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Takato S, Kakei Y, Mitsui M, Ishida Y, Suzuki M, Yamazaki C, Hayashi KI, Ishii T, Nakamura A, Soeno K, Shimada Y. Auxin signaling through SCFTIR1/AFBs mediates feedback regulation of IAA biosynthesis. Biosci Biotechnol Biochem 2017; 81:1320-1326. [DOI: 10.1080/09168451.2017.1313694] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Abstract
We previously reported that exogenous application of auxin to Arabidopsis seedlings resulted in downregulation of indole-3-acetic acid (IAA) biosynthesis genes in a feedback manner. In this study, we investigated the involvement of the SCFTIR1/AFB-mediated signaling pathway in feedback regulation of the indole-3-pyruvic acid-mediated auxin biosynthesis pathway in Arabidopsis. Application of PEO-IAA, an inhibitor of the IAA signal transduction pathway, to wild-type seedlings resulted in increased endogenous IAA levels in roots. Endogenous IAA levels in the auxin-signaling mutants axr2-1, axr3-3, and tir1-1afb1-1afb2-1afb3-1 also increased. Furthermore, YUCCA (YUC) gene expression was repressed in response to auxin treatment, and expression of YUC7 and YUC8 increased in response to PEO-IAA treatment. YUC genes were also induced in auxin-signaling mutants but repressed in TIR1-overexpression lines. These observations suggest that the endogenous IAA levels are regulated by auxin biosynthesis in a feedback manner, and the Aux/IAA and SCFTIR1/AFB-mediated auxin-signaling pathway regulates the expression of YUC genes.
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Affiliation(s)
- Shin Takato
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Marie Mitsui
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- RIKEN CSRS, Yokohama, Japan
| | - Yosuke Ishida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Masashi Suzuki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Chiaki Yamazaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ken-ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | | | - Ayako Nakamura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | | | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- RIKEN CSRS, Yokohama, Japan
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52
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Transcriptome analysis of drought-responsive genes regulated by hydrogen sulfide in wheat (Triticum aestivum L.) leaves. Mol Genet Genomics 2017. [DOI: 10.1007/s00438-017-1330-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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53
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Cheng F, Cheng Z, Meng H, Tang X. The Garlic Allelochemical Diallyl Disulfide Affects Tomato Root Growth by Influencing Cell Division, Phytohormone Balance and Expansin Gene Expression. FRONTIERS IN PLANT SCIENCE 2016; 7:1199. [PMID: 27555862 PMCID: PMC4977361 DOI: 10.3389/fpls.2016.01199] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 07/27/2016] [Indexed: 05/27/2023]
Abstract
Diallyl disulfide (DADS) is a volatile organosulfur compound derived from garlic (Allium sativum L.), and it is known as an allelochemical responsible for the strong allelopathic potential of garlic. The anticancer properties of DADS have been studied in experimental animals and various types of cancer cells, but to date, little is known about its mode of action as an allelochemical at the cytological level. The current research presents further studies on the effects of DADS on tomato (Solanum lycopersicum L.) seed germination, root growth, mitotic index, and cell size in root meristem, as well as the phytohormone levels and expression profile of auxin biosynthesis genes (FZYs), auxin transport genes (SlPINs), and expansin genes (EXPs) in tomato root. The results showed a biphasic, dose-dependent effect on tomato seed germination and root growth under different DADS concentrations. Lower concentrations (0.01-0.62 mM) of DADS significantly promoted root growth, whereas higher levels (6.20-20.67 mM) showed inhibitory effects. Cytological observations showed that the cell length of root meristem was increased and that the mitotic activity of meristematic cells in seedling root tips was enhanced at lower concentrations of DADS. In contrast, DADS at higher concentrations inhibited root growth by affecting both the length and division activity of meristematic cells. However, the cell width of the root meristem was not affected. Additionally, DADS increased the IAA and ZR contents of seedling roots in a dose-dependent manner. The influence on IAA content may be mediated by the up-regulation of FZYs and PINs. Further investigation into the underlying mechanism revealed that the expression levels of tomato EXPs were significantly affected by DADS. The expression levels of EXPB2 and beta-expansin precursor were increased after 3 d, and those of EXP1, EXPB3 and EXLB1 were increased after 5 d of DADS treatment (0.41 mM). This result suggests that tomato root growth may be regulated by multiple expansin genes at different developmental stages. Therefore, we conclude that the effects of DADS on the root growth of tomato seedlings are likely caused by changes associated with cell division, phytohormones, and the expression levels of expansin genes.
