Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco

The co-ordination between the primary carboxylating enzyme phosphoenolpyruvate carboxylase (PEPC) and the further decarboxylating enzymes is crucial to the efficiency of the CO2-concentrating mechanism in C4 plants, and investigations on more types of C4 plants are needed to fully understand their adaptation mechanisms. In this study we investigated the effect of drought on carboxylating enzyme PEPC, and the further decarboxylating NAD-malic enzyme (NAD-ME) of Salsola lanata Pall. (Chenopodiaceae) – an annual succulent C4-NAD-ME subtype desert plant. We investigated enzyme activity at the transcriptional level with real-time quantitative PCR and at the translational level by immunochemical methods, and compared S. lanata with other forms of studied C4 plants under drought stress. Results showed that only severe stress limited PEPC enzyme activity (at pH 8.0) of S. lanata significantly. Considering that PEPC enzyme activity (at pH 8.0) was not significantly affected by phosphorylation, the decrease of PEPC enzyme activity (at pH 8.0) of S. lanata under severe stress may be related with decreased PEPC mRNA. The suggestion of increased phosphorylation of the PEPC enzyme in plants under moderate stress was supported by the ratio of PEPC enzyme activity at pH 7.3/8.0, as PEPC enzyme is inhibited by L-malate and the evidence of the 50% inhibiting concentration of L-malate. NAD-ME activity decreased significantly under moderate and severe stress, and coincided with a change of leaf water content rather than the amount of α-NAD-ME mRNA and protein. Leaf dehydration may cause the decrease of NAD-ME activity under water stress. Compared with other C4 plants, the activities of PEPC and NAD-ME of S. lanata under drought stress showed distinct features.

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A comprehensive overview of miRNA targeting drought stress resistance in plants

Brazilian Journal of Biology ◽

10.1590/1519-6984.242708 ◽

2023 ◽

Vol 83 ◽

Author(s):

S. M. S. Shah ◽

F. Ullah

Keyword(s):

Drought Stress ◽

Stress Responses ◽

Crop Production ◽

Genetic Alterations ◽

Cereal Crops ◽

Transcriptional Level ◽

Gene Expressions ◽

Comprehensive Overview ◽

Defense Systems ◽

The Given

Abstract MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.

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Transcriptome changes induced by drought stress in Jerusalem artichoke (Helianthus tuberosus L.) and weighted gene co-expression network analysis (WGCNA)

10.21203/rs.3.rs-25678/v1 ◽

2020 ◽

Author(s):

Shipeng Yang ◽

Lihui Wang ◽

Qiwen Zhong ◽

Guangnan Zhang ◽

Dengshan Zhang ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Jerusalem Artichoke ◽

Northern China ◽

Qinghai Lake ◽

Helianthus Tuberosus ◽

Rna Seq ◽

Light Reaction ◽

Qinghai Province ◽

Watering Treatment

Abstract Background: Jerusalem artichoke (Helianthus tuberosus L.) is strongly resistant to stress and an important plant used for ecological management in northern China in recent years. Currently, Jerusalem artichoke has been widely planted in the area around Qinghai Lake in Qinghai Province, China. Jerusalem artichoke can not only prevent land desertification but also has maintain most of its level of production. However, there is little research on the mechanism of drought resistance of Jerusalem artichoke.Results: We conducted transcriptome sequencing under drought stress and normal watering treatment for two varieties, QY1 and QY3, with differing degrees of drought tolerance. In the three stress periods of QY1 and QY3, 5,613, 12,985 and 24,923 differentially expressed genes (DEGs) were identified, respectively. GO analysis showed that there were more DEGs in QY1 than in QY3, but there were more up-regulated genes in QY3 than in QY1. Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. The up-regulated genes in QY3 were significantly more prevalent than those in QY1 and were primarily concentrated in flavor IDS, phenylpropanoids, and the shikimate and terpenoids pathway. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. In addition, the gene analysis of the ABA key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1. A weighted gene co-expression network was constructed and divided into modules. By specifically analyzing the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase were the most significant in these pathways.Conclusions: In summary, these findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the unearthing of related genes.

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Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize

International Journal of Genomics ◽

10.1155/2017/2568706 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 14

Author(s):

Nepolean Thirunavukkarasu ◽

Rinku Sharma ◽

Nidhi Singh ◽

Kaliyugam Shiriga ◽

Sweta Mohan ◽

...

Keyword(s):

Drought Stress ◽

Stomatal Closure ◽

Gene Interactions ◽

Transcriptional Level ◽

Cell Wall Modification ◽

Drought Tolerant ◽

Expression Of Genes ◽

Proteins Metabolism ◽

Coexpression Networks ◽

Coexpression Pattern

A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.

