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Meher PK, Sahu TK, Gupta A, Kumar A, Rustgi S. ASRpro: A machine-learning computational model for identifying proteins associated with multiple abiotic stress in plants. THE PLANT GENOME 2024; 17:e20259. [PMID: 36098562 DOI: 10.1002/tpg2.20259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
One of the thrust areas of research in plant breeding is to develop crop cultivars with enhanced tolerance to abiotic stresses. Thus, identifying abiotic stress-responsive genes (SRGs) and proteins is important for plant breeding research. However, identifying such genes via established genetic approaches is laborious and resource intensive. Although transcriptome profiling has remained a reliable method of SRG identification, it is species specific. Additionally, identifying multistress responsive genes using gene expression studies is cumbersome. Thus, endorsing the need to develop a computational method for identifying the genes associated with different abiotic stresses. In this work, we aimed to develop a computational model for identifying genes responsive to six abiotic stresses: cold, drought, heat, light, oxidative, and salt. The predictions were performed using support vector machine (SVM), random forest, adaptive boosting (ADB), and extreme gradient boosting (XGB), where the autocross covariance (ACC) and K-mer compositional features were used as input. With ACC, K-mer, and ACC + K-mer compositional features, the overall accuracy of ∼60-77, ∼75-86, and ∼61-78% were respectively obtained using the SVM algorithm with fivefold cross-validation. The SVM also achieved higher accuracy than the other three algorithms. The proposed model was also assessed with an independent dataset and obtained an accuracy consistent with cross-validation. The proposed model is the first of its kind and is expected to serve the requirement of experimental biologists; however, the prediction accuracy was modest. Given its importance for the research community, the online prediction application, ASRpro, is made freely available (https://iasri-sg.icar.gov.in/asrpro/) for predicting abiotic SRGs and proteins.
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Affiliation(s)
| | | | - Ajit Gupta
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anuj Kumar
- Dep. of Microbiology and Immunology, Dalhousie Univ., Halifax, Nova Scotia, Canada
- Laboratory of Immunity, Shantou Univ. Medical College, Shantou, PRC
| | - Sachin Rustgi
- Dep. of Plant and Environmental Sciences, Pee Dee Research and Education Centre, Clemson Univ., Florence, SC, USA
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Zhou Z, Wang J, Yu Q, Lan H. Promoter activity and transcriptome analyses decipher functions of CgbHLH001 gene (Chenopodium glaucum L.) in response to abiotic stress. BMC PLANT BIOLOGY 2023; 23:116. [PMID: 36849913 PMCID: PMC9969703 DOI: 10.1186/s12870-023-04128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Our previous studies revealed that CgbHLH001 transcription factor (TF) played an important role in abiotic stress tolerance, suggesting that its promoter was a potential target in response to stress signals. In addition, the regulatory mechanism of CgbHLH001 TF is still limited. RESULTS In the present study, a 1512 bp of 5'-flanking sequence of CgbHLH001 gene was identified, and the sequence carried quite a few of cis-acting elements. The gene promoter displayed strong activity and was induced by multiple abiotic stress. A series of 5'-deletions of the promoter sequence resulted in a gradual decrease in its activity, especially, the 5' untranslated region (UTR) was necessary to drive promoter activity. Further, CgbHLH001 promoter drove its own gene overexpression ectopically at the transcriptional and translational levels, which in turn conferred the stress tolerance to transgenic Arabidopsis. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple biological regulatory processes. Differentially expressed genes (DEGs) that mediate phytohormone signal transduction and mitogen-activated protein kinase (MAPK) signaling pathway were widely induced and mostly upregulated under salt stress, and the transcription levels in PbHLH::bHLH-overexpressing transgenic lines were higher than that of 35S::bHLH overexpression. CONCLUSIONS The CgbHLH001 promoter exhibited a positive response to abiotic stress and its 5' UTR sequence enhanced the regulation of gene expression to stress. A few important pathways and putative key genes involved in salt tolerance were identified, which can be used to elucidate the mechanism of salt tolerance and decipher the regulatory mechanism of promoters to develop an adaptation strategy for desert halophytes.
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Affiliation(s)
- Zixin Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China.
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Emerging roles of NAC transcription factor in medicinal plants: progress and prospects. 3 Biotech 2021; 11:425. [PMID: 34567930 DOI: 10.1007/s13205-021-02970-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022] Open
Abstract
Transcriptional factors act as mediators in regulating stress response in plants from signal perception to processing the directed gene expression. WRKY, MYB, AP2/ERF, etc. are some of the major families of transcription factors known to mediate stress mechanisms in plants by regulating the production of secondary metabolites. NAC domain-containing proteins are among these large transcription factors families in plants. These proteins play impulsive roles in plant growth, development, and various abiotic as well as biotic stresses. They are involved in regulating the different signaling pathways of plant hormones that direct a plant's immunity against pathogens, thereby affecting their immune responses. However, their role in stress regulation or defence mechanism in plants through the secondary metabolite biosynthesis pathway is studied for very few cases. Emerging concern over the requirement of medicinal plants for the production of biocompatible drugs and antibiotics, the study of these vast, affecting proteins should be focused to improve their qualitative and quantitative production further. In medicinal plants, phytochemicals and secondary metabolites are the major biochemicals that impose antimicrobial and other medicinal properties in these plants. This review compiles the NAC transcription factors reported in selected medicinal plants and their possible roles in different mechanisms. Further, the comprehensive understanding of the molecular mechanism, genetic engineering, and regulation responses of NAC TFs in medicinal plants, can lead to improvement in stress response, immunity, and production of usable secondary metabolites.
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Kim M, Xi H, Park S, Yun Y, Park J. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Sci Rep 2021; 11:16578. [PMID: 34400697 PMCID: PMC8367991 DOI: 10.1038/s41598-021-95940-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Hong Xi
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Suhyeon Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Yunho Yun
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Jongsun Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
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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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Cheng Z, Zhang X, Zhao K, Zhou B, Jiang T. Ectopic expression of a poplar gene NAC13 confers enhanced tolerance to salinity stress in transgenic Nicotiana tabacum. JOURNAL OF PLANT RESEARCH 2020; 133:727-737. [PMID: 32643054 DOI: 10.1007/s10265-020-01213-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/28/2020] [Indexed: 05/28/2023]
Abstract
NACs are one of the major transcription factor families in plants which play an important role in plant growth and development, as well as in adverse stress responses. In this study, we cloned a salt-inducible NAC transcription factor gene (NAC13) from a poplar variety 84K, followed by transforming it into both Nicotiana tabacum and Arabidopsis thaliana. Stable expression analysis of 35S::NAC13-GFP fusion protein in Arabidopsis indicated that NAC13 protein was localized to the nucleus. We also obtained five transgenic tobacco lines. Evidence from morphological and physiological characterization and salt treatment analyses indicated that in the transgenic tobacco the salt tolerance was enhanced, suggesting that NAC13 gene may function as a positive regulator in tobacco responses to salt stress.
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Affiliation(s)
- Zihan Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Xuemei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.
