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Hua B, Wu J, Han X, Bian X, Xu Z, Sun C, Wang R, Zhang W, Liang F, Zhang H, Li S, Li Z, Wu S. Auxin homeostasis is maintained by sly-miR167-SlARF8A/B-SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits. New Phytol 2024; 241:1177-1192. [PMID: 37985404 DOI: 10.1111/nph.19391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/20/2023] [Indexed: 11/22/2023]
Abstract
The locular gel, produced by the placenta, is important for fruit flavor and seed development in tomato. However, the mechanism underlying locule and placenta development is not fully understood yet. Here, we show that two SlARF transcription factors, SlARF8B and SlARF8A (SlARF8A/B), promote the development of locular and placenta tissues. The expression of both SlARF8A and SlARF8B is repressed by sly-microRNA167 (sly-miR167), allowing for the activation of auxin downstream genes. In slarf8a, slarf8b, and slarf8a/b mutants, the auxin (IAA) levels are decreased, whereas the levels of inactive IAA conjugates including IAA-Ala, IAA-Asp, and IAA-Glu are increased. We further find that SlARF8B directly inhibits the expression of SlGH3.4, an acyl acid amino synthetase that conjugates the amino acids to IAA. Disruption of such auxin balance by the increased expression of SlGH3.4 or SlGH3.2 results in defective locular and placental tissues. Taken together, our findings reveal an important regulatory module constituted by sly-miR167-SlARF8A/B-SlGH3.4 during the development of locular and placenta tissues of tomato fruits.
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Affiliation(s)
- Bing Hua
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Junqing Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoqian Han
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinxin Bian
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhijing Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Sun
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Renyin Wang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenyan Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Huimin Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Shuang Li
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Qi Y, Wang L, Li W, Dang Z, Xie Y, Zhao W, Zhao L, Li W, Yang C, Xu C, Zhang J. Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Linum usitatissimum. Int J Mol Sci 2023; 24:11006. [PMID: 37446183 DOI: 10.3390/ijms241311006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, ARF genes have not been investigated in flax (Linum usitatissimum L.), an important oilseed and fiber crop. In this study, we comprehensively analyzed the ARF gene family and identified 33 LuARF genes unevenly distributed on the 13 chromosomes of Longya-10, an oil-use flax variety. Detailed analysis revealed wide variation among the ARF family members and predicted nuclear localization for all proteins. Nineteen LuARFs contained a complete ARF structure, including DBD, MR, and CTD, whereas the other fourteen lacked the CTD. Phylogenetic analysis grouped the LuARFs into four (I-V) clades. Combined with sequence analysis, the LuARFs from the same clade showed structural conservation, implying functional redundancy. Duplication analysis identified twenty-seven whole-genome-duplicated LuARF genes and four tandem-duplicated LuARF genes. These duplicated gene pairs' Ka/Ks ratios suggested a strong purifying selection pressure on the LuARF genes. Collinearity analysis revealed that about half of the LuARF genes had homologs in other species, indicating a relatively conserved nature of the ARFs. The promoter analysis identified numerous hormone- and stress-related elements, and the qRT-PCR experiment revealed that all LuARF genes were responsive to phytohormone (IAA, GA3, and NAA) and stress (PEG, NaCl, cold, and heat) treatments. Finally, expression profiling of LuARF genes in different tissues by qRT-PCR indicated their specific functions in stem or capsule growth. Thus, our findings suggest the potential functions of LuARFs in flax growth and response to an exogenous stimulus, providing a basis for further functional studies on these genes.
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Affiliation(s)
- Yanni Qi
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Limin Wang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wenjuan Li
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Zhao Dang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Yaping Xie
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wei Zhao
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Lirong Zhao
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Wen Li
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Chenxi Yang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Chenmeng Xu
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Jianping Zhang
- Institute of Crop, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
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Liu Y, Wang R, Yu J, Huang S, Zhang Y, Wei H, Wei Z. Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa. Int J Mol Sci 2023; 24. [PMID: 36614182 DOI: 10.3390/ijms24010740] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
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Liu R, Guo Z, Lu S. Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula. Int J Mol Sci 2021; 22:10494. [PMID: 34638833 DOI: 10.3390/ijms221910494] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.
