Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress

Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.

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Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

International Journal of Molecular Sciences ◽

10.3390/ijms21103595 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3595

Author(s):

Xinpeng Zhao ◽

Shenglong Bai ◽

Lechen Li ◽

Xue Han ◽

Jiahui Li ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Common Wheat ◽

Carbon Fixation ◽

Aegilops Tauschii ◽

Transcriptome Profiling ◽

Mapk Signaling ◽

Mitogen Activated Protein Kinase ◽

Rna Seq ◽

Alpha Linolenic Acid

As the diploid progenitor of common wheat, Aegilops tauschii is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported concerning the molecular mechanism of drought tolerance in Ae. tauschii. In this work, the drought tolerance of 155 Ae. tauschii accessions was firstly screened on the basis of their coleoptile lengths under simulated drought stress. Subsequently, two accessions (XJ002 and XJ098) with contrasting coleoptile lengths were selected and intensively analyzed on rate of water loss (RWL) as well as physiological characters, confirming the difference in drought tolerance at the seedling stage. Further, RNA-seq was utilized for global transcriptome profiling of the two accessions seedling leaves under drought stress conditions. A total of 6969 differentially expressed genes (DEGs) associated with drought tolerance were identified, and their functional annotations demonstrated that the stress response was mediated by pathways involving alpha-linolenic acid metabolism, starch and sucrose metabolism, peroxisome, mitogen-activated protein kinase (MAPK) signaling, carbon fixation in photosynthetic organisms, and glycerophospholipid metabolism. In addition, DEGs with obvious differences between the two accessions were intensively analyzed, indicating that the expression level of DEGs was basically in alignment with the physiological changes of Ae. tauschii under drought stress. The results not only shed fundamental light on the regulatory process of drought tolerance in Ae. tauschii, but also provide a new gene resource for improving the drought tolerance of common wheat.

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Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

BMC Plant Biology ◽

10.1186/s12870-020-02785-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jing Zhou ◽

Siqi Chen ◽

Wenjiao Shi ◽

Rakefet David-Schwartz ◽

Sutao Li ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Leucine Zipper ◽

Molecular Mechanisms ◽

Normal Growth ◽

Transcriptome Profiling ◽

Fatty Acyl ◽

Transferase Activity ◽

Forage Production ◽

Basic Leucine Zipper

Abstract Background Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass. Results A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions. Conclusions Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.

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Molecular Analysis of Enzymes and Metabolites Regulated Under Drought Stress in the Wild Plant Senna (Cassia Angustifolia)

Biosciences Biotechnology Research Asia ◽

10.13005/bbra/2747 ◽

2016 ◽

Vol 16 (2) ◽

pp. 307-326

Author(s):

Nadiah Al-Sulami ◽

Ahmed Atef ◽

Mohammed Al-Matary ◽

Sherif Edris ◽

Khalid M. Al-Ghamdi ◽

...

Keyword(s):