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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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Tamura K, Yoshida K, Hiraoka Y, Sakaguchi D, Chikugo A, Mochida K, Kojoma M, Mitsuda N, Saito K, Muranaka T, Seki H. The Basic Helix-Loop-Helix Transcription Factor GubHLH3 Positively Regulates Soyasaponin Biosynthetic Genes in Glycyrrhiza uralensis. PLANT & CELL PHYSIOLOGY 2018; 59:778-791. [PMID: 29648666 DOI: 10.1093/pcp/pcy046] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 05/06/2023]
Abstract
Glycyrrhiza uralensis (licorice) is a widely used medicinal plant belonging to the Fabaceae. Its main active component, glycyrrhizin, is an oleanane-type triterpenoid saponin widely used as a medicine and as a natural sweetener. Licorice also produces other triterpenoids, including soyasaponins. Recent studies have revealed various oxidosqualene cyclases and cytochrome P450 monooxygenases (P450s) required for the biosynthesis of triterpenoids in licorice. Of these enzymes, β-amyrin synthase (bAS) and β-amyrin C-24 hydroxylase (CYP93E3) are involved in the biosynthesis of soyasapogenol B (an aglycone of soyasaponins) from 2,3-oxidosqualene. Although these biosynthetic enzyme genes are known to be temporally and spatially expressed in licorice, the regulatory mechanisms underlying their expression remain unknown. Here, we identified a basic helix-loop-helix (bHLH) transcription factor, GubHLH3, that positively regulates the expression of soyasaponin biosynthetic genes. GubHLH3 preferentially activates transcription from promoters of CYP93E3 and CYP72A566, the second P450 gene newly identified and shown to be responsible for C-22β hydroxylation in soyasapogenol B biosynthesis, in transient co-transfection assays of promoter-reporter constructs and transcription factors. Overexpression of GubHLH3 in transgenic hairy roots of G. uralensis enhanced the expression levels of bAS, CYP93E3 and CYP72A566. Moreover, soyasapogenol B and sophoradiol (22β-hydroxy-β-amyrin), an intermediate between β-amyrin and soyasapogenol B, were increased in transgenic hairy root lines overexpressing GubHLH3. We found that soyasaponin biosynthetic genes and GubHLH3 were co-ordinately up-regulated by methyl jasmonate (MeJA). These results suggest that GubHLH3 regulates MeJA-responsive expression of soyasaponin biosynthetic genes in G. uralensis. The regulatory mechanisms of triterpenoid biosynthesis in legumes are compared and discussed.
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Affiliation(s)
- Keita Tamura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Koki Yoshida
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Yasuko Hiraoka
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan
| | - Daiki Sakaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Ayaka Chikugo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Keiichi Mochida
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046 Japan
| | - Mareshige Kojoma
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu, Hokkaido, 061-0293 Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566 Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675 Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Zhang L, Yao L, Zhang N, Yang J, Zhu X, Tang X, Calderón-Urrea A, Si H. Lateral Root Development in Potato Is Mediated by Stu-mi164 Regulation of NAC Transcription Factor. FRONTIERS IN PLANT SCIENCE 2018; 9:383. [PMID: 29651294 PMCID: PMC5884874 DOI: 10.3389/fpls.2018.00383] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/08/2018] [Indexed: 05/23/2023]
Abstract
The NAC designation is derived from petunia (Petunia hybrida) gene NO APICAL MERISTEM (NAM) and Arabidopsis genes ATAF1/ATAF2 and CUP-SHAPED COTYLEDON2 (CUC2), which belongs to the family of plant-specific transcription factors (TFs), and plays important role in plant development processes, such as response to biotic and abiotic stress, and hormone signaling. MicroRNAs (miRNAs) are a class of small, non-coding endogenous RNAs which play versatile and significant role in plant stress response and development via negatively affecting gene expression at a post-transcriptional level. Here, we showed that Stu-mi164 had a complementary sequence in the CDS sequence of potato NAC TFs, and that NAC expression exhibited significant differences under osmotic stress. We measured expression levels of the Stu-mi164 target gene StNAC262 between control and PEG-treated plants using real-time PCR, and the results demonstrated that they had inverse relationship. We suggested that Stu-miR164 might drive overexpression of NAC gene under osmotic stress in potato. To confirm the regulation of NAC TFs by Stu-mi164, we developed transgenic plants, using Agrobacterium tumefaciens-mediated transformation, of the potato cultivars "Gannongshu 2" and "Kexin 3" overexpressing the Stu-mi164 or the TF StNAC262. Real-time PCR analysis of transgenic potato plants under osmotic (PEG) stress, showed that potato plants overexpressing Stu-mi164 had reduced expression of StNAC262 and their osmotic resistance decreased. Furthermore, these plants had low number of lateral roots although the same length as the control. Our findings support the regulatory role of Stu-miRNAs in controlling plant response to osmotic stress via StNAC262.
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Affiliation(s)
- Li Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lei Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Alejandro Calderón-Urrea
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Department of Biology, California State University, Fresno, CA, United States
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Dias LP, de Oliveira-Busatto LA, Bodanese-Zanettini MH. The differential expression of soybean [Glycine max (L.) Merrill] WRKY genes in response to water deficit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:288-300. [PMID: 27343875 DOI: 10.1016/j.plaphy.2016.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 05/21/2023]
Abstract
Drought is today, and perhaps even more in the future, the main challenge for grain crops, resulting in a drastic yield reduction. Thus, it is of great interest to obtain soybean genotypes tolerant to water deficit. The drought tolerance trait is difficult to obtain through classical breeding due to its polygenic basis. In this context, genetic engineering is presented as a way to achieve this attribute. The ability to modulate the expression of many genes placed the transcription factors as promising biotechnological targets to develop stress tolerant cultivars. The WRKY proteins form a large family of transcription factors that are involved in important physiological and biochemical processes in plants, including the response to water deficit. In this study, the expression pattern determined by qPCR showed that, GmWRKY6, GmWRKY46, GmWRKY56, GmWRKY106 and GmWRKY149 genes are differentially expressed between a drought tolerant and a susceptible soybean genotype in water stress conditions. The in silico promoter and coexpression analysis indicate that these genes act in a stress physiological background.
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Affiliation(s)
- Letícia Pereira Dias
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Luisa Abruzzi de Oliveira-Busatto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
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11
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Ong Q, Nguyen P, Thao NP, Le L. Bioinformatics Approach in Plant Genomic Research. Curr Genomics 2016; 17:368-78. [PMID: 27499685 PMCID: PMC4955030 DOI: 10.2174/1389202917666160331202956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/11/2015] [Accepted: 09/18/2015] [Indexed: 11/22/2022] Open
Abstract
The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity.
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Affiliation(s)
- Quang Ong
- Plant Abiotic Stress Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuc Nguyen
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
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12
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Rahman H, Ramanathan V, Nallathambi J, Duraialagaraja S, Muthurajan R. Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice. BMC Biotechnol 2016; 16 Suppl 1:35. [PMID: 27213684 PMCID: PMC4896240 DOI: 10.1186/s12896-016-0261-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background NAC proteins (NAM (No apical meristem), ATAF (Arabidopsis transcription activation factor) and CUC (cup-shaped cotyledon)) are plant-specific transcription factors reported to be involved in regulating growth, development and stress responses. Salinity responsive transcriptome profiling in a set of contrasting finger millet genotypes through RNA-sequencing resulted in the identification of a NAC homolog (EcNAC 67) exhibiting differential salinity responsive expression pattern. Methods Full length cDNA of EcNAC67 was isolated, characterized and validated for its role in abiotic stress tolerance through agrobacterium mediated genetic transformation in a rice cultivar ASD16. Results Bioinformatics analysis of putative NAC transcription factor (TF) isolated from a salinity tolerant finger millet showed its genetic relatedness to NAC67 family TFs in related cereals. Putative transgenic lines of rice over-expressing EcNAC67 were generated through Agrobacterium mediated transformation and presence/integration of transgene was confirmed through PCR and southern hybridization analysis. Transgenic rice plants harboring EcNAC67 showed enhanced tolerance against drought and salinity under greenhouse conditions. Transgenic rice plants were found to possess higher root and shoot biomass during stress and showed better revival ability upon relief from salinity stress. Upon drought stress, transgenic lines were found to maintain higher relative water content and lesser reduction in grain yield when compared to non-transgenic ASD16 plants. Drought induced spikelet sterility was found to be much lower in the transgenic lines than the non-transgenic ASD16. Conclusion Results revealed the significant role of EcNAC67 in modulating responses against dehydration stress in rice. No detectable abnormalities in the phenotypic traits were observed in the transgenic plants under normal growth conditions. Results indicate that EcNAC67 can be used as a novel source for engineering tolerance against drought and salinity stress in rice and other crop plants. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0261-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hifzur Rahman
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India
| | - Valarmathi Ramanathan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India
| | - Jagedeeshselvam Nallathambi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India
| | - Sudhakar Duraialagaraja
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India.
