scholarly journals A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 267 ◽  
Author(s):  
Feng Yu ◽  
Zengdong Tan ◽  
Tian Fang ◽  
Kaiyuan Tang ◽  
Kun Liang ◽  
...  
Keyword(s):  
Early Stage ◽  
Primary Root ◽  
Dynamic Environment ◽  
Polymerase Chain Reaction Analysis ◽  
Mapk Signaling ◽  
Maize Seedlings ◽  
Root Tips ◽  
Waterlogging Tolerance ◽  
Hypoxia Response ◽  
Waterlogging Stress

Waterlogging stress (WS) in a dynamic environment seriously limits plant growth, development, and yield. The regulatory mechanism underlying WS conditions at an early stage in maize seedlings is largely unknown. In the present study, the primary root tips of B73 seedlings were sampled before (0 h) and after (2 h, 4 h, 6 h, 8 h, 10 h, and 12 h) WS and then subjected to transcriptome sequencing, resulting in the identification of differentially expressed protein-coding genes (DEpcGs) and long non-coding RNAs (DElncRs) in response to WS. These DEpcGs were classified into nine clusters, which were significantly enriched in several metabolic pathways, such as glycolysis and methionine metabolism. Several transcription factor families, including AP2-EREBP, bZIP, NAC, bHLH, and MYB, were also significantly enriched. In total, 6099 lncRNAs were identified, of which 3190 were DElncRs. A co-expression analysis revealed lncRNAs to be involved in 11 transcription modules, 10 of which were significantly associated with WS. The DEpcGs in the four modules were enriched in the hypoxia response pathways, including phenylpropanoid biosynthesis, MAPK signaling, and carotenoid biosynthesis, in which 137 DElncRs were also co-expressed. Most of the co-expressed DElncRs were co-localized with previously identified quantitative trait loci associated with waterlogging tolerance. A quantitative reverse transcription-polymerase chain reaction analysis of DEpcG and DElncR expression among the 32 maize genotypes after 4 h of WS verified significant expression correlations between them as well as significant correlation with the phenotype of waterlogging tolerance. Moreover, the high proportion of hypoxia response elements in the promoter region increased the reliability of the DElncRs identified in this study. These results provide a comprehensive transcriptome in response to WS at an early stage of maize seedlings and expand our understanding of the regulatory network involved in hypoxia in plants.

Comparable and adaptable strategies to waterlogging stress regulated by adventitious roots between two contrasting species

2021 ◽  
Author(s):  
Dadong Li ◽  
El-Hadji Malick Cisse ◽  
Luyao Guo ◽  
Juan Zhang ◽  
Lingfeng Miao ◽  
...  
Keyword(s):  
Morphological Changes ◽  
Primary Root ◽  
Woody Species ◽  
Plant Morphology ◽  
Net Photosynthesis ◽  
Waterlogging Tolerance ◽  
Root Porosity ◽  
Waterlogging Stress ◽  
Exogenous Aba ◽  
Cortex Area

Abstract Cleistocalyx operculatus and Syzygium cumini possess a certain waterlogging tolerance. However, the comparable and adaptable strategies to waterlogging stress between these two species on the basis of waterlogging adventitious root (AR) regulation were still unclear. In this study, the plant performances in response to AR regulation based on AR removal and exogenous hormone application were investigated in terms of plant morphology, physiology, photosynthesis, and AR traits. Results showed that C. operculatus possesses stronger waterlogging tolerance than S. cumini based on waterlogging tolerance coefficient, which is mainly due to the higher root biomass, root porosity, and length and activity of ARs, and shorter emergence time of ARs in C. operculatus than in S. cumini. The AR-R treatment increased activity and porosity of primary root, and induce a large amount of up-vertical ARs from the primary root systems in C. operculatus, while similar adaptive morphological changes in roots did not occur in AR-R treated S. cumini. Exogenous ABA application had better effects on alleviating waterlogging damages than exogenous IAA in balancing endogenous hormones (ABA and ZR), promoting ARs development (porosity and activity, and the ratio of cortex area to stele area), improving photosynthesis process and antioxidant system (soluble protein, free proline, and peroxidase). Moreover, under waterlogging conditions, exogenous ABA application induced greater increases in net photosynthesis rate (A), stomatal conductance (gs), chlorophyll b (Chl b), and carotenoid (Caro) in S. cumini than in C. operculatus, which suggested that S. cumini responded more positively and efficiently to exogenous ABA application than C. operculatus under waterlogging conditions. Thus, the findings provided new insights into the waterlogging adaptable strategies in waterlogging tolerant woody species on the basis of ARs, and could provide scientific guidance for the application of these two species during revegetation activities in wetlands.

