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Xue Z, Ferrand M, Gilbault E, Zurfluh O, Clément G, Marmagne A, Huguet S, Jiménez-Gómez JM, Krapp A, Meyer C, Loudet O. Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis. THE PLANT CELL 2024; 36:3378-3398. [PMID: 38916908 PMCID: PMC11371182 DOI: 10.1093/plcell/koae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 01/24/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024]
Abstract
Understanding plant responses to individual stresses does not mean that we understand real-world situations, where stresses usually combine and interact. These interactions arise at different levels, from stress exposure to the molecular networks of the stress response. Here, we built an in-depth multiomic description of plant responses to mild water (W) and nitrogen (N) limitations, either individually or combined, among 5 genetically different Arabidopsis (Arabidopsis thaliana) accessions. We highlight the different dynamics in stress response through integrative traits such as rosette growth and the physiological status of the plants. We also used transcriptomic and metabolomic profiling during a stage when the plant response was stabilized to determine the wide diversity in stress-induced changes among accessions, highlighting the limited reality of a "universal" stress response. The main effect of the W × N interaction was an attenuation of the N-deficiency syndrome when combined with mild drought, but to a variable extent depending on the accession. Other traits subject to W × N interactions are often accession specific. Multiomic analyses identified a subset of transcript-metabolite clusters that are critical to stress responses but essentially variable according to the genotype factor. Including intraspecific diversity in our descriptions of plant stress response places our findings in perspective.
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Affiliation(s)
- Zeyun Xue
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Marina Ferrand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Olivier Zurfluh
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - José M Jiménez-Gómez
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Anne Krapp
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Christian Meyer
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
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Wang JL, Wang M, Zhang L, Li YX, Li JJ, Li YY, Pu ZX, Li DY, Liu XN, Guo W, Di DW, Li XF, Guo GQ, Wu L. WAV E3 ubiquitin ligases mediate degradation of IAA32/34 in the TMK1-mediated auxin signaling pathway during apical hook development. Proc Natl Acad Sci U S A 2024; 121:e2314353121. [PMID: 38635634 PMCID: PMC11047095 DOI: 10.1073/pnas.2314353121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
Auxin regulates plant growth and development through downstream signaling pathways, including the best-known SCFTIR1/AFB-Aux/IAA-ARF pathway and several other less characterized "noncanonical" pathways. Recently, one SCFTIR1/AFB-independent noncanonical pathway, mediated by Transmembrane Kinase 1 (TMK1), was discovered through the analyses of its functions in Arabidopsis apical hook development. Asymmetric accumulation of auxin on the concave side of the apical hook triggers DAR1-catalyzed release of the C-terminal of TMK1, which migrates into the nucleus, where it phosphorylates and stabilizes IAA32/34 to inhibit cell elongation, which is essential for full apical hook formation. However, the molecular factors mediating IAA32/34 degradation have not been identified. Here, we show that proteins in the CYTOKININ INDUCED ROOT WAVING 1 (CKRW1)/WAVY GROWTH 3 (WAV3) subfamily act as E3 ubiquitin ligases to target IAA32/34 for ubiquitination and degradation, which is inhibited by TMK1c-mediated phosphorylation. This antagonistic interaction between TMK1c and CKRW1/WAV3 subfamily E3 ubiquitin ligases regulates IAA32/34 levels to control differential cell elongation along opposite sides of the apical hook.
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Affiliation(s)
- Jun-Li Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Ming Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing210008, People’s Republic of China
| | - Li Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Basic Forestry and Proteomics Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou350002, People’s Republic of China
| | - You-Xia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Jing-Jing Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Yu-Yang Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Zuo-Xian Pu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Dan-Yang Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Xing-Nan Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Wang Guo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Dong-Wei Di
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, People’s Republic of China
| | - Xiao-Feng Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Guang-Qin Guo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
| | - Lei Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou730000, People’s Republic of China
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Xing Y, Liu C, Zheng C, Li H, Yin H. Evolution and function analysis of auxin response factors reveal the molecular basis of the developed root system of Zygophyllum xanthoxylum. BMC PLANT BIOLOGY 2024; 24:81. [PMID: 38302884 PMCID: PMC10835889 DOI: 10.1186/s12870-023-04717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND As a xerophytic shrub, forming developed root system dominated with lateral roots is one of the effective strategies for Zygophyllum xanthoxylum to adapt to desert habitat. However, the molecular mechanism of lateral root formation in Z. xanthoxylum is still unclear. Auxin response factors (ARFs) are a master family of transcription factors (TFs) in auxin-mediated biological processes including root growth and development. RESULTS Here, to determine the relationship between ARFs and root system formation in Z. xanthoxylum, a total of 30 potential ZxARF genes were first identified, and their classifications, evolutionary relationships, duplication events and conserved domains were characterized. 107 ARF protein sequences from alga to higher plant species including Z. xanthoxylum are split into A, B, and C 3 Clades, consisting with previous studies. The comparative analysis of ARFs between xerophytes and mesophytes showed that A-ARFs of xerophytes expanded considerably more than that of mesophytes. Furthermore, in this Clade, ZxARF5b and ZxARF8b have lost the important B3 DNA-binding domain partly and completely, suggesting both two proteins may be more functional in activating transcription by dimerization with AUX/IAA repressors. qRT-PCR results showed that all A-ZxARFs are high expressed in the roots of Z. xanthoxylum, and they were significantly induced by drought stress. Among these A-ZxARFs, the over-expression assay showed that ZxARF7c and ZxARF7d play positive roles in lateral root formation. CONCLUSION This study provided the first comprehensive overview of ZxARFs and highlighted the importance of A-ZxARFs in the lateral root development.