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13
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Chai C, Wang Y, Valliyodan B, Nguyen HT. Comprehensive Analysis of the Soybean (Glycine max) GmLAX Auxin Transporter Gene Family. FRONTIERS IN PLANT SCIENCE 2016; 7:282. [PMID: 27014306 PMCID: PMC4783406 DOI: 10.3389/fpls.2016.00282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/22/2016] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin plays a critical role in regulation of plant growth and development as well as plant responses to abiotic stresses. This is mainly achieved through its uneven distribution in plant via a polar auxin transport process. Auxin transporters are major players in polar auxin transport. The AUXIN RESISTENT 1/LIKE AUX1 (AUX/LAX) auxin influx carriers belong to the amino acid permease family of proton-driven transporters and function in the uptake of indole-3-acetic acid (IAA). In this study, genome-wide comprehensive analysis of the soybean AUX/LAX (GmLAX) gene family, including phylogenic relationships, chromosome localization, and gene structure, was carried out. A total of 15 GmLAX genes, including seven duplicated gene pairs, were identified in the soybean genome. They were distributed on 10 chromosomes. Despite their higher percentage identities at the protein level, GmLAXs exhibited versatile tissue-specific expression patterns, indicating coordinated functioning during plant growth and development. Most GmLAXs were responsive to drought and dehydration stresses and auxin and abscisic acid (ABA) stimuli, in a tissue- and/or time point- sensitive mode. Several GmLAX members were involved in responding to salt stress. Sequence analysis revealed that promoters of GmLAXs contained different combinations of stress-related cis-regulatory elements. These studies suggest that the soybean GmLAXs were under control of a very complex regulatory network, responding to various internal and external signals. This study helps to identity candidate GmLAXs for further analysis of their roles in soybean development and adaption to adverse environments.
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Affiliation(s)
| | | | | | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
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14
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W-box and G-box elements play important roles in early senescence of rice flag leaf. Sci Rep 2016; 6:20881. [PMID: 26864250 PMCID: PMC4749992 DOI: 10.1038/srep20881] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 01/01/2023] Open
Abstract
Plant cis-elements play important roles in global regulation of gene expression. Based on microarray data from rice flag leaves during early senescence, we identified W-box and G-box cis-elements as positive regulators of senescence in the important rice variety Minghui 63. Both cis-elements were bound by leaf senescence-specific proteins in vitro and influenced senescence in vivo. Furthermore, combination of the two elements drove enhanced expression during leaf senescence, and copy numbers of the cis-elements significantly affected the levels of expression. The W-box is the cognate cis-element for WRKY proteins, while the G-box is the cognate cis-element for bZIP, bHLH and NAC proteins. Consistent with this, WRKY, bZIP, bHLH and NAC family members were overrepresented among transcription factor genes up-regulated according during senescence. Crosstalk between ABA, CTK, BR, auxin, GA and JA during senescence was uncovered by comparing expression patterns of senescence up-regulated transcription factors. Together, our results indicate that hormone-mediated signaling could converge on leaf senescence at the transcriptional level through W-box and G-box elements. Considering that there are very few documented early senescence-related cis-elements, our results significantly contribute to understanding the regulation of flag leaf senescence and provide prioritized targets for stay-green trait improvement.
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15
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Joshi R, Wani SH, Singh B, Bohra A, Dar ZA, Lone AA, Pareek A, Singla-Pareek SL. Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2016; 7:1029. [PMID: 27471513 PMCID: PMC4943945 DOI: 10.3389/fpls.2016.01029] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
Increasing vulnerability of plants to a variety of stresses such as drought, salt and extreme temperatures poses a global threat to sustained growth and productivity of major crops. Of these stresses, drought represents a considerable threat to plant growth and development. In view of this, developing staple food cultivars with improved drought tolerance emerges as the most sustainable solution toward improving crop productivity in a scenario of climate change. In parallel, unraveling the genetic architecture and the targeted identification of molecular networks using modern "OMICS" analyses, that can underpin drought tolerance mechanisms, is urgently required. Importantly, integrated studies intending to elucidate complex mechanisms can bridge the gap existing in our current knowledge about drought stress tolerance in plants. It is now well established that drought tolerance is regulated by several genes, including transcription factors (TFs) that enable plants to withstand unfavorable conditions, and these remain potential genomic candidates for their wide application in crop breeding. These TFs represent the key molecular switches orchestrating the regulation of plant developmental processes in response to a variety of stresses. The current review aims to offer a deeper understanding of TFs engaged in regulating plant's response under drought stress and to devise potential strategies to improve plant tolerance against drought.
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Affiliation(s)
- Rohit Joshi
- Plant Stress Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar, India
| | - Balwant Singh
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses ResearchKanpur, India
| | - Zahoor A. Dar
- Dryland Agricultural Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of KashmirBudgam, India
| | - Ajaz A. Lone
- Dryland Agricultural Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of KashmirBudgam, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
- *Correspondence: Sneh L. Singla-Pareek,
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16
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Achieving Crop Stress Tolerance and Improvement—an Overview of Genomic Techniques. Appl Biochem Biotechnol 2015; 177:1395-408. [DOI: 10.1007/s12010-015-1830-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/02/2015] [Indexed: 01/09/2023]
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17
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Yan J, Wang B, Zhong Y, Yao L, Cheng L, Wu T. The soybean R2R3 MYB transcription factor GmMYB100 negatively regulates plant flavonoid biosynthesis. PLANT MOLECULAR BIOLOGY 2015; 89:35-48. [PMID: 26231207 DOI: 10.1007/s11103-015-0349-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 07/23/2015] [Indexed: 05/02/2023]
Abstract
Soybean flavonoids, a group of important signaling molecules in plant-environment interaction, ubiquitously exist in soybean and are tightly regulated by many genes. Here we reported that GmMYB100, a gene encoding a R2R3 MYB transcription factor, is involved in soybean flavonoid biosynthesis. GmMYB100 is mainly expressed in flowers, leaves and immature embryo, and its level is decreased after pod ripening. Subcellular localization assay indicates that GmMYB100 is a nuclear protein. GmMYB100 has transactivation ability revealed by a yeast functional assay; whereas bioinformatic analysis suggests that GmMYB100 has a negative function in flavonoid biosynthesis. GmMYB100-overexpression represses the transcript levels of flavonoid-related genes in transgenic soybean hairy roots and Arabidopsis, and inhibits isoflavonoid (soybean) and flavonol (Arabidopsis) production in transgenic plants. Furthermore, the transcript levels of six flavonoid-related genes and flavonoid (isoflavonoid and flavone aglycones) accumulation are elevated in the GmMYB100-RNAi transgenic hairy roots. We also demonstrate that GmMYB100 protein depresses the promoter activities of soybean chalcone synthase and chalcone isomerase. These findings indicate that GmMYB100 is a negative regulator in soybean flavonoid biosynthesis pathway.
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Affiliation(s)
- Junhui Yan
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Biao Wang
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China.
| | - Yunpeng Zhong
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Luming Yao
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Linjing Cheng
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Tianlong Wu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
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18
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Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance. BMC Genomics 2015; 16:596. [PMID: 26268547 PMCID: PMC4534118 DOI: 10.1186/s12864-015-1743-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 06/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome sequencing provides the most comprehensive collection of an organism's genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biology. However, to achieve this impact in the area of crop improvement, significant efforts are still required on functional genomics, including the areas of gene annotation, cloning, expression profiling, and functional validation. RESULTS Here we report our efforts in generating the first transcription factor (TF) open reading frame (ORF)eome resource associated with drought resistance in soybean (Glycine max), a major oil/protein crop grown worldwide. This study provides a highly annotated soybean TF-ORFeome associated with drought resistance. It contains information from experimentally verified protein-coding sequences (CDS), expression profiling under several abiotic stresses (drought, salinity, dehydration and ABA), and computationally predicted protein subcellular localization and cis-regulatory elements (CREs) analysis. All the information is available to plant researchers through a freely accessible and user-friendly database, Soybean Knowledge Base (SoyKB). CONCLUSIONS The soybean TF-ORFeome provides a valuable public resource for functional genomics studies, especially in the area of plant abiotic stresses. It will accelerate findings in the areas of abiotic stresses and lead to the generation of crops with enhanced resistance to multiple stresses.
