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Singlet oxygen induces cell wall thickening and stomatal density reducing by transcriptome reprogramming

JOURNAL OF BIOLOGICAL CHEMISTRY 2023年第12期299卷 105481页

作者： Zhang, Zhong-Wei Fu, Yu-Fan Yang, Xin-Yue Yuan, Ming Zheng, Xiao-Jian Luo, Xiao-Feng Zhang, Meng-Yao Xie, Lin-Bei Shu, Kai Reinbothe, Steffen Reinbothe, Christiane Wu, Fan Feng, Ling-Yang Du, Jun-Bo Wang, Chang-Quan Gao, Xue-Song Chen, Yang-Er Zhang, Yan-Yan Li, Yang Tao, Qi Lan, Ting Tang, Xiao-Yan Zeng, Jian Chen, Guang-Deng Yuan, Shu Sichuan Agr Univ Coll Resources Chengdu Peoples R China Minist Nat Resources Key Lab Invest & Monitoring Protect & Utilizat Cul Chengdu Peoples R China Sichuan Agr Univ Coll Life Sci Yaan Peoples R China Northwestern Polytech Univ Sch Ecol & Environm Xian Peoples R China Univ Grenoble Alpes Lab Genet Mol Plantes & Biol Environm & Syst BEeSy Grenoble France Sichuan Prov Acad Nat Resource Sci Chengdu Peoples R China Sichuan Agr Univ Coll Agron Chengdu Peoples R China

Singlet oxygen (1O2) has a very short half-life of 10-5 s;however, it is a strong oxidant that causes growth arrest and necrotic lesions on plants. Its signaling pathway remains largely unknown. The Arabidopsis flu (fluorescent) mutant accumulates a high level of 1O2 and shows drastic changes in nuclear gene expression. Only two plastid proteins, EX1 (executer 1) and EX2 (executer 2), have been identified in the singlet oxygen signaling. Here, we found that the transcription factor abscisic acid insensitive 4 (ABI4) binds the promoters of genes responsive to 1O2-signals. Inactivation of the ABI4 protein in the flu/abi4 double mutant was sufficient to compromise the changes of almost all 1O2-responsive-genes and rescued the lethal phenotype of flu grown under light/dark cycles, similar to the flu/ex1/ex2 triple mutant. In addition to cell death, we reported for the first time that 1O2 also induces cell wall thickening and stomatal development defect. Contrastingly, no apparent growth arrest was observed for the flu mutant under normal light/dim light cycles, but the cell wall thickening (doubled) and stomatal density reduction (by two-thirds) still occurred. These results offer a new idea for breeding stress tolerant plants.

关键词： ABI4 cell wall singlet oxygen stomatal development transcriptome reprogramming

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Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development

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BMC PLANT BIOLOGY 2019年第1期19卷 197-197页

作者： Ma, Chuanyu Li, Bo Wang, Lina Xu, Ming-liang Lizhu, E. Jin, Hongyu Wang, Zhicheng Ye, Jian-rong China Agr Univ Natl Maize Improvement Ctr 2 West Yuanmingyuan Rd Beijing 100193 Peoples R China

BackgroundDuring maize early kernel development, the dramatic transcriptional reprogramming determines the rate of developmental progression, and phytohormone plays critical role in these important processes. To investigate the phytohormone levels and transcriptome reprogramming profiles during maize early kernel development, two maize inbreds with similar genetic background but different mature kernel sizes (ILa and ILb) were *** levels of indole-3-acetic acid (IAA) were increased continuously in maize kernels from 5days after pollination (DAP) to 10 DAP. ILa had smaller mature kernels than ILb, and ILa kernels had significantly lower IAA levels and significantly higher SA levels than ILb at 10 DAP. The different phytohormone profiles correlated with different transcriptional reprogramming in the two kernels. The global transcriptomes in ILa and ILb kernels were strikingly different at 5 DAP, and their differences peaked at 8 DAP. Functional analysis showed that the biggest transcriptome difference between the two kernels is those response to biotic and abiotic stresses. Further analyses indicated that the start of dramatic transcriptional reprogramming and the onset of significantly enriched functional categories, especially the plant hormone signal transduction and starch and sucrose metabolism, was earlier in ILa than in ILb, whereas more significant enrichment of those functional categories occurred at later stage of kernel development in *** results indicate that later onset of the significantly enriched functional categories, coincide with their stronger activities at a later developmental stage and higher IAA level, are necessary for young kernels to undergo longer mitotic activity and finally develop a larger kernel size. The different onset times and complex interactions of the important functional categories, especially phytohormone signal, and carbohydrate metabolism, form the most important molecular regulators mediating mai

