Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition

Wang, Tengfei; Zhang, Xiujun

doi:10.1186/s12870-021-03185-1

Cited by 11 publications

(7 citation statements)

References 72 publications

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“…Compared with mock plants, 461 differentially expressed genes (DEGs) and 301 DEGs were obtained from SA-treated plants and drm2 mutants from 28,959 expressing genes of Arabidopsis, respectively ( p < 0.05 ). These results are consistent with previous studies (Stroud et al 2014 ; Wang and Zhang 2021 ). Interestingly, 35 DEGs were shared by drm2 and SA treatment (Fig.…”

Section: Resultssupporting

confidence: 94%

Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

Chai

Liu

et al. 2022

Stress Biology

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DNA methylation is an important epigenetic marker for the suppression of transposable elements (TEs) and the regulation of plant immunity. However, little is known how RNA viruses counter defense such antiviral machinery. In this study, the change of DNA methylation in turnip mosaic virus (TuMV)-infected cells was analyzed by whole genome bisulfite sequencing. Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells, the majority of differentially methylated regions (DMRs) in the CHH and CHG contexts were associated with hypermethylation. Gene expression analysis showed that the expression of two methylases (DRM2 and CMT3) and three demethylases (ROS3, DML2, DML3) was significantly increased and decreased in TuMV-infected cells, respectively. Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes. Finally, we found TuMV-encoded NIb, the viral RNA-dependent RNA polymerase, was able to induce the expression of DRM2. In conclusion, this study discovered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.

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Section: Resultssupporting

confidence: 94%

Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

Chai

Liu

et al. 2022

Stress Biology

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“…In Arabidopsis, most vesicular trafficking to the plasma membrane is driven by SYP121/122 through their assembly with the R-SNAREs VAMP721/722 and the Qb+c-SNARE SNAP33 [ 57 ]. Wang and Zhang found that SYP121 and SYP122 are hub genes that play a key role in plant growth-to-defense transition [ 58 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the SNARE Family in Cultivated Peanut (Arachis hypogaea L.) Reveals That Some Members Are Involved in Stress Responses

Peng

Liu

et al. 2023

IJMS

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The superfamily of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediates membrane fusion during vesicular transport between endosomes and the plasma membrane in eukaryotic cells, playing a vital role in plant development and responses to biotic and abiotic stresses. Peanut (Arachis hypogaea L.) is a major oilseed crop worldwide that produces pods below ground, which is rare in flowering plants. To date, however, there has been no systematic study of SNARE family proteins in peanut. In this study, we identified 129 putative SNARE genes from cultivated peanut (A. hypogaea) and 127 from wild peanut (63 from Arachis duranensis, 64 from Arachis ipaensis). We sorted the encoded proteins into five subgroups (Qa-, Qb-, Qc-, Qb+c- and R-SNARE) based on their phylogenetic relationships with Arabidopsis SNAREs. The genes were unevenly distributed on all 20 chromosomes, exhibiting a high rate of homolog retention from their two ancestors. We identified cis-acting elements associated with development, biotic and abiotic stresses in the promoters of peanut SNARE genes. Transcriptomic data showed that expression of SNARE genes is tissue-specific and stress inducible. We hypothesize that AhVTI13b plays an important role in the storage of lipid proteins, while AhSYP122a, AhSNAP33a and AhVAMP721a might play an important role in development and stress responses. Furthermore, we showed that three AhSNARE genes (AhSYP122a, AhSNAP33a and AhVAMP721) enhance cold and NaCl tolerance in yeast (Saccharomyces cerevisiae), especially AhSNAP33a. This systematic study provides valuable information about the functional characteristics of AhSNARE genes in the development and regulation of abiotic stress responses in peanut.

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“…Determining the stress-triggering events would require an alternative experimental approach as adult plants with constitutive transgene expression and pheromone production probably represent an already well-established defensive state. To better understand the events prompting the transition from the normal to stressed state and its major regulatory players ( Wang and Zhang, 2021 ), sampling after production initiation in a well-regulated and non-leaky inducible expression system (e.g. Garcia-Perez et al., 2022 ; Kallam et al., 2022 ) could give more conclusive insights.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromones

et al. 2022

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Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants (“Sexy Plants”, SxP) that successfully produce a blend of moth (Lepidoptera) sex pheromone compounds (Z)-11-hexadecen-1-ol and (Z)-11-hexadecenyl acetate. However, efficient biosynthesis of sex pheromones resulted in growth and developmental penalty, diminishing the potential for commercial use of SxP in biomanufacturing. To gain insight into the underlying molecular responses, we analysed the whole-genome transcriptome and evaluated it in relation to growth and pheromone production in low- and high-producing transgenic plants of v1.0 and v1.2 SxP lines. In our study, high-producing SxPv1.2 plants accumulated the highest amounts of pheromones but still maintained better growth compared to v1.0 high producers. For an in-depth biological interpretation of the transcriptomic data, we have prepared a comprehensive functional N. benthamiana genome annotation as well as gene translations to Arabidopsis thaliana, enabling functional information transfer by using Arabidopsis knowledge networks. Differential gene expression analysis, contrasting pheromone producers to wild-type plants, revealed that while only a few genes were differentially regulated in low-producing plants, high-producing plants exhibited vast transcriptional reprogramming. They showed signs of stress-like response, manifested as downregulation of photosynthesis-related genes and significant differences in expression of hormonal signalling and secondary metabolism-related genes, the latter presumably leading to previously reported volatilome changes. Further network analyses confirmed stress-like response with activation of jasmonic acid and downregulation of gibberellic acid signalling, illuminating the possibility that the observed growth penalty was not solely a consequence of a higher metabolic burden imposed upon constitutive expression of a heterologous biosynthetic pathway, but rather the result of signalling pathway perturbation. Our work presents an example of comprehensive transcriptomic analyses of disadvantageous stress signalling in N. benthamiana biofactory that could be applied to other bioproduction systems.

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Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition

Cited by 11 publications

References 72 publications

Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

Genome-Wide Analysis of the SNARE Family in Cultivated Peanut (Arachis hypogaea L.) Reveals That Some Members Are Involved in Stress Responses

Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromones

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