Drought Stress ◽

Molecular Mechanisms ◽

De Novo ◽

Mitogen Activated Protein Kinase ◽

Wild Plant ◽

Allene Oxide ◽

Time Points ◽

Cassia Angustifolia ◽

Kegg Analysis ◽

In The Wild

This study aimed at studying differential presence of enzymes metabolites via KEGG analysis of trasncriptomes of the wild plant species senna (Cassia angustifolia Vahl.) due to watering. Senna is a shrub of the family Caesalpiniaceae with important applications in pharmaceuticals. Firstly, RNA-Seq datasets were produced by next-generation sequencing (NGS) of Illumina Miseq of leaf (day 1) in order to detect the influence of watering at day 2. Samples were harvested at three time points (e.g., dawn, midday and dusk) of the two days. de novo assembled datasets and number of annotated genes exceeded 2000 genes. As cluster analysis of gene expression almost showed no discrete differences at the transcriptome level due to watering within time points of dawn and dusk, the study focused mainly on those of the midday across the two days. KEGG analysis for genes whose differential expression between the two days was ≥5 FC resulted in a number of enzymes that were found repressed due to watering, thus likely participate in the molecular mechanisms utilized by the organism to adapt to the long-lasting drought stress. The recovered regulated metabolites and enzymes included abscisic acid (ABA) receptor PYL4 and PYL9, auxin response factor (ARF) 5 and 15, ARF (or Aux/IAA) proteins IAA7 and IAA14, indole-3-pyruvate (or flavin) monooxygenase, phosphoinositide phosphatase SAC1 and SAC6, pre-mRNA splicing factors 8, 8A, 19, 40A and ISY1, and serine/arginine-rich splicing regultors SCL33, RS31 and RS34. The two pathways tryptophan metabolism and plant hormone signal transduction likely crosstalk in senna (C. angustifolia) towards the maintenance of normal growth under adverse condition. Many other regulated metabolites and proteins in senna (C. angustifolia) including brassinosteroid, heat shock protein 95s, ATPase, several protein kinases such as mitogen-activated protein kinase (MAPK) and cytochrome c oxidase. Other enzymes include phospholipase C2 and allene oxide cyclase as well as isochorismate pathway were also regulated in senna (C. angustifolia). In conclusion, we think that we have scoped the light on the possible regulated metabolites under drought stress that might confer drought stress tolerance in the wild plant senna (C. angustifolia).

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Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration

BMC Genomics ◽

10.1186/s12864-021-08284-9 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Yiqin Wang ◽

Zhifen Yang ◽

Luxi Shi ◽

Rui Yang ◽

Hao Guo ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Fruit Body ◽

Mitogen Activated Protein Kinase ◽

Edible Fungus ◽

Mitogen Activated Protein ◽

Health Related ◽

Caffeine Metabolism

Abstract Background Drought stress severely restricts edible fungus production. The genus Auricularia has a rare drought tolerance, a rehydration capability, and is nutrient rich. Results The key genes and metabolic pathways involved in drought-stress and rehydration were investigated using a transcriptome analysis to clarify the relevant molecular mechanisms. In total, 173.93 Mb clean reads, 26.09 Gb of data bulk, and 52,954 unigenes were obtained. Under drought-stress and rehydration conditions, 14,235 and 8539 differentially expressed genes, respectively, were detected. ‘Tyrosine metabolic’, ‘caffeine metabolism’, ‘ribosome’, ‘phagosome’, and ‘proline and arginine metabolism’, as well as ‘peroxisome’ and ‘mitogen-activated protein kinase signaling’ pathways, had major roles in A. fibrillifera responses to drought stress. ‘Tyrosine’ and ‘caffeine metabolism’ might reveal unknown mechanisms for the antioxidation of A. fibrillifera under drought-stress conditions. During the rehydration process, ‘diterpenoid biosynthesis’, ‘butanoate metabolism’, ‘C5-branched dibasic acid’, and ‘aflatoxin biosynthesis’ pathways were significantly enriched. Gibberellins and γ-aminobutyric acid were important in the recovery of A. fibrillifera growth after rehydration. Many genes related to antibiotics, vitamins, and other health-related ingredients were found in A. fibrillifera. Conclusion These findings suggested that the candidate genes and metabolites involved in crucial biological pathways might regulate the drought tolerance or rehydration of Auricularia, shedding light on the corresponding mechanisms and providing new potential targets for the breeding and cultivation of drought-tolerant fungi.

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Flavonoids improve drought tolerance of maize seedlings by regulating the homeostasis of reactive oxygen species

Plant and Soil ◽

10.1007/s11104-020-04814-8 ◽

2021 ◽

Author(s):

Baozhu Li ◽

Ruonan Fan ◽

Guiling Sun ◽

Ting Sun ◽

Yanting Fan ◽

...

