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Mochdia K, Tamaki S. Transcription Factor-Based Genetic Engineering in Microalgae. PLANTS 2021; 10:plants10081602. [PMID: 34451646 PMCID: PMC8399792 DOI: 10.3390/plants10081602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are key components of gene regulatory networks. Advances in high-throughput sequencing have facilitated the rapid acquisition of whole genome assembly and TF repertoires in microalgal species. In this review, we summarize recent advances in gene discovery and functional analyses, especially for transcription factors in microalgal species. Specifically, we provide examples of the genome-scale identification of transcription factors in genome-sequenced microalgal species and showcase their application in the discovery of regulators involved in various cellular functions. Herein, we highlight TF-based genetic engineering as a promising framework for designing microalgal strains for microalgal-based bioproduction.
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Affiliation(s)
- Keiichi Mochdia
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama 244-0813, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
- School of Information and Data Sciences, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521, Japan
- Correspondence: ; Tel.: +81-045-503-9111
| | - Shun Tamaki
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
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Subba P, Narayana Kotimoole C, Prasad TSK. Plant Proteome Databases and Bioinformatic Tools: An Expert Review and Comparative Insights. ACTA ACUST UNITED AC 2019; 23:190-206. [DOI: 10.1089/omi.2019.0024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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Ogita S, Nomura T, Kato Y, Uehara-Yamaguchi Y, Inoue K, Yoshida T, Sakurai T, Shinozaki K, Mochida K. Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells. Sci Rep 2018; 8:11347. [PMID: 30054534 PMCID: PMC6063902 DOI: 10.1038/s41598-018-29645-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/16/2018] [Indexed: 01/24/2023] Open
Abstract
Highly-lignified culms of bamboo show distinctive anatomical and mechanical properties compared with the culms of other grass species. A cell culture system for Phyllostachys nigra has enabled investigating the alterations in cellular states associated with secondary cell wall formation during its proliferation and lignification in woody bamboos. To reveal transcriptional changes related to lignification in bamboo, we analyzed transcriptome in P. nigra cells treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) and the synthetic cytokinin benzylaminopurine (BA) by RNA-seq analysis. We found that some genes putatively involved in cell wall biogenesis and cell division were up-regulated in response to the 2,4-D treatment, and the induction of lignification by the BA treatment was correlated with up-regulation of genes involved in the shikimate pathway. We also found that genes encoding MYB transcription factors (TFs) show correlated expression patterns with those encoding cinnamyl alcohol dehydrogenase (CAD), suggesting that MYB TFs presumably regulate secondary cell wall formation in the bamboo cells. These findings suggest that cytokinin signaling may regulate lignification in P. nigra cells through coordinated transcriptional regulation and metabolic alterations. Our results have also produced a useful resource for better understanding of secondary cell wall formation in bamboo plants.
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Affiliation(s)
- Shinjiro Ogita
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, 5562 Nanatuka, Shobara, Hiroshima, 727-0023, Japan. .,Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yukiko Uehara-Yamaguchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Interdisciplinary Science Unit, Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. .,RIKEN, Baton Zone Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan. .,Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan.
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Genome-wide identification and phylogenetic, comparative genomic, alternative splicing, and expression analyses of TCP genes in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 2017; 45:D1040-D1045. [PMID: 27924042 DOI: 10.1093/nar/gkw98] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/12/2016] [Indexed: 05/22/2023] Open
Abstract
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
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Affiliation(s)
- Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Feng Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P.R. China
| | - De-Chang Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Yu-Qi Meng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Jingchu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
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Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 2016; 45:D1040-D1045. [PMID: 27924042 PMCID: PMC5210657 DOI: 10.1093/nar/gkw982] [Citation(s) in RCA: 1174] [Impact Index Per Article: 146.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/12/2016] [Indexed: 12/12/2022] Open
Abstract
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
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Affiliation(s)
- Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Feng Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P.R. China
| | - De-Chang Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Yu-Qi Meng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Jingchu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China
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Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. BMC Genomics 2014; 15:818. [PMID: 25261191 PMCID: PMC4189582 DOI: 10.1186/1471-2164-15-818] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 09/23/2014] [Indexed: 12/21/2022] Open
Abstract
Background Transcription factors (TFs) contain DNA-binding domains (DBDs) and regulate gene expression by binding to specific DNA sequences. In addition, there are proteins, called transcription coregulators (TCs), which lack DBDs but can alter gene expression through interaction with TFs or RNA Polymerase II. Therefore, it is interesting to identify and classify the TFs and TCs in a genome. In this study, maize (Zea mays) and foxtail millet (Setaria italica), two important species for the study of C4 photosynthesis and kranz anatomy, were selected. Result We conducted a comprehensive genome-wide annotation of TFs and TCs in maize B73 and in two strains of foxtail millet, Zhang gu and Yugu1, and classified them into families. To gain additional support for our predictions, we searched for their homologous genes in Arabidopsis or rice and studied their gene expression level using RNA-seq and microarray data. We identified many new TF and TC families in these two species, and described some evolutionary and functional aspects of the 9 new maize TF families. Moreover, we detected many pseudogenes and transposable elements in current databases. In addition, we examined tissue expression preferences of TF and TC families and identified tissue/condition-specific TFs and TCs in maize and millet. Finally, we identified potential C4-related TF and TC genes in maize and millet. Conclusions Our results significantly expand current TF and TC annotations in maize and millet. We provided supporting evidence for our annotation from genomic and gene expression data and identified TF and TC genes with tissue preference in expression. Our study may facilitate the study of regulation of gene expression, tissue morphogenesis, and C4 photosynthesis in maize and millet. The data we generated in this study are available at http://sites.google.com/site/jjlmmtf. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-818) contains supplementary material, which is available to authorized users.