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Affiliation(s)
- Chenglin Chai
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqin Wang
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Silvas Prince
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Lydia Michel
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Science, Informatics Institute, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Genome-wide identification and expression analysis of the CaNAC family members in chickpea during development, dehydration and ABA treatments. PLoS One 2014; 9:e114107. [PMID: 25479253 PMCID: PMC4257607 DOI: 10.1371/journal.pone.0114107] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/02/2014] [Indexed: 02/07/2023] Open
Abstract
The plant-specific NAC transcription factors (TFs) play important roles in regulation of diverse biological processes, including development, growth, cell division and responses to environmental stimuli. In this study, we identified the members of the NAC TF family of chickpea (Cicer arietinum) and assess their expression profiles during plant development and under dehydration and abscisic acid (ABA) treatments in a systematic manner. Seventy-one CaNAC genes were detected from the chickpea genome, including 8 membrane-bound members of which many might be involved in dehydration responses as judged from published literature. Phylogenetic analysis of the chickpea and well-known stress-related Arabidopsis and rice NACs enabled us to predict several putative stress-related CaNACs. By exploring available transcriptome data, we provided a comprehensive expression atlas of CaNACs in various tissues at different developmental stages. With the highest interest in dehydration responses, we examined the expression of the predicted stress-related and membrane-bound CaNACs in roots and leaves of chickpea seedlings, subjected to well-watered (control), dehydration and ABA treatments, using real-time quantitative PCR (RT-qPCR). Nine-teen of the 23 CaNACs examined were found to be dehydration-responsive in chickpea roots and/or leaves in either ABA-dependent or -independent pathway. Our results have provided a solid foundation for selection of promising tissue-specific and/or dehydration-responsive CaNAC candidates for detailed in planta functional analyses, leading to development of transgenic chickpea varieties with improved productivity under drought.
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Thu NBA, Hoang XLT, Doan H, Nguyen TH, Bui D, Thao NP, Tran LSP. Differential expression analysis of a subset of GmNAC genes in shoots of two contrasting drought-responsive soybean cultivars DT51 and MTD720 under normal and drought conditions. Mol Biol Rep 2014. [PMID: 24985975 DOI: 10.1007/s11105-014-0825-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
NAC transcription factors are known to be involved in regulation of plant responses to drought stress. In this study, the expression of 23 drought-responsive GmNAC genes was assessed in the shoot tissues of DT51 and MTD720, the two soybean varieties with contrasting drought-responsive phenotypes, by real-time quantitative PCR (RT-qPCR) under normal and drought conditions. Results indicated that expression profile of GmNAC genes was genotype-dependent, and six GmNACs (GmNAC019, 043, 062, 085, 095 and 101) had higher transcript levels in the shoots of the drought-tolerant DT51 in comparison with the drought-sensitive MTD720 under drought. Our study suggests a positive correlation between the higher drought tolerance degree of DT51 versus MTD720 and the up-regulation of at least these six drought-responsive GmNACs in the shoot tissues. Furthermore, on the basis of our analysis, three genes, GmNAC043, 085 and 101, were identified as promising candidates for development of drought-tolerant soybean cultivars by genetic engineering.
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Affiliation(s)
- Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
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21
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Thu NBA, Hoang XLT, Doan H, Nguyen TH, Bui D, Thao NP, Tran LSP. Differential expression analysis of a subset of GmNAC genes in shoots of two contrasting drought-responsive soybean cultivars DT51 and MTD720 under normal and drought conditions. Mol Biol Rep 2014; 41:5563-9. [PMID: 24985975 DOI: 10.1007/s11033-014-3507-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
NAC transcription factors are known to be involved in regulation of plant responses to drought stress. In this study, the expression of 23 drought-responsive GmNAC genes was assessed in the shoot tissues of DT51 and MTD720, the two soybean varieties with contrasting drought-responsive phenotypes, by real-time quantitative PCR (RT-qPCR) under normal and drought conditions. Results indicated that expression profile of GmNAC genes was genotype-dependent, and six GmNACs (GmNAC019, 043, 062, 085, 095 and 101) had higher transcript levels in the shoots of the drought-tolerant DT51 in comparison with the drought-sensitive MTD720 under drought. Our study suggests a positive correlation between the higher drought tolerance degree of DT51 versus MTD720 and the up-regulation of at least these six drought-responsive GmNACs in the shoot tissues. Furthermore, on the basis of our analysis, three genes, GmNAC043, 085 and 101, were identified as promising candidates for development of drought-tolerant soybean cultivars by genetic engineering.
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Affiliation(s)
- Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
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Hiz MC, Canher B, Niron H, Turet M. Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PLoS One 2014; 9:e92598. [PMID: 24651267 PMCID: PMC3961409 DOI: 10.1371/journal.pone.0092598] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/24/2014] [Indexed: 12/02/2022] Open
Abstract
Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.
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Affiliation(s)
- Mahmut Can Hiz
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
- * E-mail:
| | - Balkan Canher
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Harun Niron
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Muge Turet
- Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey
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Quach TN, Tran LSP, Valliyodan B, Nguyen HTM, Kumar R, Neelakandan AK, Guttikonda SK, Sharp RE, Nguyen HT. Functional analysis of water stress-responsive soybean GmNAC003 and GmNAC004 transcription factors in lateral root development in arabidopsis. PLoS One 2014; 9:e84886. [PMID: 24465446 PMCID: PMC3900428 DOI: 10.1371/journal.pone.0084886] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 11/27/2013] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis, NAC (NAM, ATAF and CUC) transcription factors have been found to promote lateral root number through the auxin signaling pathway. In the present study, the role of water stress-inducible soybean GmNAC003 and GmNAC004 genes in the enhancement of lateral root development under water deficit conditions was investigated. Both genes were highly expressed in roots, leaves and flowers of soybean and were strongly induced by water stress and moderately induced by a treatment with abscisic acid (ABA). They showed a slight response to treatment with 2,4-dichlorophenoxyacetic acid (2,4-D). The transgenic Arabidopsis plants overexpressing GmNAC004 showed an increase in lateral root number and length under non-stress conditions and maintained higher lateral root number and length under mild water stress conditions compared to the wild-type (WT), while the transgenic plants overexpressing GmNAC003 did not show any response. However, LR development of GmNAC004 transgenic Arabidopsis plants was not enhanced in the water-stressed compared to the well-watered treatment. In the treatment with ABA, LR density of the GmNAC004 transgenic Arabidopsis was less suppressed than that of the WT, suggesting that GmNAC004 counteracts ABA-induced inhibition of lateral root development. In the treatment with 2,4-D, lateral root density was enhanced in both GmNAC004 transgenic Arabidopsis and WT plants but the promotion was higher in the transgenic plants. Conversely, in the treatment with naphthylphthalamic acid (NPA), lateral root density was inhibited and there was no difference in the phenotype of the GmNAC004 transgenic Arabidopsis and WT plants, indicating that auxin is required for the action of GmNAC004. Transcript analysis for a number of known auxin and ABA related genes showed that GmNAC004's role may suppress ABA signaling but promote auxin signaling to increase lateral root development in the Arabidopsis heterologous system.
