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Lopes NDS, Santos AS, de Novais DPS, Pirovani CP, Micheli F. Pathogenesis-related protein 10 in resistance to biotic stress: progress in elucidating functions, regulation and modes of action. FRONTIERS IN PLANT SCIENCE 2023; 14:1193873. [PMID: 37469770 PMCID: PMC10352611 DOI: 10.3389/fpls.2023.1193873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 07/21/2023]
Abstract
Introduction The Family of pathogenesis-related proteins 10 (PR-10) is widely distributed in the plant kingdom. PR-10 are multifunctional proteins, constitutively expressed in all plant tissues, playing a role in growth and development or being induced in stress situations. Several studies have investigated the preponderant role of PR-10 in plant defense against biotic stresses; however, little is known about the mechanisms of action of these proteins. This is the first systematic review conducted to gather information on the subject and to reveal the possible mechanisms of action that PR-10 perform. Methods Therefore, three databases were used for the article search: PubMed, Web of Science, and Scopus. To avoid bias, a protocol with inclusion and exclusion criteria was prepared. In total, 216 articles related to the proposed objective of this study were selected. Results The participation of PR-10 was revealed in the plant's defense against several stressor agents such as viruses, bacteria, fungi, oomycetes, nematodes and insects, and studies involving fungi and bacteria were predominant in the selected articles. Studies with combined techniques showed a compilation of relevant information about PR-10 in biotic stress that collaborate with the understanding of the mechanisms of action of these molecules. The up-regulation of PR-10 was predominant under different conditions of biotic stress, in addition to being more expressive in resistant varieties both at the transcriptional and translational level. Discussion Biological models that have been proposed reveal an intrinsic network of molecular interactions involving the modes of action of PR-10. These include hormonal pathways, transcription factors, physical interactions with effector proteins or pattern recognition receptors and other molecules involved with the plant's defense system. Conclusion The molecular networks involving PR-10 reveal how the plant's defense response is mediated, either to trigger susceptibility or, based on data systematized in this review, more frequently, to have plant resistance to the disease.
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Affiliation(s)
- Natasha dos Santos Lopes
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Ariana Silva Santos
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Diogo Pereira Silva de Novais
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Meditérranéennes et Tropicales (UMR AGAP Institut), Montpellier, France
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Song J, Sajad S, Xia D, Jiang S. Identification of F-box gene family in Brassica oleracea and expression analysis in response to low-temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107717. [PMID: 37150011 DOI: 10.1016/j.plaphy.2023.107717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/09/2023]
Abstract
Unfavorable climatic conditions, such as low temperatures, often hinder the growth and production of crops worldwide. The F-box protein-encoding gene family performs an essential role in plant stress resistance. However, a comprehensive analysis of the F-box gene family in cabbage (Brassica oleracea var capitata L.) has not been reported yet. In this study, genome-wide characterization of F-box proteins in cabbage yielded 303 BoFBX genes and 224 BoFBX genes unevenly distributed on 9 chromosomes of cabbage. Phylogenetic analysis of 303 BoFBX genes was classified into nine distinct subfamily groups (GI-GIX). Analysis of the gene structure of BoFBX genes indicated that most genes within the same clade are highly conserved. In addition, tissue-specific expression analysis revealed that six F-box genes in cabbage showed the highest expression in rosette leaves, followed by roots and stems and the lowest expression was observed in the BoFBX156 gene. In contrast, the expression of the other five genes, BoFBX100, BoFBX117, BoFBX136, BoFBX137 and BoFBX213 was observed to be upregulated in response to low-temperature stress. Moreover, we found that the expression level of the BoFBX gene in the cold-tolerant cultivar "ZG" was higher than that in cold-sensitive "YC" with the extension of stress duration, while expression levels of each gene in "ZG" were higher than "YC" at 24 h. Knowledge of the various functions provided by BoFBXs genes and their expression patterns provides a firm theoretical foundation for explaining the functions of BoFBXs, thereby contributing to the molecular breeding process of cabbage.