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Affiliation(s)
- Ying Xing
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Chunli Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Chuan Zheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hongju Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Luo D, Shi L, Sun Z, Qi F, Liu H, Xue L, Li X, Liu H, Qu P, Zhao H, Dai X, Dong W, Zheng Z, Huang B, Fu L, Zhang X. Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut ( Arachis hypogaea L.). Genes (Basel) 2024; 15:160. [PMID: 38397150 PMCID: PMC10887910 DOI: 10.3390/genes15020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut (Arachis hypogaea L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value -log10(p) = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the Arahy.MIX90M locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut.
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Affiliation(s)
- Dandan Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Shi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Hongfei Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lulu Xue
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaona Li
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Han Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pengyu Qu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Huanhuan Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaodong Dai
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- National Innovation Center for Bio-Breeding Industry, Xinxiang 453500, China
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Du Q, Song K, Wang L, Du L, Du H, Li B, Li H, Yang L, Wang Y, Liu P. Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Eucommia ulmoides Oliver. PLANTS (BASEL, SWITZERLAND) 2024; 13:136. [PMID: 38202444 PMCID: PMC10780705 DOI: 10.3390/plants13010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
As a primary approach to nutrient propagation for many woody plants, cutting roots is essential for the breeding and production of Eucommia ulmoides Oliver. In this study, hormone level, transcriptomics, and metabolomics analyses were performed on two E. ulmoides varieties with different adventitious root (AR) formation abilities. The higher JA level on the 0th day and the lower JA level on the 18th day promoted superior AR development. Several hub genes executed crucial roles in the crosstalk regulation of JA and other hormones, including F-box protein (EU012075), SAUR-like protein (EU0125382), LOB protein (EU0124232), AP2/ERF transcription factor (EU0128499), and CYP450 protein (EU0127354). Differentially expressed genes (DEGs) and metabolites of AR formation were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis pathways. The up-regulated expression of PAL, CCR, CAD, DFR, and HIDH genes on the 18th day could contribute to AR formation. The 130 cis-acting lncRNAs had potential regulatory functions on hub genes in the module that significantly correlated with JA and DEGs in three metabolism pathways. These revealed key molecules, and vital pathways provided more comprehensive insight for the AR formation mechanism of E. ulmoides and other plants.
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Affiliation(s)
- Qingxin Du
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Kangkang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai’an 271018, China
| | - Lu Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
| | - Lanying Du
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
| | - Hongyan Du
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
| | - Bin Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Haozhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
| | - Panfeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Q.D.); (L.W.); (L.D.); (H.D.)
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Hung SHW, Yeh PH, Huang TC, Huang SY, Wu IC, Liu CH, Lin YH, Chien PR, Huang FC, Ho YN, Kuo CH, Hwang HH, Chiang EPI, Huang CC. A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions. ISME COMMUNICATIONS 2024; 4:ycae041. [PMID: 38707842 PMCID: PMC11070113 DOI: 10.1093/ismeco/ycae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 05/07/2024]
Abstract
In response to climate change, the nature of endophytes and their applications in sustainable agriculture have attracted the attention of academics and agro-industries. This work focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of these isolates through in planta salinity stress alleviation assay using Arabidopsis. The endophytic strain Priestia megaterium BP01R2, which can promote plant growth and salinity tolerance, was further characterized through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, the cyclodipeptide cyclo(L-Ala-Gly), which was identified by metabolomics analysis, was confirmed to contribute to the alleviation of salinity stress in stressed plants via exogenous supplementation. In this study, we used multi-omics approaches to investigate the genomics, metabolomics, and tropisms of endophytes, as well as the transcriptomics of plants in response to the endophyte. The results revealed the potential molecular mechanisms underlying the occurrence of biostimulant-based plant-endophyte symbioses with possible application in sustainable agriculture.
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Affiliation(s)
- Shih-Hsun Walter Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
| | - Pin-Hsien Yeh
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Tsai-Ching Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Shao-Yu Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - I-Chen Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chia-Ho Liu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yu-Hsi Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Pei-Ru Chien
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Fan-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung 202301, Taiwan
- Centre of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
| | - Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
| | - En-Pei Isabel Chiang
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
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Ran J, Ding Q, Wang G, Shen Y, Gao Z, Gao Y, Ma X, Hou X. The Developmental Mechanism of the Root System of Cultivated Terrestrial Watercress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3523. [PMID: 37895987 PMCID: PMC10610301 DOI: 10.3390/plants12203523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023]
Abstract
A well-developed root system is crucial for the rapid growth, asexual reproduction, and adaptation to the drought environments of the watercress. After analyzing the transcriptome of the watercress root system, we found that a high concentration of auxin is key to its adaptation to dry conditions. For the first time, we obtained DR5::EGFP watercress, which revealed the dynamic distribution of auxin in watercress root development under drought conditions. Via the application of naphthylphthalamic acid (NPA), 4-biphenylboronic acid (BBO), ethylene (ETH), abscisic acid (ABA), and other factors, we confirmed that auxin has a significant impact on the root development of watercress. Finally, we verified the role of auxin in root development using 35S::NoYUC8 watercress and showed that the synthesis of auxin in the root system mainly depends on the tryptophan, phenylalanine, and tyrosine amino acids (TAA) synthesis pathway. After the level of auxin increases, the root system of the watercress develops toward adaptation to dry environments. The formation of root aerenchyma disrupts the concentration gradient of auxin and is a key factor in the differentiation of lateral root primordia and H cells in watercress.