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Affiliation(s)
- Truyen N. Quach
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Lam-Son Phan Tran
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Babu Valliyodan
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Hanh TM. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Rajesh Kumar
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Anjanasree K. Neelakandan
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Satish Kumar Guttikonda
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Robert E. Sharp
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
| | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
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Thao NP, Thu NBA, Hoang XLT, Van Ha C, Tran LSP. Differential expression analysis of a subset of drought-responsive GmNAC genes in two soybean cultivars differing in drought tolerance. Int J Mol Sci 2013; 14:23828-41. [PMID: 24322442 PMCID: PMC3876080 DOI: 10.3390/ijms141223828] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 12/26/2022] Open
Abstract
The plant-specific NAC transcription factors play important roles in plant response to drought stress. Here, we have compared the expression levels of a subset of GmNAC genes in drought-tolerant DT51 and drought-sensitive MTD720 under both normal and drought stress conditions aimed at identifying correlation between GmNAC expression levels and drought tolerance degree, as well as potential GmNAC candidates for genetic engineering. The expression of 23 selected dehydration-responsive GmNACs was assessed in both stressed and unstressed root tissues of DT51 and MTD720 using real-time quantitative PCR. The results indicated that expression of GmNACs was genotype-dependent. Seven and 13 of 23 tested GmNACs showed higher expression levels in roots of DT51 in comparison with MTD720 under normal and drought stress conditions, respectively, whereas none of them displayed lower transcript levels under any conditions. This finding suggests that the higher drought tolerance of DT51 might be positively correlated with the higher induction of the GmNAC genes during water deficit. The drought-inducible GmNAC011 needs to be mentioned as its transcript accumulation was more than 76-fold higher in drought-stressed DT51 roots relative to MTD720 roots. Additionally, among the GmNAC genes examined, GmNAC085, 092, 095, 101 and 109 were not only drought-inducible but also more highly up-regulated in DT51 roots than in that of MTD720 under both treatment conditions. These data together suggest that GmNAC011, 085, 092, 095, 101 and 109 might be promising candidates for improvement of drought tolerance in soybean by biotechnological approaches.
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Affiliation(s)
- Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh 70000, Vietnam; E-Mails: (N.B.A.T.); (X.L.T.H.)
| | - Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh 70000, Vietnam; E-Mails: (N.B.A.T.); (X.L.T.H.)
| | - Xuan Lan Thi Hoang
- School of Biotechnology, International University, Vietnam National University HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh 70000, Vietnam; E-Mails: (N.B.A.T.); (X.L.T.H.)
| | - Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; E-Mail:
- National Key Laboratory of Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham Van Dong Street, Hanoi 10000, Vietnam
- Post-Graduate Program, Vietnamese Academy of Agricultural Science, Thanhtri, Hanoi 10000, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; E-Mail:
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25
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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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26
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Hassan NM, El-Bastawisy ZM, El-Sayed AK, Ebeed HT, Nemat Alla MM. Roles of dehydrin genes in wheat tolerance to drought stress. J Adv Res 2013; 6:179-88. [PMID: 25750752 PMCID: PMC4348445 DOI: 10.1016/j.jare.2013.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 01/24/2023] Open
Abstract
Physiological parameters and expression levels of drought related genes were analyzed in early vegetative stage of two bread wheat cultivars (Sids and Gmiza) differ in drought tolerance capacity. Both cultivars were imposed to gradual water depletion started on day 17 till day 32 after sowing. Sids, the more tolerant cultivar to drought showed higher fresh and dry weights than the drought sensitive genotype, Gmiza. Under water stress, Sids had higher membrane stability index (MSI), lower accumulated H2O2 and higher activity of the antioxidant enzymes; catalase (CAT), guaiacol peroxidase (GPX), ascorbate peroxidase (APX) and superoxide dismutase (SOD) than Gmiza. On the other hand, the differential expression patterns of the genes dhn, wcor and dreb were observed due to water deficit intensity according to cultivar’s tolerance to drought. The DNA sequence alignment of dun showed high similarity of about 80–92% identities with other related plants. The most striking overall observed trend was the highly induction in the expression of dun, wcor and dreb in leaves of the tolerant genotype, Sids under severe water stress.
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Affiliation(s)
- Nemat M Hassan
- Botany Department, Faculty of Science, Damietta University, Egypt
| | | | | | - Heba T Ebeed
- Botany Department, Faculty of Science, Damietta University, Egypt
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27
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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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28
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Nie DM, Ouyang YD, Wang X, Zhou W, Hu CG, Yao J. Genome-wide analysis of endosperm-specific genes in rice. Gene 2013; 530:236-47. [PMID: 23948082 DOI: 10.1016/j.gene.2013.07.088] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 12/31/2022]
Abstract
The endosperm of the cereal crop is an important nutrient source for humans. It also acts as a critical integrator of plant seed growth and development. Despite its importance, the comprehensive understanding in regulating of endosperm development in rice remains elusive. Here, we performed a genomic survey comprising the identification and functional characterization of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data and Gene Ontology (GO) analysis. A total of 151 endosperm-specific genes were identified, and the expression patterns of 13 selected genes were confirmed by qRT-PCR analysis. Promoter regions of the endosperm-specific expression genes were analyzed by PLACE Signal Scan Search. The results indicated that some motifs were involved in endosperm-specific expression regulation, and some cis-elements were responsible for hormone regulation. The bootstrap analysis indicated that the RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. GO analysis indicated that these genes could be classified into 12 groups, namely, transcription factor, stress/defense, seed storage protein (SSP), carbohydrate and energy metabolism, seed maturation, protein metabolism, lipid metabolism, transport, cell wall related, hormone related, signal transduction, and one unclassified group. Taken together, our results provide informative clues for further functional characterization of the endosperm-specific genes, which facilitate the understanding of the molecular mechanism in rice endosperm development.
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Affiliation(s)
- Dong-Ming Nie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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29
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Cabreira C, Cagliari A, Bücker-Neto L, Wiebke-Strohm B, de Freitas LB, Marcelino-Guimarães FC, Nepomuceno AL, Margis-Pinheiro MMAN, Bodanese-Zanettini MH. The Lesion Simulating Disease (LSD) gene family as a variable in soybean response to Phakopsora pachyrhizi infection and dehydration. Funct Integr Genomics 2013; 13:323-38. [DOI: 10.1007/s10142-013-0326-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/20/2013] [Accepted: 05/27/2013] [Indexed: 12/13/2022]
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30
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. DNA Res 2013; 20:151-62. [PMID: 23284086 PMCID: PMC3628445 DOI: 10.1093/dnares/dss040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/10/2012] [Indexed: 12/11/2022] Open
Abstract
Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Biomass Engineering Program, 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
| | - Takuhiro Yoshida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Kazuo Shinozaki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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31
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Chung E, Kim KM, Lee JH. Genome-wide analysis and molecular characterization of heat shock transcription factor family in Glycine max. J Genet Genomics 2013; 40:127-35. [PMID: 23522385 DOI: 10.1016/j.jgg.2012.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/04/2012] [Accepted: 12/07/2012] [Indexed: 11/16/2022]
Abstract
Heat shock transcription factors (Hsfs) play an essential role on the increased tolerance against heat stress by regulating the expression of heat-responsive genes. In this study, a genome-wide analysis was performed to identify all of the soybean (Glycine max) GmHsf genes based on the latest soybean genome sequence. Chromosomal location, protein domain, motif organization, and phylogenetic relationships of 26 non-redundant GmHsf genes were analyzed compared with AtHsfs (Arabidopsis thaliana Hsfs). According to their structural features, the predicted members were divided into the previously defined classes A-C, as described for AtHsfs. Transcript levels and subcellular localization of five GmHsfs responsive to abiotic stresses were analyzed by real-time RT-PCR. These results provide a fundamental clue for understanding the complexity of the soybean GmHsf gene family and cloning the functional genes in future studies.
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Affiliation(s)
- Eunsook Chung
- BK21 Center for Silver-Bio Industrialization, College of Natural Resources and Life Science, Dong-A University, Hadan 2 dong, Sahagu, Busan 604-714, Republic of Korea
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32
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Abstract
Soybean (Glycine max) is one of the most important crops in legume family. Soybean and soybean-based products are also considered as popular food for human and animal husbandry. With its high oil content, soybean has become a potential resource for the production of renewable fuel. However, soybean is considered one of the most drought-sensitive crops, with approximately 40% reduction of the yield in the worst years. Recent research progresses in elucidation of biochemical, morphological and physiological responses as well as molecular mechanisms of plant adaptation to drought stress in model plants have provided a solid foundation for translational genomics of soybean toward drought tolerance. In this review, we will summarize the recent advances in development of drought-tolerant soybean cultivars by gene transfer.