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Affiliation(s)
| | - Zhihui Cheng
- Department of Vegetable Science, College of Horticulture, Northwest A&F UniversityYangling, China
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54
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Naser V, Shani E. Auxin response under osmotic stress. PLANT MOLECULAR BIOLOGY 2016; 91:661-72. [PMID: 27052306 DOI: 10.1007/s11103-016-0476-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/28/2016] [Indexed: 05/18/2023]
Abstract
The phytohormone auxin (indole-3-acetic acid, IAA) is a small organic molecule that coordinates many of the key processes in plant development and adaptive growth. Plants regulate the auxin response pathways at multiple levels including biosynthesis, metabolism, transport and perception. One of the most striking aspects of plant plasticity is the modulation of development in response to changing growth environments. In this review, we explore recent findings correlating auxin response-dependent growth and development with osmotic stresses. Studies of water deficit, dehydration, salt, and other osmotic stresses point towards direct and indirect molecular perturbations in the auxin pathway. Osmotic stress stimuli modulate auxin responses by affecting auxin biosynthesis (YUC, TAA1), transport (PIN), perception (TIR/AFB, Aux/IAA), and inactivation/conjugation (GH3, miR167, IAR3) to coordinate growth and patterning. In turn, stress-modulated auxin gradients drive physiological and developmental mechanisms such as stomata aperture, aquaporin and lateral root positioning. We conclude by arguing that auxin-mediated growth inhibition under abiotic stress conditions is one of the developmental and physiological strategies to acclimate to the changing environment.
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Affiliation(s)
- Victoria Naser
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Eilon Shani
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978, Tel Aviv, Israel.
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55
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Phytohormones and their metabolic engineering for abiotic stress tolerance in crop plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.01.010] [Citation(s) in RCA: 501] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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56
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Different cucumber CsYUC genes regulate response to abiotic stresses and flower development. Sci Rep 2016; 6:20760. [PMID: 26857463 PMCID: PMC4746583 DOI: 10.1038/srep20760] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/07/2016] [Indexed: 12/22/2022] Open
Abstract
The phytohormone auxin is essential for plant growth and development, and YUCCA (YUC) proteins catalyze a rate-limiting step for endogenous auxin biosynthesis. Despite YUC family genes have been isolated from several species, systematic expression analyses of YUCs in response to abiotic stress are lacking, and little is known about the function of YUC homologs in agricultural crops. Cucumber (Cucumis sativus L.) is a world cultivated vegetable crop with great economical and nutritional value. In this study, we isolated 10 YUC family genes (CsYUCs) from cucumber and explored their expression pattern under four types of stress treatments. Our data showed that CsYUC8 and CsYUC9 were specifically upregulated to elevate the auxin level under high temperature. CsYUC10b was dramatically increased but CsYUC4 was repressed in response to low temperature. CsYUC10a and CsYUC11 act against the upregulation of CsYUC10b under salinity stress, suggesting that distinct YUC members participate in different stress response, and may even antagonize each other to maintain the proper auxin levels in cucumber. Further, CsYUC11 was specifically expressed in the male flower in cucumber, and enhanced tolerance to salinity stress and regulated pedicel and stamen development through auxin biosynthesis in Arabidopsis.
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57
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Wang Q, An B, Wei Y, Reiter RJ, Shi H, Luo H, He C. Melatonin Regulates Root Meristem by Repressing Auxin Synthesis and Polar Auxin Transport in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 28018411 DOI: 10.3389/fpls.201601882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) plays important roles in regulating both biotic and abiotic stress tolerance, biological rhythms, plant growth and development. Sharing the same substrate (tryptophan) for the biosynthesis, melatonin and auxin also have similar effects in plant development. However, the specific function of melatonin in modulating plant root growth and the relationship between melatonin and auxin as well as underlying mechanisms are still unclear. In this study, we found high concentration of melatonin remarkably inhibited root growth in Arabidopsis by reducing root meristem size. Further studies showed that melatonin negatively regulated auxin biosynthesis, the expression of PINFORMED (PIN) proteins as well as auxin response in Arabidopsis. Moreover, the root growth of the triple mutant pin1pin3pin7 was more tolerant than that of wild-type in response to melatonin treatment, suggesting the essential role of PIN1/3/7 in melatonin-mediated root growth. Combination treatment of melatonin and 5-Triiodobenzoic acid (TIBA) did not enhance melatonin-mediated reduction of root meristem size, indicating that polar auxin transport (PAT) may be necessary for the regulation of root meristem size by melatonin treatment. Taken together, this study indicates that melatonin regulates root growth in Arabidopsis, through auxin synthesis and polar auxin transport, at least partially.