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Affiliation(s)
- Jianghua Song
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China.
| | - Shoukat Sajad
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
| | - Dongjian Xia
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
| | - Shuhan Jiang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
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Chen Y, Yang W, Gao R, Chen Y, Zhou Y, Xie J, Zhang F. Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice ( Oryza rufipogon Griff.) Responding to Salt Stress. Int J Mol Sci 2023; 24:ijms24044069. [PMID: 36835475 PMCID: PMC9960954 DOI: 10.3390/ijms24044069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.
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Affiliation(s)
- Yong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Rifang Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yaling Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.X.); (F.Z.)
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4
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Li S, Xing K, Qanmber G, Chen G, Liu L, Guo M, Hou Y, Lu L, Qu L, Liu Z, Yang Z. GhBES1 mediates brassinosteroid regulation of leaf size by activating expression of GhEXO2 in cotton (Gossypium hirsutum). PLANT MOLECULAR BIOLOGY 2023; 111:89-106. [PMID: 36271986 DOI: 10.1007/s11103-022-01313-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
We proposed a working model of BR to promote leaf size through cell expansion. In the BR signaling pathway, GhBES1 affects cotton leaf size by binding to and activating the expression of the E-box element in the GhEXO2 promoter region. Brassinosteroid (BR) is an essential phytohormone that controls plant growth. However, the mechanisms of BR regulation of leaf size remain to be determined. Here, we found that the BR deficient cotton mutant pagoda1 (pag1) had a smaller leaf size than wild-type CRI24. The expression of EXORDIUM (GhEXO2) gene, was significantly downregulated in pag1. Silencing of BRI1-EMS-SUPPRESSOR 1 (GhBES1), inhibited leaf cell expansion and reduced leaf size. Overexpression of GhBES1.4 promoted leaf cell expansion and enlarged leaf size. Expression analysis showed GhEXO2 expression positively correlated with GhBES1 expression. In plants, altered expression of GhEXO2 promoted leaf cell expansion affecting leaf size. Furthermore, GhBES1.4 specifically binds to the E-box elements in the GhEXO2 promoter, inducing its expression. RNA-seq data revealed many down-regulated genes related to cell expansion in GhEXO2 silenced plants. In summary, we discovered a novel mechanism of BR regulation of leaf size through GhBES1 directly activating the expression of GhEXO2.
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Affiliation(s)
- Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Kun Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Biology (Hebei Base), Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoquan Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Yan Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lingbo Qu
- College of Chemistry, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China.
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, 450001, Zhengzhou, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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5
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Pruthi R, Chapagain S, Coronejo S, Singh L, Subudhi PK. Quantitative trait loci, candidate genes, and breeding lines to improve salt tolerance at the flowering and seedling stages in rice. Food Energy Secur 2022. [DOI: 10.1002/fes3.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences Louisiana State University Agricultural Center Baton Rouge Louisiana USA
| | - Sandeep Chapagain
- School of Plant, Environmental, and Soil Sciences Louisiana State University Agricultural Center Baton Rouge Louisiana USA
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences Louisiana State University Agricultural Center Baton Rouge Louisiana USA
| | - Lovepreet Singh
- School of Plant, Environmental, and Soil Sciences Louisiana State University Agricultural Center Baton Rouge Louisiana USA
| | - Prasant Kumar Subudhi
- School of Plant, Environmental, and Soil Sciences Louisiana State University Agricultural Center Baton Rouge Louisiana USA
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6
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Yang Z, Zhang H, Tan X, Wei Z, Wen C, Sun Z, Sun B, Chen J. Insights Into the Effect of Rice Stripe Virus P2 on Rice Defense by Comparative Proteomic Analysis. Front Microbiol 2022; 13:897589. [PMID: 35747367 PMCID: PMC9209781 DOI: 10.3389/fmicb.2022.897589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022] Open
Abstract
Rice stripe virus (RSV) has a serious effect on rice production. Our previous research had shown that RSV P2 plays important roles in RSV infection, so in order to further understand the effect of P2 on rice, we used Tandem Mass Tag (TMT) quantitative proteomics experimental system to analyze the changes of protein in transgenic rice expressing P2 for the first time. The results of proteomics showed that a total of 4,767 proteins were identified, including 198 up-regulated proteins and 120 down-regulated proteins. Functional classification results showed that differentially expressed proteins (DEPs) were mainly localized in chloroplasts and mainly involved in the metabolic pathways. Functional enrichment results showed that DEPs are mainly involved in RNA processing and splicing. We also verified the expression of several DEPs at the mRNA level and the interaction of a transcription factor (B7EPB8) with RSV P2. This research is the first time to use proteomics technology to explore the mechanism of RSV infection in rice with the RSV P2 as breakthrough point. Our findings provide valuable information for the study of RSV P2 and RSV infection mechanism.