关键词： Phytohormone Defense response Maize early kernel development transcriptome reprogramming Auxin

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reprogramming of phytopathogen transcriptome by a non-bactericidal pesticide residue alleviates its virulence in rice

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Fundamental Research 2022年第2期2卷 198-207页

作者： Haruna Matsumoto Yuan Qian Xiaoyan Fan Sunlu Chen Yanxia Nie Kun Qiao Dandan Xiang Xinzhong Zhang Meng Li Bo Guo Peilin Shen Qiangwei Wang Yunlong Yu Tomislav Cemava Mengcen Wang State Key Laboratory of Rice Biology&Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects Institute of Pesticide and Environmental ToxicologyZhejiang UniversityHangzhou 310058China Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Institute of Environmental Biotechnology Graz University of TechnologyPetersgasse 128010 GrazAustria Global Education Program for AgriScience Frontiers Graduate School of AgricultureHokkaido UniversitySapporo 0608589Japan State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China Ecology and Environmental Sciences Center South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China Key laboratory of South Subtropical Fruit Biology and Genetic Resource Uilization(MOA) Instiute of Fruit Tree ResearchGuangdong Acadermy of Agricultural SciencesGuangzhou 510640China Tea Research Instiute Chinese Academy of Agriculural SciencesHangzhou 310008China Shanghai Intermnational Studies University Shanghai 200083China Xiaoshan Agricultural Comprehensive Development Zone&Management Committee Hangzhou 311200China

Bacteria equipped with virulence systems based on highly bioactive small molecules can circumvent their host's defense *** employing this strategy are currently threatening global rice *** the present study,variations in the virulence of the highly destructive Barkholderiaplantarii were observed in different rice-producing *** environment-linked variation was not attributable to any known host-related or external ***-occurrence analyses indicated a connection between reduced virulence and 5-Amino-l,3,4-thiadiazole-2-thiol(ATT),a non-bactericidal organic ***,which accumulates in rice plants during metabolization of specific agrochemicals,was found to reduce virulence factor secretion by *** up to 88.8%and inhibit pathogen virulence by hijacking an upstream signaling *** assessment of the newly discovered virulence inhibitor resulted in mechanistic insights into positive effects of ATT accumulation in plant *** of virulence alleviation were deciphered by integrating high-throughput data,gene knockout mutants,and molecular interaction ***,a histidine protein kinase in a two-component system that regulates virulence factor secretion,is likely the molecular target antagonized by *** findings provide novel insights into virulence modulation in an important plant-pathogen system that relies on the host's metabolic activity and subsequent signaling interference.