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A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. Nat Protoc 2014; 9:2180-93. [PMID: 25144269 DOI: 10.1038/nprot.2014.146] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.
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Legué V, Rigal A, Bhalerao RP. Adventitious root formation in tree species: involvement of transcription factors. PHYSIOLOGIA PLANTARUM 2014; 151:192-8. [PMID: 24666319 DOI: 10.1111/ppl.12197] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/27/2014] [Accepted: 03/24/2014] [Indexed: 05/23/2023]
Abstract
Adventitious rooting is an essential step in the vegetative propagation of economically important horticultural and woody species. Populus has emerged as an experimental model for studying processes that are important in tree growth and development. It is highly useful for molecular genetic analysis of adventitious roots in trees. In this short review, we will highlight the recent progress made in the identification of transcription factors involved in the control of adventitious rooting in woody species. Their regulation will be discussed.
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Affiliation(s)
- Valérie Legué
- INRA and Université de Lorraine, UMR Interactions Arbres/Micro-organismes 1136, F-54280, Champenoux, France; Clermont Université, Université Blaise-Pascal, UMR 547 PIAF, BP 10448, F-63000, Clermont-Ferrand, France; INRA, UMR 547 PIAF, F-63100, Clermont-Ferrand, France
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Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 2014; 42:D1182-7. [PMID: 24174544 PMCID: PMC3965000 DOI: 10.1093/nar/gkt1016] [Citation(s) in RCA: 619] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 11/25/2022] Open
Abstract
With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences.
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Affiliation(s)
- Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, P.R. China
| | | | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, P.R. China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, P.R. China
| | - Jingchu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, P.R. China
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Van Ha C, Le DT, Nishiyama R, Watanabe Y, Sulieman S, Tran UT, Mochida K, Van Dong N, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress. DNA Res 2013; 20:511-24. [PMID: 23810914 PMCID: PMC3789561 DOI: 10.1093/dnares/dst027] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/28/2013] [Indexed: 12/20/2022] Open
Abstract
In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many of which were formed by genome duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain and an auxin/indole acetic acid (AUX/IAA) dimerization domain, whereas the remaining eight members lack the dimerization domain. Phylogenetic analysis of the ARFs from soybean and Arabidopsis revealed both similarity and divergence between the two ARF families, as well as enabled us to predict the functions of the GmARFs. Using quantitative real-time polymerase chain reaction (qRT-PCR) and available soybean Affymetrix array and Illumina transcriptome sequence data, a comprehensive expression atlas of GmARF genes was obtained in various organs and tissues, providing useful information about their involvement in defining the precise nature of individual tissues. Furthermore, expression profiling using qRT-PCR and microarray data revealed many water stress-responsive GmARFs in soybean, albeit with different patterns depending on types of tissues and/or developmental stages. Our systematic analysis has identified excellent tissue-specific and/or stress-responsive candidate GmARF genes for in-depth in planta functional analyses, which would lead to potential applications in the development of genetically modified soybean cultivars with enhanced drought tolerance.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
- Post-Graduate Program, Vietnamese Academy of Agricultural Science, Thanhtri, Hanoi, Vietnam
| | - Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Saad Sulieman
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
| | - Nguyen Van Dong
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | | | - Kazuo Shinozaki
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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