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RNA-Seq reveals different responses to drought in Neotropical trees from savannas and seasonally dry forests

BMC Plant Biology ◽

10.1186/s12870-021-03244-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Mariane B. Sobreiro ◽

Rosane G. Collevatti ◽

Yuri L. A. dos Santos ◽

Ludmila F. Bandeira ◽

Francis J. F. Lopes ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Drought Stress ◽

Phenotypic Plasticity ◽

Tree Species ◽

Block Design ◽

Limiting Factors ◽

Transcriptional Level ◽

Rna Seq ◽

Seasonally Dry

Abstract Background Water is one of the main limiting factors for plant growth and crop productivity. Plants constantly monitor water availability and can rapidly adjust their metabolism by altering gene expression. This leads to phenotypic plasticity, which aids rapid adaptation to climate changes. Here, we address phenotypic plasticity under drought stress by analyzing differentially expressed genes (DEG) in four phylogenetically related neotropical Bignoniaceae tree species: two from savanna, Handroanthus ochraceus and Tabebuia aurea, and two from seasonally dry tropical forests (SDTF), Handroanthus impetiginosus and Handroanthus serratifolius. To the best of our knowledge, this is the first report of an RNA-Seq study comparing tree species from seasonally dry tropical forest and savanna ecosystems. Results Using a completely randomized block design with 4 species × 2 treatments (drought and wet) × 3 blocks (24 plants) and an RNA-seq approach, we detected a higher number of DEGs between treatments for the SDTF species H. serratifolius (3153 up-regulated and 2821 down-regulated under drought) and H. impetiginosus (332 and 207), than for the savanna species. H. ochraceus showed the lowest number of DEGs, with only five up and nine down-regulated genes, while T. aurea exhibited 242 up- and 96 down-regulated genes. The number of shared DEGs among species was not related to habitat of origin or phylogenetic relationship, since both T. aurea and H impetiginosus shared a similar number of DEGs with H. serratifolius. All four species shared a low number of enriched gene ontology (GO) terms and, in general, exhibited different mechanisms of response to water deficit. We also found 175 down-regulated and 255 up-regulated transcription factors from several families, indicating the importance of these master regulators in drought response. Conclusion Our findings show that phylogenetically related species may respond differently at gene expression level to drought stress. Savanna species seem to be less responsive to drought at the transcriptional level, likely due to morphological and anatomical adaptations to seasonal drought. The species with the largest geographic range and widest edaphic-climatic niche, H. serratifolius, was the most responsive, exhibiting the highest number of DEG and up- and down-regulated transcription factors (TF).

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Drought Stress-Mediated Transcriptome Profile Reveals NCED as a Key Player Modulating Drought Tolerance in Populus davidiana

Frontiers in Plant Science ◽

10.3389/fpls.2021.755539 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sang-Uk Lee ◽

Bong-Gyu Mun ◽

Eun-Kyung Bae ◽

Jae-Young Kim ◽

Hyun-Ho Kim ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Responses ◽

Expression Patterns ◽

Pcr Analysis ◽

Transcriptional Level ◽

Rna Seq ◽

Drought Tolerant ◽

Populus Davidiana ◽

Strict Regulation

Populus trichocarpa has been studied as a model poplar species through biomolecular approaches and was the first tree species to be genome sequenced. In this study, we employed a high throughput RNA-sequencing (RNA-seq) mediated leaf transcriptome analysis to investigate the response of four different Populus davidiana cultivars to drought stress. Following the RNA-seq, we compared the transcriptome profiles and identified two differentially expressed genes (DEGs) with contrasting expression patterns in the drought-sensitive and tolerant groups, i.e., upregulated in the drought-tolerant P. davidiana groups but downregulated in the sensitive group. Both these genes encode a 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme required for abscisic acid (ABA) biosynthesis. The high-performance liquid chromatography (HPLC) measurements showed a significantly higher ABA accumulation in the cultivars of the drought-tolerant group following dehydration. The Arabidopsis nced3 loss-of-function mutants showed a significantly higher sensitivity to drought stress, ~90% of these plants died after 9 days of drought stress treatment. The real-time PCR analysis of several key genes indicated a strict regulation of drought stress at the transcriptional level in the P. davidiana drought-tolerant cultivars. The transgenic P. davidiana NCED3 overexpressing (OE) plants were significantly more tolerant to drought stress as compared with the NCED knock-down RNA interference (RNAi) lines. Further, the NCED OE plants accumulated a significantly higher quantity of ABA and exhibited strict regulation of drought stress at the transcriptional level. Furthermore, we identified several key differences in the amino acid sequence, predicted structure, and co-factor/ligand binding activity of NCED3 between drought-tolerant and susceptible P. davidiana cultivars. Here, we presented the first evidence of the significant role of NCED genes in regulating ABA-dependent drought stress responses in the forest tree P. davidiana and uncovered the molecular basis of NCED3 evolution associated with increased drought tolerance.