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Affiliation(s)
- Zihang Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiaoxiang Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Bingjian Sun,
| | - Jianping Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- Jianping Chen,
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7
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Song Z, Zhang C, Jin P, Tetteh C, Dong X, Luo S, Zhang S, Li X, Liu Y, Zhang H. The cell-type specific role of Arabidopsis bZIP59 transcription factor in plant immunity. PLANT, CELL & ENVIRONMENT 2022; 45:1843-1861. [PMID: 35199374 DOI: 10.1111/pce.14299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/21/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Stomatal movement participates in plant immunity by directly affecting the invasion of bacteria, but the genes that regulate stomatal immunity have not been well identified. Here, we characterised the function of the bZIP59 transcription factor from Arabidopsis thaliana, which is constitutively expressed in guard cells. The bzip59 mutant is partially impaired in stomatal closure induced by Pseudomonas syringae pv. tomato strain (Pst) DC3000 and is more susceptible to Pst DC3000 infection. By contrast, the line overexpressing bZIP59 enhances resistance to Pst DC3000 infection. Furthermore, the bzip59 mutant is also partially impaired in stomatal closure induced by flagellin flg22 derived from Pst DC3000, and epistasis analysis revealed that bZIP59 acts upstream of reactive oxygen species (ROS) and nitric oxide (NO) and downstream of salicylic acid signalling in flg22-induced stomatal closure. In addition, the bzip59 mutant showed resistance and sensitivity to Sclerotinia sclerotiorum and Tobacco mosaic virus that do not invade through stomata, respectively. Collectively, our results demonstrate that bZIP59 plays an important role in the stomatal immunity and reveal that the same transcription factor can positively and negatively regulate disease resistance against different pathogens.
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Affiliation(s)
- Zhiqiang Song
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Cheng Zhang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Pinyuan Jin
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Charles Tetteh
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Xueshuo Dong
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Sheng Luo
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Siyi Zhang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Xinyuan Li
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yingjun Liu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Huajian Zhang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Department of Plant Pathology, School of Plant Protection, College of Plant Protection, Anhui Agricultural University, Hefei, China
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8
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Khan ZH, Dang S, Memaya MB, Bhadouriya SL, Agarwal S, Mehrotra S, Gupta D, Mehrotra R. Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner. G3 GENES|GENOMES|GENETICS 2022; 12:6550508. [PMID: 35302624 PMCID: PMC9073683 DOI: 10.1093/g3journal/jkac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/24/2022] [Indexed: 12/03/2022]
Abstract
Cis-regulatory elements are regions of noncoding DNA that regulate the transcription of neighboring genes. The study of cis-element architecture that functions in transcription regulation are essential. AAAG and ACGT are a class of cis-regulatory elements, known to interact with Dof and bZIP transcription factors respectively, and are known to regulate the expression of auxin response, gibberellin response, floral development, light response, seed storage proteins genes, biotic and abiotic stress genes in plants. Analysis of the frequency of occurrence of AAAG and ACGT motifs from varying spacer lengths (0–30 base pair) between these 2 motifs in both possible orientations—AAAG (N) ACGT and ACGT (N) AAAG, in the promoters and genome of Arabidopsis thaliana which indicated preferred orientation of AAAG (N) ACGT over ACGT (N) AAAG across the genome and in promoters. Further, microarray analysis revealed the involvement of these motifs in the genes downregulated under jasmonic acid response in an orientation-independent manner. These results were further confirmed by the transient expression studies with promoter-reporter cassettes carrying AAAG and ACGT motifs in both orientations. Furthermore, cluster analysis on genes with AAAG (N) ACGT and ACGT (N) AAAG motifs orientations revealed clusters of genes to be involved in ABA signaling, transcriptional regulation, DNA binding, and metal ion binding. These findings can be utilized in designing synthetic promoters for the development of stress-tolerant transgenic plants and also provides an insight into the roles of these motifs in transcriptional regulation.
