Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

Lü, Shuai; Chen, Yaoyu; Wang, Surong; Han, Binying; Zhao, Chunrong; Xue, Penghui; Zhang, Yue; Fang, Hui; Wang, Baohua; Cao, Yunying

doi:10.3389/fpls.2022.1043757

Cited by 7 publications

(3 citation statements)

References 92 publications

(102 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consequently, it is hypothesized that CIPKs may influence the production of citric acid by modulating intracellular Ca 2+ levels in plants. The OsCIPK17 gene in rice has been demonstrated to enhance rice drought resistance and play a role in the citric acid accumulation within the citrate cycle [ 80 ]. Ca 2+ have the potential to enhance soybean tolerance to aluminum ions (Al 3+ ) by stimulating citric acid secretion and mitigating oxidative stress damage [ 81 ].…”

Section: Discussionmentioning

confidence: 99%

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake

Chen,

Feng,

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.

show abstract

Section: Discussionmentioning

confidence: 99%

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake

Chen,

Feng,

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

show abstract

“…In contrast, genes and metabolites related to sugar metabolism were less changed in ‘Pacific Early’, indicating that ‘Pacific Early’ failed to produce more osmoregulatory substances to resist drought stress. The TCA cycle is an important component of plant energy metabolism [ 21 , 23 , 47 ]. In this study, in ‘Jilv3’ under drought stress, the TCA cycle was enhanced by the upregulation of related DEGs, including SDH , CS , SDH , and IDH , which could efficiently improve the utilization of malic acid, citric acid, and succinic acid.…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of transcriptomics and metabolomics of garden asparagus (Asparagus officinalis L.) under drought stress

Zhang,

Han,

Wang

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

Background Drought is a leading environmental factor affecting plant growth. To explore the drought tolerance mechanism of asparagus, this study analyzed the responses of two asparagus varieties, namely, ‘Jilv3’ (drought tolerant) and ‘Pacific Early’ (drought sensitive), to drought stress using metabolomics and transcriptomics. Results In total, 2,567 and 7,187 differentially expressed genes (DEGs) were identified in ‘Pacific Early’ and ‘Jilv3’, respectively, by comparing the transcriptome expression patterns between the normal watering treatment and the drought stress treatment. These DEGs were significantly enriched in the amino acid biosynthesis, carbon metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. In ‘Jilv3’, DEGs were also enriched in the following energy metabolism-related pathways: citrate cycle (TCA cycle), glycolysis/gluconeogenesis, and pyruvate metabolism. This study also identified 112 and 254 differentially accumulated metabolites (DAMs) in ‘Pacific Early’ and ‘Jilv3’ under drought stress compared with normal watering, respectively. The amino acid, flavonoid, organic acid, and soluble sugar contents were more significantly enhanced in ‘Jilv3’ than in ‘Pacific Early’. According to the metabolome and transcriptome analysis, in ‘Jilv3’, the energy supply of the TCA cycle was improved, and flavonoid biosynthesis increased. As a result, its adaptability to drought stress improved. Conclusions These findings help to better reveal the molecular mechanism underlying how asparagus responds to drought stress and improve researchers’ ability to screen drought-tolerant asparagus varieties as well as breed new varieties.

show abstract

“…In another study, the transcriptome and metabolome of Cyclocarya paliurus under different PEG concentrations were analyzed, and WGCNA revealed that 3 key modules, 8 structural genes and 14 regulatory transcription factors regulate sugar metabolism under drought stress (Li et al, 2023a). By combining transcriptomics and metabolomics, researchers showed that OsCIPK17 positively regulates drought resistance in rice and is involved in the accumulation of citrate in the TCA cycle (Lu et al, 2023). Transcriptome and metabolome analyses of Illicium difengpi under drought stress and water replenishment revealed that there were more genes with upregulated expression than genes with downregulated expression, and water replenishment treatment induced the stable expression of 65.25% of genes (Zhang et al, 2024).…”

Section: Introductionmentioning

confidence: 99%

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Chen,

Zhong,

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

IntroductionWatermelon is an annual vine of the family Cucurbitaceae. Watermelon plants produce a fruit that people love and have important nutritional and economic value. With global warming and deterioration of the ecological environment, abiotic stresses, including drought, have become important factors that impact the yield and quality of watermelon plants. Previous research on watermelon drought resistance has included analyzing homologous genes based on known drought-responsive genes and pathways in other species.MethodsHowever, identifying key pathways and genes involved in watermelon drought resistance through high-throughput omics methods is particularly important. In this study, RNA-seq and metabolomic analysis were performed on watermelon plants at five time points (0 h, 1 h, 6 h, 12 h and 24 h) before and after drought stress.ResultsTranscriptomic analysis revealed 7829 differentially expressed genes (DEGs) at the five time points. The DEGs were grouped into five clusters using the k-means clustering algorithm. The functional category for each cluster was annotated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; different clusters were associated with different time points after stress. A total of 949 metabolites were divided into 10 categories, with lipids and lipid-like molecules accounting for the most metabolites. Differential expression analysis revealed 22 differentially regulated metabolites (DRMs) among the five time points. Through joint analysis of RNA-seq and metabolome data, the 6-h period was identified as the critical period for watermelon drought resistance, and the starch and sucrose metabolism, plant hormone signal transduction and photosynthesis pathways were identified as important regulatory pathways involved in watermelon drought resistance. In addition, 15 candidate genes associated with watermelon drought resistance were identified through joint RNA-seq and metabolome analysis combined with weighted correlation network analysis (WGCNA). Four of these genes encode transcription factors, including bHLH (Cla97C03G068160), MYB (Cla97C01G002440), HSP (Cla97C02G033390) and GRF (Cla97C02G042620), one key gene in the ABA pathway, SnRK2-4 (Cla97C10G186750), and the GP-2 gene (Cla97C05G105810), which is involved in the starch and sucrose metabolism pathway.DiscussionIn summary, our study provides a theoretical basis for elucidating the molecular mechanisms underlying drought resistance in watermelon plants and provides new genetic resources for the study of drought resistance in this crop.

show abstract

Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

Cited by 7 publications

References 92 publications

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake

Integrated analysis of transcriptomics and metabolomics of garden asparagus (Asparagus officinalis L.) under drought stress

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Contact Info

Product

Resources

About