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Affiliation(s)
- Nguyen Phuong Thao
- International University, Vietnam National University-HCMC, St block 6, Linh Trung ward, Thu Duc district, HCM city, Vietnam
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33
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Le DT, Nishiyama R, Watanabe Y, Tanaka M, Seki M, Ham LH, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis. PLoS One 2012; 7:e49522. [PMID: 23189148 PMCID: PMC3505142 DOI: 10.1371/journal.pone.0049522] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 10/09/2012] [Indexed: 12/15/2022] Open
Abstract
The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46,093 soybean genes, which were predicted with high confidence among approximately 66,000 putative genes, 41,059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Le Huy Ham
- National Key Laboratory of Plant Cell Biotechnology and Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
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34
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Ma Y, Qin F, Tran LSP. Contribution of genomics to gene discovery in plant abiotic stress responses. MOLECULAR PLANT 2012; 5:1176-8. [PMID: 22930735 DOI: 10.1093/mp/sss085] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Yun Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100039, China
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35
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Huang H, Wang Y, Wang S, Wu X, Yang K, Niu Y, Dai S. Transcriptome-wide survey and expression analysis of stress-responsive NAC genes in Chrysanthemum lavandulifolium. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 193-194:18-27. [PMID: 22794915 DOI: 10.1016/j.plantsci.2012.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 05/22/2023]
Abstract
The plant-specific NAC (NAM, ATAF, and CUC) transcription factor family plays a vital role in various plant growth and developmental processes as well as in stress resistance. Using RNA sequencing, we found that the ClNAC genes (ClNAC1-44) were the most strongly up-regulated transcription factor family in Chrysanthemum lavandulifolium leaves under salt treatment. We carried out reverse transcriptase polymerase chain reaction to monitor ClNAC genes response against multiple stresses and hormonal treatments including salt, drought, cold, heat, abscisic acid and salicylic acid treatments. The results showed that 35 ClNAC genes were differentially expressed in different organ, and 32 ClNAC genes could respond to at least 2 kinds of treatments. Quantitative real time polymerase chain reaction showed that 10 ClNAC genes belonging to 7 different subfamilies could respond to at least 5 kinds of treatments. Over 50-fold variation in transcriptional levels of ClNAC17 and ClNAC21 genes was observed under 6 different types of treatments. In the present study, high-level expression of ClNAC genes under abiotic stresses and hormonal treatments suggests that the NAC transcription factors play important roles in abiotic stress tolerance and adaptation.
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Affiliation(s)
- He Huang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China
| | - Yi Wang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China
| | - Shunli Wang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China; College of Life Science, Beijing Forestry University, Beijing 100038, China
| | - Xuan Wu
- College of Foresty, Beijing Forestry University, Beijing 100038, China
| | - Ke Yang
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China; School of Forestry and Environmental Studies, Yale University, New Haven, CT 06511, USA
| | - Yajing Niu
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China
| | - Silan Dai
- College of Landscape Architecture, Beijing Forestry University, Beijing 100038, China.
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36
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Soares-Cavalcanti NM, Belarmino LC, Kido EA, Pandolfi V, Marcelino-Guimarães FC, Rodrigues FA, Pereira GAG, Benko-Iseppon AM. Overall picture of expressed Heat Shock Factors in Glycine max, Lotus japonicus and Medicago truncatula. Genet Mol Biol 2012; 35:247-59. [PMID: 22802710 PMCID: PMC3392877 DOI: 10.1590/s1415-47572012000200006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Heat shock (HS) leads to the activation of molecular mechanisms, known as HS-response, that prevent damage and enhance survival under stress. Plants have a flexible and specialized network of Heat Shock Factors (HSFs), which are transcription factors that induce the expression of heat shock proteins. The present work aimed to identify and characterize the Glycine max HSF repertory in the Soybean Genome Project (GENOSOJA platform), comparing them with other legumes (Medicago truncatula and Lotus japonicus) in view of current knowledge of Arabidopsis thaliana. The HSF characterization in leguminous plants led to the identification of 25, 19 and 21 candidate ESTs in soybean, Lotus and Medicago, respectively. A search in the SuperSAGE libraries revealed 68 tags distributed in seven HSF gene types. From the total number of obtained tags, more than 70% were related to root tissues (water deficit stress libraries vs. controls), indicating their role in abiotic stress responses, since the root is the first tissue to sense and respond to abiotic stress. Moreover, as heat stress is related to the pressure of dryness, a higher HSF expression was expected at the water deficit libraries. On the other hand, expressive HSF candidates were obtained from the library inoculated with Asian Soybean Rust, inferring crosstalk among genes associated with abiotic and biotic stresses. Evolutionary relationships among sequences were consistent with different HSF classes and subclasses. Expression profiling indicated that regulation of specific genes is associated with the stage of plant development and also with stimuli from other abiotic stresses pointing to the maintenance of HSF expression at a basal level in soybean, favoring its activation under heat-stress conditions.
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Affiliation(s)
- Nina M Soares-Cavalcanti
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
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Vidal RO, do Nascimento LC, Mondego JMC, Pereira GAG, Carazzolle MF. Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 2012; 35:331-4. [PMID: 22802718 PMCID: PMC3392885 DOI: 10.1590/s1415-47572012000200014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both cultivars. Our method identified more than 6,000 SNPs in tolerant and sensitive Brazilian cultivars in those drought stress related genes. Among these SNPs, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (MYB, WRKY) related to tolerance to abiotic stress.
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Affiliation(s)
- Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Anai T, Sato S, Yamazaki T, Lü S, Wu H, Tabata S, Harada K. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A 2012; 109:E2155-64. [PMID: 22619331 PMCID: PMC3420212 DOI: 10.1073/pnas.1117982109] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene (E1). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity.
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Affiliation(s)
- Zhengjun Xia
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Satoshi Watanabe
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Tetsuya Yamada
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yasutaka Tsubokura
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | | | - Hong Zhai
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Shusei Sato
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu 292-0812, Japan; and
| | - Toshimasa Yamazaki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Shixiang Lü
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Hongyan Wu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu 292-0812, Japan; and
| | - Kyuya Harada
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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Puranik S, Sahu PP, Srivastava PS, Prasad M. NAC proteins: regulation and role in stress tolerance. TRENDS IN PLANT SCIENCE 2012; 17:369-81. [PMID: 22445067 DOI: 10.1016/j.tplants.2012.02.004] [Citation(s) in RCA: 599] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 01/31/2012] [Accepted: 02/16/2012] [Indexed: 05/17/2023]
Abstract
The plant-specific NAC (NAM, ATAF1,2 and CUC2) proteins constitute a major transcription factor family renowned for their roles in several developmental programs. Despite their highly conserved DNA-binding domains, their remarkable diversification across plants reflects their numerous functions. Lately, they have received much attention as regulators in various stress signaling pathways which may include interplay of phytohormones. This review summarizes the recent progress in research on NACs highlighting the proteins' potential for engineering stress tolerance against various abiotic and biotic challenges. We discuss regulatory components and targets of NAC proteins in the context of their prospective role for crop improvement strategies via biotechnological intervention.
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Affiliation(s)
- Swati Puranik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Mao X, Zhang H, Qian X, Li A, Zhao G, Jing R. TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2933-46. [PMID: 22330896 PMCID: PMC3350912 DOI: 10.1093/jxb/err462] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 05/18/2023]
Abstract
Environmental stresses such as drought, salinity, and cold are major factors that significantly limit agricultural productivity. NAC transcription factors play essential roles in response to various abiotic stresses. However, the paucity of wheat NAC members functionally characterized to date does not match the importance of this plant as a world staple crop. Here, the function of TaNAC2 was characterized in Arabidopsis thaliana. A fragment of TaNAC2 was obtained from suppression subtractive cDNA libraries of wheat treated with polyethylene glycol, and its full-length cDNA was obtained by searching a full-length wheat cDNA library. Gene expression profiles indicated that TaNAC2 was involved in response to drought, salt, cold, and abscisic acid treatment. To test its function, transgenic Arabidopsis lines overexpressing TaNAC2-GFP controlled by the cauliflower mosaic virus 35S promoter were generated. Overexpression of TaNAC2 resulted in enhanced tolerances to drought, salt, and freezing stresses in Arabidopsis, which were simultaneously demonstrated by enhanced expression of abiotic stress-response genes and several physiological indices. Therefore, TaNAC2 has potential for utilization in transgenic breeding to improve abiotic stress tolerances in crops.