Keyword(s):

Free Radicals ◽

Drought Stress ◽

Drought Tolerance ◽

Infrared Imaging ◽

Oxygen Free Radicals ◽

Transcriptome Profiling ◽

Far Infrared ◽

Drought Treatment ◽

Physiological Characterization ◽

Oxidative Damages

Abstract Background and aims As drought threatens the yield and quality of maize (Zea mays L.), it is important to dissect the molecular basis of maize drought tolerance. Flavonoids, participate in the scavenging of oxygen free radicals and alleviate stress-induced oxidative damages. This study aims to dissect the function of flavonoids in the improvement of maize drought tolerance. Methods Using far-infrared imaging screening, we previously isolated a drought overly insensitivity (doi) mutant from an ethyl methanesulfonate (EMS)-mutagenized maize library and designated it as doi57. In this study, we performed a physiological characterization and transcriptome profiling of doi57 in comparison to corresponding wild-type B73 under drought stress. Results Under drought stress, doi57 seedlings displayed lower leaf-surface temperature (LST), faster water loss, and better performance in growth than B73. Transcriptome analysis reveals that key genes involved in flavonoid biosynthesis are enriched among differentially expressed genes in doi57. In line with these results, more flavonols and less hydrogen peroxide (H2O2) were accumulated in guard cells of doi57 than in those of B73 with the decrease of soil water content (SWC). Moreover, the capacity determined from doi57 seedling extracts to scavenge oxygen free radicals was more effective than that of B73 under the drought treatment. Additionally, doi57 seedlings had higher photosynthetic rates, stomatal conductance, transpiration rates, and water use efficiency than B73 exposed to drought stress, resulting in high biomass and greater root/shoot ratios in doi57 mutant plants. Conclusion Flavonoids may facilitate maize seedling drought tolerance by lowering drought-induced oxidative damage as well regulating stomatal movement.

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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Targeting MDM2-dependent serine metabolism as a therapeutic strategy for liposarcoma

Science Translational Medicine ◽

10.1126/scitranslmed.aay2163 ◽

2020 ◽

Vol 12 (547) ◽

pp. eaay2163

Author(s):

Madi Y. Cissé ◽

Samuel Pyrdziak ◽

Nelly Firmin ◽

Laurie Gayte ◽

Maud Heuillet ◽

...

Keyword(s):

Therapeutic Strategy ◽

Molecular Mechanisms ◽

De Novo ◽

Negative Regulator ◽

Nucleotide Synthesis ◽

Metabolic Functions ◽

Xenograft Models ◽

Well Differentiated ◽

Serine Metabolism

Well-differentiated and dedifferentiated liposarcomas (LPSs) are characterized by a systematic amplification of the MDM2 oncogene, which encodes a key negative regulator of the p53 pathway. The molecular mechanisms underlying MDM2 overexpression while sparing wild-type p53 in LPS remain poorly understood. Here, we show that the p53-independent metabolic functions of chromatin-bound MDM2 are exacerbated in LPS and mediate an addiction to serine metabolism that sustains nucleotide synthesis and tumor growth. Treatment of LPS cells with Nutlin-3A, a pharmacological inhibitor of the MDM2-p53 interaction, stabilized p53 but unexpectedly enhanced MDM2-mediated control of serine metabolism by increasing its recruitment to chromatin, likely explaining the poor clinical efficacy of this class of MDM2 inhibitors. In contrast, genetic or pharmacological inhibition of chromatin-bound MDM2 by SP141, a distinct MDM2 inhibitor triggering its degradation, or interfering with de novo serine synthesis, impaired LPS growth both in vitro and in clinically relevant patient-derived xenograft models. Our data indicate that targeting MDM2 functions in serine metabolism represents a potential therapeutic strategy for LPS.

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In Vitro Assessment of Kurdish Rice Genotypes in Response to PEG-Induced Drought Stress

Applied Sciences ◽

10.3390/app10134471 ◽

2020 ◽

Vol 10 (13) ◽

pp. 4471

Author(s):

Didar Rahim ◽

Petr Kalousek ◽

Nawroz Tahir ◽

Tomáš Vyhnánek ◽

Petr Tarkowski ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Growth Parameters ◽