scholarly journals Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with MiRNAs and Target Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Vol 22 (15) ◽  
pp. 8197
Author(s):  
Kinga Kęska ◽  
Michał Wojciech Szcześniak ◽  
Adela Adamus ◽  
Małgorzata Czernicka
Keyword(s):  
Target Genes ◽  
Recovery Period ◽  
Sufficient Information ◽  
Low Oxygen ◽  
Waterlogging Tolerance ◽  
Cucumis Sativus L ◽  
Waterlogging Stress ◽  
Non Coding Rna

Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.

scholarly journals Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium hybrid ‘Zhongshanshan 406’

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 225
Author(s):  
Lei Xuan ◽  
Jianfeng Hua ◽  
Fan Zhang ◽  
Zhiquan Wang ◽  
Xiaoxiao Pei ◽  
...  
Keyword(s):  
Ethanol Metabolism ◽  
Flooding Tolerance ◽  
Transcriptome Data ◽  
Low Oxygen ◽  
Anaerobic Conditions ◽  
Waterlogging Tolerance ◽  
Waterlogging Stress ◽  
Adh Genes ◽  
Oxygen Conditions ◽  
Stems And Leaves

The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4 (GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406’.

Effect of Icariin on Osteoclasts and Its Mechanism

2020 ◽  
Vol 10 (12) ◽  
pp. 1807-1812
Author(s):  
Xiaoxiao Wu ◽  
Xi Fu ◽  
Xiabing Qin
Keyword(s):  
Transcription Factors ◽  
Bone Resorption ◽  
Bone Loss ◽  
Mapk Pathway ◽  
Early Stage ◽  
Osteoclast Differentiation ◽  
Mapk Signaling ◽  
Therapeutic Drug ◽  
Actin Ring ◽  
B Subunit

Background: The paper aimed to elucidate the molecular mechanism of Icariin regulating RANKLinduced osteoclast-ogenesis and bone resorption, and to investigate whether Icariin could be a potential therapeutic drug for diseases of bone loss related to osteoclast. Material and methods: Osteoclasts were cultured. MTT to determine cell viability. Von Kossa to determine the effect of Icariin on bone resorption. F-actin ring staining to measure the expressions of various proteins, and WB method was used to measure the expression of p-65. Results: MTT showed that Icariin is not toxic to osteoclasts. The bone resorption result showed that RANKL-mediated osteoclast bone resorption was reduced in the early stage, and the higher the intervention concentration, the smaller the bone resorption area. F-actin ring staining indicated that it is possible to reduce the differentiation and bone resorption capacity of osteoclasts by hindering the formation of F-actin ring in the early stage, and in a concentration-dependentmanner. Significantly reduced the expressions of key transcription factors-NFATc1 and c-Fos. It significantly inhibited the phosphorylation and nucleation of NF-κB subunit p65 induced by RANKL, and significantly inhibited the phosphorylation of ERK and p38 proteins in the MAPK pathway activated by RANKL. Conclusion: Icariin can effectively inhibit osteoclast differentiation, F-actin ring formation, and bone resorption. By inhibiting the key transcription factors NFATc1 and c-Fos to down-regulate related expressions, thereby impeding osteoclast differentiation, Icariin may regulate key transcription factors NFATc1 and c-Fos through NF-κB and MAPK signaling pathways. Studies have suggested that Icariin could be a potential treatment for diseases of bone loss related to osteoclasts.