关键词： Phytopathogen Virulence factor transcriptome reprogramming Agrochemical Pesticide Rice

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Irregular transcriptome reprogramming probably causes thec developmental failure of embryos produced by interspecies somatic cell nuclear transfer between the Przewalski's gazelle and the bovine

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BMC GENOMICS 2014年第1期15卷 1-14页

作者： Zuo, Yongchun Gao, Yu Su, Guanghua Bai, Chunling Wei, Zhuying Liu, Kun Li, Qianzhong Bou, Shorgan Li, Guangpeng Inner Mongolia Univ Key Lab Natl Educ Key Lab Herbivore Reprod Biotechnol & Breeding Minist Mammalian Reprod Biol & BiotechnolMinist Hohhot 010070 Peoples R China Inner Mongolia Univ Sch Phys Sci & Technol Lab Theoret Biophys Hohhot 010021 Peoples R China Inner Mongolia Univ Key Lab Natl Educ Minist Mammalian Reprod Biol & Biotechnol Hohhot 010070 Peoples R China

Background: Interspecies somatic cell nuclear transfer (iSCNT) has been regarded as a potential alternative for rescuing highly endangered species and can be used as a model for studying nuclear-cytoplasmic interactions. However, iSCNT embryos often fail to produce viable offspring. The alterations in normal molecular mechanisms contributing to extremely poor development are for the most part unknown. Results: Przewalski's gazelle-bovine iSCNT embryos (PBNT) were produced by transferring Przewalski's gazelle fibroblast nuclei into enucleated bovine oocytes. The percentages of PBNT embryos that developed to morula/blastocyst stages were extremely low even with the use of various treatments that included different SCNT protocols and treatment of embryos with small molecules. Transcriptional microarray analyses of the cloned embryos showed that the upregulation of reprogramming-associated genes in bovine-bovine SCNT (BBNT) embryos was significantly higher than those observed in PBNT embryos (1527: 643). In all, 139 transcripts related to various transcription regulation factors (TFs) were unsuccessfully activated in the iSCNT embryos. Maternal degradation profiles showed that 1515 genes were uniquely downregulated in the BBNT embryos, while 343 genes were downregulated in the PBNT embryos. Incompatibilities between mitochondrial DNA (mtDNA) and nuclear DNA revealed that the TOMM (translocase of outer mitochondrial membrane)/TIMM (translocase of inner mitochondrial membrane) complex-associated genes in BBNT embryos had the highest expression levels, while the PBNT embryos exhibited much lower expression rates. Conclusions: Improper degradation of maternal transcripts, incomplete activation of TFs and abnormal expression of genes associated with mitochondrial function in PBNT embryos likely contributed to incomplete reprogramming of the donor cell nuclei and therefore led to the developmental failure of these cloned embryos.

关键词： Interspecies somatic cell nuclear transfer (iSCNT) transcriptome reprogramming Embryonic genome activation Transcriptional regulation Mitochondrial DNA

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Irregular transcriptome reprogramming probably caused embryo developmental failure of interspecies nuclear transfer between the Przewalski's gazelle and the bovine

Irregular transcriptome reprogramming probably caused embryo...

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第六届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会

作者：左永春郜宇苏广华李前忠李光鹏哺乳动物生殖生物学及生物技术教育部重点实验室内蒙古大学呼和浩特010070 理论生物物理实验室物理科学与技术学院内蒙古大学呼和浩特010021

Methods: Interspecies somatic cell nuclear transfer (iSCNT) has been regarded as a potential alternative in rescuing highly endangered species and can be used as a model for studying nuclear-cytoplasmic ***, iSCNT embryos often fail to produce viable *** alterations of normal molecular mechanisms contributing to extremely poor development is for the most part unknown.

关键词： SCNT transcriptome reprogramming embryonic genome activation transcriptional regulation mitochondrial DNA

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The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

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PLANT BIOTECHNOLOGY JOURNAL 2023年第11期21卷 2291-2306页

作者： Zhou, Leilei Gao, Guangtong Li, Xiaojing Wang, Weihao Tian, Shiping Qin, Guozheng Chinese Acad Sci Inst Bot Key Lab Plant Resources Beijing Peoples R China China Natl Bot Garden Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China

Fruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5-methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2, the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlbCA3 encoding a beta-carbonic anhydrase and SlFAD3 encoding a omega-3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2-mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2. We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of Sl beta CA3 and SlFAD3. Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2, as a multifunctional gene, participates in modulating the trade-off between fruit ripening and disease resistance.