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Affiliation(s)
- Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, The University of Texas Health Science Center San Antonio, TX, USA
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
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58
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Zhu Z, Sun B, Xu X, Chen H, Zou L, Chen G, Cao B, Chen C, Lei J. Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:1285. [PMID: 27625663 PMCID: PMC5003845 DOI: 10.3389/fpls.2016.01285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/11/2016] [Indexed: 05/09/2023]
Abstract
Plants are constantly challenged by environmental stresses, including drought and high salinity. Improvement of drought and osmotic stress tolerance without yield decrease has been a great challenge in crop improvement. The Arabidopsis ENHANCED DROUGHT TOLERANCE1/HOMEODOMAIN GLABROUS11 (AtEDT1/HDG11), a protein of the class IV HD-Zip family, has been demonstrated to significantly improve drought tolerance in Arabidopsis, rice, and pepper. Here, we report that AtEDT1/HDG11 confers drought and osmotic stress tolerance in the Chinese kale. AtEDT1/HDG11-overexpression lines exhibit auxin-overproduction phenotypes, such as long hypocotyls, tall stems, more root hairs, and a larger root system architecture. Compared with the untransformed control, transgenic lines have significantly reduced stomatal density. In the leaves of transgenic Chinese kale plants, proline (Pro) content and reactive oxygen species-scavenging enzyme activity was significantly increased after drought and osmotic stress, particularly compared to wild kale. More importantly, AtEDT1/HDG11-overexpression leads to abscisic acid (ABA) hypersensitivity, resulting in ABA inhibitor germination and induced stomatal closure. Consistent with observed phenotypes, the expression levels of auxin, ABA, and stress-related genes were also altered under both normal and/or stress conditions. Further analysis showed that AtEDT1/HDG11, as a transcription factor, can target the auxin biosynthesis gene YUCC6 and ABA response genes ABI3 and ABI5. Collectively, our results provide a new insight into the role of AtEDT1/HDG11 in enhancing abiotic stress resistance through auxin- and ABA-mediated signaling response in Chinese kale.
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Affiliation(s)
- Zhangsheng Zhu
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Binmei Sun
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Xiaoxia Xu
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Hao Chen
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Lifang Zou
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Bihao Cao
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Changming Chen
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- *Correspondence: Jianjun Lei, Changming Chen,
| | - Jianjun Lei
- College of Horticulture, South China Agricultural UniversityGuangzhou, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Biology, Innovation and Utilization for Germplasm Resources in Horticultural Crops in Southern China, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- *Correspondence: Jianjun Lei, Changming Chen,
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59
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Chai C, Subudhi PK. Comprehensive Analysis and Expression Profiling of the OsLAX and OsABCB Auxin Transporter Gene Families in Rice (Oryza sativa) under Phytohormone Stimuli and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2016; 7:593. [PMID: 27200061 PMCID: PMC4853607 DOI: 10.3389/fpls.2016.00593] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/18/2016] [Indexed: 05/20/2023]
Abstract
The plant hormone auxin regulates many aspects of plant growth and developmental processes. Auxin gradient is formed in plant as a result of polar auxin transportation by three types of auxin transporters such as OsLAX, OsPIN, and OsABCB. We report here the analysis of two rice auxin transporter gene families, OsLAX and OsABCB, using bioinformatics tools, publicly accessible microarray data, and quantitative RT-PCR. There are 5 putative OsLAXs and 22 putative OsABCBs in rice genome, which were mapped on 8 chromosomes. The exon-intron structure of OsLAX genes and properties of deduced proteins were relatively conserved within grass family, while that of OsABCB genes varied greatly. Both constitutive and organ/tissue specific expression patterns were observed in OsLAXs and OsABCBs. Analysis of evolutionarily closely related "gene pairs" together with organ/tissue specific expression revealed possible "function gaining" and "function losing" events during rice evolution. Most OsLAX and OsABCB genes were regulated by drought and salt stress, as well as hormonal stimuli [auxin and Abscisic Acid (ABA)], which suggests extensive crosstalk between abiotic stresses and hormone signaling pathways. The existence of large number of auxin and stress related cis-regulatory elements in promoter regions might account for their massive responsiveness of these genes to these environmental stimuli, indicating complexity of regulatory networks involved in various developmental and physiological processes. The comprehensive analysis of OsLAX and OsABCB auxin transporter genes in this study would be helpful for understanding the biological significance of these gene families in hormone signaling and adaptation of rice plants to unfavorable environments.
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60
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Wang Q, An B, Wei Y, Reiter RJ, Shi H, Luo H, He C. Melatonin Regulates Root Meristem by Repressing Auxin Synthesis and Polar Auxin Transport in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:1882. [PMID: 28018411 PMCID: PMC5156734 DOI: 10.3389/fpls.2016.01882] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/29/2016] [Indexed: 05/18/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) plays important roles in regulating both biotic and abiotic stress tolerance, biological rhythms, plant growth and development. Sharing the same substrate (tryptophan) for the biosynthesis, melatonin and auxin also have similar effects in plant development. However, the specific function of melatonin in modulating plant root growth and the relationship between melatonin and auxin as well as underlying mechanisms are still unclear. In this study, we found high concentration of melatonin remarkably inhibited root growth in Arabidopsis by reducing root meristem size. Further studies showed that melatonin negatively regulated auxin biosynthesis, the expression of PINFORMED (PIN) proteins as well as auxin response in Arabidopsis. Moreover, the root growth of the triple mutant pin1pin3pin7 was more tolerant than that of wild-type in response to melatonin treatment, suggesting the essential role of PIN1/3/7 in melatonin-mediated root growth. Combination treatment of melatonin and 5-Triiodobenzoic acid (TIBA) did not enhance melatonin-mediated reduction of root meristem size, indicating that polar auxin transport (PAT) may be necessary for the regulation of root meristem size by melatonin treatment. Taken together, this study indicates that melatonin regulates root growth in Arabidopsis, through auxin synthesis and polar auxin transport, at least partially.