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Affiliation(s)
- Zaiba H Khan
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani , Zuarinagar, Goa 403726, India
| | - Siddhant Dang
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani , Pilani, Jhunjhunu, Rajasthan 333031, India
| | - Mounil B Memaya
- Department of Computer Science and Information Systems, Birla Institute of Technology and Science-Pilani , Zuarinagar, Sancoale, Goa 403726, India
| | - Sneha L Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani , Zuarinagar, Goa 403726, India
| | - Swati Agarwal
- Department of Computer Science and Information Systems, Birla Institute of Technology and Science-Pilani , Zuarinagar, Sancoale, Goa 403726, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani , Zuarinagar, Goa 403726, India
| | - Divya Gupta
- Faculty of Bioscience, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University , Barabanki, Uttar Pradesh 225003, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani , Zuarinagar, Goa 403726, India
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9
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Su C, Cui J, Liu Y, Luan Y. Genome-wide identification and characterization of the tomato F-box associated (FBA) protein family and expression analysis of their responsiveness to Phytophthora infestans. Gene 2022; 821:146335. [PMID: 35182672 DOI: 10.1016/j.gene.2022.146335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/22/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022]
Abstract
Late blight caused by Phytophthora infestans brings huge economic losses to the production of tomato (Solanum lycopersicum) every year. F-box proteins participate in plants response to phytohormones and biotic stress, whereas as the largest subfamily of F-box superfamily, the detailed information about F-box associated (SlFBA) family in tomato has been rarely reported. In this study, a total of 46 tomato FBA genes were identified based on the latest genome annotation. Phylogenetic analysis revealed that the FBA proteins from tomato and 6 different plant species were clustered into 7 distinct clades. The SlFBA genes were unevenly distributed on 11 chromosomes of tomato, mainly concentrated in the regions with high gene density. Tandem duplications and purification selection contribute to the expansion and evolution of the SlFBA gene family. Transcriptome analysis revealed that the SlFBA genes were differentially expressed in different tissues with obvious tissue-specific expression patterns. There were 18 SlFBA genes differentially expressed in P. infestans-resistant and -susceptible tomato, among which, 3 SlFBA genes might play positive roles in tomato resistance to P. infestans. Taken together, this study systematically analyzed the SlFBA genes family for the first time and identified the candidate SlFBA genes that affect tomato resistance to P. infestans, which provided important genetic and breeding resources for improving tomato resistance to pathogens.
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Affiliation(s)
- Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China
| | - Jun Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yarong Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China.
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10
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Zhou H, Zhang F, Zhai F, Su Y, Zhou Y, Ge Z, Tilak P, Eirich J, Finkemeier I, Fu L, Li Z, Yang J, Shen W, Yuan X, Xie Y. Rice GLUTATHIONE PEROXIDASE1-mediated oxidation of bZIP68 positively regulates ABA-independent osmotic stress signaling. MOLECULAR PLANT 2022; 15:651-670. [PMID: 34793984 DOI: 10.1016/j.molp.2021.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/11/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Osmotic stress caused by drought and high salinity is a significant environmental threat that limits plant growth and agricultural yield. Redox regulation plays an important role in plant stress responses, but the mechanisms by which plants perceive and transduce redox signals are still underexplored. Here, we report a critical function for the thiol peroxidase GPX1 in osmotic stress response in rice, where it serves as a redox sensor and transducer. GPX1 is quickly oxidized upon exposure to osmotic stress and forms an intramolecular disulfide bond, which is required for the activation of bZIP68, a VRE-like basic leucine zipper (bZIP) transcription factor involved in the ABA-independent osmotic stress response pathway. The disulfide exchange between GPX1 and bZIP68 induces homo-tetramerization of bZIP68 and thus positively regulates osmotic stress response by regulating osmotic-responsive gene expression. Furthermore, we discovered that the nuclear translocation of GPX1 is regulated by its acetylation under osmotic stress. Taken together, our findings not only uncover the redox regulation of the GPX1-bZIP68 module during osmotic stress but also highlight the coordination of protein acetylation and redox signaling in plant osmotic stress responses.