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Affiliation(s)
- Jiajun Ran
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
- Anhui Jianghuai Horticulture Seeds Co., Ltd., Hefei 230000, China
| | - Qiang Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Guangpeng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Yunlou Shen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Zhanyuan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Yue Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Xiaoqing Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (J.R.); (Q.D.); (G.W.); (Y.S.); (Z.G.); (Y.G.); (X.M.)
- Nanjing Suman Plasma Engineering Research Institute Co., Ltd., Nanjing 211162, China
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Ahkami AH. Systems biology of root development in Populus: Review and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111818. [PMID: 37567482 DOI: 10.1016/j.plantsci.2023.111818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.
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Affiliation(s)
- Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
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9
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Chen W, Shan W, Niu T, Ye T, Sun Q, Zhang J. Insight into regulation of adventitious root formation by arbuscular mycorrhizal fungus and exogenous auxin in tea plant (Camellia sinensis L.) cuttings. FRONTIERS IN PLANT SCIENCE 2023; 14:1258410. [PMID: 37790788 PMCID: PMC10544935 DOI: 10.3389/fpls.2023.1258410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023]
Abstract
Introduction Adventitious root (AR) development, affected by various biotic and abiotic factors, is the most important procedure in tea plant (Camellia sinensis L.) cutting propagation. Establishing symbiotic relationships with most terrestrial plants, AMF (Arbuscular mycorrhizal fungus) can mediate the AR formation of several herbaceous and woody plants in previous studies. Methods In this paper, effects of combined application of AMF and exogenous auxin on AR formation of cuttings from different tea plant varieties ('Pingyangtezao', 'Longjing 43' and 'Longjingchangye') were studied. Then we also performed RNA-Seq analysis with 'Pingyangtezao' cuttings aiming to find the possible auxin-related pathway of AM fungal regulation on AR formation. To accurately uncover the regulatory mechanism of AMF on AR formation of tea cuttings, rooting process were separated into four stages (S0, non-rooting; S1, AR protrusion; S2, AR formation and S3, AR elongation) at the same sampling time. Results and Discussion Results showed that IBA treatment increased the mycorrhizal colonization rate, especially in 'Pingyangtezao' variety (from 37.58% to 46.29%). Both inoculating AMF and addition of IBA promoted the AR formation, and rooting of different tea plant varieties showed different dependence on auxin. AMF could alleviate the effect of auxin-related inhibitors (2,3,5-triiodobenzoic acid, L-α-(Aminooxy)-β-phenylpropionic acid and α-(phenylethyl-2-oxo)-IAA) on rooting of tea cuttings, even though the colonization of AMF was hindered at various degrees. Transcriptomic analysis showed that different numbers of differentially expressed genes (DEGs) at various rooting stages of tea cuttings with the most at S2 stage (1360 DEGs), indicating the increasing regulation by AMF with the development of AR. Similar trend was found in auxin-related DEGs, and family genes of YUC, GH, PIN, LAX, SAUR, AUX, and ABP involved in the AM fungal regulation on AR formation of tea cuttings. Additionally, AMF strongly mediated auxin transport and signal transduction pathways in tea cuttings as showed by the results of correlation analysis. Overall, interaction of AMF and exogenous auxin in promoting rooting and the preliminary mechanism of AMF regulating AR formation of tea cuttings was deciphered in this paper, which may provide a basis for further deep mechanistic research and cutting propagation of tea production.
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Affiliation(s)
| | | | | | | | | | - Jiaxia Zhang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Huangshan, China
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10
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Yin C, Sun A, Zhou Y, Liu K, Wang P, Ye W, Fang Y. The dynamics of Arabidopsis H2A.Z on SMALL AUXIN UP RNAs regulates abscisic acid-auxin signaling crosstalk. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad131. [PMID: 37022978 DOI: 10.1093/jxb/erad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Extreme environmental changes threaten plant survival and worldwide food production. In response to osmotic stresses, plant hormone ABA activates stress responses and restricts plant growth. However, the epigenetic regulation of the ABA signaling and ABA-auxin crosstalk are not well known. Here we report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has altered ABA signaling and stress performances. RNA-sequencing data showed that a majority of stress related genes are activated in h2a.z-kd. In addition, we revealed that ABA directly promotes the deposition of H2A.Z on SMALL AUXIN UP RNAs (SAURs), which is involved in ABA-repressed SAUR expression. Moreover, we found that ABA represses the transcription of H2A.Z genes through suppressing ARF7/19-HB22/25 module. Our results shed light on a dynamic and reciprocal regulation hub through H2A.Z deposition on SAURs and ARF7/19-HB22/25-mediated H2A.Z transcription to integrate ABA/auxin signaling and regulate stress responses in Arabidopsis.
