| Literature DB >> 30120651 |
Chao Chen1, Yonghua Zhang2, Pan Ye2, Xiaofeng Ma2, Chaoxing Zheng2, Genfa Zhang3.
Abstract
There is a growing awareness that some dual-function enzymes may provide a directly evidence that metabolism could feed into the regulation of gene expression via metabolic enzymes. However, the mechanism by which metabolic enzymes control gene expression to optimize plant stress responses remains largely unknown in Arabidopsis thaliana. LOS2/ENO2 is a bifunctional gene transcribed a functional RNA that translates a full-length version of the ENO2 protein and a truncated version of the MBP-1 protein. Here, we report that eno2 negatively regulates plant tolerance to salinity stress. NaCl treatment caused the death of the mutant eno2/eno2 homozygote earlier than the wild type (WT) Arabidopsis. To understand the mechanism by which the mutant eno2 had a lower NaCl tolerance, an analysis of the expressed sequence tag (EST) dataset from the WT and mutant eno2 Arabidopsis was conducted. Firstly, the most identified up- and down-regulated genes are senescence-associated gene 12 (SAG12) and isochorismate mutase-related gene, which are associated with salicylic acid (SA) inducible plant senescence and endogenous SA synthesis, respectively. Secondly, the differentially regulated by salt stress genes in mutant eno2 are largely enriched Gene Ontology(GO) terms associated with various kinds of response to stimulations. Thirdly, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping, we find that knocking out ENO2-influenced genes were most enriched into metabolite synthesis with extra plant-pathogen interaction pathway and plant hormone signal transduction pathway. Briefly, with the translation shifting function, LOS2/ENO2 not only influenced the genes involved in SA synthesis and transduction, but also influenced genes that participate in metabolite synthesis in cytoplasm and gene expression variation in nuclear under salt stress.Entities:
Keywords: Arabidopsis; Gene expression; Mutant eno2; NaCl stress
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Year: 2018 PMID: 30120651 PMCID: PMC6156758 DOI: 10.1007/s11033-018-4292-7
Source DB: PubMed Journal: Mol Biol Rep ISSN: 0301-4851 Impact factor: 2.316
Fig. 1Localization of T-DNA insertion and expression variation of ENO2. a Localization of T-DNA. The down-arrow demonstrates the orientation of the inserted T-DNA in the ENO2 gene. RB and LB show the right and left T-DNA border, respectively. Black lines indicate introns and filled bars indicate exons. b RT-PCR of ENO2 gene in WT plants and eno2 mutants. Actin-2 indicates the housekeeping gene as a control
Fig. 2Decreased resistance of eno2 mutant to NaCl stress. Four-week-old WT and eno2 plants were treated with 300 mM NaCl. Phenotypes were observed at 0th (on the day prior to the commencement of the salt stress treatment), 12th, and 18th day
Fig. 3Differentially expressed genes (DEGs) analysis of WT and eno2 mutant libraries. X-axis shows the log10 value of WT plant RPKM, and Y-axis represents the log10 value of eno2 mutant. The red and green dots denote the significantly different expression in each dataset (two-fold change), whereas the blue dot indicates no significant difference in the expression of the genes
The process ontology terms of DEGs with corrected p value less than 0.05
| Gene ontology term | Cluster frequency | Genome frequency of use | Corrected |
|---|---|---|---|
| Response to stimulus | 1111 out of 2215 genes, 50.2% | 7620 out of 20,969 genes, 36.3% | 4.57E−42 |
| Response to stress | 654 out of 2215 genes, 29.5% | 3859 out of 20,969 genes, 18.4% | 7.47E−39 |
| Defense response | 238 out of 2215 genes, 10.7% | 1057 out of 20,969 genes, 5.0% | 3.85E−28 |
| Response to oxygen-containing compound | 189 out of 2215 genes, 8.5% | 789 out of 20,969 genes, 3.8% | 2.91E−25 |
| Response to organic substance | 390 out of 2215 genes, 17.6% | 2330 out of 20,969 genes, 11.1% | 2.44E−19 |
| Response to biotic stimulus | 207 out of 2215 genes, 9.3% | 1020 out of 20,969 genes, 4.9% | 3.54E−18 |
| Response to carbohydrate stimulus | 115 out of 2215 genes, 5.2% | 436 out of 20,969 genes, 2.1% | 4.60E−18 |
| Response to abiotic stimulus | 388 out of 2215 genes, 17.5% | 2403 out of 20,969 genes, 11.5% | 2.21E−16 |
| Response to chemical stimulus | 520 out of 2215 genes, 23.5% | 3517 out of 20,969 genes, 16.8% | 5.58E−15 |
| Response to other organism | 177 out of 2215 genes, 8.0% | 901 out of 20,969 genes, 4.3% | 9.42E−14 |
| Response to endogenous stimulus | 318 out of 2215 genes, 14.4% | 2013 out of 20,969 genes, 9.6% | 1.64E−11 |
| Multi-organism process | 193 out of 2215 genes, 8.7% | 1091 out of 20,969 genes, 5.2% | 1.84E−10 |