scholarly journals Effects of Phosphate Shortage on Root Growth and Hormone Content of Barley Depend on Capacity of the Roots to Accumulate ABA

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1722
Author(s):  
Lidiya Vysotskaya ◽  
Guzel Akhiyarova ◽  
Arina Feoktistova ◽  
Zarina Akhtyamova ◽  
Alla Korobova ◽  
...  
Keyword(s):  
Root Growth ◽  
Lateral Roots ◽  
Primary Root ◽  
Growth Responses ◽  
Root Tips ◽  
P Deficiency ◽  
Root Branching ◽  
Auxin Concentration ◽  
Shoot Mass ◽  
Primary Root Length

Although changes in root architecture in response to the environment can optimize mineral and water nutrient uptake, mechanisms regulating these changes are not well-understood. We investigated whether P deprivation effects on root development are mediated by abscisic acid (ABA) and its interactions with other hormones. The ABA-deficient barley mutant Az34 and its wild-type (WT) were grown in P-deprived and P-replete conditions, and hormones were measured in whole roots and root tips. Although P deprivation decreased growth in shoot mass similarly in both genotypes, only the WT increased primary root length and number of lateral roots. The effect was accompanied by ABA accumulation in root tips, a response not seen in Az34. Increased ABA in P-deprived WT was accompanied by decreased concentrations of cytokinin, an inhibitor of root extension. Furthermore, P-deficiency in the WT increased auxin concentration in whole root systems in association with increased root branching. In the ABA-deficient mutant, P-starvation failed to stimulate root elongation or promote branching, and there was no decline in cytokinin and no increase in auxin. The results demonstrate ABA’s ability to mediate in root growth responses to P starvation in barley, an effect linked to its effects on cytokinin and auxin concentrations.

scholarly journals Phosphorylation of Msx1 promotes cell proliferation through the Fgf9/18-MAPK signaling pathway during embryonic limb development

2020 ◽  
Vol 48 (20) ◽  
pp. 11452-11467
Author(s):  
Yenan Yang ◽  
Xiaoli Zhu ◽  
Xiang Jia ◽  
Wanwan Hou ◽  
Guoqiang Zhou ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Limb Development ◽  
Early Stage ◽  
Control Cell ◽  
Cell Lineage ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Mitogen Activated Protein ◽  
Embryonic Limb ◽  
Underlying Mechanisms

Abstract Msh homeobox (Msx) is a subclass of homeobox transcriptional regulators that control cell lineage development, including the early stage of vertebrate limb development, although the underlying mechanisms are not clear. Here, we demonstrate that Msx1 promotes the proliferation of myoblasts and mesenchymal stem cells (MSCs) by enhancing mitogen-activated protein kinase (MAPK) signaling. Msx1 directly binds to and upregulates the expression of fibroblast growth factor 9 (Fgf9) and Fgf18. Accordingly, knockdown or antibody neutralization of Fgf9/18 inhibits Msx1-activated extracellular signal-regulated kinase 1/2 (Erk1/2) phosphorylation. Mechanistically, we determined that the phosphorylation of Msx1 at Ser136 is critical for enhancing Fgf9 and Fgf18 expression and cell proliferation, and cyclin-dependent kinase 1 (CDK1) is apparently responsible for Ser136 phosphorylation. Furthermore, mesenchymal deletion of Msx1/2 results in decreased Fgf9 and Fgf18 expression and Erk1/2 phosphorylation, which leads to serious defects in limb development in mice. Collectively, our findings established an important function of the Msx1-Fgf-MAPK signaling axis in promoting cell proliferation, thus providing a new mechanistic insight into limb development.

scholarly journals RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 213
Author(s):  
Yu Xu ◽  
Junjie Zou ◽  
Hongyan Zheng ◽  
Miaoyun Xu ◽  
Xuefeng Zong ◽  
...  
Keyword(s):  
Cell Wall ◽  
Root Growth ◽  
Primary Root ◽  
Glutathione Metabolism ◽  
Auxin Signaling ◽  
Antioxidant Enzyme Activities ◽  
Rna Seq ◽  
Root Tips ◽  
Primary Roots ◽  
Quercetin Treatment

Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.