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Affiliation(s)
- Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Zhou
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Kunpeng Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenjing Ye
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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Tao GY, Xie YH, Li WF, Li KP, Sun C, Wang HM, Sun XM. LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1. Commun Biol 2023; 6:372. [PMID: 37020138 PMCID: PMC10076273 DOI: 10.1038/s42003-023-04731-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kui-Peng Li
- Guangxi Forestry Research Institute, Guangxi, 530009, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hong-Ming Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu, 741000, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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12
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Fu H, Wei X, Chen Q, Yong S, Liu Q, Dang J, Wu D, Liang G, Guo Q. Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea ( Camellia gymnogyna Chang) under red light quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1154169. [PMID: 37025148 PMCID: PMC10070859 DOI: 10.3389/fpls.2023.1154169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
As the formation of adventitious roots (AR) is an important component of in vitro regeneration of tea plants, the propagation and preservation of Huangshan Bitter tea (Camellia gymnogyna Chang) cuttings have been hindered due to its lower rooting rate. As light is a crucial environmental factor that affects AR formation, this study aimed to investigate the special role of red light (RL) in the formation of AR in Huangshan Bitter tea plants, which has not been well understood. Huangshan Bitter tea plants were induced with white light (control, WL) and red light (660 nm, RL) qualities 36 days after induced treatment (DAI) to investigate dynamic AR formation and development, anatomical observation, hormones content change, and weighted gene co-expression network analysis (WGCNA) of the transcriptome. Results showed that RL promoted the rooting rate and root characteristics compared to WL. Anatomical observations demonstrated that root primordium was induced earlier by RL at the 4 DAI. RL positively affected IAA, ZT and GA3 content and negatively influenced ABA from the 4 to 16 DAI. RNA-seq and analysis of differential expression genes (DEGs) exhibited extensive variation in gene expression profiles between RL and WL. Meanwhile, the results of WGCNA and correlation analysis identified three highly correlated modules and hub genes mainly participated in 'response to hormone', 'cellular glucan metabolic progress', and 'response to auxin'. Furthermore, the proportion of transcription factors (TFs) such as ethylene response factor (ERF), myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WRKYGQK (WRKY) were the top four in DEGs. These results suggested that the AR-promoting potential of red light was due to complex hormone interactions in tea plants by regulating the expression of related genes. This study provided an important reference to shorten breeding cycles and accelerate superiority in tea plant propagation and preservation.
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Affiliation(s)
- Hao Fu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Xu Wei
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Qian Chen
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Shunyuan Yong
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Qinjin Liu
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
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13
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Li Y, Luo J, Chen R, Zhou Y, Yu H, Chu Z, Lu Y, Gu X, Wu S, Wang P, Kuang H, Ouyang B. Folate shapes plant root architecture by affecting auxin distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:969-985. [PMID: 36587293 DOI: 10.1111/tpj.16093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/26/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.
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Affiliation(s)
- Ying Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jinying Luo
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhuannan Chu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Liu Z, Yuan Y, Wang L, Zhao X, Wang L, Wang L, Zhao Z, Zhao X, Chu Y, Gao Y, Yang F, Wang Y, Zhang Q, Zhao J, Liu M. Three Novel Adenylate Cyclase Genes Show Significant Biological Functions in Plant. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1149-1161. [PMID: 36601683 DOI: 10.1021/acs.jafc.2c07683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Adenylate cyclase is the key enzyme solely synthesizing cAMP which participates in cell metabolism regulations and functions as an intracellular second messenger. However, the biological functions of plant ACs have not been elucidated clearly for their poor conservative sequences and low detectable cAMP. We performed a systematic study of plant ACs by using Chinese jujube, whose fruit exhibits the highest cAMP content among plants. Three novel ACs were identified from Chinese jujube, and two types of methods including in vitro and in vivo were used to certificate ZjAC1-3 which can catalyze the conversion of ATP into cAMP. The biological functions of significant accelerations of seed germination, root growth, and flowering were found via overexpression of these AC genes in Arabidopsis, and these functions of ACs were further demonstrated by treating the AC-overexpressing transgenic lines and wild type Arabidopsis with bithionol and dibutyryl-cAMP. At last, transcriptome data revealed that the underlying mechanism of the biological functions of ACs might be regulation of the key genes involved in the circadian rhythm pathway and the hormone signal transduction pathway. This research established a foundation for further investigating plant AC genes and provided strong evidence for cAMP serving as a signaling molecule in plants.
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Affiliation(s)
- Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei 071001, China
| | - Ye Yuan
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- "Dongzao" Research Institute of Zhanhua District, Binzhou, Shandong 256800, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China
| | - Zhihui Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xin Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yuetong Chu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yaning Gao
- Beijing Pharma and Biotech Center, Beijing 100176, China
| | - Fangyuan Yang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yulu Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Qiong Zhang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei 071001, China
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Wang J, Sun N, Zheng L, Zhang F, Xiang M, Chen H, Deng XW, Wei N. Brassinosteroids promote etiolated apical structures in darkness by amplifying the ethylene response via the EBF-EIN3/PIF3 circuit. THE PLANT CELL 2023; 35:390-408. [PMID: 36321994 PMCID: PMC9806594 DOI: 10.1093/plcell/koac316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Germinated plants grow in darkness until they emerge above the soil. To help the seedling penetrate the soil, most dicot seedlings develop an etiolated apical structure consisting of an apical hook and folded, unexpanded cotyledons atop a rapidly elongating hypocotyl. Brassinosteroids (BRs) are necessary for etiolated apical development, but their precise role and mechanisms remain unclear. Arabidopsis thaliana SMALL AUXIN UP RNA17 (SAUR17) is an apical-organ-specific regulator that promotes production of an apical hook and closed cotyledons. In darkness, ethylene and BRs stimulate SAUR17 expression by transcription factor complexes containing PHYTOCHROME-INTERACTING FACTORs (PIFs), ETHYLENE INSENSITIVE 3 (EIN3), and its homolog EIN3-LIKE 1 (EIL1), and BRASSINAZOLE RESISTANT1 (BZR1). BZR1 requires EIN3 and PIFs for enhanced DNA-binding and transcriptional activation of the SAUR17 promoter; while EIN3, PIF3, and PIF4 stability depends on BR signaling. BZR1 transcriptionally downregulates EIN3-BINDING F-BOX 1 and 2 (EBF1 and EBF2), which encode ubiquitin ligases mediating EIN3 and PIF3 protein degradation. By modulating the EBF-EIN3/PIF protein-stability circuit, BRs induce EIN3 and PIF3 accumulation, which underlies BR-responsive expression of SAUR17 and HOOKLESS1 and ultimately apical hook development. We suggest that in the etiolated development of apical structures, BRs primarily modulate plant sensitivity to darkness and ethylene.