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Yang H, Klopotek Y, Hajirezaei MR, Zerche S, Franken P, Druege U. Role of auxin homeostasis and response in nitrogen limitation and dark stimulation of adventitious root formation in petunia cuttings. Ann Bot 2019; 124:1053-1066. [PMID: 31181150 PMCID: PMC6881223 DOI: 10.1093/aob/mcz095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/05/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Adventitious root (AR) formation in Petunia hybrida is inhibited by low nitrogen fertilization of stock plants but promoted by dark incubation of cuttings before planting. We investigated whether the plant hormone auxin is involved in nitrogen- and dark-mediated AR formation. METHODS Concentrations of indole-3-acetic acid (IAA) and RNA accumulation of genes controlling auxin homeostasis and function were monitored in the stem base in response to high versus low nitrogen supply to stock plants and to temporal dark vs. light exposure of cuttings by use of GC-MS/MS, a petunia-specific microarray and quantitative RT-PCR. Auxin source capacity, polar auxin transport in cuttings and auxin concentration in the rooting zone were manipulated to investigate the functional contribution of auxin homeostasis and response to the effects of nitrogen fertilization and dark exposure on rooting. KEY RESULTS The nitrogen content of cuttings had only a marginal effect on IAA concentration in the stem base. Dark incubation enhanced the accumulation of IAA in the stem base during AR induction independent of nitrogen level. Early IAA accumulation in the dark depended on the upper shoot as an auxin source and was enhanced after apical IAA supply. Dark exposure stimulated RNA accumulation of auxin-related genes. In particular, expression of Ph-PIN1 and of genes controlling auxin signalling, including Ph-IAA14, Ph-ARF8, Ph-ARF10 and Ph-SAUR14, was enhanced, while the latter four were repressed in nitrogen-limited cuttings, particularly in the dark. Dark stimulation of rooting depended on polar auxin transport. Basal auxin application partially substituted the effect of dark exposure on rooting, whereas the auxin response of AR formation was strongly depressed by nitrogen limitation. CONCLUSIONS Increased auxin delivery from the upper shoot and enhanced auxin signalling in the stem base contribute to dark-stimulated AR formation, while nitrogen limitation inhibits AR formation downstream of the auxin signal.
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Affiliation(s)
- Huaiyu Yang
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Erfurt, Germany
| | - Yvonne Klopotek
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Erfurt, Germany
| | | | - Siegfried Zerche
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Erfurt, Germany
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Erfurt, Germany
| | - Uwe Druege
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Erfurt, Germany
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Carey NS, Krogan NT. The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav 2017; 12:e1307492. [PMID: 28340328 PMCID: PMC6322905 DOI: 10.1080/15592324.2017.1307492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 06/01/2023]
Abstract
Plants react to environmental cues by altering their growth and development, which can include organ tropic responses. These differential growth responses are triggered by the hormone auxin, and AUXIN RESPONSE FACTORs (ARFs) have been implicated in numerous organ tropisms in Arabidopsis thaliana. Surprisingly, despite being critical for light capture and overall plant morphology, inflorescence stem tropic responses remain relatively understudied, with presumed direct links to ARF function yet to be established. Here, we show that the expression patterns of ARF5/MONOPTEROS and ARF7/NONPHOTOTROPIC HYPOCOTYL4 are consistent with roles in inflorescence stem tropisms. Mutation of these factors does not alter inflorescence stem responses to gravity or unilateral auxin application, meaning their participation in these processes is presumably masked by functional redundancies. Future resolution of these redundancies will likely require higher order arf mutant combinations, guided by detailed expression analyses of ARFs in the inflorescence stem.