Effect of bypass kinase pathways on acquired CDK4/6 inhibitor resistance.

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 379-379
Author(s):  
Renee De Leeuw ◽  
Christopher McNair ◽  
Matthew Joseph Schiewer ◽  
Neermala Poudel Neupane ◽  
Michael Augello ◽  
...  
Keyword(s):  
Mapk Pathway ◽  
Early Stage ◽  
Mapk Signaling ◽  
Cross Resistance ◽  
Mek Inhibitors ◽  
Mesenchymal Transition ◽  
Inhibitor Resistance ◽  
Tumor Types

379 Background: Cyclin Dependent Kinase-4/6 (CDK4/6) kinase inhibitors have shown clinical benefit in treatment of solid tumor types, including breast cancer. However, resistance is common, and the underpinning mechanisms of action are not well understood. Given the dependence of CDK4/6 inhibitors on retinoblastoma tumor suppressor (RB) function for activity, this class of agents may be particularly effective in tumor types for which RB loss is infrequent or occurs late in tumor progression. Methods: Here, models of acquired palbociclib resistance were generated in early stage, RB positive cancers, wherein it was shown acquired palbociclib resistance resulted in cross-resistance to other CDK4/6 inhibitors under clinical testing. Results: Cells showing acquired resistance exhibited aggressive in vitro and in vivo phenotypes without genetic loss of RB or RB pathway members, including enhanced proliferative capacity, migratory potential, and characteristics of epithelial to mesenchymal transition. Further analyses through integration of RNA sequencing and phospho-proteomics identified activation of the MAPK signaling pathway as a mediator of CDK4/6 inhibitor resistance, capable of bypassing CDK4/6 activity. However, this altered kinase dependence resulted in sensitization to MEK inhibitors, suggestive of new clinical opportunities in CDK4/6 resistant tumors. Conclusions: In sum, the studies herein not only identify activation of the MAPK pathway as capable of bypassing the CDK4/6 requirement and promoting aggressive tumor characteristics, but nominate MEK inhibitors as potential mechanisms to treat or prevent CDK4/6 inhibitor resistance.

Effect of organic pollutant treatment on the growth of pea and maize seedlings

2012 ◽  
Vol 7 (1) ◽  
pp. 159-166 ◽  
Author(s):  
Marie Kummerová ◽  
Štěpán Zezulka ◽  
Lucie Váňová ◽  
Helena Fišerová
Keyword(s):  
Zea Mays ◽  
Seed Germination ◽  
Lateral Roots ◽  
Organic Pollutant ◽  
Primary Root ◽  
Dry Weight ◽  
Considerable Effect ◽  
Maize Seedlings ◽  
Polycyclic Aromatic ◽  
Primary And Lateral Roots

AbstractThis study confirmed the considerable effect of polycyclic aromatic hydrocarbon fluoranthene (FLT; 0.01, 0.1, 1, 4 and 7 mg/l) exposure on the germination of seeds, growth and root morphology of seedlings in Zea mays and Pisum sativum. Seed germination was significantly inhibited at FLT≥0.01 mg/l in maize and at ≥1 mg/l in pea. The amount of released ethylene after 3 days of germination was significantly increased in both species at FLT≥0.1 mg/l. After 7 days of seedling cultivation a significant decrease in the dry weight of roots and shoots occurred in maize at FLT≥0.1 mg/l while in pea similar effect was observed at ≥1 mg/l. The total length of primary and lateral roots was significantly reduced by FLT≥1 mg/l in maize and by 4 and 7 mg/l in pea. The length of the non-branched part of the primary root was significantly reduced by FLT≥0.1 mg/l in maize and ≥0.01 mg/l in pea. In both species the number of lateral roots was significantly increased at FLT≤1 mg/l and inhibited at concentrations of 4 and 7 mg/l. Fluoranthene content in roots and shoots of both species positively correlated with the FLT treatment.

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