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Kim JS, Chae S, Jun KM, Lee GS, Jeon JS, Kim KD, Kim YK. Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice. PLANTA 2021; 253:40. [PMID: 33475863 PMCID: PMC7819943 DOI: 10.1007/s00425-021-03572-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/08/2021] [Indexed: 05/20/2023]
Abstract
The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5' upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.
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Affiliation(s)
- Joung Sug Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - SongHwa Chae
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene BioTech Inc., 16-4 Dongbaekjungang-ro 16beon-gil, Giheung-gu, Yongin, Gyeonggi-do, 17015, Republic of Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54875, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Republic of Korea
| | - Kyung Do Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea
| | - Yeon-Ki Kim
- Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea.
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Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming. Nat Commun 2020; 11:5845. [PMID: 33203871 PMCID: PMC7672089 DOI: 10.1038/s41467-020-19624-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/20/2020] [Indexed: 02/04/2023] Open
Abstract
Pathogens utilize multiple types of effectors to modulate plant immunity. Although many apoplastic and cytoplasmic effectors have been reported, nuclear effectors have not been well characterized in fungal pathogens. Here, we characterize two nuclear effectors of the rice blast pathogen Magnaporthe oryzae. Both nuclear effectors are secreted via the biotrophic interfacial complex, translocated into the nuclei of initially penetrated and surrounding cells, and reprogram the expression of immunity-associated genes by binding on effector binding elements in rice. Their expression in transgenic rice causes ambivalent immunity: increased susceptibility to M. oryzae and Xanthomonas oryzae pv. oryzae, hemibiotrophic pathogens, but enhanced resistance to Cochliobolus miyabeanus, a necrotrophic pathogen. Our findings help remedy a significant knowledge deficiency in the mechanism of M. oryzae–rice interactions and underscore how effector-mediated manipulation of plant immunity by one pathogen may also affect the disease severity by other pathogens. Plant pathogens secrete various effectors to manipulate host immunity. Here, Kim et al. describe two Magnaporthe oryzae effectors that translocate into the nuclei of infected rice cells and reprogram expression of immunity-associated genes, increasing susceptibility to hemibiotrophic pathogens.
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3
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Kim JE, Nam H, Park J, Choi GJ, Lee YW, Son H. Characterization of the CCAAT-binding transcription factor complex in the plant pathogenic fungus Fusarium graminearum. Sci Rep 2020; 10:4898. [PMID: 32184445 PMCID: PMC7078317 DOI: 10.1038/s41598-020-61885-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/05/2020] [Indexed: 12/18/2022] Open
Abstract
The CCAAT sequence is a ubiquitous cis-element of eukaryotic promoters, and genes containing CCAAT sequences have been shown to be activated by the CCAAT-binding transcription factor complex in several eukaryotic model organisms. In general, CCAAT-binding transcription factors form heterodimers or heterotrimeric complexes that bind to CCAAT sequences within the promoters of target genes and regulate various cellular processes. To date, except Hap complex, CCAAT-binding complex has been rarely reported in fungi. In this study, we characterized two CCAAT-binding transcription factors (Fct1 and Fct2) in the plant pathogenic fungus Fusarium graminearum. Previously, FCT1 and FCT2 were shown to be related to DNA damage response among eight CCAAT-binding transcription factors in F. graminearum. We demonstrate that the nuclear CCAAT-binding complex of F. graminearum has important functions in various fungal developmental processes, not just DNA damage response but virulence and mycotoxin production. Moreover, the results of biochemical and genetic analyses revealed that Fct1 and Fct2 may form a complex and play distinct roles among the eight CCAAT-binding transcription factors encoded by F. graminearum. To the best of our knowledge, the results of this study represent a substantial advancement in our understanding of the molecular mechanisms underlying the functions of CCAAT-binding factors in eukaryotes.
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Affiliation(s)
- Jung-Eun Kim
- Research Institute of Agriculture and Life Sciences and Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea
| | - Hyejin Nam
- Research Institute of Agriculture and Life Sciences and Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea
| | - Jiyeun Park
- Research Institute of Agriculture and Life Sciences and Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea
| | - Gyung Ja Choi
- Therapeutic & Biotechnology Division, Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Yin-Won Lee
- Research Institute of Agriculture and Life Sciences and Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea
| | - Hokyoung Son
- Research Institute of Agriculture and Life Sciences and Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea.