Oryza Sativa L ◽

Polymorphic Information Content ◽

Callus Growth ◽

Antioxidant Systems ◽

In Vitro Tests ◽

Rice Genotypes

Rice (Oryza sativa L.) is productively affected by different environmental factors, including biotic and abiotic stress. The objectives of this research were to evaluate the genetic distinction among Kurdish rice genotypes using the simple sequence repeats (SSRs) molecular markers and to perform in vitro tests to characterize the drought tolerance of six local rice genotypes. The polymorphic information content (PIC) varied from 0.38 to 0.84 with an average of 0.56. The genetic distance ranged from 0.33 to 0.88. Drought stress had a significant impact (p ≤ 0.05) on callus growth parameters. Enzymatic antioxidant systems were predicted and exhibited a significant variation. The findings revealed that proline levels increase in proportion to polyethylene glycol (PEG) concentrations. Kalar and Gwll Swr genotypes showed the worst performances in phenotypic and biochemical traits, while Choman and Shawre exhibited the best phenotypic and biochemical performances. A positive and substantial relationship between callus fresh weight (CFW) and callus dry weight (CDW) was found under stressful and optimized conditions. Callus induction (CI) was positively and significantly associated with the catalase activity (CAT) in all stressed treatments. Based on the results for callus growth and the biochemical parameters under stress conditions, a remarkable genotype distinction, based on the tolerance reaction, was noted as follows: PEG resistant > susceptible, Choman > Shawre > White Bazyan > Red Bazyan > Gwll Swr > Kalar. The CI and CAT characteristics were considered as reliable predictors of drought tolerance in rice genotypes.

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IQGAP1 binds AMPK and is required for maximum AMPK activation

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.016193 ◽

2020 ◽

pp. jbc.RA120.016193

Author(s):

Andrew C. Hedman ◽

Zhigang Li ◽

Laëtitia Gorisse ◽

Swetha Parvathaneni ◽

Chase J. Morgan ◽

...

Keyword(s):

Protein Kinase ◽

Intracellular Signaling ◽

Energy Homeostasis ◽

Molecular Mechanisms ◽

Direct Interaction ◽

Mitogen Activated Protein Kinase ◽

Null Cell ◽

Ampk Signaling ◽

In Cells

AMP-activated protein kinase (AMPK) is a fundamental component of a protein kinase cascade that is an energy sensor. AMPK maintains energy homeostasis in the cell by promoting catabolic and inhibiting anabolic pathways. Activation of AMPK requires phosphorylation by the liver kinase B1 or by the Ca2+ /calmodulin-dependent protein kinase kinase 2 (CaMKK2). The scaffold protein IQGAP1 regulates intracellular signaling pathways, such as the mitogen-activated protein kinase and AKT signaling cascades. Recent work implicates the participation of IQGAP1 in metabolic function, but the molecular mechanisms underlying these effects are poorly understood. Here, using several approaches including binding analysis with fusion proteins, siRNA-mediated gene silencing, RT-PCR, and knockout mice, we investigated whether IQGAP1 modulates AMPK signaling. In vitro analysis reveals that IQGAP1 binds directly to the α1 subunit of AMPK. In addition, we observed a direct interaction between IQGAP1 and CaMKK2, which is mediated by the IQ domain of IQGAP1. Both CaMKK2 and AMPK associate with IQGAP1 in cells. The ability of metformin and increased intracellular free Ca2+ concentrations to activate AMPK is reduced in cells lacking IQGAP1. Importantly, Ca2+-stimulated AMPK phosphorylation was rescued by re-expression of IQGAP1 in IQGAP1-null cell lines. Comparison of the fasting response in wild-type and IQGAP1-null mice revealed that transcriptional regulation of the gluconeogenesis genes PCK1 and G6PC and the fatty acid synthesis genes FASN and ACC1 is impaired in IQGAP1-null mice. Our data disclose a previously unidentified functional interaction between IQGAP1 and AMPK and suggest that IQGAP1 modulates AMPK signaling.

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Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

Microorganisms ◽

10.3390/microorganisms8091329 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1329

Author(s):

Zhiqiang Pang ◽

Ying Zhao ◽

Peng Xu ◽

Diqiu Yu

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Plant Growth ◽

Upland Rice ◽

Oryza Sativa L ◽

Soluble Sugar ◽

Stress Conditions ◽

Rice Roots ◽

Microbial Resources

Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.

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