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Affiliation(s)
- Jiajun Wang
- School of Life Sciences, Southwest University, Chongqing 400715, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ning Sun
- Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lidan Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fangfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Mengda Xiang
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China
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16
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Liu C, Bai L, Cao P, Li S, Huang SX, Wang J, Li L, Zhang J, Zhao J, Song J, Sun P, Zhang Y, Zhang H, Guo X, Yang X, Tan X, Liu W, Wang X, Xiang W. Novel Plant Growth Regulator Guvermectin from Plant Growth-Promoting Rhizobacteria Boosts Biomass and Grain Yield in Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16229-16240. [PMID: 36515163 DOI: 10.1021/acs.jafc.2c07072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Food is a fundamental human right, and global food security is threatened by crop production. Plant growth regulators (PGRs) play an essential role in improving crop yield and quality, and this study reports on a novel PGR, termed guvermectin (GV), isolated from plant growth-promoting rhizobacteria, which can promote root and coleoptile growth, tillering, and early maturing in rice. GV is a nucleoside analogue like cytokinin (CK), but it was found that GV significantly promoted root and hypocotyl growth, which is different from the function of CK in Arabidopsis. The Arabidopsis CK receptor triple mutant ahk2-2 ahk3-3 cre1-12 still showed a GV response. Moreover, GV led different growth-promoting traits from auxin, gibberellin (GA), and brassinosteroid (BR) in Arabidopsis and rice. The results from a four-year field trial involving 28 rice varieties showed that seed-soaking treatment with GV increased the yields by 6.2 to 19.6%, outperforming the 4.0 to 10.8% for CK, 1.6 to 16.9% for BR, and 2.2 to 7.1% for GA-auxin-BR mixture. Transcriptome analysis demonstrated that GV induced different transcriptome patterns from CK, auxin, BR, and GA, and SAUR genes may regulate GV-mediated plant growth and development. This study suggests that GV represents a novel PGR with a unique signal perception and transduction pathway in plants.
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Affiliation(s)
- Chongxi Liu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Lu Bai
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Peng Cao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jidong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Lei Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ji Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Peng Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xiaowei Guo
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xilang Yang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xinqiu Tan
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Liu R, Wen SS, Sun TT, Wang R, Zuo WT, Yang T, Wang C, Hu JJ, Lu MZ, Wang LQ. PagWOX11/12a positively regulates the PagSAUR36 gene that enhances adventitious root development in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7298-7311. [PMID: 36001042 DOI: 10.1093/jxb/erac345] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Adventitious root (AR) development is an extremely complex biological process that is affected by many intrinsic factors and extrinsic stimuli. Some WUSCHEL-related homeobox (WOX) transcription factors have been reported to play important roles in AR development, but their functional relationships with auxin signaling are poorly understood, especially the developmental plasticity of roots in response to adversity stress. Here, we identified that the WOX11/12a-SMALL AUXIN UP RNA36 (SAUR36) module mediates AR development through the auxin pathway in poplar, as well as under salt stress. PagWOX11/12a displayed inducible expression during AR development, and overexpression of PagWOX11/12a significantly promoted AR development and increased salt tolerance in poplar, whereas dominant repression of PagWOX11/12a produced the opposite phenotype. PagWOX11/12a proteins directly bind to the SAUR36 promoter to regulate SAUR36 transcription, and this binding was enhanced during salt stress. Genetic modification of PagWOX11/12a-PagSAUR36 expression revealed that the PagWOX11/12a-PagSAUR36 module is crucial for controlling AR development via the auxin pathway. Overall, our results indicate that a novel WOX11-SAUR-auxin signaling regulatory module is required for AR development in poplar. These findings provide key insights and a better understanding of the involvement of WOX11 in root developmental plasticity in saline environments.
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Affiliation(s)
- Rui Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
| | - Shuang-Shuang Wen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
| | - Ting-Ting Sun
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Rui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wen-Teng Zuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
| | - Tao Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jian-Jun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liu-Qiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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18
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Sun A, Yin C, Ma M, Zhou Y, Zheng X, Tu X, Fang Y. Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:1721-1733. [PMID: 36017638 DOI: 10.1111/nph.18440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.
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Affiliation(s)
- Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Min Ma
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoyun Zheng
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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19
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Transcription Factor IAA27 Positively Regulates P Uptake through Promoted Adventitious Root Development in Apple Plants. Int J Mol Sci 2022; 23:ijms232214029. [PMID: 36430505 PMCID: PMC9695701 DOI: 10.3390/ijms232214029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Phosphate (P) deficiency severely limits the growth and production of plants. Adventitious root development plays an essential role in responding to low phosphorus stress for apple plants. However, the molecular mechanisms regulating adventitious root growth and development in response to low phosphorus stress have remained elusive. In this study, a mutation (C-T) in the coding region of the apple AUXIN/INDOLE-3-ACETIC ACID 27 (IAA27) gene was identified. MdIAA27T-overexpressing transgenic apple improved the tolerance to phosphorus deficiency, which grew longer and denser adventitious roots and presented higher phosphorous content than the control plants under low phosphorus conditions, while the overexpression of MdIAA27C displayed the opposite trend. Moreover, the heterologous overexpression of MdIAA27 in tobacco yielded the same results, supporting the aforementioned findings. In vitro and in vivo assays showed that MdIAA27 directly interacted with AUXIN RESPONSE FACTOR (ARF8), ARF26 and ARF27, which regulated Small Auxin-Up RNA 76 (MdSAUR76) and lateral organ boundaries domain 16 (MdLBD16) transcription. The mutation in IAA27 resulted in altered interaction modes, which in turn promoted the release of positive ARFs to upregulate SAUR76 and LBD16 expression in low phosphorus conditions. Altogether, our studies provide insights into how the allelic variation of IAA27 affects adventitious root development in response to low phosphorus stress.