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4
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Moon SJ, Park HJ, Kim TH, Kang JW, Lee JY, Cho JH, Lee JH, Park DS, Byun MO, Kim BG, Shin D. OsTGA2 confers disease resistance to rice against leaf blight by regulating expression levels of disease related genes via interaction with NH1. PLoS One 2018; 13:e0206910. [PMID: 30444888 PMCID: PMC6239283 DOI: 10.1371/journal.pone.0206910] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/22/2018] [Indexed: 11/21/2022] Open
Abstract
How plants defend themselves from microbial infection is one of the most critical issues for sustainable crop production. Some TGA transcription factors belonging to bZIP superfamily can regulate disease resistance through NPR1-mediated immunity mechanisms in Arabidopsis. Here, we examined biological roles of OsTGA2 (grouped into the same subclade as Arabidopsis TGAs) in bacterial leaf blight resistance. Transcriptional level of OsTGA2 was accumulated after treatment with salicylic acid, methyl jasmonate, and Xathomonas oryzae pv. Oryzae (Xoo), a bacterium causing serious blight of rice. OsTGA2 formed homo- and hetero-dimer with OsTGA3 and OsTGA5 and interacted with rice NPR1 homologs 1 (NH1) in rice. Results of quadruple 9-mer protein-binding microarray analysis indicated that OsTGA2 could bind to TGACGT DNA sequence. Overexpression of OsTGA2 increased resistance of rice to bacterial leaf blight, although overexpression of OsTGA3 resulted in disease symptoms similar to wild type plant upon Xoo infection. Overexpression of OsTGA2 enhanced the expression of defense related genes containing TGA binding cis-element in the promoter such as AP2/EREBP 129, ERD1, and HOP1. These results suggest that OsTGA2 can directly regulate the expression of defense related genes and increase the resistance of rice against bacterial leaf blight disease.
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Affiliation(s)
- Seok-Jun Moon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Republic of Korea
| | - Hee Jin Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
| | - Tae-Heon Kim
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Ju-Won Kang
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Ji-Yoon Lee
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Jun-Hyun Cho
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Jong-Hee Lee
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Dong-Soo Park
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Myung-Ok Byun
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Republic of Korea
| | - Beom-Gi Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Republic of Korea
| | - Dongjin Shin
- Paddy Crop Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
- * E-mail:
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Minh-Thu PT, Kim JS, Chae S, Jun KM, Lee GS, Kim DE, Cheong JJ, Song SI, Nahm BH, Kim YK. A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice. Mol Cells 2018; 41:781-798. [PMID: 30078233 PMCID: PMC6125423 DOI: 10.14348/molcells.2018.0203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Plants have evolved strategies to cope with drought stress by maximizing physiological capacity and adjusting developmental processes such as flowering time. The WOX13 orthologous group is the most conserved among the clade of WOX homeodomain-containing proteins and is found to function in both drought stress and flower development. In this study, we isolated and characterized OsWOX13 from rice. OsWOX13 was regulated spatially in vegetative organs but temporally in flowers and seeds. Overexpression of OsWOX13 (OsWOX13-ov) in rice under the rab21 promoter resulted in drought resistance and early flowering by 7-10 days. Screening of gene expression profiles in mature leaf and panicles of OsWOX13-ov showed a broad spectrum of effects on biological processes, such as abiotic and biotic stresses, exerting a cross-talk between responses. Protein binding microarray and electrophoretic mobility shift assay analyses supported ATTGATTG as the putative cis-element binding of OsWOX13. OsDREB1A and OsDREB1F, drought stress response transcription factors, contain ATTGATTG motif(s) in their promoters and are preferentially expressed in OsWOX13-ov. In addition, Heading date 3a and OsMADS14, regulators in the flowering pathway and development, were enhanced in OsWOX13-ov. These results suggest that OsWOX13 mediates the stress response and early flowering and, thus, may be a regulator of genes involved in drought escape.