| Secondary metabolic process | 108 out of 2215 genes, 4.9% | 525 out of 20,969 genes, 2.5% | 6.00E−09 |
| Secondary metabolite biosynthetic process | 80 out of 2215 genes, 3.6% | 356 out of 20,969 genes, 1.7% | 3.92E−08 |
| Response to hormone stimulus | 282 out of 2215 genes, 12.7% | 1864 out of 20,969 genes, 8.9% | 9.05E−08 |
| Signaling | 299 out of 2215 genes, 13.5% | 2078 out of 20,969 genes, 9.9% | 5.39E−06 |
| Phenylpropanoid biosynthetic process | 58 out of 2215 genes, 2.6% | 252 out of 20,969 genes, 1.2% | 7.25E−06 |
| Phenylpropanoid metabolic process | 64 out of 2215 genes, 2.9% | 293 out of 20,969 genes, 1.4% | 1.10E−05 |
| Cell death | 70 out of 2215 genes, 3.2% | 336 out of 20,969 genes, 1.6% | 1.81E−05 |
| Death | 70 out of 2215 genes, 3.2% | 336 out of 20,969 genes, 1.6% | 1.81E−05 |
| Response to reactive oxygen species | 31 out of 2215 genes, 1.4% | 100 out of 20,969 genes, 0.5% | 1.83E−05 |
| Single-organism biosynthetic process | 127 out of 2215 genes, 5.7% | 744 out of 20,969 genes, 3.5% | 2.60E−05 |
| Flavonoid biosynthetic process | 33 out of 2215 genes, 1.5% | 113 out of 20,969 genes, 0.5% | 3.32E−05 |
| Ketone biosynthetic process | 35 out of 2215 genes, 1.6% | 125 out of 20,969 genes, 0.6% | 4.21E−05 |
| Response to oxidative stress | 37 out of 2215 genes, 1.7% | 137 out of 20,969 genes, 0.7% | 4.96E−05 |
| Response to osmotic stress | 153 out of 2215 genes, 6.9% | 965 out of 20,969 genes, 4.6% | 0.00014 |
| Flavonoid metabolic process | 33 out of 2215 genes, 1.5% | 121 out of 20,969 genes, 0.6% | 0.00019 |
| Programmed cell death | 58 out of 2215 genes, 2.6% | 291 out of 20,969 genes, 1.4% | 0.00132 |
| Cellular ketone metabolic process | 35 out of 2215 genes, 1.6% | 144 out of 20,969 genes, 0.7% | 0.0017 |
| Immune system process | 59 out of 2215 genes, 2.7% | 304 out of 20,969 genes, 1.4% | 0.00264 |
| Monocarboxylic acid metabolic process | 92 out of 2215 genes, 4.2% | 543 out of 20,969 genes, 2.6% | 0.00294 |
| Cell wall modification | 29 out of 2215 genes, 1.3% | 112 out of 20,969 genes, 0.5% | 0.00333 |
| Defense response to fungus | 34 out of 2215 genes, 1.5% | 142 out of 20,969 genes, 0.7% | 0.00341 |
| Response to fungus | 34 out of 2215 genes, 1.5% | 144 out of 20,969 genes, 0.7% | 0.00474 |
| Jasmonic acid metabolic process | 16 out of 2215 genes, 0.7% | 44 out of 20,969 genes, 0.2% | 0.0049 |
| Response to light intensity | 31 out of 2215 genes, 1.4% | 130 out of 20,969 genes, 0.6% | 0.00982 |
| Immune effector process | 17 out of 2215 genes, 0.8% | 52 out of 20,969 genes, 0.2% | 0.01302 |
| Response to radiation | 147 out of 2215 genes, 6.6% | 1003 out of 20,969 genes, 4.8% | 0.02057 |
| Cell wall organization | 41 out of 2215 genes, 1.9% | 201 out of 20,969 genes, 1.0% | 0.02502 |
| Response to water deprivation | 21 out of 2215 genes, 0.9% | 79 out of 20,969 genes, 0.4% | 0.04666 |
Differentially expressed salinity tolerance related genes
| Process Ontology term | GeneID | WT_24 h-RPKM | eno2_24 h-RPKM | log2 Ratio | FDR | Description |
|---|---|---|---|---|---|---|
| Response to salt stress/hyperosmotic salinity response | AT1G05680.1 | 7.901282047 | 85.60965475 | 3.437614841 | 0 | Symbols: UGT74E2 | Uridine diphosphate glycosyltransferase 74E2 |
| Response to salt stress | AT5G64000.1 | 4.637864696 | 21.66939811 | 2.224126445 | 7.91E−54 | Symbols: SAL2, ATSAL2 | Inositol monophosphatase family protein |
| Response to salt stress | AT5G60270.1 | 1.156503206 | 7.482285588 | 2.693709767 | 7.27E−44 | Symbols: LECRK-I.7 | Concanavalin A-like lectin protein kinase family protein |
| Response to salt stress | AT5G09290.1 | 1.708224293 | 6.512534541 | 1.930721703 | 1.48E−13 | Symbols: | Inositol monophosphatase family protein |
| Response to salt stress/hyperosmotic salinity response | AT1G05675.1 | 0.237445936 | 1.87277171 | 2.979504076 | 1.73E−08 | Symbols: | UDP-Glycosyltransferase superfamily protein |
| Response to salt stress | AT3G21370.1 | 0.781954259 | 0.001 | − 9.610940408 | 2.13E−07 | Symbols: BGLU19 | beta glucosidase 19 |
| response to salt stress | AT5G63990.1 | 0.965002378 | 2.707512504 | 1.488363598 | 4.85E−05 | Symbols: | Inositol monophosphatase family protein |
| Response to salt stress | AT5G19000.2 | 1.836643156 | 0.606054045 | − 1.599552992 | 8.21E−05 | Symbols: BPM1 | BTB-POZ and MATH domain 1 |
Fig. 4Scatter plot of KEGG pathway enrichment statistics. The RichFactor refers to the ratio generated from dividing DEG numbers parsed in a special pathway by the total number of genes parsed in the same pathway. Greater RichFactor means greater intensiveness. Q-value is the corrected p value ranging from 0 to 1; lower values mean greater intensiveness. The figure demonstrates the enrichment degree of the top 20 entries to the pathway