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Affiliation(s)
- Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, The University of Texas Health Science Center San Antonio, TX, USA
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
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61
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Mittag J, Gabrielyan A, Ludwig-Müller J. Knockout of GH3 genes in the moss Physcomitrella patens leads to increased IAA levels at elevated temperature and in darkness. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:339-49. [PMID: 26520677 DOI: 10.1016/j.plaphy.2015.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 05/21/2023]
Abstract
Two proteins of the GRETCHEN HAGEN3 (GH3) family of acyl acid amido synthetases from the moss Physcomitrella patens conjugate indole-3-acetic acid (IAA) to a series of amino acids. The possible function of altered auxin levels in the moss in response to two different growth perturbations, elevated temperatures and darkness, was analyzed using a) the recently described double knockout lines in both P. patens GH3 genes (GH3-doKO) and b) a previously characterized line harboring an auxin-inducible soybean GH3 promoter::reporter fused to β-glucuronidase (G1-GUS). The GUS activity as marker of the auxin response increased at higher temperatures and after cultivation in the darkness for a period of up to four weeks. Generally, the double knockout plants grew more slowly than the wild type (WT). The altered growth conditions influenced the phenotypes of the double knockout lines differently from that of WT moss. Higher temperatures negatively affected GH3-doKO plants compared to WT which was shown by stronger loss of chlorophyll. On the other hand, a positive effect was found on the concentrations of free IAA which increased at 28 °C in the GH3-doKO lines compared to WT plants. A different factor, namely darkness vs. a light/dark cycle caused the adverse phenotype concerning chlorophyll concentrations. Mutant moss plants showed higher chlorophyll concentrations than WT and these correlated with higher free IAA in the plant population that was classified as green. Our data show that growth perturbations result in higher free IAA levels in the GH3-doKO mutants, but in one case - growth in darkness - the mutants could cope better with the condition, whereas at elevated temperatures the mutants were more sensitive than WT. Thus, GH3 function in P. patens WT could lie in the regulation of IAA concentrations under unfavorable environmental conditions.
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Affiliation(s)
- Jennifer Mittag
- Institute of Botany, Technische Universität Dresden, 01062 Dresden, Germany
| | | | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, 01062 Dresden, Germany.
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62
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Cha JY, Kim WY, Kang SB, Kim JI, Baek D, Jung IJ, Kim MR, Li N, Kim HJ, Nakajima M, Asami T, Sabir JSM, Park HC, Lee SY, Bohnert HJ, Bressan RA, Pardo JM, Yun DJ. A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis. Nat Commun 2015; 6:8041. [PMID: 26314500 PMCID: PMC4560777 DOI: 10.1038/ncomms9041] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/11/2015] [Indexed: 11/10/2022] Open
Abstract
YUCCA (YUC) proteins constitute a family of flavin monooxygenases (FMOs), with an important role in auxin (IAA) biosynthesis. Here we report that Arabidopsis plants overexpressing YUC6 display enhanced IAA-related phenotypes and exhibit improved drought stress tolerance, low rate of water loss and controlled ROS accumulation under drought and oxidative stresses. Co-overexpression of an IAA-conjugating enzyme reduces IAA levels but drought stress tolerance is unaffected, indicating that the stress-related phenotype is not based on IAA overproduction. YUC6 contains a previously unrecognized FAD- and NADPH-dependent thiol-reductase activity (TR) that overlaps with the FMO domain involved in IAA biosynthesis. Mutation of a conserved cysteine residue (Cys-85) preserves FMO but suppresses TR activity and stress tolerance, whereas mutating the FAD- and NADPH-binding sites, that are common to TR and FMO domains, abolishes all outputs. We provide a paradigm for a single protein playing a dual role, regulating plant development and conveying stress defence responses.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Sun Bin Kang
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Dongwon Baek
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - In Jung Jung
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Mi Ri Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ning Li
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hyun-Jin Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Masatoshi Nakajima
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Hyeong Cheol Park
- Department of Ecological Adaptation, National Institute of Ecology, Seocheon 325-813, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hans J Bohnert
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ray A Bressan
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jose M Pardo
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas, Sevilla 41012, Spain
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
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63
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Suzuki M, Yamazaki C, Mitsui M, Kakei Y, Mitani Y, Nakamura A, Ishii T, Soeno K, Shimada Y. Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis. PLANT CELL REPORTS 2015; 34:1343-52. [PMID: 25903543 DOI: 10.1007/s00299-015-1791-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 05/23/2023]
Abstract
The IPyA pathway, the major auxin biosynthesis pathway, is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels. The phytohormone auxin plays an important role in plant growth and development, and levels of active free auxin are determined by biosynthesis, conjugation, and polar transport. Unlike conjugation and polar transport, little is known regarding the regulatory mechanism of auxin biosynthesis. We discovered that expression of genes encoding indole-3-pyruvic acid (IPyA) pathway enzymes is regulated by elevated or reduced active auxin levels. Expression levels of TAR2, YUC1, YUC2, YUC4, and YUC6 were downregulated in response to synthetic auxins [1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D)] exogenously applied to Arabidopsis thaliana L. seedlings. Concomitantly, reduced levels of endogenous indole-3-acetic acid (IAA) were observed. Alternatively, expression of these YUCCA genes was upregulated by the auxin biosynthetic inhibitor kynurenine in Arabidopsis seedlings, accompanied by reduced IAA levels. These results indicate that expression of YUCCA genes is regulated by active auxin levels. Similar results were also observed in auxin-overproduction and auxin-deficient mutants. Exogenous application of IPyA to Arabidopsis seedlings preincubated with kynurenine increased endogenous IAA levels, while preincubation with 2,4-D reduced endogenous IAA levels compared to seedlings exposed only to IPyA. These results suggest that in vivo conversion of IPyA to IAA was enhanced under reduced auxin levels, while IPyA to IAA conversion was depressed in the presence of excess auxin. Based on these results, we propose that the IPyA pathway is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels.