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Affiliation(s)
| | | | | | | | | | - Ruilian Jing
- To whom correspondence should be addressed. E-mail:
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Nishiyama R, Le DT, Watanabe Y, Matsui A, Tanaka M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency. PLoS One 2012; 7:e32124. [PMID: 22355415 PMCID: PMC3280229 DOI: 10.1371/journal.pone.0032124] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/19/2012] [Indexed: 01/04/2023] Open
Abstract
Soil destruction by abiotic environmental conditions, such as high salinity, has resulted in dramatic losses of arable land, giving rise to the need of studying mechanisms of plant adaptation to salt stress aimed at creating salt-tolerant plants. Recently, it has been reported that cytokinins (CKs) regulate plant environmental stress responses through two-component systems. A decrease in endogenous CK levels could enhance salt and drought stress tolerance. Here, we have investigated the global transcriptional change caused by a reduction in endogenous CK content under both normal and salt stress conditions. Ten-day-old Arabidopsis thaliana wild-type (WT) and CK-deficient ipt1,3,5,7 plants were transferred to agar plates containing either 0 mM (control) or 200 mM NaCl and maintained at normal growth conditions for 24 h. Our experimental design allowed us to compare transcriptome changes under four conditions: WT-200 mM vs. WT-0 mM, ipt1,3,5,7-0 mM vs. WT-0 mM, ipt1,3,5,7-200 mM vs. ipt1,3,5,7-0 mM and ipt1,3,5,7-200 mM vs. WT-200 mM NaCl. Our results indicated that the expression of more than 10% of all of the annotated Arabidopsis genes was altered by CK deficiency under either normal or salt stress conditions when compared to WT. We found that upregulated expression of many genes encoding either regulatory proteins, such as NAC, DREB and ZFHD transcription factors and the calcium sensor SOS3, or functional proteins, such as late embryogenesis-abundant proteins, xyloglucan endo-transglycosylases, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins, may contribute to improved salt tolerance of CK-deficient plants. We also demonstrated that the downregulation of photosynthesis-related genes and the upregulation of several NAC genes may cause the altered morphological phenotype of CK-deficient plants. This study highlights the impact of CK regulation on the well-known stress-responsive signaling pathways, which regulate plant adaptation to high salinity as well as other environmental stresses.
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Affiliation(s)
- Rie Nishiyama
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Dung Tien Le
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Hanoi, Vietnam
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- * E-mail:
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Ayarpadikannan S, Chung E, Cho CW, So HA, Kim SO, Jeon JM, Kwak MH, Lee SW, Lee JH. Exploration for the salt stress tolerance genes from a salt-treated halophyte, Suaeda asparagoides. PLANT CELL REPORTS 2012; 31:35-48. [PMID: 21874516 DOI: 10.1007/s00299-011-1137-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 05/12/2023]
Abstract
Salinity stress severely affects plant growth and development causing crop loss worldwide. Suaeda asparagoides is a salt-marsh euhalophyte widely distributed in southwestern foreshore of Korea. To isolate salt tolerance genes from S. asparagoides, we constructed a cDNA library from leaf tissues of S. asparagoides that was treated with 200 mM NaCl. A total of 1,056 clones were randomly selected for EST sequencing, and 932 of them produced readable sequence. By sequence analysis, we identified 538 unigenes and registered each in National Center for Biotechnology Information. The 80 salt stress related genes were selected to study their differential expression. Reverse transcription-PCR and Northern blot analysis revealed that 23 genes were differentially expressed under the high salinity stress conditions in S. asparagoides. They are functionally diverse including transport, signal transduction, transcription factor, metabolism and stress associated protein, and unknown function. Among them dehydrin (SaDhn) and RNA binding protein (SaRBP1) were examined for their abiotic stress tolerance in yeast (Saccharomyces cerevisiae). Yeast overexpressing SaDhn and SaRBP1 showed enhanced tolerance to osmotic, freezing and heat shock stresses. This study provides the evidence that SaRBP1 and SaDhn from S. asparagoides exert abiotic stress tolerance in yeast. Information of salt stress related genes from S. asparagoides would contribute for the accumulating genetic resources to improve osmotic tolerance in plants.
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Affiliation(s)
- Selvam Ayarpadikannan
- BK21 Center for Silver-Bio Industrialization, College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
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de Almeida Barros B, da Silva WG, Moreira MA, de Barros EG. In silico characterization and expression analysis of the multigene family encoding the Bowman-Birk protease inhibitor in soybean. Mol Biol Rep 2012; 39:327-34. [PMID: 21556767 DOI: 10.1007/s11033-011-0742-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/27/2011] [Indexed: 03/03/2023]
Abstract
The Bowman-Birk (BBI) protease inhibitors can be used as source of sulfur amino acids, can regulate endogenous protease activity during seed germination and during the defense response of plants to pathogens. In soybean this family has not been fully described. The goal of this work was to characterize in silico and analyze the expression of the members of this family in soybean. We identified 11 potential BBI genes in the soybean genome. In each one of them at least a characteristic BBI conserved domain was detected in addition to a potential signal peptide. The sequences have been positioned in the soybean physical map and the promoter regions were analyzed with respect to known regulatory elements. Elements related to seed-specific expression and also to response to biotic and abiotic stresses have been identified. Based on the in silico analysis and also on quantitative RT-PCR data it was concluded that BBI-A, BBI-CII and BBI-DII are expressed specifically in the seed. The expression profiles of these three genes are similar along seed development. Their expressions reach a maximum in the intermediate stages and decrease as the seed matures. The BBI-DII transcripts are the most abundant ones followed by those of BBI-A and BBI-CII.
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Affiliation(s)
- Beatriz de Almeida Barros
- Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011; 52:2017-38. [PMID: 22156726 PMCID: PMC3233218 DOI: 10.1093/pcp/pcr153] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
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45
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Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011. [PMID: 22156726 DOI: 10.1093/pcp/pc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
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46
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Heis MD, Ditmer EM, de Oliveira LA, Frazzon APG, Margis R, Frazzon J. Differential expression of cysteine desulfurases in soybean. BMC PLANT BIOLOGY 2011; 11:166. [PMID: 22099069 PMCID: PMC3233524 DOI: 10.1186/1471-2229-11-166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 11/18/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Iron-sulfur [Fe-S] clusters are prosthetic groups required to sustain fundamental life processes including electron transfer, metabolic reactions, sensing, signaling, gene regulation and stabilization of protein structures. In plants, the biogenesis of Fe-S protein is compartmentalized and adapted to specific needs of the cell. Many environmental factors affect plant development and limit productivity and geographical distribution. The impact of these limiting factors is particularly relevant for major crops, such as soybean, which has worldwide economic importance. RESULTS Here we analyze the transcriptional profile of the soybean cysteine desulfurases NFS1, NFS2 and ISD11 genes, involved in the biogenesis of [Fe-S] clusters, by quantitative RT-PCR. NFS1, ISD11 and NFS2 encoding two mitochondrial and one plastid located proteins, respectively, are duplicated and showed distinct transcript levels considering tissue and stress response. NFS1 and ISD11 are highly expressed in roots, whereas NFS2 showed no differential expression in tissues. Cold-treated plants showed a decrease in NFS2 and ISD11 transcript levels in roots, and an increased expression of NFS1 and ISD11 genes in leaves. Plants treated with salicylic acid exhibited increased NFS1 transcript levels in roots but lower levels in leaves. In silico analysis of promoter regions indicated the presence of different cis-elements in cysteine desulfurase genes, in good agreement with differential expression of each locus. Our data also showed that increasing of transcript levels of mitochondrial genes, NFS1/ISD11, are associated with higher activities of aldehyde oxidase and xanthine dehydrogenase, two cytosolic Fe-S proteins. CONCLUSIONS Our results suggest a relationship between gene expression pattern, biochemical effects, and transcription factor binding sites in promoter regions of cysteine desulfurase genes. Moreover, data show proportionality between NFS1 and ISD11 genes expression.
