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Integrated ATAC-Seq and RNA-Seq Data Analysis to Reveal OsbZIP14 Function in Rice in Response to Heat Stress. Int J Mol Sci 2023; 24:ijms24065619. [PMID: 36982696 PMCID: PMC10057503 DOI: 10.3390/ijms24065619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Transcription factors (TFs) play critical roles in mediating the plant response to various abiotic stresses, particularly heat stress. Plants respond to elevated temperatures by modulating the expression of genes involved in diverse metabolic pathways, a regulatory process primarily governed by multiple TFs in a networked configuration. Many TFs, such as WRKY, MYB, NAC, bZIP, zinc finger protein, AP2/ERF, DREB, ERF, bHLH, and brassinosteroids, are associated with heat shock factor (Hsf) families, and are involved in heat stress tolerance. These TFs hold the potential to control multiple genes, which makes them ideal targets for enhancing the heat stress tolerance of crop plants. Despite their immense importance, only a small number of heat-stress-responsive TFs have been identified in rice. The molecular mechanisms underpinning the role of TFs in rice adaptation to heat stress still need to be researched. This study identified three TF genes, including OsbZIP14, OsMYB2, and OsHSF7, by integrating transcriptomic and epigenetic sequencing data analysis of rice in response to heat stress. Through comprehensive bioinformatics analysis, we demonstrated that OsbZIP14, one of the key heat-responsive TF genes, contained a basic-leucine zipper domain and primarily functioned as a nuclear TF with transcriptional activation capability. By knocking out the OsbZIP14 gene in the rice cultivar Zhonghua 11, we observed that the knockout mutant OsbZIP14 exhibited dwarfism with reduced tiller during the grain-filling stage. Under high-temperature treatment, it was also demonstrated that in the OsbZIP14 mutant, the expression of the OsbZIP58 gene, a key regulator of rice seed storage protein (SSP) accumulation, was upregulated. Furthermore, bimolecular fluorescence complementation (BiFC) experiments uncovered a direct interaction between OsbZIP14 and OsbZIP58. Our results suggested that OsbZIP14 acts as a key TF gene through the concerted action of OsbZIP58 and OsbZIP14 during rice filling under heat stress. These findings provide good candidate genes for genetic improvement of rice but also offer valuable scientific insights into the mechanism of heat tolerance stress in rice.
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Zhu F, Li M, Yan M, Qiao F, Jiang X. Integrated Transcriptome Analysis and Single-Base Resolution Methylomes of Watermelon ( Citrullus lanatus) Reveal Epigenome Modifications in Response to Osmotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:769712. [PMID: 34912359 PMCID: PMC8667863 DOI: 10.3389/fpls.2021.769712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
DNA methylation plays an important role against adverse environment by reshaping transcriptional profile in plants. To better understand the molecular mechanisms of watermelon response to osmotic stress, the suspension cultured watermelon cells were treated with 100mM mannitol, and then a methylated cytosines map was generated by whole genome bisulfite sequencing (WGBS). Combined with transcriptome sequencing, the effects of osmotic stress on differentially methylated expressed genes (DMEGs) were assessed. It was found that genes related to plant hormone synthesis, signal transduction, osmoregulatory substance-related and reactive oxygen species scavenging-related enzyme could rapidly respond to osmotic stress. The overall methylation level of watermelon decreased after osmotic stress treatment, and demethylation occurred in CG, CHG, and CHH contexts. Moreover, differentially methylated expressed genes (DMEGs) were significantly enriched in RNA transport, starch and sucrose metabolism, plant hormone signal transduction and biosynthesis of secondary metabolites, especially in biosynthesis of osmolytes synthase genes. Interestingly, demethylation of a key enzyme gene Cla014489 in biosynthesis of inositol upregulated its expression and promoted accumulation of inositol, which could alleviate the inhibition of cell growth caused by osmotic stress. Meanwhile, a recombinant plasmid pET28a-Cla014489 was constructed and transferred into Escherichia coli BL21 for prokaryotic expression and the expression of ClMIPS protein could improve the tolerance of E. coli to osmotic stress. The effect of methylation level on the expression properties of inositol and its related genes was further confirmed by application of DNA methylation inhibitor 5-azacytidine. These results provide a preliminary insight into the altered methylation levels of watermelon cells in response to osmotic stress and suggest a new mechanism that how watermelon cells adapt to osmotic stress.