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Soil Water Deficit and Fertilizer Placement Effects on Root Biomass Distribution, Soil Water Extraction, Water Use, Yield, and Yield Components of Soybean [Glycine max (L.) Merr.] Grown in 1-m Rooting Columns

Frontiers in Plant Science ◽

10.3389/fpls.2021.581127 ◽

2021 ◽

Vol 12 ◽

Author(s):

Michael Gebretsadik Gebre ◽

Hugh James Earl

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Soil Water ◽

Water Use ◽

Yield Components ◽

Dry Matter ◽

Soil Depth ◽

Mild Drought ◽

Watering Treatment ◽

Pod Number

Typical small-pot culture systems are not ideal for controlled environment phenotyping for drought tolerance, especially for root-related traits. We grew soybean plants in a greenhouse in 1-m rooting columns filled with amended field soil to test the effects of drought stress on water use, root growth, shoot growth, and yield components. There were three watering treatments, beginning at first flower: watered daily to 100% of the maximum soil water holding capacity (control), 75% (mild drought stress), or 50% (drought stress). We also tested whether applying fertilizer throughout the 1-m soil depth instead of only in the top 30 cm would modify root distribution by depth in the soil profile and thereby affect responses to drought stress. Distributing the fertilizer over the entire 1-m soil depth altered the root biomass distribution and volumetric soil water content profile at first flower, but these effects did not persist to maturity and thus did not enhance drought tolerance. Compared to the control (100%) watering treatment, the 50% watering treatment significantly reduced seed yield by 40%, pod number by 42%, seeds per pod by 3%, shoot dry matter by 48%, root dry matter by 53%, and water use by 52%. Effects of the 75% watering treatment were intermittent between the 50 and 100%. The 50% treatment significantly increased root-to-shoot dry matter ratio by 23%, harvest index by 17%, and water-use efficiency by 7%. Seed size was not affected by either fertilizer or watering treatments. More than 65% of the total root dry matter was distributed in the upper 20 cm of the profile in all watering treatments. However, the two drought stress treatments, especially the mild drought stress, had a greater proportion of root dry matter located in the deeper soil layers. The overall coefficient of variation for seed yield was low at 5.3%, suggesting good repeatability of the treatments. Drought stress imposed in this culture system affected yield components similarly to what is observed in the field, with pod number being the component most strongly affected. This system should be useful for identifying variation among soybean lines for a wide variety of traits related to drought tolerance.

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Drought-Induced Responses of Nitrogen Metabolism in Ipomoea batatas

Plants ◽

10.3390/plants9101341 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1341

Author(s):

Houqiang Xia ◽

Tao Xu ◽

Jing Zhang ◽

Ke Shen ◽

Zongyun Li ◽

...

Keyword(s):

Drought Stress ◽

Ipomoea Batatas ◽

Glutamate Synthase ◽

Ammonium Nitrogen ◽

Transcriptional Level ◽

Peg 6000 ◽

Metabolism Enzymes ◽

N Metabolism ◽

Leaves And Roots ◽

Different Response

This study investigated the effect of water stress, simulated by the polyethylene glycol (PEG-6000) method, on nitrogen (N) metabolism in leaves and roots of hydroponically grown sweet potato seedlings, Xushu 32 (X32) and Ningzishu 1 (N1). The concentrations of PEG-6000 treatments were 0%, 5% and 10% (m/v). The results showed that the drought-treated plants showed a decline leaf relative water content, and revealed severe growth inhibition, compared with the 0% treatment. Under drought stress, the decline in biomass of the leaf and stem was more noticeable than in root biomass for X32, leading to a higher root to shoot ratio. Drought stress increased the nitrate nitrogen (NO3−-N) and protein in leaves, but reduced all the activities of N-metabolism enzymes and the transcriptional levels of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (GOGAT); in roots, NO3−-N and NR had opposite trends. The leaf ammonium nitrogen (NH4+-N), GS and amino acid had different trends between X32 and N1 under drought stress. Furthermore, the transcriptional level of nitrate transporter genes NRT1.1 in leaves and roots were upregulated under drought stress, except in N1 roots. In conclusion, NR determined the different response to drought in leaves for X32 and N1, and GS and GOGAT determined the response to drought in roots, respectively.

