamine Biosynthesis ◽  
Polyamine Content ◽  
Transgenic Lines

Drought is a serious problem, which causes heavy yield losses for rice. Heat-shock factors (HSFs) had been implicated in tolerance to drought and high temperature. However, there has not been much functional characterization and mechanism clarification in rice. Previously, we found an HSF gene, OsHSFA3, was highly related with drought tolerance after screening from 10,000 different samples. Herein, we cloned the OsHSFA3 from rice and overexpressed it in Arabidopsis thaliana to study its regulatory mechanism of drought tolerance. Phenotypic and physiological assays of the transgenic Arabidopsis lines showed that overexpression of OsHSFA3 confers drought tolerance by reducing water loss and reactive oxygen species (ROS) levels, whereas it increases abscisic acid (ABA) levels. However, enzymatic antioxidants such as activity levels of superoxide dismutase, peroxidase and catalase were not significantly different between wild type and transgenic lines. Instead, we observed a significant increase in polyamine content, which was correlated with increased AtADC1, AtADC2, SPDS1 and SPMS expression levels. In silico and in vivo analyses confirmed that OsHSFA3 is a nuclear-localized gene. In addition, OsHSFA3 can bind to the promoter of AtADC1 and OsADC via a yeast one-hybrid assay. Overall, this study reveals that OsHSFA3 improves drought tolerance in Arabidopsis not only by increasing ABA levels, but also by modulating polyamine levels to maintain ROS homeostasis, therefore it could be a strong candidate to develop drought-tolerant rice cultivars.

scholarly journals Analysis of Differentially Expressed Transcripts in Apolygus lucorum (Meyer-Dür) Exposed to Different Temperature Coefficient Insecticides

2020 ◽  
Vol 21 (2) ◽  
pp. 658 ◽  
Author(s):  
Jingjie An ◽  
Chang Liu ◽  
Ya’nan Dou ◽  
Zhanlin Gao ◽  
Zhihong Dang ◽  
...  
Keyword(s):  
Temperature Effect ◽  
Temperature Coefficient ◽  
Transcriptome Profiling ◽  
Underlying Mechanism ◽  
Green Plant ◽  
Rna Seq ◽  
Biochemical Processes ◽  
Apolygus Lucorum ◽  
Gene Information ◽  
Physiological And Biochemical

The existence of a temperature effect of insecticides frustrated the control of the green plant bug Apolygus lucorum (Meyer-Dür). Previous studies mostly focused on the application of insecticides, but the underlying mechanism remains incompletely understood. Here, we report a transcriptome profiling of A. lucorum treated by three kinds of temperature coefficient insecticides (TCIs) (positive TCI: imidacloprid, negative TCI: b-cypermethrin and non-effect TCI: phoxim) at 15 °C, 25 °C and 35 °C by using next- and third-generation RNA-Seq methods. A total of 34,739 transcripts were annotated from 277.74 Gb of clean data. There were more up-regulated transcripts than down-regulated transcripts in all three kinds of TCI treatments. Further Venn diagrams indicate the regulatory transcripts and regulatory modes were different at the three temperatures. The responses to imidacloprid involved more detox and stress response transcripts such as cytochrome P450 (CYP450), carboxylesterase (CarE) and catalase (CAT) at 35 °C, which was the case for beta-cypermethrin at 15 °C. UDP-glucuronyltransferase (UGT) and heat shock protein (HSP) transcripts were heavily involved, and thus deserve particular note in the temperature effect of insecticides. This high-confidence transcriptome atlas provides improved gene information for further study on the insecticide temperature effect related physiological and biochemical processes of A. lucorum.

scholarly journals Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiaofang Xie ◽  
Zhiwei Chen ◽  
Binghui Zhang ◽  
Huazhong Guan ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanism ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Cell Death Pathways ◽  
Rnai Line ◽  
Transgenic Lines

Abstract Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

scholarly journals FurA-Dependent Microcystin Synthesis under Copper Stress in Microcystis aeruginosa

2020 ◽  
Vol 8 (6) ◽  
pp. 832
Author(s):  
Yuanyuan Chen ◽  
Jiaojiao Yin ◽  
Jin Wei ◽  
Xuezhen Zhang
Keyword(s):  
Microcystis Aeruginosa ◽  
Iron Uptake ◽  
Copper Ions ◽  
Copper Ion ◽  
Underlying Mechanism ◽  
Cyanobacterial Blooms ◽  
Copper Stress ◽  
Rna Seq ◽  
Treatment Groups ◽  
The Relationship

Massive blooms of cyanobacteria frequently occur with microcystin (MC) production. Cyanobacteria are exposed to copper stresses such as copper algaecides which are often used to remove cyanobacterial blooms. However, copper increased the MC production of cyanobacteria, and the underlying mechanism remains unclear. The present study investigated the relationship between copper exposure (0.5 and 3 µM) and MC synthesis in Microcystis aeruginosa PCC 7806. The study concluded that the content of intracellular MCs increased by nearly two times both in 0.5 and 3 µM copper. High-throughput RNA sequencing (RNA-seq) provided evidence that copper mainly attacked Fe–S clusters, with evidence of changes in iron, sulfur, iron uptake regulators (fur), glutaredoxins and dehydratase genes. The transcription of numbers of genes implicated in iron uptake, MC synthesis and furA was also evaluated with quantitative real-time PCR (qRT-PCR). In these three Cu treatment groups, the amount of MCs increased as copper elevated. As the expression of mcyD gene was directly regulated by FurA and copper ions affected the expression of the FurA-related genes, we believed that MC synthesis genes were controlled by copper. This study has made a further understanding of the mechanism of the increase in MC synthesis of M. aeruginosa PCC 7806 treated with copper-based algaecides. We aimed to understand the mechanism of copper ion influencing the synthesis of MCs.

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