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Affiliation(s)
- Fangming Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Mingyan Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Manwen Yan
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Xuefei Jiang
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University (HNU), Haikou, China
- Key Laboratory of Tropical Agritourism in Greenhouse of Haikou, College of Horticulture, Hainan University (HNU), Haikou, China
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Branco I, Choupina A. Bioinformatics: new tools and applications in life science and personalized medicine. Appl Microbiol Biotechnol 2021; 105:937-951. [PMID: 33404829 DOI: 10.1007/s00253-020-11056-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022]
Abstract
While we have a basic understanding of the functioning of the gene when coding sequences of specific proteins, we feel the lack of information on the role that DNA has on specific diseases or functions of thousands of proteins that are produced. Bioinformatics combines the methods used in the collection, storage, identification, analysis, and correlation of this huge and complex information. All this work produces an "ocean" of information that can only be "sailed" with the help of computerized methods. The goal is to provide scientists with the right means to explain normal biological processes, dysfunctions of these processes which give rise to disease and approaches that allow the discovery of new medical cures. Recently, sequencing platforms, a large scale of genomes and transcriptomes, have created new challenges not only to the genomics but especially for bioinformatics. The intent of this article is to compile a list of tools and information resources used by scientists to treat information from the massive sequencing of recent platforms to new generations and the applications of this information in different areas of life sciences including medicine. KEY POINTS: • Biological data mining • Omic approaches • From genotype to phenotype.
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Affiliation(s)
- Iuliia Branco
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Altino Choupina
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance. BMC Genomics 2015; 16:596. [PMID: 26268547 PMCID: PMC4534118 DOI: 10.1186/s12864-015-1743-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 06/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome sequencing provides the most comprehensive collection of an organism's genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biology. However, to achieve this impact in the area of crop improvement, significant efforts are still required on functional genomics, including the areas of gene annotation, cloning, expression profiling, and functional validation. RESULTS Here we report our efforts in generating the first transcription factor (TF) open reading frame (ORF)eome resource associated with drought resistance in soybean (Glycine max), a major oil/protein crop grown worldwide. This study provides a highly annotated soybean TF-ORFeome associated with drought resistance. It contains information from experimentally verified protein-coding sequences (CDS), expression profiling under several abiotic stresses (drought, salinity, dehydration and ABA), and computationally predicted protein subcellular localization and cis-regulatory elements (CREs) analysis. All the information is available to plant researchers through a freely accessible and user-friendly database, Soybean Knowledge Base (SoyKB). CONCLUSIONS The soybean TF-ORFeome provides a valuable public resource for functional genomics studies, especially in the area of plant abiotic stresses. It will accelerate findings in the areas of abiotic stresses and lead to the generation of crops with enhanced resistance to multiple stresses.
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Affiliation(s)
- Chenglin Chai
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqin Wang
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Silvas Prince
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Lydia Michel
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Science, Informatics Institute, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Muthuswamy A, Eapen SJ. Research on Plant Pathogenic Fungi in the Genomics Era: From Sequence Analysis to Systems Biology. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Xia Z, Zhai H, Lü S, Wu H, Zhang Y. Recent achievement in gene cloning and functional genomics in soybean. ScientificWorldJournal 2013; 2013:281367. [PMID: 24311973 PMCID: PMC3842071 DOI: 10.1155/2013/281367] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/18/2013] [Indexed: 11/18/2022] Open
Abstract
Soybean is a model plant for photoperiodism as well as for symbiotic nitrogen fixation. However, a rather low efficiency in soybean transformation hampers functional analysis of genes isolated from soybean. In comparison, rapid development and progress in flowering time and photoperiodic response have been achieved in Arabidopsis and rice. As the soybean genomic information has been released since 2008, gene cloning and functional genomic studies have been revived as indicated by successfully characterizing genes involved in maturity and nematode resistance. Here, we review some major achievements in the cloning of some important genes and some specific features at genetic or genomic levels revealed by the analysis of functional genomics of soybean.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Shixiang Lü
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yupeng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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