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20
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Li M, Liu C, Hepworth SR, Ma C, Li H, Li J, Wang SM, Yin H. SAUR15 interaction with BRI1 activates plasma membrane H+-ATPase to promote organ development of Arabidopsis. PLANT PHYSIOLOGY 2022; 189:2454-2466. [PMID: 35511168 PMCID: PMC9343009 DOI: 10.1093/plphys/kiac194] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/25/2022] [Indexed: 05/13/2023]
Abstract
Brassinosteroids (BRs) are an important group of plant steroid hormones that regulate growth and development. Several members of the SMALL AUXIN UP RNA (SAUR) family have roles in BR-regulated hypocotyl elongation and root growth. However, the mechanisms are unclear. Here, we show in Arabidopsis (Arabidopsis thaliana) that SAUR15 interacts with cell surface receptor-like kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1) in BR-treated plants, resulting in enhanced BRI1 phosphorylation status and recruitment of the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1. Genetic and phenotypic assays indicated that the SAUR15 effect on BRI1 can be uncoupled from BRASSINOSTEROID INSENSITIVE 2 activity. Instead, we show that SAUR15 promotes BRI1 direct activation of plasma membrane H+-ATPase (PM H+-ATPase) via phosphorylation. Consequently, SAUR15-BRI1-PM H+-ATPase acts as a direct, PM-based mode of BR signaling that drives cell expansion to promote the growth and development of various organs. These data define an alternate mode of BR signaling in plants.
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Affiliation(s)
- Mengzhan Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Chunli Liu
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Shelley R Hepworth
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People’s Republic of China
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Chaofan Ma
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Hong Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, People’s Republic of China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, People’s Republic of China
| | | | - Hongju Yin
- Authors for correspondence: (H.Y.) and (S.M.W.)
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21
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Yun F, Huang D, Zhang M, Wang C, Deng Y, Gao R, Hou X, Liu Z, Liao W. Comprehensive transcriptome analysis unravels the crucial genes during adventitious root development induced by carbon monoxide in Cucumis sativus L. Mol Biol Rep 2022; 49:11327-11340. [PMID: 35906509 DOI: 10.1007/s11033-022-07797-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/29/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Carbon monoxide (CO) has been reported to be participated in adventitious rooting. However, knowledge about the interrelationship between CO and phytohormones during rooting is obscure. The molecular mechanism of CO-induced rooting is currently unclear. METHODS AND RESULTS The roles of CO in adventitious rooting in Cucumis sativus L. at the transcriptional level were investigated. The results show that 10 μM hematin (a CO donor) has a significant positive effect on adventitious rooting in cucumber. A total of 1792 differentially expressed genes (DEGs; 1103 up-regulated and 689 down-regulated) were identified in hematin treatment by RNA sequencing analysis. There were 37, 18 and 19 DEGs significantly enriched in plant hormone signal transduction, sucrose and starch metabolism, and phenylalanine metabolism, respectively. Both transcriptome and real-time quantitative PCR results showed that the expressions of AUX22D, IAA6, SAUR21, SAUR24, GH3.5, CYCD3-3, TIFY10a, TIFY10A and TIF9 promoted the accumulation of IAA, BR, JA and SA in plant hormone signal transduction. The up-regulation of HK3, TPPF, otsB, TPS7, TPS9 and the down-regulation of AGPS1, AGPS3 increased the content of starch and total sugar by mediating the activity of some critical enzymes, including HK, TPS, TPP and AGP. PER47, PER61, PER24, PER66, PER4 and CCR2 increased the lignin content. CONCLUSION Our results suggest that CO could promote the accumulation of plant hormones, starch, sugar and lignin during adventitious rooting by regulating the expression of some related genes, including AUX22D, IAA6, SAUR21, SAUR24, GH3.5, CYCD3-3, TIFY10a, TIFY10A, TIF9 HK3, otsB, TPS7, TPS9, AGPS1, AGPS3, PER47, PER61, PER24, PER66, PER4, and CCR2. Thus, we provides an interesting candidate gene list for further studies on the molecular mechanisms of adventitious rooting.
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Affiliation(s)
- Fahong Yun
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Dengjing Huang
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Meiling Zhang
- College of Science, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Yuzheng Deng
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Rong Gao
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Xuemei Hou
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Zesheng Liu
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, 1 Yingmen Village, Anning District, Lanzhou, 730070, China.
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22
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Lv W, He X, Guo H, Lan H, Jiao Y, Li L, Lian Y, Wang Z, Xin Z, Ren Y, Lin T. Genome-Wide Identification of TaSAUR Gene Family Members in Hexaploid Wheat and Functional Characterization of TaSAUR66-5B in Improving Nitrogen Use Efficiency. Int J Mol Sci 2022; 23:ijms23147574. [PMID: 35886923 PMCID: PMC9319360 DOI: 10.3390/ijms23147574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. Although Small Auxin Up-regulated RNAs (SAURs) participate in diverse biological processes, the function of SAURs in the nitrogen starvation response has not been well-studied. Here, we identified 308 TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of most TaSAURs contain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of the TaSAUR family members, a nitrogen starvation responsive gene, TaSAUR66-5B, can promote the growth of Arabidopsis and wheat roots. In addition, overexpression of TaSAUR66-5B in Arabidopsis up-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpression TaSAUR66-5B may promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression of TaSAUR66-5B in wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of the TaSAUR gene family and lays a foundation for elucidating the functions of TaSAURs in improving nitrogen utilization efficiency in wheat.