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Affiliation(s)
- Masashi Suzuki
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
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64
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Robert HS, Crhak Khaitova L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5029-42. [PMID: 26019252 DOI: 10.1093/jxb/erv256] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.
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Affiliation(s)
- Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Lucie Crhak Khaitova
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Souad Mroue
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Eva Benková
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
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65
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Jung H, Lee DK, Choi YD, Kim JK. OsIAA6, a member of the rice Aux/IAA gene family, is involved in drought tolerance and tiller outgrowth. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:304-12. [PMID: 26025543 DOI: 10.1016/j.plantsci.2015.04.018] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/24/2015] [Accepted: 04/26/2015] [Indexed: 05/20/2023]
Abstract
Auxin signaling is a fundamental part of many plant growth processes and stress responses and operates through Aux/IAA protein degradation and the transmission of the signal via auxin response factors (ARFs). A total of 31 Aux/IAA genes have been identified in rice (Oryza sativa), some of which are induced by drought stress. However, the mechanistic link between Aux/IAA expression and drought responses is not well understood. In this study we found that the rice Aux/IAA gene OsIAA6 is highly induced by drought stress and that its overexpression in transgenic rice improved drought tolerance, likely via the regulation of auxin biosynthesis genes. We observed that OsIAA6 was specifically expressed in the axillary meristem of the basal stem, which is the tissue that gives rise to tillers. A knock-down mutant of OsIAA6 showed abnormal tiller outgrowth, apparently due to the regulation of the auxin transporter OsPIN1 and the rice tillering inhibitor OsTB1. Our results confirm that the OsIAA6 gene is involved in drought stress responses and the control of tiller outgrowth.
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Affiliation(s)
- Harin Jung
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea.
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea.
| | - Yang Do Choi
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea.
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66
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Kikuchi A, Huynh HD, Endo T, Watanabe K. Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato. BREEDING SCIENCE 2015; 65:85-102. [PMID: 25931983 PMCID: PMC4374567 DOI: 10.1270/jsbbs.65.85] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/23/2014] [Indexed: 05/20/2023]
Abstract
Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.
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67
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Hu W, Zuo J, Hou X, Yan Y, Wei Y, Liu J, Li M, Xu B, Jin Z. The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress. FRONTIERS IN PLANT SCIENCE 2015; 6:742. [PMID: 26442055 PMCID: PMC4569978 DOI: 10.3389/fpls.2015.00742] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/31/2015] [Indexed: 05/18/2023]
Abstract
Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Jiao Zuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Xiaowan Hou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Yunxie Wei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Meiying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- *Correspondence: Biyu Xu, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua County, Haikou City, Hainan Province 571101, China
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- Zhiqiang Jin, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Yilong W Road 2, Longhua County, Haikou City, Hainan Province 570102, China
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68
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Zhang J, Yin Z, White F. TAL effectors and the executor R genes. FRONTIERS IN PLANT SCIENCE 2015; 6:641. [PMID: 26347759 PMCID: PMC4542534 DOI: 10.3389/fpls.2015.00641] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/02/2015] [Indexed: 05/19/2023]
Abstract
Transcription activator-like (TAL) effectors are bacterial type III secretion proteins that function as transcription factors in plants during Xanthomonas/plant interactions, conditioning either host susceptibility and/or host resistance. Three types of TAL effector associated resistance (R) genes have been characterized-recessive, dominant non-transcriptional, and dominant TAL effector-dependent transcriptional based resistance. Here, we discuss the last type of R genes, whose functions are dependent on direct TAL effector binding to discrete effector binding elements in the promoters. Only five of the so-called executor R genes have been cloned, and commonalities are not clear. We have placed the protein products in two groups for conceptual purposes. Group 1 consists solely of the protein from pepper, BS3, which is predicted to have catalytic function on the basis of homology to a large conserved protein family. Group 2 consists of BS4C-R, XA27, XA10, and XA23, all of which are relatively short proteins from pepper or rice with multiple potential transmembrane domains. Group 2 members have low sequence similarity to proteins of unknown function in closely related species. Firm predictions await further experimentation on these interesting new members to the R gene repertoire, which have potential broad application in new strategies for disease resistance.