关键词： SlDML2 defence response transcriptome reprogramming Botrytis cinerea tomato

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Unveiling functional module associated with fungal disease stress in barley (Hordeum vulgare)

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BIOCHEMISTRY AND BIOPHYSICS REPORTS 2025年 41卷 101958页

作者： Panahi, Bahman Hamid, Rasmieh Agr Res Educ & Extens Org AREEO Agr Biotechnol Res Inst Iran ABRII Dept Genom Branch Northwest & West Reg Tabriz 5156915-598 Iran Agr Res Educ & Extens Org AREEO Cotton Res Inst Iran CRII Dept Plant Breeding Gorgan Iran

Fungal infections pose a considerable threat to the cultivation of barley (Hordeum vulgare) and often limit the crop yield. During infection, the transcriptome undergoes extensive reprogramming involving several regulatory pathways. To address this complexity, we performed a comprehensive meta-analysis and co-expression network analysis using rigorously curated RNA-seq datasets from three different fungal diseases. Pre-processing of the data, including batch effect correction, ensured high-quality integration of the datasets. Module-trait relationship (MTR) analysis identified functional modules associated with fungal disease response. Hub genes within these modules were prioritized by multi-model centrality analyses using Cytoscape, which considered the metrics Degree, Closeness, Betweenness and Maximum Clique Centrality together with the MCODE algorithm to detect densely connected subclusters. These hub genes were further validated by cross-validation and receiver operating characteristic (ROC) curve analysis and achieved AUC values greater than 0.7, confirming their robustness. A total of 6688 consistently expressed genes were identified, including 879 upregulated and 701 downregulated genes. Co-expression networks revealed 19 different gene modules, six of which were significantly associated with the response of barley to fungal infection. The blue module in particular was associated with immune responses such as activation of the MAPK cascade and pathogen recognition, while the green module correlated with defence mechanisms and secondary metabolism. The hub genes within these modules showed high predictive power for fungal resistance, as shown by the AUC values of the ROC curve of over 0.7, emphasizing their potential as biomarkers. This study uniquely integrates multiple RNA-seq datasets to identify novel regulatory networks and hub genes, including 345 transcription factors (TFs) from different families, with MYB and bHLH being particularly abundant. The res

关键词： Fungal stress Barley Co-expression network analysis transcriptome reprogramming Regulatory pathways

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DNA Methylation: Toward Crop Disease Resistance Improvement

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TRENDS IN PLANT SCIENCE 2019年第12期24卷 1137-1150页

作者： Tirnaz, Soodeh Batley, Jacqueline Univ Western Australia Sch Biol Sci Perth WA 6009 Australia

Crop diseases, in conjunction with climate change, are a major threat to global crop production. DNA methylation is an epigenetic mark and is involved in plants' biological processes, including development, stress adaptation, and genome evolution. By providing a new source of variation, DNA methylation introduces novel direction to both scientists and breeders with its potential in disease resistance enhancement. Here, we discuss the impact of pathogen-induced DNA methylation modifications on a host's transcriptome reprogramming and genome stability, as part of the plant's defense mechanisms. We also highlight the knowledge gaps that need to be investigated for understanding the entire role of DNA methylation in plant pathogen interactions. This will ultimately assist breeders toward improving resistance and decreasing yield losses.