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Affiliation(s)
- Pham-Thi Minh-Thu
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Joung Sug Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Songhwa Chae
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54875,
Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826,
Korea
| | - Sang Ik Song
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Baek Hie Nahm
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 17058,
Korea
| | - Yeon-Ki Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
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6
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Franco-Zorrilla JM, Solano R. Identification of plant transcription factor target sequences. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:21-30. [PMID: 27155066 DOI: 10.1016/j.bbagrm.2016.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/01/2016] [Accepted: 05/02/2016] [Indexed: 12/15/2022]
Abstract
Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription factors (TFs) in a sequence-specific manner, and their identification could help to elucidate the regulatory networks that underlie plant physiological responses to developmental programs or to environmental adaptation. Here we review recent advances in high throughput methodologies for the identification of plant TF binding sites. Several approaches offer a map of the TF binding locations in vivo and of the dynamics of the gene regulatory networks. As an alternative, high throughput in vitro methods provide comprehensive determination of the DNA sequences recognized by TFs. These advances are helping to decipher the regulatory lexicon and to elucidate transcriptional network hierarchies in plants in response to internal or external cues. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- José M Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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7
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Kim HK, Jo SM, Kim GY, Kim DW, Kim YK, Yun SH. A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum. PLoS Genet 2015; 11:e1005486. [PMID: 26334536 PMCID: PMC4559316 DOI: 10.1371/journal.pgen.1005486] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 08/06/2015] [Indexed: 01/12/2023] Open
Abstract
Fusarium graminearum, the causal agent of Fusarium head blight in cereal crops, produces sexual progeny (ascospore) as an important overwintering and dissemination strategy for completing the disease cycle. This homothallic ascomycetous species does not require a partner for sexual mating; instead, it carries two opposite mating-type (MAT) loci in a single nucleus to control sexual development. To gain a comprehensive understanding of the regulation of sexual development in F. graminearum, we used in-depth and high-throughput analyses to examine the target genes controlled transcriptionally by two-linked MAT loci (MAT1-1, MAT1-2). We hybridized a genome-wide microarray with total RNAs from F. graminearum mutants that lacked each MAT locus individually or together, and overexpressed MAT1-2-1, as well as their wild-type progenitor, at an early stage of sexual development. A comparison of the gene expression levels revealed a total of 1,245 differentially expressed genes (DEGs) among all of the mutants examined. Among these, genes involved in metabolism, cell wall organization, cellular response to stimuli, cell adhesion, fertilization, development, chromatin silencing, and signal transduction, were significantly enriched. Protein binding microarray analysis revealed the presence of putative core DNA binding sequences (ATTAAT or ATTGTT) for the HMG (high mobility group)-box motif in the MAT1-2-1 protein. Targeted deletion of 106 DEGs revealed 25 genes that were specifically required for sexual development, most of which were regulated transcriptionally by both the MAT1-1 and MAT1-2 loci. Taken together with the expression patterns of key target genes, we propose a regulatory pathway for MAT-mediated sexual development, in which both MAT loci may be activated by several environmental cues via chromatin remodeling and/or signaling pathways, and then control the expression of at least 1,245 target genes during sexual development via regulatory cascades and/or networks involving several downstream transcription factors and a putative RNA interference pathway.
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Affiliation(s)
- Hee-Kyoung Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Seong-Mi Jo
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Gi-Yong Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Da-Woon Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Yeon-Ki Kim
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, Republic of Korea
| | - Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
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8
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Abstract
Sequence-specific protein-DNA interactions mediate most regulatory processes underlying gene expression, such as transcriptional regulation by transcription factors (TFs) or chromatin organization. Current knowledge about DNA-binding specificities of TFs is based mostly on low- to medium-throughput methodologies that are time-consuming and often fail to identify DNA motifs recognized by a TF with lower affinity but retaining biological relevance. The use of protein-binding microarrays (PBMs) offers a high-throughput alternative for the identification of protein-DNA specificities. PBM consists in an array of pseudorandomized DNA sequences that are optimized to include all the possible 10- or 11-mer DNA sequences, allowing the determination of binding specificities of most eukaryotic TFs. PBMs that can be synthesized by several manufacturing companies as single-stranded DNA are converted into double-stranded in a simple primer extension reaction. The protein of interest fused to an epitope tag is then incubated onto the PBM, and specific DNA-protein complexes are revealed in a series of immunological reactions coupled to a fluorophore. After scanning and quantifying PBMs, specific DNA motifs recognized by the protein are identified with ready-to-use scripts, generating comprehensive but accessible information about the DNA-binding specificity of the protein. This chapter describes detailed procedures for preparation of double-stranded PBMs, incubation with recombinant protein, and detection of protein-DNA complexes. Finally, we outline some cues for evaluating the biological role of DNA motifs obtained in vitro.