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Affiliation(s)
- Junli Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- *Correspondence: Junli Zhang, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA,
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Frank White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
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69
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Shi H, Chen L, Ye T, Liu X, Ding K, Chan Z. Modulation of auxin content in Arabidopsis confers improved drought stress resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:209-17. [PMID: 24992887 DOI: 10.1016/j.plaphy.2014.06.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/13/2014] [Indexed: 05/18/2023]
Abstract
Auxin is a well-known plant phytohormone that is involved in multiple plant growth processes and stress responses. In this study, auxin response was significantly modulated under drought stress condition. The iaaM-OX transgenic lines with higher endogenous indole-3-acetic acid (IAA) level and IAA pre-treated wild type (WT) plants exhibited enhanced drought stress resistance, while the yuc1yuc2yuc6 triple mutants with lower endogenous IAA level showed decreased stress resistance in comparison to non-treated WT plants. Additionally, endogenous and exogenous auxin positively modulated the expression levels of multiple abiotic stress-related genes (RAB18, RD22, RD29A, RD29B, DREB2A, and DREB2B), and positively affected reactive oxygen species (ROS) metabolism and underlying antioxidant enzyme activities. Moreover, auxin significantly modulated some carbon metabolites including amino acids, organic acids, sugars, sugar alcohols and aromatic amines. Notably, endogenous and exogenous auxin positively modulated root architecture especially the lateral root number. Taken together, this study demonstrated that auxin might participate in the positive regulation of drought stress resistance, through regulation of root architecture, ABA-responsive genes expression, ROS metabolism, and metabolic homeostasis, at least partially.
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Affiliation(s)
- Haitao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Li Chen
- College of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Tiantian Ye
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaodong Liu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Kejian Ding
- College of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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70
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Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. BIOINFORMATICS (OXFORD, ENGLAND) 2014; 151:3-12. [PMID: 24695404 DOI: 10.1111/ppl.12098] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/30/2013] [Accepted: 08/15/2013] [Indexed: 05/09/2023]
Abstract
MOTIVATION Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. RESULTS The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. AVAILABILITY AND IMPLEMENTATION Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anthony M Bolger
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Marc Lohse
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Bjoern Usadel
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
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71
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Dash PK, Cao Y, Jailani AK, Gupta P, Venglat P, Xiang D, Rai R, Sharma R, Thirunavukkarasu N, Abdin MZ, Yadava DK, Singh NK, Singh J, Selvaraj G, Deyholos M, Kumar PA, Datla R. Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum). GM CROPS & FOOD 2014; 5:106-19. [PMID: 25072186 DOI: 10.4161/gmcr.29742] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A robust phenotypic plasticity to ward off adverse environmental conditions determines performance and productivity in crop plants. Flax (linseed), is an important cash crop produced for natural textile fiber (linen) or oilseed with many health promoting products. This crop is prone to drought stress and yield losses in many parts of the world. Despite recent advances in drought research in a number of important crops, related progress in flax is very limited. Since, response of this plant to drought stress has not been addressed at the molecular level; we conducted microarray analysis to capture transcriptome associated with induced drought in flax. This study identified 183 differentially expressed genes (DEGs) associated with diverse cellular, biophysical and metabolic programs in flax. The analysis also revealed especially the altered regulation of cellular and metabolic pathways governing photosynthesis. Additionally, comparative transcriptome analysis identified a plethora of genes that displayed differential regulation both spatially and temporally. These results revealed co-regulated expression of 26 genes in both shoot and root tissues with implications for drought stress response. Furthermore, the data also showed that more genes are upregulated in roots compared to shoots, suggesting that roots may play important and additional roles in response to drought in flax. With prolonged drought treatment, the number of DEGs increased in both tissue types. Differential expression of selected genes was confirmed by qRT-PCR, thus supporting the suggested functional association of these intrinsic genes in maintaining growth and homeostasis in response to imminent drought stress in flax. Together the present study has developed foundational and new transcriptome data sets for drought stress in flax.