关键词： plant disease epigenetics transcriptome reprogramming genome stability plant breeding

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BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models

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CANCER CELL 2019年第5期35卷 752-+页

作者： Zhao, Xiaohong Ren, Yuan Lawlor, Matthew Shah, Bijal D. Park, Paul M. C. Lwin, Tint Wang, Xuefeng Liu, Kenian Wang, Michelle Gao, Jing Li, Tao Xu, Mousheng Silva, Ariosto S. Lee, Kaplan Zhang, Tinghu Koomen, John M. Jiang, Huijuan Sudalagunta, Praneeth R. Meads, Mark B. Cheng, Fengdong Bi, Chengfeng Fu, Kai Fan, Huitao Dalton, William S. Moscinski, Lynn C. Shain, Kenneth H. Sotomayor, Eduardo M. Wang, Gang Greg Gray, Nathanael S. Cleveland, John L. Qi, Jun Tao, Jianguo H Lee Moffitt Canc Ctr & Res Inst Chem Biol & Mol Med Program Tampa FL 33612 USA Dana Farber Canc Inst Dept Canc Biol Boston MA 02215 USA H Lee Moffitt Canc Ctr & Res Inst Dept Malignant Hematol Tampa FL 33612 USA H Lee Moffitt Canc Ctr & Res Inst Dept Biostat & Bioinformat Tampa FL 33612 USA H Lee Moffitt Canc Ctr & Res Inst Dept Lab Med & Hematopathol Tampa FL 33612 USA Chinese Acad Med Sci Natl Canc Ctr Dept VIP Med Serv Canc Hosp Beijing 100021 Peoples R China Peking Union Med Coll Beijing 100021 Peoples R China H Lee Moffitt Canc Ctr & Res Inst Dept Canc Physiol Tampa FL 33612 USA BayCare Labs LLC Tampa FL 33634 USA H Lee Moffitt Canc Ctr & Res Inst Dept Mol Oncol Tampa FL 33612 USA Tianjin Med Univ Dept Hematol Gen Hosp Tianjin 300052 Peoples R China George Washington Univ Dept Hematol & Oncol Washington DC 20052 USA Univ Nebraska Med Ctr Dept Pathol & Microbiol Omaha NE 68106 USA Univ North Carolina Chapel Hill Dept Biochem & Biophys Lineberger Comprehens Canc Ctr Sch Med Chapel Hill NC 27599 USA Harvard Med Sch Dept Biol Chem & Mol Pharmacol Boston MA 02215 USA H Lee Moffitt Canc Ctr & Res Inst Dept Tumor Biol Tampa FL 33612 USA Harvard Med Sch Dept Med Boston MA 02215 USA

Drug-tolerant "persister" tumor cells underlie emergence of drug-resistant clones and contribute to relapse and disease progression. Here we report that resistance to the BCL-2 targeting drug ABT-199 in models of mantle cell lymphoma and double-hit lymphoma evolves from outgrowth of persister clones displaying loss of 18q21 amplicons that harbor BCL2. Further, persister status is generated via adaptive super-enhancer remodeling that reprograms transcription and offers opportunities for overcoming ABT-199 resistance. Notably, pharmacoproteomic and pharmacogenomic screens revealed that persisters are vulnerable to inhibition of the transcriptional machinery and especially to inhibition of cyclin-dependent kinase 7 (CDK7), which is essential for the transcriptional reprogramming that drives and sustains ABT-199 resistance. Thus, transcription-targeting agents offer new approaches to disable drug resistance in B-cell lymphomas.

关键词： drug resistance drug persister ABT-199 BCL2 super-enhancer remodeling transcriptome reprogramming CDK7 THZ1 mantle cell lymphoma double-hit lymphoma

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Emerging Themes in Regulation of Global mRNA Turnover in cis

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TRENDS IN BIOCHEMICAL SCIENCES 2017年第1期42卷 16-27页

作者： Chen, Chyi-Ying A. Shyu, Ann-Bin Univ Texas Hlth Sci Ctr Houston McGovern Med Sch Dept Biochem & Mol Biol Houston TX 77030 USA

mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N-6-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis. Here, we discuss the discovery and molecular dissection of these mechanisms in relation to how they impact the intrinsic decay rate of mRNA in eukaryotes, leading to transcriptome reprogramming.

关键词： alternative polyadenylation codon optimality m6A mRNA turnover transcriptome reprogramming

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