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Affiliation(s)
- Weizeng Lv
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Xue He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Haojuan Guo
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Haibin Lan
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yanqing Jiao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Le Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yanhao Lian
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Zhiqiang Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Zeyu Xin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
| | - Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
- Correspondence: (Y.R.); (T.L.)
| | - Tongbao Lin
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (W.L.); (H.G.); (H.L.); (Y.J.); (L.L.); (Y.L.); (Z.W.); (Z.X.)
- Correspondence: (Y.R.); (T.L.)
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Xu D, Yang C, Fan H, Qiu W, Huang B, Zhuo R, He Z, Li H, Han X. Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance. PLANTS (BASEL, SWITZERLAND) 2022; 11:1273. [PMID: 35567274 PMCID: PMC9103128 DOI: 10.3390/plants11091273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Auxin response factors (ARFs) play important roles in plant development and environmental adaption. However, the function of ARFs in cadmium (Cd) accumulation are still unknown. Here, 23 SaARFs were detected in the genome of hyperaccumulating ecotype of Sedum alfredii Hance (HE), and they were not evenly distributed on the chromosomes. Their protein domains remained highly conservative. SaARFs in the phylogenetic tree can be divided into three groups. Genes in the group Ⅰ contained three introns at most. However, over ten introns were found in other two groups. Collinearity relationships were exhibited among ten SaARFs. The reasons for generating SaARFs may be segmental duplication and rearrangements. Collinearity analysis among different species revealed that more collinear genes of SaARFs can be found in the species with close relationships of HE. A total of eight elements in SaARFs promoters were related with abiotic stress. The qRT-PCR results indicated that four SaARFs can respond to Cd stress. Moreover, that there may be functional redundancy among six SaARFs. The adaptive selection and functional divergence analysis indicated that SaARF4 may undergo positive selection pressure and an adaptive-evolution process. Overexpressing SaARF4 effectively declined Cd accumulation. Eleven single nucleotide polymorphism (SNP) sites relevant to Cd accumulation can be detected in SaARF4. Among them, only one SNP site can alter the sequence of the SaARF4 protein, but the SaARF4 mutant of this site did not cause a significant difference in cadmium content, compared with wild-type plants. SaARFs may be involved in Cd-stress responses, and SaARF4 may be applied for decreasing Cd accumulation of plants.
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Affiliation(s)
- Dong Xu
- Key Laboratory of Three Gorges Regional Plant Genetic & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, China; (D.X.); (C.Y.)
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Chunyu Yang
- Key Laboratory of Three Gorges Regional Plant Genetic & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, China; (D.X.); (C.Y.)
| | - Huijin Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Biyun Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetic & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, China; (D.X.); (C.Y.)
| | - Haiying Li
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (H.F.); (W.Q.); (B.H.); (R.Z.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Zanin FC, Freitas NC, Pinto RT, Máximo WPF, Diniz LEC, Paiva LV. The SAUR gene family in coffee: genome-wide identification and gene expression analysis during somatic embryogenesis. Mol Biol Rep 2022; 49:1973-1984. [PMID: 35034287 DOI: 10.1007/s11033-021-07011-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Small auxin-up RNA (SAUR) genes form a wide family supposedly involved in different physiological and developmental processes in plants such as leaf senescence, auxin signaling and transport, hypocotyl development and tolerance to abiotic stresses. The transcription of SAUR genes is quickly induced by auxins, a group of phytohormones of major importance on embryo development. To better understand the distribution and expression profile of such still not explored family in Coffea sp., especially during the development of somatic embryogenesis (SE), SAUR members were characterized in silico using the available Coffea canephora genome data and analyzed for gene expression by RT-qPCR in C. arabica embryogenic samples. METHODS AND RESULTS Over C. canephora genome 31 CcSAURs were distributed by 11 chromosomes. Out of these 31 gene members, 5 SAURs were selected for gene expression analysis in C. arabica embryogenic materials. CaSAUR12 and CaSAUR18 were the members highly expressed through almost all plant materials. The other genes had more expression in at least one of the developing embryo stages or plantlets. The CaSAUR12 was the only member to exhibit an increased expression in both non-embryogenic calli and the developing embryo stages. CONCLUSION The identification of SAUR family on C. canephora genome followed by the analysis of gene expression profile across coffee somatic embryogenesis process on C. arabica represents a further additional step towards a better comprehension of molecular components acting on SE. Along with new research about this gene family such knowledge may support studies about clonal propagation methods via somatic embryogenesis to help the scientific community towards improvements into coffee crop.
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Affiliation(s)
- Fabiana Couto Zanin
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras (UFLA), Lavras, MG, 37200000, Brazil
| | - Natália Chagas Freitas
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras (UFLA), Lavras, MG, 37200000, Brazil
| | - Renan Terassi Pinto
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras (UFLA), Lavras, MG, 37200000, Brazil
| | - Wesley Pires Flausino Máximo
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras (UFLA), Lavras, MG, 37200000, Brazil
| | | | - Luciano Vilela Paiva
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras (UFLA), Lavras, MG, 37200000, Brazil.