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Affiliation(s)
- Heng Zhou
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Feng Zhang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Fengchao Zhai
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ye Su
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ying Zhou
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhenglin Ge
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Priyadarshini Tilak
- Institute for Biology and Biotechnology of Plants, University of Muenster, 48149 Muenster, Germany
| | - Jürgen Eirich
- Institute for Biology and Biotechnology of Plants, University of Muenster, 48149 Muenster, Germany
| | - Iris Finkemeier
- Institute for Biology and Biotechnology of Plants, University of Muenster, 48149 Muenster, Germany
| | - Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center 17 for Protein Sciences ⋅ Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zongmin Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center 17 for Protein Sciences ⋅ Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center 17 for Protein Sciences ⋅ Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wenbiao Shen
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yanjie Xie
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
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11
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Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 ( TabZIP96) under Freezing Stress in Wheat ( Triticum aestivum). Int J Mol Sci 2022; 23:ijms23042351. [PMID: 35216467 PMCID: PMC8874521 DOI: 10.3390/ijms23042351] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 01/07/2023] Open
Abstract
The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.
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12
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Han H, Xu F, Li Y, Yu L, Fu M, Liao Y, Yang X, Zhang W, Ye J. Genome-wide characterization of bZIP gene family identifies potential members involved in flavonoids biosynthesis in Ginkgo biloba L. Sci Rep 2021; 11:23420. [PMID: 34862430 PMCID: PMC8642526 DOI: 10.1038/s41598-021-02839-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/18/2021] [Indexed: 11/28/2022] Open
Abstract
Ginkgo biloba L. is an ancient relict plant with rich pharmacological activity and nutritional value, and its main physiologically active components are flavonoids and terpene lactones. The bZIP gene family is one of the largest gene families in plants and regulates many processes including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. In this study, genome-wide distribution of the bZIP transcription factors was screened from G. biloba database in silico analysis. A total of 40 bZIP genes were identified in G. biloba and were divided into 10 subclasses. GbbZIP members in the same group share a similar gene structure, number of introns and exons, and motif distribution. Analysis of tissue expression pattern based on transcriptome indicated that GbbZIP08 and GbbZIP15 were most highly expressed in mature leaf. And the expression level of GbbZIP13 was high in all eight tissues. Correlation analysis and phylogenetic tree analysis suggested that GbbZIP08 and GbbZIP15 might be involved in the flavonoid biosynthesis. The transcriptional levels of 20 GbbZIP genes after SA, MeJA, and low temperature treatment were analyzed by qRT-PCR. The expression level of GbbZIP08 was significantly upregulated under 4°C. Protein–protein interaction network analysis indicated that GbbZIP09 might participate in seed germination by interacting with GbbZIP32. Based on transcriptome and degradome data, we found that 32 out of 117 miRNAs were annotated to 17 miRNA families. The results of this study may provide a theoretical foundation for the functional validation of GbbZIP genes in the future.
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Affiliation(s)
- Huan Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yuting Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Li Yu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Mingyue Fu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China. .,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, Hubei, China.
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
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13
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Chen S, Han X, Yang L, Li Q, Shi Y, Li H, Chen L, Sun B, Shi Y, Yang X. Identification and functional analyses of host factors interacting with the 17-kDa protein of Barley yellow dwarf virus-GAV. Sci Rep 2021; 11:8453. [PMID: 33875710 PMCID: PMC8055683 DOI: 10.1038/s41598-021-87836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Barley yellow dwarf viruses (BYDVs) cause significant economic losses on barley, wheat, and oats worldwide. 17-kDa protein (17K) of BYDVs plays a key role in viral infection in plants, whereas the underlying regulation mechanism of 17K in virus infection remains elusive. In this study, we determined that 17K of BYDV-GAV, the most common species found in China in recent years, was involved in viral pathogenicity. To identify the host factors interacting with 17K, the full length coding sequence of 17K was cloned into pGBKT7 to generate the bait plasmid pGBKT7-17K. 114 positive clones were identified as possible host factors to interact with 17K through screening a tobacco cDNA library. Gene ontology enrichment analysis showed that they were classified into 35 functional groups, involving three main categories including biological processes (BP), cellular components (CC), and molecular functions (MF). Kyoto Encyclopedia of Genes and Genome (KEGG) analysis indicated the acquired genes were assigned to 49 KEGG pathways. The majority of these genes were involved in glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, and glycolysis/gluconeogenesis. The interactions between 17K and the 27 proteins with well-documented annotations were verified by conducting yeast two-hybrid assays and 12 of the 27 proteins were verified to interact with 17K. To explore the putative function of the 12 proteins in BYDV-GAV infection, the subcellular localization and expression alterations in the presence of BYDV-GAV were monitored. The results showed that, under the condition of BYDV-GAV infection, RuBisCo, POR, and PPD5 were significantly up-regulated, whereas AEP and CAT1 were significantly down-regulated. Our findings provide insights into the 17K-mediated BYDV-GAV infection process.