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An abscisic acid (ABA) homeostasis regulated by its production, catabolism and transport in peanut leaves in response to drought stress

10.1101/569848 ◽

2019 ◽

Author(s):

Haitao Long ◽

Zhao Zheng ◽

Yajun Zhang ◽

Pengzhan Xing ◽

Xiaorong Wan ◽

...

Keyword(s):

Drought Stress ◽

De Novo ◽

Transcriptional Level ◽

Uridine Diphosphate ◽

High Sequence Identity ◽

Regulatory Circuit ◽

Catabolic Genes ◽

Permissible Range ◽

Aba Catabolism ◽

Important Pathway

AbstractABA is an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to drought stress. Two production pathways,de novobiosynthesis and hydrolysis of glucose-conjugated ABA by β-glucosidase (BG), increase cellular ABA levels in plants. ABA catabolism via hydroxylation by 8’-hydroxylase (CYP707A), or conjugation by uridine diphosphate glucosyltransferase (UGT), decreases cellular ABA levels. The transport of ABA through ATP-binding cassette (ABC)-containing transporter proteins, members of ABC transporter G family (ABCG), across plasma membrane (PM) is another important pathway to regulate cellular ABA levels. In this study, based on our previously constructed transcriptome of peanut leaves in response to drought stress, fourteen candidate genes involved in ABA production (includingAhZEP,AhNCED1andAhNCED3,AhABA2,AhAAO1andAhAAO2,AhABA3,AhBG11andAhBG24), catabolism (includingAhCYP707A3,AhUGT71K1andAhUGT73B4) and transport (includingAhABCG22-1andAhABCG22-2), were identified homologously and phylogenetically, and further analyzed at the transcriptional level by real-time RT-PCR, simultaneously determining ABA levels in peanut leaves in response to drought. The high sequence identity and very similar subcellular localization of the proteins deduced from 14 identified genes involved in ABA production, catabolism and transport with the reported corresponding enzymes in databases suggest their similar roles in regulating cellular ABA levels. In response to drought stress, ABA accumulation levels in peanut leaves agree very well with the up-regulated expressions of ABA-producing genes (AhZEP,AhNCED1,AhAAO2,AhABA3,AhBG11andAhBG24) and PM-localized ABA importer genes (AhABCG22-1andAhABCG22-2), although the expression of ABA catabolic genes (AhCYP707A3andAhUGT71K1) was also up-regulated. It is likely that drought-responsive induction of catabolic genes helps not only to maintain ABA levels within a permissible range, but also to prepare the plant for degradation of ABA after removal of the stress. These results suggest that ABA homeostasis in peanut leaves in response to drought may be coordinated by a master regulatory circuit that involves production, catabolism, and as well as transport.

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Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor

Phytobiomes Journal ◽

10.1094/pbiomes-07-20-0052-r ◽

2020 ◽

Author(s):

Heidi Wipf ◽

Thảo-Nguyên Bùi ◽

Devin Coleman-Derr

Keyword(s):

Drought Stress ◽

Sorghum Bicolor ◽

Alpha Diversity ◽

Crop Productivity ◽

Seedling Roots ◽

Microbe Interactions ◽

C 30 ◽

Watering Treatment ◽

Microbiome Assembly

Water deficit and extreme temperatures regularly and considerably reduce crop productivity. While several studies have explored the role of the plant microbiome in drought tolerance, it remains to be determined how the often co-occurring factor of heat conjunctly shapes plant-microbe interactions. In order to compare the roles temperature and drought stress play in plant microbial recruitment, we conducted a growth chamber experiment with a series of temperatures (22°C, 30°C, and 38°C) and watering (drought versus watered) conditions in Sorghum bicolor, sampling soil mixtures and seedling roots at 7 and 21 days post initial stress initiation. We found that bacterial root communities had the lowest alpha diversity when under drought and at 38°C, and that temperature influenced the beta diversity of soil mixture and root microbiomes to a greater extent than watering treatment. Additionally, we observed that the relative abundances of Actinobacteria increased both under drought and incrementally with higher temperatures. Further, unique Actinobacteria were indicator species of either temperature or watered conditions and were one of the top phyla whose indicators are predominantly of high temperatures in watered conditions. Together, these data suggest that heat and drought stress differentially impact microbiome assembly in significant ways and unique Actinobacteria may be recruited under either stress. This work informs our understandings of how abiotic stresses shape crop microbiomes, as well as highlights the need for additional work to describe what mechanisms may be involved in host-mediated microbial recruitment and adaptation under various stresses in field-based studies.

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