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Affiliation(s)
| | - Naden T. Krogan
- Department of Biology, American University, Washington DC, USA
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Krogan NT, Marcos D, Weiner AI, Berleth T. The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol 2016; 212:42-50. [PMID: 27441727 PMCID: PMC5596637 DOI: 10.1111/nph.14107] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/19/2016] [Indexed: 05/18/2023]
Abstract
The regulatory effect auxin has on its own transport is critical in numerous self-organizing plant patterning processes. However, our understanding of the molecular mechanisms linking auxin signal transduction and auxin transport is still fragmentary, and important regulatory genes remain to be identified. To track a key link between auxin signaling and auxin transport in development, we established an Arabidopsis thaliana genetic background in which fundamental patterning processes in both shoot and root were essentially abolished and the expression of PIN FORMED (PIN) auxin efflux facilitators was dramatically reduced. In this background, we demonstrate that activating a steroid-inducible variant of the auxin response factor (ARF) MONOPTEROS (MP) is sufficient to restore patterning and PIN gene expression. Further, we show that MP binds to distinct promoter elements of multiple genetically defined PIN genes. Our work identifies a direct regulatory link between central, well-characterized genes involved in auxin signal transduction and auxin transport. The steroid-inducible MP system directly demonstrates the importance of this molecular link in multiple patterning events in embryos, shoots and roots, and provides novel options for interrogating the properties of self-regulated auxin-based patterning in planta.
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Affiliation(s)
- Naden T. Krogan
- American University, Department of Biology, 4400 Massachusetts
Avenue NW, Washington D.C. 20016, United States
- To whom correspondence should be addressed:
Tel: (202) 885-2203,
Tel: (416) 946-3734
| | - Danielle Marcos
- University of Toronto, Department of Cell and Systems Biology, 25
Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Aaron I. Weiner
- American University, Department of Biology, 4400 Massachusetts
Avenue NW, Washington D.C. 20016, United States
| | - Thomas Berleth
- University of Toronto, Department of Cell and Systems Biology, 25
Willcocks Street, Toronto, Ontario M5S 3B2, Canada
- To whom correspondence should be addressed:
Tel: (202) 885-2203,
Tel: (416) 946-3734
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Shen C, Yue R, Sun T, Zhang L, Xu L, Tie S, Wang H, Yang Y. Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula. Front Plant Sci 2015; 6:73. [PMID: 25759704 PMCID: PMC4338661 DOI: 10.3389/fpls.2015.00073] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/27/2015] [Indexed: 05/18/2023]
Abstract
Auxin response factors (ARFs) bind specifically to auxin response elements (AuxREs) in the promoters of down-stream target genes and play roles in plant responses to diverse environmental factors. Using the latest updated Medicago truncatula reference genome sequence, a comprehensive characterization and analysis of 24 MtARF (M. truncatula ARF) genes were performed. To uncover the basic information and functions of MtARF genes during symbiosis, we analyzed the expression patterns of MtARF genes during the early phase of Sinorhizobium meliloti infection. The systematic analysis indicated that changes in MtARF gene expression occur during these early stages of infection, suggesting a functional role in symbiosis. Furthermore, the roles of MtARF-mediated auxin signaling in symbiosis were tested in the infection resistant mutant (dmi3). The expression responses of MtARFs to S. meliloti infection were attenuated in the mutant compared to wild-type A17. In summary, our results show that changes in MtARF gene expression occur during the response to S. meliloti infection, suggesting that members of this family may have important roles in the symbiotic interaction.
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Affiliation(s)
- Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Runqing Yue
- Henan Academy of Agricultural SciencesZhengzhou, China
| | - Tao Sun
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Lei Zhang
- Department of Plant Pathology, Washington State UniversityPullman, WA, USA
| | - Luqin Xu
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Shuanggui Tie
- Henan Academy of Agricultural SciencesZhengzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- *Correspondence: Huizhong Wang and Yanjun Yang, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou 310036, China e-mail: ;
| | - Yanjun Yang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- *Correspondence: Huizhong Wang and Yanjun Yang, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou 310036, China e-mail: ;
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