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9
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Casado-Vela J, Fuentes M, Franco-Zorrilla JM. Screening of Protein–Protein and Protein–DNA Interactions Using Microarrays. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:231-81. [DOI: 10.1016/b978-0-12-800453-1.00008-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Jung C, Kim YK, Oh NI, Shim JS, Seo JS, Choi YD, Nahm BH, Cheong JJ. Quadruple 9-mer-based protein binding microarray analysis confirms AACnG as the consensus nucleotide sequence sufficient for the specific binding of AtMYB44. Mol Cells 2012; 34:531-7. [PMID: 23161171 PMCID: PMC3887824 DOI: 10.1007/s10059-012-0209-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 10/10/2012] [Accepted: 10/15/2012] [Indexed: 02/02/2023] Open
Abstract
AtMYB44 is a member of the R2R3 MYB subgroup 22 transcription factors and regulates diverse cellular responses in Arabidopsis thaliana. We performed quadruple 9-merbased protein binding microarray (PBM) analysis, which revealed that full-size AtMYB44 recognized and bound to the consensus sequence AACnG, where n represents A, G, C or T. The consensus sequence was confirmed by electrophoretic mobility shift assay (EMSA) with a truncated AtMYB44 protein containing the N-terminal side R2R3 domain. This result indicates that the R2R3 domain alone is sufficient to exhibit AtMYB44 binding specificity. The sequence AACnG is the type I binding site for MYB transcription factors, including all members of the subgroup 22. EMSA showed that the R2R3 domain protein binds in vitro to promoters of randomly selected Arabidopsis genes that contain the consensus binding sequence. This implies that AtMYB44 binds to any promoter region that contains the consensus sequence, without determining their functional activity or specificity. The C-terminal side transcriptional activation domain of AtMYB44 contains an asparagine-rich fragment, NINNTTSSRHNHNN (aa 215-228), which, among the members of subgroup 22, is unique to AtMYB44. A transcriptional activation assay in yeast showed that this fragment is included in a region (aa 200-240) critical for the ability of AtMYB44 to function as a transcriptional activator. We hypothesize that the C-terminal side of the protein, but not the N-terminal side of the R2R3 domain, contributes to the functional activity and specificity of AtMYB44 through interactions with other regulators generated by each of a variety of stimuli.
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Affiliation(s)
- Choonkyun Jung
- Center for Food and Bioconvergence, Seoul National University, Seoul 151-921,
Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Yeon-Ki Kim
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 449-728,
Korea
| | - Nam Iee Oh
- Center for Food and Bioconvergence, Seoul National University, Seoul 151-921,
Korea
| | - Jae Sung Shim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Jun Sung Seo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Yang Do Choi
- Center for Food and Bioconvergence, Seoul National University, Seoul 151-921,
Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Baek Hie Nahm
- Genomics Genetics Institute, GreenGene Biotech Inc., Yongin 449-728,
Korea
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728,
Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 151-921,
Korea
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Convenient determination of protein-binding DNA sequences using quadruple 9-mer-based microarray and DsRed-monomer fusion protein. Methods Mol Biol 2012; 786:65-77. [PMID: 21938620 DOI: 10.1007/978-1-61779-292-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein-binding DNA microarray (PBM) is one of the high-throughput methods to define DNA sequences which potentially bind to a given DNA-binding protein. Quadruple 9-mer-based protein-binding DNA microarray, named Q9-PBM, is designed in such a way that target probes are synthesized as quadruples of all possible 9-mer combinations. Also, recombinant proteins fused with DsRed-monomer fluorescent protein are conveniently constructed. Q9-PBM confirms the well-known DNA-binding sequences of Cbf1 and CBF1/DREB1B transcription factors, and also identifies the adjacent sequences. Moreover, Q9-PBM is applied to elucidate the unidentified cis-acting element of the OsNAC6 rice transcription factor. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.