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25
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Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R. Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PLANT PHYSIOLOGY 2021; 187:2656-2673. [PMID: 34636851 PMCID: PMC8644285 DOI: 10.1093/plphys/kiab441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
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Affiliation(s)
- Changyu Yi
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang 31008, China
| | - Qian Chen
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University (Burwood Campus), Burwood VIC 3125, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
- Author for communication:
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26
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Hu QQ, Shu JQ, Li WM, Wang GZ. Role of Auxin and Nitrate Signaling in the Development of Root System Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:690363. [PMID: 34858444 PMCID: PMC8631788 DOI: 10.3389/fpls.2021.690363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/25/2021] [Indexed: 06/12/2023]
Abstract
The plant root is an important storage organ that stores indole-3-acetic acid (IAA) from the apical meristem, as well as nitrogen, which is obtained from the external environment. IAA and nitrogen act as signaling molecules that promote root growth to obtain further resources. Fluctuations in the distribution of nitrogen in the soil environment induce plants to develop a set of strategies that effectively improve nitrogen use efficiency. Auxin integrates the information regarding the nitrate status inside and outside the plant body to reasonably distribute resources and sustainably construct the plant root system. In this review, we focus on the main factors involved in the process of nitrate- and auxin-mediated regulation of root structure to better understand how the root system integrates the internal and external information and how this information is utilized to modify the root system architecture.
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Di DW, Sun L, Wang M, Wu J, Kronzucker HJ, Fang S, Chu J, Shi W, Li G. WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and indole-3-acetic acid-conjugating genes and by inhibiting ammonium efflux in the root elongation zone. THE NEW PHYTOLOGIST 2021; 232:190-207. [PMID: 34128546 DOI: 10.1111/nph.17554] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 05/11/2023]
Abstract
Ammonium (NH4+ ) is toxic to root growth in most plants, even at moderate concentrations. Transcriptional regulation is one of the most important mechanisms in the response of plants to NH4+ toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear. Here, RNA-seq analysis was performed on Arabidopsis roots to screen for ammonium-responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH4+ , was selected. We defined the role of WRKY46 using mutation and overexpression assays, and characterized the regulation of NUDX9 and indole-3-acetic acid (IAA)-conjugating genes by WRKY46 via yeast one-hybrid and electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative real-time polymerase chain reaction (ChIP-qPCR). Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH4+ -suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA-conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and to inhibit their transcription, thus positively regulating free IAA content and stabilizing protein N-glycosylation, leading to an inhibition of NH4+ efflux in the root elongation zone (EZ). We identify TF involvement in the regulation of NH4+ efflux in the EZ, and show that WRKY46 inhibits NH4+ efflux by negative regulation of NUDX9 and IAA-conjugating genes.
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Affiliation(s)
- Dong-Wei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Li Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, 210095, China
| | - Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingjing Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Herbert J Kronzucker
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shuang Fang
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Guangjie Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Li J, Foster R, Ma S, Liao SJ, Bliss S, Kartika D, Wang L, Wu L, Eamens AL, Ruan YL. Identification of transcription factors controlling cell wall invertase gene expression for reproductive development via bioinformatic and transgenic analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1058-1074. [PMID: 33650173 DOI: 10.1111/tpj.15218] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Cell wall invertase (CWIN) hydrolyses sucrose into glucose and fructose in the extracellular matrix and plays crucial roles in assimilate partitioning and sugar signalling. However, the molecular regulators controlling CWIN gene transcription remain unknown. As the first step to address this issue, we performed bioinformatic and transgenic studies, which identified a cohort of transcription factors (TFs) modulating CWIN gene expression in Arabidopsis thaliana. Comprehensive bioinformatic analyses identified 18 TFs as putative regulators of the expression of AtCWIN2 and AtCWIN4 that are predominantly expressed in Arabidopsis reproductive organs. Among them, MYB21, ARF6, ARF8, AP3 and CRC were subsequently shown to be the most likely regulators of CWIN gene expression based on molecular characterization of the respective mutant of each candidate TF. More specifically, the obtained data indicate that ARF6, ARF8 and MYB21 regulate CWIN2 expression in the anthers and CWIN4 in nectaries, anthers and petals, whereas AP3 and CRC were determined primarily to regulate the transcriptional activity of CWIN4. TF-promoter interaction assays demonstrated that ARF6 and ARF8 directly control CWIN2 and CWIN4 transcription with AP3 activating CWIN4. The involvement of ARF8 in regulating CWIN4 expression was further supported by the finding that enhanced CWIN4 expression partially recovered the short silique phenotype displayed by the arf8-3 mutant. The identification of the five TFs regulating CWIN expression serves as a launching pad for future studies to dissect the upstream molecular network underpinning the transcription of CWINs and provides a new avenue, potentially, to engineer assimilate allocation and reproductive development for improving seed yield.
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Affiliation(s)
- Jun Li
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ryan Foster
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Si Ma
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Sheng-Jin Liao
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Samuel Bliss
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Dewi Kartika
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Lu Wang
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Limin Wu
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Andrew L Eamens
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Yong-Ling Ruan
- School of Environmental & Life Sciences and Australia-China Research Centre for Crop Improvement, The University of Newcastle, Callaghan, NSW, 2308, Australia
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Favero DS, Lambolez A, Sugimoto K. Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:392-420. [PMID: 32986276 DOI: 10.1111/tpj.14996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.
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Affiliation(s)
- David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
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Li SW. Molecular Bases for the Regulation of Adventitious Root Generation in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:614072. [PMID: 33584771 PMCID: PMC7876083 DOI: 10.3389/fpls.2021.614072] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 05/08/2023]
Abstract
The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.
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31
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Copeland C. SAUR15 Connects Auxin Perception to Lateral and Adventitious Root Formation. PLANT PHYSIOLOGY 2020; 184:558-559. [PMID: 33020320 PMCID: PMC7536690 DOI: 10.1104/pp.20.01089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Charles Copeland
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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