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Affiliation(s)
- Siyu Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyu Han
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lingling Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qinglun Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yajuan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Linlin Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xue Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
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14
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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15
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Wang Y, Hou Y, Qiu J, Wang H, Wang S, Tang L, Tong X, Zhang J. Abscisic acid promotes jasmonic acid biosynthesis via a 'SAPK10-bZIP72-AOC' pathway to synergistically inhibit seed germination in rice (Oryza sativa). THE NEW PHYTOLOGIST 2020; 228:1336-1353. [PMID: 32583457 PMCID: PMC7689938 DOI: 10.1111/nph.16774] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/15/2020] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) and jasmonic acid (JA) both inhibit seed germination, but their interactions during this process remain elusive. Here, we report the identification of a 'SAPK10-bZIP72-AOC' pathway, through which ABA promotes JA biosynthesis to synergistically inhibit rice seed germination. Using biochemical interaction and phosphorylation assays, we show that SAPK10 exhibits autophosphorylation activity on the 177th serine, which enables it to phosphorylate bZIP72 majorly on 71st serine. The SAPK10-dependent phosphorylation enhances bZIP72 protein stability as well as the DNA-binding ability to the G-box cis-element of AOC promoter, thereby elevating the AOC transcription and the endogenous concentration of JA. Blocking of JA biosynthesis significantly alleviated the ABA sensitivity on seed germination, suggesting that ABA-imposed inhibition partially relied on the elevated concentration of JA. Our findings shed a novel insight into the molecular networks of ABA-JA synergistic interaction during rice seed germination.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Yuxuan Hou
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Jiehua Qiu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Huimei Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Shuang Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
- College of Life ScienceYangtze UniversityJingzhou434025China
| | - Liqun Tang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Xiaohong Tong
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
| | - Jian Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhou311400China
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16
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F-Box Gene D5RF Is Regulated by Agrobacterium Virulence Protein VirD5 and Essential for Agrobacterium-Mediated Plant Transformation. Int J Mol Sci 2020; 21:ijms21186731. [PMID: 32937889 PMCID: PMC7555846 DOI: 10.3390/ijms21186731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/16/2022] Open
Abstract
We previously reported that the Agrobacterium virulence protein VirD5 possesses transcriptional activation activity, binds to a specific DNA element D5RE, and is required for Agrobacterium-mediated stable transformation, but not for transient transformation. However, direct evidence for a role of VirD5 in plant transcriptional regulation has been lacking. In this study, we found that the Arabidopsis gene D5RF (coding for VirD5 response F-box protein, At3G49480) is regulated by VirD5. D5RF has two alternative transcripts of 930 bp and 1594 bp that encode F-box proteins of 309 and 449 amino acids, designated as D5RF.1 and D5RF.2, respectively. D5RF.2 has a N-terminal extension of 140 amino acids compared to D5RF.1, and both of them are located in the plant cell nucleus. The promoter of the D5RF.1 contains two D5RE elements and can be activated by VirD5. The expression of D5RF is downregulated when the host plant is infected with virD5 deleted Agrobacterium. Similar to VirD5, D5RF also affects the stable but not transient transformation efficiency of Agrobacterium. Some pathogen-responsive genes are downregulated in the d5rf mutant. In conclusion, this study further confirmed Agrobacterium VirD5 as the plant transcription activator and identified Arabidopsis thalianaD5RF.1 as the first target gene of VirD5 in regulation.
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17
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Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U. RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. Int J Mol Sci 2019; 21:E167. [PMID: 31881735 PMCID: PMC6981605 DOI: 10.3390/ijms21010167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
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Affiliation(s)
- Isiaka Ibrahim Muhammad
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Sze Ling Kong
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Siti Nor Akmar Abdullah
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
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