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Affiliation(s)
- Prasanta K Dash
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Yongguo Cao
- National Research Council of Canada; Saskatoon, SK Canada
| | - Abdul K Jailani
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Payal Gupta
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | | | - Daoquan Xiang
- National Research Council of Canada; Saskatoon, SK Canada
| | - Rhitu Rai
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Rinku Sharma
- Indian Agricultural Research Institute; PUSA Campus; New Delhi, India
| | | | - Malik Z Abdin
- Faculty of Science; Hamdard University; Hamdard Nagar, New Delhi, India
| | - Devendra K Yadava
- Indian Agricultural Research Institute; PUSA Campus; New Delhi, India
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology; PUSA Campus; New Delhi, India
| | - Jas Singh
- Eastern Cereal and Oilseed Research Centre; Agriculture and Agri-Food Canada; Ottawa, ON Canada
| | | | - Mike Deyholos
- Department of Biological Sciences; University of Alberta; Edmonton, AB Canada
| | | | - Raju Datla
- National Research Council of Canada; Saskatoon, SK Canada
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72
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Chen Q, Dai X, De-Paoli H, Cheng Y, Takebayashi Y, Kasahara H, Kamiya Y, Zhao Y. Auxin overproduction in shoots cannot rescue auxin deficiencies in Arabidopsis roots. PLANT & CELL PHYSIOLOGY 2014; 55:1072-9. [PMID: 24562917 PMCID: PMC4051135 DOI: 10.1093/pcp/pcu039] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
Auxin plays an essential role in root development. It has been a long-held dogma that auxin required for root development is mainly transported from shoots into roots by polarly localized auxin transporters. However, it is known that auxin is also synthesized in roots. Here we demonstrate that a group of YUCCA (YUC) genes, which encode the rate-limiting enzymes for auxin biosynthesis, plays an essential role in Arabidopsis root development. Five YUC genes (YUC3, YUC5, YUC7, YUC8 and YUC9) display distinct expression patterns during root development. Simultaneous inactivation of the five YUC genes (yucQ mutants) leads to the development of very short and agravitropic primary roots. The yucQ phenotypes are rescued by either adding 5 nM of the natural auxin, IAA, in the growth media or by expressing a YUC gene in the roots of yucQ. Interestingly, overexpression of a YUC gene in shoots in yucQ causes the characteristic auxin overproduction phenotypes in shoots; however, the root defects of yucQ are not rescued. Our data demonstrate that localized auxin biosynthesis in roots is required for normal root development and that auxin transported from shoots is not sufficient for supporting root elongation and root gravitropic responses.
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Affiliation(s)
- Qingguo Chen
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Henrique De-Paoli
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Youfa Cheng
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Hiroyuki Kasahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Yuji Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
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73
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Yang C, Liu J, Dong X, Cai Z, Tian W, Wang X. Short-term and continuing stresses differentially interplay with multiple hormones to regulate plant survival and growth. MOLECULAR PLANT 2014; 7:841-55. [PMID: 24499771 DOI: 10.1093/mp/ssu013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The stress phytohormone, abscisic acid (ABA), plays important roles in facilitating plants to survive and grow well under a wide range of stress conditions. Previous gene expression studies mainly focused on plant responses to short-term ABA treatment, but the effect of sustained ABA treatment and their difference are poorly studied. Here, we treated plants with ABA for 1 h or 9 d, and our genome-wide analysis indicated the differentially regulated genes under the two conditions were tremendously different. We analyzed other hormones' signaling changes by using their whole sets of known responsive genes as reporters and integrating feedback regulation of their biosynthesis. We found that, under short-term ABA treatment, signaling outputs of growth-promoting hormones, brassinosteroids and gibberellins, and a biotic stress-responsive hormone, jasmonic acid, were significantly inhibited, while auxin and ethylene signaling outputs were promoted. However, sustained ABA treatment repressed cytokinin and gibberellin signaling, but stimulated auxin signaling. Using several sets of hormone-related mutants, we found candidates in corresponding hormonal signaling pathways, including receptors or transcription regulators, are essential in responding to ABA. Our findings indicate interactions of ABA-dependent stress signals with hormones at different levels are involved in plants to survive under transient stress and to adapt to continuing stressful environments.
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Affiliation(s)
- Cangjing Yang
- a State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
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Kazan K. Auxin and the integration of environmental signals into plant root development. ANNALS OF BOTANY 2013; 112:1655-65. [PMID: 24136877 PMCID: PMC3838554 DOI: 10.1093/aob/mct229] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 08/12/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Auxin is a versatile plant hormone with important roles in many essential physiological processes. In recent years, significant progress has been made towards understanding the roles of this hormone in plant growth and development. Recent evidence also points to a less well-known but equally important role for auxin as a mediator of environmental adaptation in plants. SCOPE This review briefly discusses recent findings on how plants utilize auxin signalling and transport to modify their root system architecture when responding to diverse biotic and abiotic rhizosphere signals, including macro- and micro-nutrient starvation, cold and water stress, soil acidity, pathogenic and beneficial microbes, nematodes and neighbouring plants. Stress-responsive transcription factors and microRNAs that modulate auxin- and environment-mediated root development are also briefly highlighted. CONCLUSIONS The auxin pathway constitutes an essential component of the plant's biotic and abiotic stress tolerance mechanisms. Further understanding of the specific roles that auxin plays in environmental adaptation can ultimately lead to the development of crops better adapted to stressful environments.