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12
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Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
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13
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Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R. Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:700-11. [PMID: 21284757 DOI: 10.1111/j.1365-313x.2011.04519.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Transcriptional regulation depends on the specificity of transcription factors (TFs) recognizing cis regulatory sequences in the promoters of target genes. Current knowledge about DNA-binding specificities of TFs is based mostly on low- to medium-throughput methodologies, revealing DNA motifs bound by a TF with high affinity. These strategies are time-consuming and often fail to identify DNA motifs recognized by a TF with lower affinity but retaining biological relevance. Here we report on the development of a protein-binding microarray (PBM11) containing all possible double-stranded 11-mers for the determination of DNA-binding specificities of TFs. The large number of sequences in the PBM11 allows accurate and high-throughput quantification of TF-binding sites, outperforming previous methods. We applied this tool to determine binding site specificities of two Arabidopsis TFs, MYC2 and ERF1, rendering the G-box and the GCC-box, respectively, as their highest-affinity binding sites. In addition, we identified variants of the G-box recognized by MYC2 with high and medium affinity, whereas ERF1 only recognized GCC variants with low affinity, indicating that ERF1 binding to DNA has stricter base requirements than MYC2. Analysis of transcriptomic data revealed that high- and medium-affinity binding sites have biological significance, probably representing relevant cis-acting elements in vivo. Comparison of promoter sequences with putative orthologs from closely related species demonstrated a high degree of conservation of all the identified DNA elements. The combination of PBM11, transcriptomic data and phylogenomic footprinting provides a straightforward method for the prediction of biologically active cis-elements, and thus for identification of in vivo DNA targets of TFs.
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Affiliation(s)
- Marta Godoy
- Genomics Unit, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049-Madrid, Spain
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14
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Shin D, Moon SJ, Han S, Kim BG, Park SR, Lee SK, Yoon HJ, Lee HE, Kwon HB, Baek D, Yi BY, Byun MO. Expression of StMYB1R-1, a novel potato single MYB-like domain transcription factor, increases drought tolerance. PLANT PHYSIOLOGY 2011; 155:421-32. [PMID: 21030505 PMCID: PMC3075785 DOI: 10.1104/pp.110.163634] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 10/26/2010] [Indexed: 05/18/2023]
Abstract
Potato (Solanum tuberosum) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms for such stresses in potato are largely unknown. To identify stress-related factors in potato, we previously carried out a genetic screen of potato plants exposed to abiotic environmental stress conditions using reverse northern-blot analysis. A cDNA encoding a putative R1-type MYB-like transcription factor (StMYB1R-1) was identified as a putative stress-response gene. Here, the transcript levels of StMYB1R-1 were enhanced in response to several environmental stresses in addition to drought but were unaffected by biotic stresses. The results of intracellular targeting and quadruple 9-mer protein-binding microarray analysis indicated that StMYB1R-1 localizes to the nucleus and binds to the DNA sequence (G)/(A)GATAA. Overexpression of a StMYB1R-1 transgene in potato plants improved plant tolerance to drought stress while having no significant effects on other agricultural traits. Transgenic plants exhibited reduced rates of water loss and more rapid stomatal closing than wild-type plants under drought stress conditions. In addition, overexpression of StMYB1R-1 enhanced the expression of drought-regulated genes such as AtHB-7, RD28, ALDH22a1, and ERD1-like. Thus, the expression of StMYB1R-1 in potato enhanced drought tolerance via regulation of water loss. These results indicated that StMYB1R-1 functions as a transcription factor involved in the activation of drought-related genes.
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MESH Headings
- Abscisic Acid/pharmacology
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Amino Acid Sequence
- Base Sequence
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- DNA, Plant/metabolism
- Dehydration
- Droughts
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/genetics
- Molecular Sequence Data
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/isolation & purification
- Plant Proteins/metabolism
- Plant Stomata/drug effects
- Plant Stomata/physiology
- Plants, Genetically Modified
- Protein Binding/drug effects
- Protein Structure, Tertiary
- Protein Transport/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Solanum tuberosum/drug effects
- Solanum tuberosum/genetics
- Solanum tuberosum/physiology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Up-Regulation/drug effects
- Up-Regulation/genetics
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