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Affiliation(s)
- Marta D Heis
- Biotechnology Center, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Elisabeth M Ditmer
- Biotechnology Center, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Luisa A de Oliveira
- Biotechnology Center, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Ana Paula G Frazzon
- Department of Microbiology, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Rogério Margis
- Biotechnology Center, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jeverson Frazzon
- Department of Food Science, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
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Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res 2011; 18:263-76. [PMID: 21685489 PMCID: PMC3158466 DOI: 10.1093/dnares/dsr015] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 05/24/2011] [Indexed: 01/17/2023] Open
Abstract
Plant-specific NAC transcription factors (TFs) play important roles in regulating diverse biological processes, including development, senescence, growth, cell division and responses to environmental stress stimuli. Within the soybean genome, we identified 152 full-length GmNAC TFs, including 11 membrane-bound members. In silico analysis of the GmNACs, together with their Arabidopsis and rice counterparts, revealed similar NAC architecture. Next, we explored the soybean Affymetrix array and Illumina transcriptome sequence data to analyse tissue-specific expression profiles of GmNAC genes. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis and rice as seeding sequences identified 58 of the 152 GmNACs as putative stress-responsive genes, including eight previously reported dehydration-responsive GmNACs. We could design gene-specific primers for quantitative real-time PCR verification of 38 out of 50 newly predicted stress-related genes. Twenty-five and six GmNACs were found to be induced and repressed 2-fold or more, respectively, in soybean roots and/or shoots in response to dehydration. GmNAC085, whose amino acid sequence was 39%; identical to that of well-known SNAC1/ONAC2, was the most induced gene upon dehydration, showing 390-fold and 20-fold induction in shoots and roots, respectively. Our systematic analysis has identified excellent tissue-specific and/or dehydration-responsive candidate GmNAC genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiichi Mochida
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res 2011; 18:321-32. [PMID: 21729923 PMCID: PMC3190953 DOI: 10.1093/dnares/dsr019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The interactions between transcription factors (TFs) and cis-regulatory DNA sequences control gene expression, constituting the essential functional linkages of gene regulatory networks. The aim of this study is to identify and integrate all putative TFs from six grass species: Brachypodium distachyon, maize, rice, sorghum, barley, and wheat with significant information into an integrative database (GramineaeTFDB) for comparative genomics and functional genomics. For each TF, sequence features, promoter regions, domain alignments, GO assignment, FL-cDNA information, if available, and cross-references to various public databases and genetic resources are provided. Additionally, GramineaeTFDB possesses a tool which aids the users to search for putative cis-elements located in the promoter regions of TFs and predict the functions of the TFs using cis-element-based functional prediction approach. We also supplied hyperlinks to expression profiles of those TF genes of maize, rice, and barley, for which data are available. Furthermore, information about the availability of FOX and Ds mutant lines for rice and maize TFs, respectively, are also accessible through hyperlinks. Our study provides an important user-friendly public resource for functional analyses and comparative genomics of grass TFs, and understanding of the architecture of transcriptional regulatory networks and evolution of the TFs in agriculturally important cereal crops.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Genome-wide expression profiling of soybean two-component system genes in soybean root and shoot tissues under dehydration stress. DNA Res 2011; 18:17-29. [PMID: 21208938 PMCID: PMC3041507 DOI: 10.1093/dnares/dsq032] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/29/2010] [Indexed: 11/13/2022] Open
Abstract
Two-component systems (TCSs) play vital functions in the adaptation of plants to environmental stresses. To identify soybean TCS genes involved in the regulation of drought stress response, we performed tissue-specific expression profiling of all 83 putative TCS genes in plants subjected to dehydration. Under well-watered conditions, the majority of soybean TCS genes were expressed higher in the root tissues. Additionally, a high variability in transcript abundance was observed for the TCS genes in both roots and shoots. Under dehydration, TCS genes were more responsive in shoots than in roots. Further analysis indicated that 50% more TCS genes were repressed by dehydration than induced. Specifically, 18 genes were induced by 2-fold or more, whereas 33 genes were down-regulated at least 2-fold by dehydration. TCS genes putatively involved in cytokinin and ethylene signallings strongly responded to dehydration, suggesting that crosstalk exists between different hormonal and stress pathways. Our study provides the first glance into the complex regulatory roles of soybean TCSs underlying their functions in response to dehydration. Additionally, these systematic expression analyses identified excellent dehydration-responsive candidate genes to further clarify soybean TCS functions in drought response and to enable the development of improved drought tolerance in transgenic soybeans.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiichi Mochida
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Hernandez-Garcia CM, Bouchard RA, Rushton PJ, Jones ML, Chen X, Timko MP, Finer JJ. High level transgenic expression of soybean (Glycine max) GmERF and Gmubi gene promoters isolated by a novel promoter analysis pipeline. BMC PLANT BIOLOGY 2010; 10:237. [PMID: 21050446 PMCID: PMC3095320 DOI: 10.1186/1471-2229-10-237] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/04/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Although numerous factors can influence gene expression, promoters are perhaps the most important component of the regulatory control process. Promoter regions are often defined as a region upstream of the transcriptional start. They contain regulatory elements that interact with regulatory proteins to modulate gene expression. Most genes possess their own unique promoter and large numbers of promoters are therefore available for study. Unfortunately, relatively few promoters have been isolated and characterized; particularly from soybean (Glycine max). RESULTS In this research, a bioinformatics approach was first performed to identify members of the Gmubi (G.max ubiquitin) and the GmERF (G. max Ethylene Response Factor) gene families of soybean. Ten Gmubi and ten GmERF promoters from selected genes were cloned upstream of the gfp gene and successfully characterized using rapid validation tools developed for both transient and stable expression. Quantification of promoter strength using transient expression in lima bean (Phaseolus lunatus) cotyledonary tissue and stable expression in soybean hairy roots showed that the intensity of gfp gene expression was mostly conserved across the two expression systems. Seven of the ten Gmubi promoters yielded from 2- to 7-fold higher expression than a standard CaMV35S promoter while four of the ten GmERF promoters showed from 1.5- to 2.2-times higher GFP levels compared to the CaMV35S promoter. Quantification of GFP expression in stably-transformed hairy roots of soybean was variable among roots derived from different transformation events but consistent among secondary roots, derived from the same primary transformation events. Molecular analysis of hairy root events revealed a direct relationship between copy number and expression intensity; higher copy number events displayed higher GFP expression. CONCLUSION In this study, we present expression intensity data on 20 novel soybean promoters from two different gene families, ubiquitin and ERF. We also demonstrate the utility of lima bean cotyledons and soybean hairy roots for rapid promoter analyses and provide novel insights towards the utilization of these expression systems. The soybean promoters characterized here will be useful for production of transgenic soybean plants for both basic research and commercial plant improvement.
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Affiliation(s)
- Carlos M Hernandez-Garcia
- Department of Horticulture and Crop Science, OARDC/The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - Robert A Bouchard
- Department of Horticulture and Crop Science, OARDC/The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - Paul J Rushton
- Department of Biology, University of Virginia, Charlottesville, VA 22904 USA
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007 USA
| | - Michelle L Jones
- Department of Horticulture and Crop Science, OARDC/The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - Xianfeng Chen
- Department of Microbiology, University of Virginia Health Systems, Charlottesville, VA 22908 USA
- USACE, Environmental Lab, ERDC, 3909 Halls Ferry Road, Vicksburg, MS 39180 USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904 USA
| | - John J Finer
- Department of Horticulture and Crop Science, OARDC/The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
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