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Affiliation(s)
- Kemal Kazan
- Commonwealth Scientific and Industrial Organization (CSIRO) Plant Industry, Queensland Bioscience Precinct (QBP), Brisbane, Queensland 4067, Australia
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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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76
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Hong JH, Seah SW, Xu J. The root of ABA action in environmental stress response. PLANT CELL REPORTS 2013; 32:971-83. [PMID: 23571661 DOI: 10.1007/s00299-013-1439-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/24/2013] [Accepted: 03/26/2013] [Indexed: 05/05/2023]
Abstract
The growth and development of plants are influenced by the integration of diverse endogenous and environmental signals. Acting as a mediator of extrinsic signals, the stress hormone, abscisic acid (ABA), has been shown to regulate many aspects of plant development in response to unfavourable environmental stresses, allowing the plant to cope and survive in adverse conditions, such as drought, low or high temperature, or high salinity. Here, we summarize recent evidence on the roles of ABA in environmental stress responses in the Arabidopsis root; and on how ABA crosstalks with other phytohormones to modulate root development and growth in Arabidopsis. We also review literature findings showing that, in response to environmental stresses, ABA affects the root system architecture in other plant species, such as rice.
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Affiliation(s)
- Jing Han Hong
- Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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77
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Cheol Park H, Cha JY, Yun DJ. Roles of YUCCAs in auxin biosynthesis and drought stress responses in plants. PLANT SIGNALING & BEHAVIOR 2013; 8:e24495. [PMID: 23603963 PMCID: PMC3907447 DOI: 10.4161/psb.24495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 05/21/2023]
Abstract
Auxin, a plant hormone, plays crucial roles in diverse aspects of plant growth and development reacting to and integrating environmental stimuli. Indole-3-acetic acid (IAA) is the major plant auxin that is synthesized by members of the YUCCA (YUC) family of flavin monooxygenases that catalyse a rate-limiting step. Although the paths to IAA biosynthesis are characterized in Arabidopsis, little is known about the corresponding components in potato. Recently, we isolated eight putative StYUC (Solanum tuberosum YUCCA) genes and five putative tryptophan aminotransferase genes in comparison to those found in Arabidopsis. (1) The specific domains of YUC proteins were well conserved in all StYUC amino acid sequences. Transgenic potato (Solanum tuberosum cv. Jowon) overexpressing AtYUC6 showed high-auxin and enhanced drought tolerance phenotypes. The transgenic potatoes also exhibited reduced levels of ROS (reactive oxygen species) compared to control plants. We therefore propose that YUCCA and TAA families in potato would function in the auxin biosynthesis. The overexpression of AtYUC6 in potato establishes enhanced drought tolerance through regulated ROS homeostasis.
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Abstract
Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.
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Affiliation(s)
- Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
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79
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Kim JI, Baek D, Park HC, Chun HJ, Oh DH, Lee MK, Cha JY, Kim WY, Kim MC, Chung WS, Bohnert HJ, Lee SY, Bressan RA, Lee SW, Yun DJ. Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit. MOLECULAR PLANT 2013; 6:337-49. [PMID: 22986790 DOI: 10.1093/mp/sss100] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Indole-3-acetic acid (IAA), a major plant auxin, is produced in both tryptophan-dependent and tryptophan-independent pathways. A major pathway in Arabidopsis thaliana generates IAA in two reactions from tryptophan. Step one converts tryptophan to indole-3-pyruvic acid (IPA) by tryptophan aminotransferases followed by a rate-limiting step converting IPA to IAA catalyzed by YUCCA proteins. We identified eight putative StYUC (Solanum tuberosum YUCCA) genes whose deduced amino acid sequences share 50%-70% identity with those of Arabidopsis YUCCA proteins. All include canonical, conserved YUCCA sequences: FATGY motif, FMO signature sequence, and FAD-binding and NADP-binding sequences. In addition, five genes were found with ~50% amino acid sequence identity to Arabidopsis tryptophan aminotransferases. Transgenic potato (Solanum tuberosum cv. Jowon) constitutively overexpressing Arabidopsis AtYUC6 displayed high-auxin phenotypes such as narrow downward-curled leaves, increased height, erect stature, and longevity. Transgenic potato plants overexpressing AtYUC6 showed enhanced drought tolerance based on reduced water loss. The phenotype was correlated with reduced levels of reactive oxygen species in leaves. The results suggest a functional YUCCA pathway of auxin biosynthesis in potato that may be exploited to alter plant responses to the environment.
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Affiliation(s)
- Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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